Galaxy |

Changeset 2:8947fca5f715 (2015-06-26)

Previous changeset 1:84a17b3fad1f (2015-06-26)

Commit message:
Uploaded

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/AUTHORS
--- a/GEMBASSY-1.0.3/AUTHORS Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-See README file.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/COPYING
--- a/GEMBASSY-1.0.3/COPYING Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,340 +0,0 @@\n-\t\t GNU GENERAL PUBLIC LICENSE\n-\t\t Version 2, June 1991\n-\n- Copyright (C) 1989, 1991 Free Software Foundation, Inc.\n- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA\n- Everyone is permitted to copy and distribute verbatim copies\n- of this license document, but changing it is not allowed.\n-\n-\t\t\t Preamble\n-\n- The licenses for most software are designed to take away your\n-freedom to share and change it. By contrast, the GNU General Public\n-License is intended to guarantee your freedom to share and change free\n-software--to make sure the software is free for all its users. This\n-General Public License applies to most of the Free Software\n-Foundation\'s software and to any other program whose authors commit to\n-using it. (Some other Free Software Foundation software is covered by\n-the GNU Library General Public License instead.) You can apply it to\n-your programs, too.\n-\n- When we speak of free software, we are referring to freedom, not\n-price. Our General Public Licenses are designed to make sure that you\n-have the freedom to distribute copies of free software (and charge for\n-this service if you wish), that you receive source code or can get it\n-if you want it, that you can change the software or use pieces of it\n-in new free programs; and that you know you can do these things.\n-\n- To protect your rights, we need to make restrictions that forbid\n-anyone to deny you these rights or to ask you to surrender the rights.\n-These restrictions translate to certain responsibilities for you if you\n-distribute copies of the software, or if you modify it.\n-\n- For example, if you distribute copies of such a program, whether\n-gratis or for a fee, you must give the recipients all the rights that\n-you have. You must make sure that they, too, receive or can get the\n-source code. And you must show them these terms so they know their\n-rights.\n-\n- We protect your rights with two steps: (1) copyright the software, and\n-(2) offer you this license which gives you legal permission to copy,\n-distribute and/or modify the software.\n-\n- Also, for each author\'s protection and ours, we want to make certain\n-that everyone understands that there is no warranty for this free\n-software. If the software is modified by someone else and passed on, we\n-want its recipients to know that what they have is not the original, so\n-that any problems introduced by others will not reflect on the original\n-authors\' reputations.\n-\n- Finally, any free program is threatened constantly by software\n-patents. We wish to avoid the danger that redistributors of a free\n-program will individually obtain patent licenses, in effect making the\n-program proprietary. To prevent this, we have made it clear that any\n-patent must be licensed for everyone\'s free use or not licensed at all.\n-\n- The precise terms and conditions for copying, distribution and\n-modification follow.\n-\x0c\n-\t\t GNU GENERAL PUBLIC LICENSE\n- TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION\n-\n- 0. This License applies to any program or other work which contains\n-a notice placed by the copyright holder saying it may be distributed\n-under the terms of this General Public License. The "Program", below,\n-refers to any such program or work, and a "work based on the Program"\n-means either the Program or any derivative work under copyright law:\n-that is to say, a work containing the Program or a portion of it,\n-either verbatim or with modifications and/or translated into another\n-language. (Hereinafter, translation is included without limitation in\n-the term "modification".) Each licensee is addressed as "you".\n-\n-Activities other than copying, distribution and modification are not\n-covered by this License; they are outside its scope. The act of\n-running the Program is not restricted, and the output from the Program\n-is covered only if its contents constitute a work based on the\n-Program (independent of having been made by running the Program).\n-Whet'..b'D/OR OTHER PARTIES\n-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED\n-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF\n-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS\n-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE\n-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,\n-REPAIR OR CORRECTION.\n-\n- 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR\n-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,\n-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING\n-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED\n-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY\n-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER\n-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE\n-POSSIBILITY OF SUCH DAMAGES.\n-\n-\t\t END OF TERMS AND CONDITIONS\n-\x0c\n-\t How to Apply These Terms to Your New Programs\n-\n- If you develop a new program, and you want it to be of the greatest\n-possible use to the public, the best way to achieve this is to make it\n-free software which everyone can redistribute and change under these terms.\n-\n- To do so, attach the following notices to the program. It is safest\n-to attach them to the start of each source file to most effectively\n-convey the exclusion of warranty; and each file should have at least\n-the "copyright" line and a pointer to where the full notice is found.\n-\n- <one line to give the program\'s name and a brief idea of what it does.>\n- Copyright (C) <year> <name of author>\n-\n- This program is free software; you can redistribute it and/or modify\n- it under the terms of the GNU General Public License as published by\n- the Free Software Foundation; either version 2 of the License, or\n- (at your option) any later version.\n-\n- This program is distributed in the hope that it will be useful,\n- but WITHOUT ANY WARRANTY; without even the implied warranty of\n- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n- GNU General Public License for more details.\n-\n- You should have received a copy of the GNU General Public License\n- along with this program; if not, write to the Free Software\n- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-\n-Also add information on how to contact you by electronic and paper mail.\n-\n-If the program is interactive, make it output a short notice like this\n-when it starts in an interactive mode:\n-\n- Gnomovision version 69, Copyright (C) year name of author\n- Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w\'.\n- This is free software, and you are welcome to redistribute it\n- under certain conditions; type `show c\' for details.\n-\n-The hypothetical commands `show w\' and `show c\' should show the appropriate\n-parts of the General Public License. Of course, the commands you use may\n-be called something other than `show w\' and `show c\'; they could even be\n-mouse-clicks or menu items--whatever suits your program.\n-\n-You should also get your employer (if you work as a programmer) or your\n-school, if any, to sign a "copyright disclaimer" for the program, if\n-necessary. Here is a sample; alter the names:\n-\n- Yoyodyne, Inc., hereby disclaims all copyright interest in the program\n- `Gnomovision\' (which makes passes at compilers) written by James Hacker.\n-\n- <signature of Ty Coon>, 1 April 1989\n- Ty Coon, President of Vice\n-\n-This General Public License does not permit incorporating your program into\n-proprietary programs. If your program is a subroutine library, you may\n-consider it more useful to permit linking proprietary applications with the\n-library. If this is what you want to do, use the GNU Library General\n-Public License instead of this License.\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/ChangeLog
--- a/GEMBASSY-1.0.3/ChangeLog Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-Version 0.0.1 11-Mar-2012
- Beta version.
-Version 0.0.1 09-Jun-2012
- Update, 5 methods added. Some method names changed.
-Version 0.0.1 26-Sep-2012
- Update, 1 method added.
-Version 1.0.1 07-Jul-2013
- Map method conversion.
- Document re-enforecment.
- RESTification
- EDAM ontology mapping
-Version 1.0.2 28-Oct-2013
- Update EMBOSS-6.6.0
-Version 1.0.3 09-Feb-2015
- Refactoring
- Finish RESTification
- Implement "-tai" option in "gcai"

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/INSTALL
--- a/GEMBASSY-1.0.3/INSTALL Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,370 +0,0 @@\n-Installation Instructions\n-*************************\n-\n-Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,\n-Inc.\n-\n- Copying and distribution of this file, with or without modification,\n-are permitted in any medium without royalty provided the copyright\n-notice and this notice are preserved. This file is offered as-is,\n-without warranty of any kind.\n-\n-Basic Installation\n-==================\n-\n- Briefly, the shell command `./configure && make && make install'\n-should configure, build, and install this package. The following\n-more-detailed instructions are generic; see the `README' file for\n-instructions specific to this package. Some packages provide this\n-`INSTALL' file but do not implement all of the features documented\n-below. The lack of an optional feature in a given package is not\n-necessarily a bug. More recommendations for GNU packages can be found\n-in *note Makefile Conventions: (standards)Makefile Conventions.\n-\n- The `configure' shell script attempts to guess correct values for\n-various system-dependent variables used during compilation. It uses\n-those values to create a `Makefile' in each directory of the package.\n-It may also create one or more `.h' files containing system-dependent\n-definitions. Finally, it creates a shell script `config.status' that\n-you can run in the future to recreate the current configuration, and a\n-file `config.log' containing compiler output (useful mainly for\n-debugging `configure').\n-\n- It can also use an optional file (typically called `config.cache'\n-and enabled with `--cache-file=config.cache' or simply `-C') that saves\n-the results of its tests to speed up reconfiguring. Caching is\n-disabled by default to prevent problems with accidental use of stale\n-cache files.\n-\n- If you need to do unusual things to compile the package, please try\n-to figure out how `configure' could check whether to do them, and mail\n-diffs or instructions to the address given in the `README' so they can\n-be considered for the next release. If you are using the cache, and at\n-some point `config.cache' contains results you don't want to keep, you\n-may remove or edit it.\n-\n- The file `configure.ac' (or `configure.in') is used to create\n-`configure' by a program called `autoconf'. You need `configure.ac' if\n-you want to change it or regenerate `configure' using a newer version\n-of `autoconf'.\n-\n- The simplest way to compile this package is:\n-\n- 1. `cd' to the directory containing the package's source code and type\n- `./configure' to configure the package for your system.\n-\n- Running `configure' might take a while. While running, it prints\n- some messages telling which features it is checking for.\n-\n- 2. Type `make' to compile the package.\n-\n- 3. Optionally, type `make check' to run any self-tests that come with\n- the package, generally using the just-built uninstalled binaries.\n-\n- 4. Type `make install' to install the programs and any data files and\n- documentation. When installing into a prefix owned by root, it is\n- recommended that the package be configured and built as a regular\n- user, and only the `make install' phase executed with root\n- privileges.\n-\n- 5. Optionally, type `make installcheck' to repeat any self-tests, but\n- this time using the binaries in their final installed location.\n- This target does not install anything. Running this target as a\n- regular user, particularly if the prior `make install' required\n- root privileges, verifies that the installation completed\n- correctly.\n-\n- 6. You can remove the program binaries and object files from the\n- source code directory by typing `make clean'. To also remove the\n- files that `configure' created (so you can compile the package for\n- a different kind of computer), type `make distclean'. There is\n- also a `make maintainer-clean' target, but that is intended mainly\n- for the package's developers. If you us"..b'e by the type of machine the package\n-will run on. Usually, assuming the package is built to be run on the\n-_same_ architectures, `configure\' can figure that out, but if it prints\n-a message saying it cannot guess the machine type, give it the\n-`--build=TYPE\' option. TYPE can either be a short name for the system\n-type, such as `sun4\', or a canonical name which has the form:\n-\n- CPU-COMPANY-SYSTEM\n-\n-where SYSTEM can have one of these forms:\n-\n- OS\n- KERNEL-OS\n-\n- See the file `config.sub\' for the possible values of each field. If\n-`config.sub\' isn\'t included in this package, then this package doesn\'t\n-need to know the machine type.\n-\n- If you are _building_ compiler tools for cross-compiling, you should\n-use the option `--target=TYPE\' to select the type of system they will\n-produce code for.\n-\n- If you want to _use_ a cross compiler, that generates code for a\n-platform different from the build platform, you should specify the\n-"host" platform (i.e., that on which the generated programs will\n-eventually be run) with `--host=TYPE\'.\n-\n-Sharing Defaults\n-================\n-\n- If you want to set default values for `configure\' scripts to share,\n-you can create a site shell script called `config.site\' that gives\n-default values for variables like `CC\', `cache_file\', and `prefix\'.\n-`configure\' looks for `PREFIX/share/config.site\' if it exists, then\n-`PREFIX/etc/config.site\' if it exists. Or, you can set the\n-`CONFIG_SITE\' environment variable to the location of the site script.\n-A warning: not all `configure\' scripts look for a site script.\n-\n-Defining Variables\n-==================\n-\n- Variables not defined in a site shell script can be set in the\n-environment passed to `configure\'. However, some packages may run\n-configure again during the build, and the customized values of these\n-variables may be lost. In order to avoid this problem, you should set\n-them in the `configure\' command line, using `VAR=value\'. For example:\n-\n- ./configure CC=/usr/local2/bin/gcc\n-\n-causes the specified `gcc\' to be used as the C compiler (unless it is\n-overridden in the site shell script).\n-\n-Unfortunately, this technique does not work for `CONFIG_SHELL\' due to\n-an Autoconf limitation. Until the limitation is lifted, you can use\n-this workaround:\n-\n- CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash\n-\n-`configure\' Invocation\n-======================\n-\n- `configure\' recognizes the following options to control how it\n-operates.\n-\n-`--help\'\n-`-h\'\n- Print a summary of all of the options to `configure\', and exit.\n-\n-`--help=short\'\n-`--help=recursive\'\n- Print a summary of the options unique to this package\'s\n- `configure\', and exit. The `short\' variant lists options used\n- only in the top level, while the `recursive\' variant lists options\n- also present in any nested packages.\n-\n-`--version\'\n-`-V\'\n- Print the version of Autoconf used to generate the `configure\'\n- script, and exit.\n-\n-`--cache-file=FILE\'\n- Enable the cache: use and save the results of the tests in FILE,\n- traditionally `config.cache\'. FILE defaults to `/dev/null\' to\n- disable caching.\n-\n-`--config-cache\'\n-`-C\'\n- Alias for `--cache-file=config.cache\'.\n-\n-`--quiet\'\n-`--silent\'\n-`-q\'\n- Do not print messages saying which checks are being made. To\n- suppress all normal output, redirect it to `/dev/null\' (any error\n- messages will still be shown).\n-\n-`--srcdir=DIR\'\n- Look for the package\'s source code in directory DIR. Usually\n- `configure\' can determine that directory automatically.\n-\n-`--prefix=DIR\'\n- Use DIR as the installation prefix. *note Installation Names::\n- for more details, including other options available for fine-tuning\n- the installation locations.\n-\n-`--no-create\'\n-`-n\'\n- Run the configure checks, but stop before creating any output\n- files.\n-\n-`configure\' also accepts some other, not widely useful, options. Run\n-`configure --help\' for more details.\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/Makefile.am
--- a/GEMBASSY-1.0.3/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-#
-
-SUBDIRS = src acd doc
-
-EXTRA_DIST = gsoap depcomp ltmain.sh config.sub config.guess data
-
-# tar to pick up the other directories
-# then remove any CVS subdirectories
-
-dist-hook:
- tar cBf - acd | ( cd $(distdir); tar xBf - ; cd acd; rm -rf CVS )
- tar cBf - doc | ( cd $(distdir); tar xBf - ; cd doc; rm -rf CVS; rm -rf master)
- tar cBf - include | ( cd $(distdir); tar xBf - ; cd include; rm -rf CVS )

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/Makefile.in
--- a/GEMBASSY-1.0.3/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,850 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-#\n-VPATH = @srcdir@\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgdatadir = $(datadir)/@PACKAGE@\n-pkgincludedir = $(includedir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkglibexecdir = $(libexecdir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-subdir = .\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \\\n-\t$(am__configure_deps) $(am__DIST_COMMON)\n-am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \\\n- configure.lineno config.status.lineno\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_@AM_V@)\n-am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_@AM_V@)\n-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)\n-am__v_GEN_0 = @echo " G'..b' build" ; \\\n-\t exit 1 ; \\\n-\tfi\n-\t@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \\\n-\t || { echo "ERROR: files left in build directory after distclean:" ; \\\n-\t $(distcleancheck_listfiles) ; \\\n-\t exit 1; } >&2\n-check-am: all-am\n-check: check-recursive\n-all-am: Makefile\n-installdirs: installdirs-recursive\n-installdirs-am:\n-install: install-recursive\n-install-exec: install-exec-recursive\n-install-data: install-data-recursive\n-uninstall: uninstall-recursive\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-recursive\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-recursive\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-recursive\n-\t-rm -f $(am__CONFIG_DISTCLEAN_FILES)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic distclean-libtool \\\n-\tdistclean-tags\n-\n-dvi: dvi-recursive\n-\n-dvi-am:\n-\n-html: html-recursive\n-\n-html-am:\n-\n-info: info-recursive\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-recursive\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-recursive\n-\n-install-html-am:\n-\n-install-info: install-info-recursive\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-recursive\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-recursive\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-recursive\n-\t-rm -f $(am__CONFIG_DISTCLEAN_FILES)\n-\t-rm -rf $(top_srcdir)/autom4te.cache\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-recursive\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-recursive\n-\n-pdf-am:\n-\n-ps: ps-recursive\n-\n-ps-am:\n-\n-uninstall-am:\n-\n-.MAKE: $(am__recursive_targets) install-am install-strip\n-\n-.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \\\n-\tam--refresh check check-am clean clean-cscope clean-generic \\\n-\tclean-libtool cscope cscopelist-am ctags ctags-am dist \\\n-\tdist-all dist-bzip2 dist-gzip dist-hook dist-lzip dist-shar \\\n-\tdist-tarZ dist-xz dist-zip distcheck distclean \\\n-\tdistclean-generic distclean-libtool distclean-tags \\\n-\tdistcleancheck distdir distuninstallcheck dvi dvi-am html \\\n-\thtml-am info info-am install install-am install-data \\\n-\tinstall-data-am install-dvi install-dvi-am install-exec \\\n-\tinstall-exec-am install-html install-html-am install-info \\\n-\tinstall-info-am install-man install-pdf install-pdf-am \\\n-\tinstall-ps install-ps-am install-strip installcheck \\\n-\tinstallcheck-am installdirs installdirs-am maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-generic \\\n-\tmostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \\\n-\tuninstall-am\n-\n-.PRECIOUS: Makefile\n-\n-\n-# tar to pick up the other directories\n-# then remove any CVS subdirectories\n-\n-dist-hook:\n-\ttar cBf - acd | ( cd $(distdir); tar xBf - ; cd acd; rm -rf CVS ) \n-\ttar cBf - doc | ( cd $(distdir); tar xBf - ; cd doc; rm -rf CVS; rm -rf master) \n-\ttar cBf - include | ( cd $(distdir); tar xBf - ; cd include; rm -rf CVS ) \n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/NEWS
--- a/GEMBASSY-1.0.3/NEWS Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-11/3/2012 See Changelog

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/README
--- a/GEMBASSY-1.0.3/README Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,223 +0,0 @@\n-\n-/* GEMBASSY ver 1.0.3 *********************************************************\n-\n- All rights reserved. Copyright (C) 2012-2013 by ITAYA Hidetoshi.\n-\n- This EMBASSY package is free software. You can redistribute it and/or modify\n- it under the terms of the GNU General Public License as published by the\n- Free Software Foundation, either version 2 of the License, or any later\n- version.\n-\n- See also GNU General Public License Version 2, included in this\n- package as COPYING.\n-\n-*****************************************************************************/\n-\n-\n-\n-/* About *********************************************************************\n-\n- This is an EMBASSY package for the utilization of G-language SOAP service.\n-\n- All of the tools included in this package are wrapper programs to\n- utilize G-language SOAP service, which are web APIs to access the methods\n- of G-language Genome Analysis Environment (G-language GAE); a powerful\n- workbench for genome analysis.\n-\n- Detailed documentation on G-language GAE methods are availabe at:\n- http://www.g-language.org/wiki/soap\n-\n- The EMBOSS Explorer interface is available at:\n- http://soap.g-language.org/gembassy/emboss_explorer\n-\n-*****************************************************************************/\n-\n-\n-\n-/* Installation **************************************************************\n-\n-REQUIREMENTS\n- EMBOSS (> 6.6.0) - This EMBASSY package requires EMBOSS version 6.6.0 or\n- above.\n- libcurl-devel (> 7.29.0) - Required for file POST\n-\n- A UNIX-like operating system\n-\n-INSTALLATION\n- Is EMBOSS already installed in your system?\n- Yes: Go to "EMBOSS is already installed" section.\n- No: Go to "Install from EMBOSS" section.\n-\n- Install from EMBOSS:\n- Root users\n- In the following examples we assume the downloaded EMBOSS archive filename\n- is emboss-latest.tar.gz\n-\n- 1. Download and compile EMBOSS source code\n- % wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz\n- (or "curl -O ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz")\n- % tar zxf emboss-latest.tar.gz\n- % cd EMBOSS-6.6.0\n- % ./configure\n- % make\n- % sudo make install\n-\n- 2. Make "embassy" directory in the EMBOSS-6.6.0/ directory if it does not\n- exist and go into the directory.\n- % mkdir embassy\n- % cd embassy\n-\n- 3. Download and compile the GEMBASSY source code\n- % wget http://soap.g-language.org/gembassy/source/GEMBASSSY-1.0.3.tar.gz\n- (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")\n- % tar zxvf GEMBASSY-1.0.3.tar.gz\n- % cd GEMBASSY-1.0.3\n- ( EMBOSS-6.6.0/embassy/GEMBASSY-1.0.3 )\n- % ./configure\n- % make\n- % sudo make install\n-\n- Non-root users\n- When running the \'./configure\' command do the following instead:\n- % ./configure --prefix=/PATH/TO/DIR/ (ex. --prefix=$HOME/opt)\n-\n- EMBOSS is already installed:\n- When EMBOSS is already installed, GEMBASSY must be installed to the exact\n- same directory as the existing EMBOSS.\n-\n- If non-root users wish to install GEMBASSY separately, first install the\n- EMBOSS package on top of the home directory.\n-\n- The following commands assume you have EMBOSS installed in the\n- /PATH/TO/EMBOSS/ directory.\n- % wget http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz\n- (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")\n- % tar zxf GEMBASSY-1.0.3.tar.gz\n- % cd GEMBASSY-1.0.3\n- % ./configure --prefix=/PATH/TO/EMBOSS/ (ex. --prefix=/usr/local)\n- % make\n- % make install\n-\n-\n- Installing custom EMBOSS configuration files\n- We highly recommend users to install the custom EMBOSS configuration files\n- from the KBWS package. The configuration file provides database definition\n- for various databases, allowing versatile access to various sequence\n- '..b'\n- % mv embossrc ~/.embossrc\n-\n- Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc\n- file to the corresponding directories.\n- (ex. emboss_acdroot = ~/opt/share/EMBOSS/acd)\n- (ex. emboss_data = ~/opt/share/EMBOSS/data)\n-\n- Update of EMBOSS\n- When users are upgrading EMBOSS, please be sure to uninstall old versions\n- of EMBOSS and GEMBASSY. If you override them, some older versions of files\n- may cause errors.\n-\n- NOTE - automake problem\n- If the source code is cloned from the GitHub Repository, there are\n- known problems with automake version mismatches which stop the compilation\n- of the source. Follow the steps below in (NOTE - libtool problem) to\n- solve this problem.\n-\n- NOTE - libtool problem\n- On some systems there may be compatibility problems with different\n- automake, autoconf or libtool versions. If a libtool problem\n- arises you can try deleting the following files if they exist:\n-\n- config.cache\n- ltmain.sh\n- ltconfig\n- libtool\n-\n- and then type\n- % aclocal -I m4\n- % autoconf\n- % automake -a\n-\n- and then retry make.\n-\n- If you have \'autoreconf\' in your system\n- % autoreconf -fi\n-\n- will do the trick.\n-\n-*****************************************************************************/\n-\n-\n-\n-/* QuickStart ****************************************************************\n-\n-DATABASE DEFINITION\n- The database definitions for following commands are available at\n- http://soap.g-language.org/kbws/embossrc\n- Input files used in the examples are provided in the data/ directory.\n-\n- INSTALLATION:\n- % wget http://soap.g-language.org/kbws/embossrc\n- (or "curl -O http://soap.g-language.org/kbws/embossrc")\n- % mv embossrc ~/.embossrc\n-\n- Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc\n- file to the corresponding directories.\n- (ex. emboss_acdroot = ~/share/EMBOSS/acd)\n- (ex. emboss_data = ~/share/EMBOSS/data)\n-\n-INFORMATION OF GEMBASSY TOOLS\n- List of all tools\n- For a list of all tools included in GEMBASSY use\n- % wossname -showembassy GEMBASSY\n-\n- Documentation\n- Detailed documentation are available to be viewed with the "tfm"\n- utility included in EMBOSS.\n- Here is an example for "gaminoinfo"\n- % tfm gaminoinfo\n-\n-USAGE EXAMPLE\n- The following examples show basic usages of three GEMBASSY tools and the\n- different ways of passing input. Example 1. uses database definition, 2.\n- uses the accid option, and 3. uses the sequence accession ID as input.\n- 1. ggcskew (GC skew)\n- % ggcskew -plot -graph cps refseqn:NC_000913\n- Calculates the GC skew of the input sequence\n- Created ggcskew.ps\n-\n- 2. ggcsi (GC Skew Index)\n- % ggcsi accid.fasta -accid stdout\n- GC Skew Index: an index for strand-specefic mutational bias\n- Input nucleotide sequence: refseqn:NC_000964\n- Sequence: NC_000964 GCSI: 0.214855185905019 SA: 976.152832384745 DIST: 170.245783\n-\n- 3. greporiter (Replication Origin and Terminus)\n- % greporiter -outfile stdout\n- Get the positions of replication origin and terminus\n- Input nucleotide sequence: accid.fasta\n- Sequence: NC_000913 Origin: 3923881 Terminus: 1550412\n-\n-*****************************************************************************/\n-\n-\n-\n-/* Content *******************************************************************\n-\n-gSOAP Toolkit\n- This EMBASSY package is dependant on gSOAP Toolkit for SOAP transfer,\n- included in the gsoap/ directory. It is used automatically during\n- compilation.\n-\n-*****************************************************************************/\n-\n-\n-\n-/* Contact *******************************************************************\n-\n-Hidetoshi Itaya (celery @ g-language.org)\n- Institute for Advanced Biosciences, Keio University.\n-\n-*****************************************************************************/\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/Makefile
--- a/GEMBASSY-1.0.3/acd/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,533 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# acd/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgincludedir = $(includedir)/GEMBASSY\n-pkglibdir = $(libdir)/GEMBASSY\n-pkglibexecdir = $(libexecdir)/GEMBASSY\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = x86_64-apple-darwin14.0.0\n-host_triplet = x86_64-apple-darwin14.0.0\n-subdir = acd\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_$(V))\n-am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_$(V))\n-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_$(V))\n-am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))\n-am__v_at_0 = @\n-am__v_at_1 = '..b'-e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(DATA)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(pkgdatadir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am: install-pkgdataDATA\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-pkgdataDATA\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: all all-am check check-am clean clean-generic clean-libtool \\\n-\tcscopelist-am ctags-am distclean distclean-generic \\\n-\tdistclean-libtool distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-pkgdataDATA install-ps \\\n-\tinstall-ps-am install-strip installcheck installcheck-am \\\n-\tinstalldirs maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags-am uninstall uninstall-am uninstall-pkgdataDATA\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/Makefile.am
--- a/GEMBASSY-1.0.3/acd/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,3 +0,0 @@
-
-pkgdata_DATA = *.acd
-pkgdatadir=$(prefix)/share/EMBOSS/acd

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/Makefile.in
--- a/GEMBASSY-1.0.3/acd/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,533 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-VPATH = @srcdir@\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgincludedir = $(includedir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkglibexecdir = $(libexecdir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-subdir = acd\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_@AM_V@)\n-am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_@AM_V@)\n-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_@AM_V@)\n-am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)\n-am__v_at_0 = @\n-am__v_at_1 = \n-SOURCES =\n-DIST_SOURCES =\n-am__can_run_installinfo = \\\n- case $$'..b'-e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(DATA)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(pkgdatadir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am: install-pkgdataDATA\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-pkgdataDATA\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: all all-am check check-am clean clean-generic clean-libtool \\\n-\tcscopelist-am ctags-am distclean distclean-generic \\\n-\tdistclean-libtool distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-pkgdataDATA install-ps \\\n-\tinstall-ps-am install-strip installcheck installcheck-am \\\n-\tinstalldirs maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags-am uninstall uninstall-am uninstall-pkgdataDATA\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gaaui.acd
--- a/GEMBASSY-1.0.3/acd/gaaui.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,55 +0,0 @@
-application: gaaui [
-  documentation: "Calculates various indece of amino acid usage"
-  groups: "Protein:Properties"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0613 Peptides and amino acids"
-  relations: "EDAM_operation:0250 Protein property calculation"
-  relations: "EDAM_operation:0398 Protein molecular weight calculation"
-  relations: "EDAM_operation:2574 Protein hydropathy calculation"
-  relations: "EDAM_operation:0401 Protein hydropathy calculation
-              (from sequence)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    features: "Y"
-    type: "nucleotide"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "AAINDEX entry output file"
-    knowntype: "aaindex data"
-    relations: "EDAM_data:2016 Amino acid property"
-    relations: "EDAM_data:1501 Amino acid index"
-    relations: "EDAM_data:1502 Amino acid index (chemical classes)"
-    relations: "EDAM_data:1506 Amino acid index (hydropathy)"
-    relations: "EDAM_data:1505 Amino acid index (molecular weight)"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gaminoinfo.acd
--- a/GEMBASSY-1.0.3/acd/gaminoinfo.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,42 +0,0 @@
-application: gaminoinfo [
-  documentation: "Prints out basic amino acid sequence statistics"
-  groups: "Protein:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0613 Peptides and amino acids"
-  relations: "EDAM_operation:0250 Protein property calculation"
-  relations: "EDAM_operation:0398 Protein molecular weight calculation"
-  relations: "EDAM_operation:2574 Protein hydropathy calculation"
-  relations: "EDAM_operation:0401 Protein hydropathy calculation
-              (from sequence)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "protein"
-    relations: "EDAM_data:2886 Sequence record (protein)"
-  ]
-
-endsection: input
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "AAINDEX entry output file"
-    knowntype: "aaindex data"
-    relations: "EDAM_data:2016 Amino acid property"
-    relations: "EDAM_data:1501 Amino acid index"
-    relations: "EDAM_data:1502 Amino acid index (chemical classes)"
-    relations: "EDAM_data:1506 Amino acid index (hydropathy)"
-    relations: "EDAM_data:1505 Amino acid index (molecular weight)"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gb1.acd
--- a/GEMBASSY-1.0.3/acd/gb1.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,54 +0,0 @@
-application: gb1 [
-  documentation: "Calculates strand bias of bacterial genome using B1 index"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: method [
-    information: "Choose method of 'lobry' or 'rocha'"
-    values: "lobry;rocha"
-    default: "rocha"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gb2.acd
--- a/GEMBASSY-1.0.3/acd/gb2.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,48 +0,0 @@
-application: gb2 [
-  documentation: "Calculates strand bias of bacterial genome using B2 index"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gbasecounter.acd
--- a/GEMBASSY-1.0.3/acd/gbasecounter.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,71 +0,0 @@
-application: gbasecounter [
-  documentation: "Creates a position weight matrix of oligomers around start
-                  codon"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: position [
-    information: "Either 'start' (around start codon) or 'end'
-                  (around stop codon) to create the PWM"
-    values: "start;end"
-    default: "start"
-  ]
-
-  integer: patlen [
-    information: "Length of oligomer to count"
-    default: "3"
-  ]
-
-  integer: upstream [
-    information: "Length upstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  integer: downstream [
-    information: "Length downstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Weight matrix output file"
-    knowntype: "matrix"
-    relations: "EDAM_data:1362 Position weight matrix"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gbaseentropy.acd
--- a/GEMBASSY-1.0.3/acd/gbaseentropy.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,83 +0,0 @@
-application: gbaseentropy [
-  documentation: "Calculates and graphs the sequence conservation
-                  using Shanon uncertainty (entropy)"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0160 Sequence sites and features"
-  relations: "EDAM_operation:0253 Feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: position [
-    information: "Either 'start' (around start codon) or 'end'
-                  (around stop codon) to create the PWM"
-    values: "start;end"
-    default: "start"
-  ]
-
-  integer: patlen [
-    information: "Length of oligomer to count"
-    default: "3"
-  ]
-
-  integer: upstream [
-    information: "Length upstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  integer: downstream [
-    information: "Length downstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "gbaseentropy of $(sequence.name)"
-    relations: "EDAM_data:2166 Sequence compisition plot"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gbaseinformationcontent.acd
--- a/GEMBASSY-1.0.3/acd/gbaseinformationcontent.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,84 +0,0 @@
-application: gbaseinformationcontent [
-  documentation: "Calculates and graphs the sequence conservation using
-                  information content"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0160 Sequence sites and features"
-  relations: "EDAM_operation:0253 Feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: position [
-    information: "Either 'start' (around start codon) or 'end'
-                  (around stop codon) to create the PWM"
-    values: "start;end"
-    default: "start"
-  ]
-
-  integer: upstream [
-    information: "Length upstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  integer: downstream [
-    information: "Length downstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  integer: patlen [
-    information: "Length of oligomer to count"
-    default: "3"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "gbaseinformationcontent of $(sequence.name)"
-    relations: "EDAM_data:2166 Sequence compisition plot"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gbaserelativeentropy.acd
--- a/GEMBASSY-1.0.3/acd/gbaserelativeentropy.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,83 +0,0 @@
-application: gbaserelativeentropy [
-  documentation: "Calculates and graphs the sequence conservation using
-                  Kullback-Leibler divergence (relative entropy)"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0160 Sequence sites and features"
-  relations: "EDAM_operation:0253 Feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: position [
-    information: "Either 'start' (around start codon) or 'end'
-                  (around stop codon) to create the PWM"
-    values: "start;end"
-    default: "start"
-  ]
-
-  integer: patlen [
-    information: "Length of oligomer to count"
-    default: "3"
-  ]
-
-  integer: upstream [
-    information: "Length upstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  integer: downstream [
-    information: "Length downstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "gbaserelativeentropy of $(sequence.name)"
-    relations: "EDAM_data:2166 Sequence compisition plot"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gbasezvalue.acd
--- a/GEMBASSY-1.0.3/acd/gbasezvalue.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,75 +0,0 @@
-application: gbasezvalue [
-  documentation: "Extracts conserved oligomers per position using Z-score"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: limit [
-    information: "Rank threshold for showing the conserved oligomer"
-    default: "5"
-  ]
-
-  selection: position [
-    information: "Either 'start' (around start codon) or 'end'
-                  (around stop codon) to create the PWM"
-    values: "start;end"
-    default: "start"
-  ]
-
-  integer: patlen [
-    information: "Length of oligomer to count"
-    default: "3"
-  ]
-
-  integer: upstream [
-    information: "Length upstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  integer: downstream [
-    information: "Length downstream of specified position to create PWM"
-    default: "30"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gbui.acd
--- a/GEMBASSY-1.0.3/acd/gbui.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,69 +0,0 @@
-application: gbui [
-  documentation: "Calculates base usage indices for protein-coding sequences"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0236 Sequence composition calculation"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translating using standard codon table"
-    default: "N"
-  ]
-
-  list: position [
-    information: "Codon position"
-    values: "all: Assess overall base usage of the gene;
-             1: Assess base usage at 1st position of codons;
-             2: Assess base usage at 2nd position of codons;
-             3: Assess base usage at 3rd position of codons"
-    default: "all"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
- type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gcai.acd
--- a/GEMBASSY-1.0.3/acd/gcai.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,64 +0,0 @@
-application: gcai [
-  documentation: "Calculates codon adaptation index for each gene"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translating using standard codon table"
-    default: "N"
-  ]
-
-  string: wabsent [
-    information: "W value of codons absent from a reference set to negative
-                  when excludes such codons from the calculation"
-
-    default: "-1"
-  ]
-
-  boolean: tai [
-    information: "Include when calculating tRNA adaptation index (TAI)"
-    default: "N"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gcbi.acd
--- a/GEMBASSY-1.0.3/acd/gcbi.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,58 +0,0 @@
-application: gcbi [
-  documentation: "Calculates the codon bias index (CBI)"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translating using standard codon table"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gcgr.acd
--- a/GEMBASSY-1.0.3/acd/gcgr.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,55 +0,0 @@
-application: gcgr [
-  documentation: "Creates a Chaos Game Representation of a given sequence"
-  groups: "Display"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0092 Data visualisation"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: format [
-    information: "Output file format. Dependent on 'convert' command"
-    knowntype: "output format"
-    default: "png"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: width [
-    information: "Width of image"
-    default: "1024"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  string: goutfile [
-    information: "Output file for non interactive displays"
-    knowntype: "output filename"
-    relations: "EDAM_data:2166 Sequence composition plot"
-    default: "gcgr"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gcircularmap.acd
--- a/GEMBASSY-1.0.3/acd/gcircularmap.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,54 +0,0 @@
-application: gcircularmap [
-  documentation: "Draws circular map of the genome"
-  groups: "Display"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0092 Data visualisation"
-  relations: "EDAM_topic:0621 Genome, proteome and model organisms"
-  relations: "EDAM_operation:0578 Circular map rendering"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: format [
-    information: "Output file format. Dependent on 'convert' command"
-    knowntype: "output format"
-    default: "svg"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output
-[
-  information: "Output section"
-  type: "page"
-]
-
-  string: goutfile [
-    information: "Output file for non interactive displays"
-    relations: "EDAM_data:1274 DNA map"
-    default: "gcircularmap"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gcodoncompiler.acd
--- a/GEMBASSY-1.0.3/acd/gcodoncompiler.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,91 +0,0 @@
-application: gcodoncompiler [
-  documentation: "Calculates various kinds of amino acid and codon usage data"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include to translate using standard codon table"
-    default: "N"
-  ]
-
-  boolean: startcodon [
-    information: "Include to include start codon"
-    default: "N"
-  ]
-
-  boolean: stopcodon [
-    information: "Include to include stop codon"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key (i.e. amino acids and
-                  nucleotides)"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  list: data [
-    information: "Kinds of codon usage data. R* hypothesizes amino acids which
-                  are not present in the gene"
-    values: "A0: Absolute amino acid frequency ('AA');
-             A1: Relative amino acid frequency ('RAAU');
-             C0: Absolute codon frequency ('AF');
-             C1: Relative codon frequency in a complete sequence;
-             C2: Relative codon frequency in each amino acid ('RF');
-             C3: Relative synonymous codon usage ('RSCU') ;
-             C4: Relative adaptiveness; i.e., ratio to maximum of minor codon
-                 ('W')
-             C5: Maximum (1) or minor (0) codon;
-             R0: Absolute codon frequency ('AF');
-             R1: Relative codon frequency in a complete sequence;
-             R2: Relative codon frequency in each amino acid ('RF');
-             R3: Relative synonymous codon usage ('RSCU') ;
-             R4: Relative adaptiveness; i.e., ratio to maximum of minor codon
-                 ('W')
-             R5: Maximum (1) or minor (0) codon"
-    default: "R0"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gconsensusz.acd
--- a/GEMBASSY-1.0.3/acd/gconsensusz.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,64 +0,0 @@
-application: gconsensusz [
-  documentation: "Calculates consensus in given array of sequences"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    relations: "EDAM_data:0850 Sequence set"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: high [
-    information: "Z value greater than which is significant"
-    default: "1"
-  ]
-
-  float: low [
-    information: "Z value less than which is insignificant"
-    default: "0.2"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "gconsensusz of $(sequence.name)"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gdeltaenc.acd
--- a/GEMBASSY-1.0.3/acd/gdeltaenc.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,49 +0,0 @@
-application: gdeltaenc [
-  documentation: "Calculates the codon usage bias related to translation
-                  optimization (delta ENC)"
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gdeltagcskew.acd
--- a/GEMBASSY-1.0.3/acd/gdeltagcskew.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,69 +0,0 @@
-application: gdeltagcskew [
-  documentation: "Calculates strand bias of bacterial genome using delta GC skew index"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: at [
-    information: "Include when observing AT skew instead of GC skew "
-    default: "N"
-  ]
-
-  boolean: purine [
-    information: "Include when observing purine (AG/TC) skew"
-    default: "N"
-  ]
-
-  boolean: keto [
-    information: "Include when observing keto (TG/AC) skew"
-    default: "N"
-  ]
-
-  selection: method [
-    information: "Choose the nucleotides to use 'degenerate', 'gc3', or 'all'"
-    values: "degenerate;gc3;all"
-    default: "degenerate"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gdinuc.acd
--- a/GEMBASSY-1.0.3/acd/gdinuc.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,68 +0,0 @@
-application: gdinuc [
-  documentation: "Calculates dinucleotide usage "
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translates using standard codon table"
-    default: "N"
-  ]
-
-  list: position [
-    information: "Codon position or reading frame"
-    values: "all:Assess all codon positions;
-             12:Assess the reading frame 1-2;
-             23:Assess the reading frame 2-3;
-             31:Assess the reading frame 3-1"
-    default: "all"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key (i.e. amino acids and nucleotides)"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gdistincc.acd
--- a/GEMBASSY-1.0.3/acd/gdistincc.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,56 +0,0 @@
-application: gdistincc [
-  documentation: "Calculates the distance between two loci in circular chromosomes"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:3073 Nucleic acid feature detection"
-  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  integer: first [
-    parameter: "Y"
-    information: "Position to find the distance"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "Y"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: second [
-    information: "If the second position is negative, position of replication origin is used"
-    default: "-1"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    relations: "EDAM_data:3127 Nucleic acid features (replication and
-                recombination)"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gdnawalk.acd
--- a/GEMBASSY-1.0.3/acd/gdnawalk.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,43 +0,0 @@
-application: gdnawalk [
-  documentation: "Draws DNA Walk map of the genome"
-  groups: "Display"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0092 Data visualisation"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: format [
-    information: "Output file format. Dependent on 'convert' command"
-    knowntype: "output format"
-    default: "png"
-  ]
-
-endsection: input
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  string: goutfile [
-    information: "Output file for non interactive displays"
-    knowntype: "output filename"
-    relations: "EDAM_data:1274 DNA map"
-    default: "gdnawalk"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/genc.acd
--- a/GEMBASSY-1.0.3/acd/genc.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,58 +0,0 @@
-application: genc [
-  documentation: "Calculates the effective number of codons (Nc)"
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translates using standard codon table"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key (i.e. amino acids and nucleotides)"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/genret.acd
--- a/GEMBASSY-1.0.3/acd/genret.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,68 +0,0 @@
-application: genret [
-  documentation: "Retrieves various gene features from genome flatfile"
-  groups: "Edit, Data retrieval, Feature tables"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0160 Sequence sites and features"
-  relations: "EDAM_topic:0091 Data handling"
-  relations: "EDAM_operation:2422 Data retrieval"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: gene [
-    parameter: "Y"
-    information: "List of gene name(s) to report"
-    knowntype: "sequence id list"
-    default: "*"
-  ]
-
-  string: access [
-    parameter: "Y"
-    information: "Name of gene feature to access"
-    knowntype: "feature key"
-    word: "Y"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  string: argument [
-    information: "Extra arguments to pass to method"
-    knowntype: "string"
-    default: ""
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    extension: "$(access).genret"
-    information: "Sequence output file"
-    knowntype: "sequence data"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gentrez.acd
--- a/GEMBASSY-1.0.3/acd/gentrez.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,39 +0,0 @@
-application: gentrez [
-  documentation: "Searches NCBI Entrez"
-  groups: "Data Retrieval:Text data"
-  embassy: "gembassy"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  string: database [
-    parameter: "Y"
-    information: "NCBI database to search"
-    knowntype: "name"
-    default: "pubmed"
-  ]
-
-  string: query [
-    parameter: "Y"
-    information: "Query to search"
-    knowntype: "string"
-  ]
-
-endsection: input
-
-section: output [
-        information: "Output section"
-        type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "ASCII text output file"
-    knowntype: "ascii text"
-    default: "$(database).$(query).gentrez"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gew.acd
--- a/GEMBASSY-1.0.3/acd/gew.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,58 +0,0 @@
-application: gew [
-  documentation: "Calculates a measure of synonymous codon usage evenness (Ew)"
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translates using standard codon table"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key (i.e. amino acids and nucleotides)"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gfindoriter.acd
--- a/GEMBASSY-1.0.3/acd/gfindoriter.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,61 +0,0 @@
-application: gfindoriter [
-  documentation: "Predicts the replication origin and terminus in bacterial genomes"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:3073 Nucleic acid feature detection"
-  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: window [
-    information: "Number of windows to use for Fat Fourier Transform. Only active when -lowpass option is specified. Value must be the power of two"
-    default: "4096"
-  ]
-
-  boolean: purine [
-    information: "Use purine skew for calculation"
-    default: "N"
-  ]
-
-  boolean: keto [
-    information: "Use keto skew for calculation"
-    default: "N"
-  ]
-
-  integer: lowpass [
-    information: "Lowpass filter strength in percent. Typically 95 or 99 works best"
-    default: ""
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    relations: "EDAM_data:3127 Nucleic acid features (replication and
-                recombination)"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gfop.acd
--- a/GEMBASSY-1.0.3/acd/gfop.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,52 +0,0 @@
-application: gfop [
-  documentation: "Calculates the frequency of optimal codons (Fop)"
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translates using standard codon table"
-    default: "N"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/ggcsi.acd
--- a/GEMBASSY-1.0.3/acd/ggcsi.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,74 +0,0 @@
-application: ggcsi [
-  documentation: "GC Skew Index: an index for strand-specific mutational bias"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: gcsi [
-    information: "GCSI version to use"
-    values:  "1;2"
-    default: "2"
-  ]
-
-  integer: window [
-    information: "Number of windows. Must be a power of 2"
-    default: "4096"
-  ]
-
-  boolean: purine [
-    information: "Use purine skew for calculation"
-    default: "N"
-  ]
-
-  boolean: keto [
-    information: "Use keto skew for calculation"
-    default: "N"
-  ]
-
-  boolean: at [
-    information: "Use AT skew for calculation"
-    default: "N"
-  ]
-
-  boolean: pval [
-    information: "Calculate p-value when GCSI version 2 is selected"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/ggcskew.acd
--- a/GEMBASSY-1.0.3/acd/ggcskew.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,85 +0,0 @@
-application: ggcskew [
-  documentation: "Calculates and plots the GC skew of the input sequence"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: window [
-    information: "Window size to observe"
-    default: "10000"
-  ]
-
-  integer: slide [
-    information: "Window slide size"
-    default: "10000"
-  ]
-
-  boolean: cumulative [
-    information: "Include to calculate cumulative skew"
-    default: "N"
-  ]
-
-  boolean: at [
-    information: "Include for observing AT skew instead of GC skew"
-    default: "N"
-  ]
-
-  boolean: purine [
-    information: "Include for observing purine (AG/TC) skew"
-    default: "N"
-  ]
-
-  boolean: keto [
-    information: "Include for observing keto (TG/AC) skew"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "ggcskew of $(sequence.name)"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/ggcwin.acd
--- a/GEMBASSY-1.0.3/acd/ggcwin.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,75 +0,0 @@
-application: ggcwin [
-  documentation: "Calculates and plots the GC content along the given genome"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: window [
-    information: "Window size to observe"
-    default: "10000"
-  ]
-
-  boolean: at [
-    information: "Include for observing AT skew instead of GC skew"
-    default: "N"
- ]
-
-  boolean: purine [
-    information: "Include for observing purine (AG/TC) skew"
-    default: "N"
-  ]
-
-  boolean: keto [
-    information: "Include for observing keto (TG/AC) skew"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "ggcwin of $(sequence.name)"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/ggeneskew.acd
--- a/GEMBASSY-1.0.3/acd/ggeneskew.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,87 +0,0 @@
-application: ggeneskew [
-  documentation: "Calculates and plots the gene strand bias of the given genome"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: window [
-    information: "Window size to observe"
-    default: "10000"
-  ]
-
-  integer: slide [
-    information: "Window slide size"
-    default: "10000"
-  ]
-
-  boolean: cumulative [
-    information: "Input 1 to calculate cumulative skew"
-    default: "N"
-  ]
-
-  selection: base [
-    information: "Input 'gc', 'at', 'purine', or 'keto' for observing
-                   GC/AT/Purine/Keto skews"
-    values: "none;gc;at;purine;keto"
-    default: "none"
-  ]
-
-  boolean: gctri [
-    information: "Include to use only the third codon positions"
-    default: "N"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "ggeneskew of $(sequence.name)"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/ggenomemap3.acd
--- a/GEMBASSY-1.0.3/acd/ggenomemap3.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,64 +0,0 @@
-application: ggenomemap3 [
-  documentation: "Draws the map of the genome (version 3)"
-  groups: "Display"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0092 Data visualisation"
-  relations: "EDAM_topic:0621 Genome, proteome and model organisms"
-  relations: "EDAM_operation:0573 Map rendering"
-  relations: "EDAM_operation:2466 Map annotation"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: format [
-    information: "Output file format. Dependent on 'convert' command"
-    knowntype: "output format"
-    default: "png"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: width [
-    information: "Image width"
-    default: "8192"
-  ]
-
-  integer: height [
-    information: "Image height"
-    default: "8192"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  string: goutfile [
-    information: "Output file for non interactive displays"
-    relations: "EDAM_data:1278 Genetic map"
-    default: "ggenomemap3"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/ggenomicskew.acd
--- a/GEMBASSY-1.0.3/acd/ggenomicskew.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,71 +0,0 @@
-application: ggenomicskew [
-  documentation: "Calculates and plots the GC skew in different regions of the given genome"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: divide [
-    information: "Window to divide into"
-    default: "250"
-  ]
-
-  boolean: at [
-    information: "Input 1 when observing AT skew instead of GC skew"
-    default: "N"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "ggenomicskew of $(sequence.name)"
-    multiple: "4"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gicdi.acd
--- a/GEMBASSY-1.0.3/acd/gicdi.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,58 +0,0 @@
-application: gicdi [
-  documentation: "Calculates the intrinsic codon deviation index (ICDI)"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translating using standard codon table"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gkmertable.acd
--- a/GEMBASSY-1.0.3/acd/gkmertable.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,55 +0,0 @@
-application: gkmertable [
-  documentation: "Creates an image showing all k-mer abundance within a sequence"
-  groups: "Display"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0092 Data visualisation"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: format [
-    information: "Output file format. Dependent on 'convert' command"
-    knowntype: "output format"
-    default: "png"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: k [
-    information: "Length of oligomer"
-    default: "6"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  string: goutfile [
-    information: "Output file for non interactive displays"
-    knowntype: "output filename"
-    relations: "EDAM_data:2166 Sequence composition plot"
-    default: "gkmertable"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gldabias.acd
--- a/GEMBASSY-1.0.3/acd/gldabias.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,61 +0,0 @@
-application: gldabias [
-  documentation: "Calculates strand bias of bacterial genome using linear
-                  discriminant analysis (LDA)"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: coefficients [
-    information: "Show LDA coefficients"
-    default: "0"
-  ]
-
-  selection: variable [
-    information: "Data to use for LDA. Either 'base', 'codonbase', 'codon', or
-                  'amino'"
-    values: "base;codonbase;codon;amino"
-    default: "codon"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gnucleotideperiodicity.acd
--- a/GEMBASSY-1.0.3/acd/gnucleotideperiodicity.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,71 +0,0 @@
-application: gnucleotideperiodicity [
-  documentation: "Checks the periodicity of certain oligonucleotides"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: window [
-    information: "Window size to seek periodicity"
-    default: "50"
-  ]
-
-  string: nucleotide [
-    information: "Nucleotide to search"
-    knowntype: "nucleotide codes"
-    default: "aa"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "ggcskew of $(sequence.name)"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/goligomercounter.acd
--- a/GEMBASSY-1.0.3/acd/goligomercounter.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,54 +0,0 @@
-application: goligomercounter [
-  documentation: "Counts the number of given oligomers in a sequence"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: oligomer [
-    parameter: "Y"
-    knowntype: "nucleotide codes"
-    information: "Oligomer to count"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: window [
-    information: "Int window size"
-    default: ""
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/goligomersearch.acd
--- a/GEMBASSY-1.0.3/acd/goligomersearch.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,59 +0,0 @@
-application: goligomersearch [
-  documentation: "Searches oligomers in given sequence"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: oligomer [
-    parameter: "Y"
-    knowntype: "nucleotide codes"
-    information: "Oligomer to search"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: return [
-    information: "'position' to return list of positions where oligomers are
-                  found, 'oligo' to return list of oligomers found ordered by
-                  positions, 'both' to return a hash with positions as keys and
-                  oligomers as values, 'distribution' to return four values
-                  about the distribution of given oligomer"
-    values: "position;oligo;both;distribution"
-    default: "position"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gp2.acd
--- a/GEMBASSY-1.0.3/acd/gp2.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,47 +0,0 @@
-application: gp2 [
-  documentation: "Calculates the P2 index of each gene"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gpalindrome.acd
--- a/GEMBASSY-1.0.3/acd/gpalindrome.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,63 +0,0 @@
-application: gpalindrome [
-  documentation: "Searches palindrome sequences"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: shortest [
-    information: "Shortest palindrome to search"
-    default: "4"
-  ]
-
-  integer: loop [
-    information: "Longest stem loop to allow"
-    default: "0"
-  ]
-
-  boolean: gtmatch [
-    information: "If 1, allows g-t match"
-    default: "0"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gphx.acd
--- a/GEMBASSY-1.0.3/acd/gphx.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,58 +0,0 @@
-application: gphx [
-  documentation: "Identifies predicted highly expressed genes"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translating using standard codon table"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gqueryarm.acd
--- a/GEMBASSY-1.0.3/acd/gqueryarm.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,50 +0,0 @@
-application: gqueryarm [
-  documentation: "Gets the replication arm name (left or right) from the given position"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:3073 Nucleic acid feature detection"
-  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  integer: position [
-    parameter: "Y"
-    information: "Position to query"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-        information: "Output section"
-        type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    relations: "EDAM_data:1276 Nucleic acid features"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gquerystrand.acd
--- a/GEMBASSY-1.0.3/acd/gquerystrand.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,57 +0,0 @@
-application: gquerystrand [
-  documentation: "Gets the strand name (leading or lagging) from the given position"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:3073 Nucleic acid feature detection"
-  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  integer: position [
-    parameter: "Y"
-    information: "Position to query"
-    default: "0"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  selection: direction [
-    information: "Strand of the querying position either 'direct' or 'complement'"
-    values: "direct;complement"
-    default: "direct"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-        information: "Output section"
-        type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    relations: "EDAM_data:1276 Nucleic acid features"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/greporiter.acd
--- a/GEMBASSY-1.0.3/acd/greporiter.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,69 +0,0 @@
-application: greporiter [
-  documentation: "Gets the positions of replication origin and terminus"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:3073 Nucleic acid feature detection"
-  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: oriloc [
-    information: "Include Oriloc for prediction"
-    default: "N"
-  ]
-
-  boolean: gcskew [
-    information: "Include to use GC skew shift-point for prediction"
-    default: "N"
-  ]
-
-  integer: difthreshold [
-    information: "Distance between the GC skew shift point and predicted dif
-                  site expressed as the precentage of genome size, used as a
-                  threshold to retrieve dif sequence from the database"
-    default: "0"
-  ]
-
-  boolean: dbonly [
-    information: "Include to only use values available in databases and to
-                  suppress prediction"
-    default: "N"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    relations: "EDAM_data:3127 Nucleic acid features (replication and
-                recombination)"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gscs.acd
--- a/GEMBASSY-1.0.3/acd/gscs.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,58 +0,0 @@
-application: gscs [
-  documentation: "Calculates the scaled chi-square"
-  groups: "Nucleic:Codon usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: translate [
-    information: "Include when translates using standard codon table"
-    default: "N"
-  ]
-
-  string: delkey [
-    information: "Regular expression to delete key (i.e. amino acids and nucleotides)"
-    knowntype: "regular expression"
-    default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gseq2png.acd
--- a/GEMBASSY-1.0.3/acd/gseq2png.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,60 +0,0 @@
-application: gseq2png [
-  documentation: "Converts a sequence to PNG image"
-  groups: "Display"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0092 Data visualisation"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-  string: format [
-    information: "Output file format. Dependent on 'convert' command"
-    knowntype: "output format"
-    default: "png"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: width [
-    information: "Width of the image"
-    default: "640"
-  ]
-
-  integer: window [
-    information: "Window size of a sequence to represent each pixel"
-    default: "20"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  string: goutfile [
-    information: "Output file for non interactive displays"
-    knowntype: "output filename"
-    relations: "EDAM_data:2166 Sequence composition plot"
-    default: "gseq2png"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gseqinfo.acd
--- a/GEMBASSY-1.0.3/acd/gseqinfo.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,36 +0,0 @@
-application: gseqinfo [
-  documentation: "Prints out basic nucleotide sequence statistics"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gshuffleseq.acd
--- a/GEMBASSY-1.0.3/acd/gshuffleseq.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,46 +0,0 @@
-application: gshuffleseq [
-  documentation: "Creates randomized sequence with conserved k-mer composition"
-  groups: "Nucleic:Mutation"
-  embassy: "gembassy"
-  groups: "Nucleic:Mutation, Protein:Mutation"
-  relations: "EDAM_topic:0091 Data handling"
-  relations: "EDAM_topic:0199 Genetic variation"
-  relations: "EDAM_operation:0367 Sequence mutation and randomization"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "any"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: k [
-    information: "Sequence k-mer to preserve composition"
-    default: "1"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  seqout: outseq [
-    parameter: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gsignature.acd
--- a/GEMBASSY-1.0.3/acd/gsignature.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,64 +0,0 @@
-application: gsignature [
-  documentation: "Calculates oligonucleotide usage (genomic signature)"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: wordlength [
-    information: "Word length"
-    default: "2"
-  ]
-
-  boolean: bothstrand [
-    information: "Include to use both strands direct used otherwise"
-    default: "Y"
-  ]
-
-  boolean: oe [
-    information: "Use observed (0) or O/E (1) value"
-    information: "Include to use O/E value observed values used otherwise"
-    default: "Y"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Program compseq output file"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gsvalue.acd
--- a/GEMBASSY-1.0.3/acd/gsvalue.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,52 +0,0 @@
-application: gsvalue [
-  documentation: "Calculates the strength of selected codon usage bias (S)"
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  boolean: sharp [
-    information: "Include to use the 40 genes used by Sharp instead of ribosomal proteins"
-    default: "N"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gviewcds.acd
--- a/GEMBASSY-1.0.3/acd/gviewcds.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,71 +0,0 @@
-application: gviewcds [
-  documentation: "Displays a graph of nucleotide contents around start and stop codons"
-  groups: "Nucleic:Composition"
-  embassy: "gembassy"
-  relations: "EDAM_topic:0157 Sequence composition analysis"
-  relations: "EDAM_operation:0377 Sequence composition calculation
-              (nucleic acid)"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  integer: length [
-    information: "Length in bases to show around start/stop codons"
-    default: "100"
-  ]
-
-  integer: gap [
-    information: "Gap shown in graph in between start/stop codon neighbors"
-    default: "3"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  toggle: plot [
-    information: "Include to plot result"
-    default: "Y"
-  ]
-
-  xygraph: graph [
-    standard: "$(plot)"
-    gtitle: "gviewcds of $(sequence.name)"
-    multiple: "4"
-  ]
-
-  outfile: outfile [
-    standard: "@(!$(plot))"
-    nullok: "Y"
-    nulldefault: "$(plot)"
-    information: "Program compseq output file (optional)"
-    knowntype: "compseq output"
-    relations: "EDAM_data:3086 Nucleic acid sequence composition"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/acd/gwvalue.acd
--- a/GEMBASSY-1.0.3/acd/gwvalue.acd Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,61 +0,0 @@
-application: gwvalue [
-  documentation: "Calculates the 'relative adaptiveness of each codon' (W)"
-  groups: "Nucleic:Codon Usage"
-  embassy: "gembassy"
-  relations: "EDAM_operation:0286 Codon usage analysis"
-  relations: "EDAM_topic:0107 Codon usage analysis"
-]
-
-section: input [
-  information: "Input section"
-  type: "page"
-]
-
-  seqall: sequence [
-    parameter: "Y"
-    type: "nucleotide"
-    features: "Y"
-    relations: "EDAM_data:0849 Sequence record"
-  ]
-
-endsection: input
-
-section: advanced [
-  information: "Advanced section"
-  type: "page"
-]
-
-  string: include [
-    information: "Regular expression to include genes in a reference set a
-                  reference set in several studies are in-built 1: Nakamura
-                  and Tabata, 2: Sharp and Li, 3: Sakai et al."
-    knowntype: "regular expression"
-    default: "ribosomal.*protein"
-  ]
-
-  string: exclude [
-    information: "Regular expression to exclude genes from a reference set"
-    knowntype: "regular expression"
-    default: "[Mm]itochondrial"
-  ]
-
-  boolean: accid [
-    information: "Include to use sequence accession ID as query"
-    default: "N"
-  ]
-
-endsection: advanced
-
-section: output [
-  information: "Output section"
-  type: "page"
-]
-
-  outfile: outfile [
-    parameter: "Y"
-    information: "Codon usage output file"
-    knowntype: "codon usage"
-    relations: "EDAM_data:2865 Codon usage bias"
-  ]
-
-endsection: output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/aclocal.m4
--- a/GEMBASSY-1.0.3/aclocal.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b"@@ -1,1165 +0,0 @@\n-# generated automatically by aclocal 1.15 -*- Autoconf -*-\n-\n-# Copyright (C) 1996-2014 Free Software Foundation, Inc.\n-\n-# This file is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-m4_ifndef([AC_CONFIG_MACRO_DIRS], [m4_defun([_AM_CONFIG_MACRO_DIRS], [])m4_defun([AC_CONFIG_MACRO_DIRS], [_AM_CONFIG_MACRO_DIRS($@)])])\n-m4_ifndef([AC_AUTOCONF_VERSION],\n- [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl\n-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,\n-[m4_warning([this file was generated for autoconf 2.69.\n-You have another version of autoconf. It may work, but is not guaranteed to.\n-If you have problems, you may need to regenerate the build system entirely.\n-To do so, use the procedure documented by the package, typically 'autoreconf'.])])\n-\n-# Copyright (C) 2002-2014 Free Software Foundation, Inc.\n-#\n-# This file is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# AM_AUTOMAKE_VERSION(VERSION)\n-# ----------------------------\n-# Automake X.Y traces this macro to ensure aclocal.m4 has been\n-# generated from the m4 files accompanying Automake X.Y.\n-# (This private macro should not be called outside this file.)\n-AC_DEFUN([AM_AUTOMAKE_VERSION],\n-[am__api_version='1.15'\n-dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to\n-dnl require some minimum version. Point them to the right macro.\n-m4_if([$1], [1.15], [],\n- [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl\n-])\n-\n-# _AM_AUTOCONF_VERSION(VERSION)\n-# -----------------------------\n-# aclocal traces this macro to find the Autoconf version.\n-# This is a private macro too. Using m4_define simplifies\n-# the logic in aclocal, which can simply ignore this definition.\n-m4_define([_AM_AUTOCONF_VERSION], [])\n-\n-# AM_SET_CURRENT_AUTOMAKE_VERSION\n-# -------------------------------\n-# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.\n-# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.\n-AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],\n-[AM_AUTOMAKE_VERSION([1.15])dnl\n-m4_ifndef([AC_AUTOCONF_VERSION],\n- [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl\n-_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])\n-\n-# AM_AUX_DIR_EXPAND -*- Autoconf -*-\n-\n-# Copyright (C) 2001-2014 Free Software Foundation, Inc.\n-#\n-# This file is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets\n-# $ac_aux_dir to '$srcdir/foo'. In other projects, it is set to\n-# '$srcdir', '$srcdir/..', or '$srcdir/../..'.\n-#\n-# Of course, Automake must honor this variable whenever it calls a\n-# tool from the auxiliary directory. The problem is that $srcdir (and\n-# therefore $ac_aux_dir as well) can be either absolute or relative,\n-# depending on how configure is run. This is pretty annoying, since\n-# it makes $ac_aux_dir quite unusable in subdirectories: in the top\n-# source directory, any form will work fine, but in subdirectories a\n-# relative path needs to be adjusted first.\n-#\n-# $ac_aux_dir/missing\n-# fails when called from a subdirectory if $ac_aux_dir is relative\n-# $top_srcdir/$ac_aux_dir/missing\n-# fails if $ac_aux_dir is absolute,\n-# fails when called from a subdirectory in a VPATH build with\n-# a relative $ac_aux_dir\n-#\n-# The reason of the latter failure is that $top_srcdir and $ac_aux_dir\n-# are both pr"..b'${TAR-tar}\'])\n-\n-# We\'ll loop over all known methods to create a tar archive until one works.\n-_am_tools=\'gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none\'\n-\n-m4_if([$1], [v7],\n- [am__tar=\'$${TAR-tar} chof - "$$tardir"\' am__untar=\'$${TAR-tar} xf -\'],\n-\n- [m4_case([$1],\n- [ustar],\n- [# The POSIX 1988 \'ustar\' format is defined with fixed-size fields.\n- # There is notably a 21 bits limit for the UID and the GID. In fact,\n- # the \'pax\' utility can hang on bigger UID/GID (see automake bug#8343\n- # and bug#13588).\n- am_max_uid=2097151 # 2^21 - 1\n- am_max_gid=$am_max_uid\n- # The $UID and $GID variables are not portable, so we need to resort\n- # to the POSIX-mandated id(1) utility. Errors in the \'id\' calls\n- # below are definitely unexpected, so allow the users to see them\n- # (that is, avoid stderr redirection).\n- am_uid=`id -u || echo unknown`\n- am_gid=`id -g || echo unknown`\n- AC_MSG_CHECKING([whether UID \'$am_uid\' is supported by ustar format])\n- if test $am_uid -le $am_max_uid; then\n- AC_MSG_RESULT([yes])\n- else\n- AC_MSG_RESULT([no])\n- _am_tools=none\n- fi\n- AC_MSG_CHECKING([whether GID \'$am_gid\' is supported by ustar format])\n- if test $am_gid -le $am_max_gid; then\n- AC_MSG_RESULT([yes])\n- else\n- AC_MSG_RESULT([no])\n- _am_tools=none\n- fi],\n-\n- [pax],\n- [],\n-\n- [m4_fatal([Unknown tar format])])\n-\n- AC_MSG_CHECKING([how to create a $1 tar archive])\n-\n- # Go ahead even if we have the value already cached. We do so because we\n- # need to set the values for the \'am__tar\' and \'am__untar\' variables.\n- _am_tools=${am_cv_prog_tar_$1-$_am_tools}\n-\n- for _am_tool in $_am_tools; do\n- case $_am_tool in\n- gnutar)\n- for _am_tar in tar gnutar gtar; do\n- AM_RUN_LOG([$_am_tar --version]) && break\n- done\n- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "\'"$$tardir"\'\n- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "\'"$tardir"\'\n- am__untar="$_am_tar -xf -"\n- ;;\n- plaintar)\n- # Must skip GNU tar: if it does not support --format= it doesn\'t create\n- # ustar tarball either.\n- (tar --version) >/dev/null 2>&1 && continue\n- am__tar=\'tar chf - "$$tardir"\'\n- am__tar_=\'tar chf - "$tardir"\'\n- am__untar=\'tar xf -\'\n- ;;\n- pax)\n- am__tar=\'pax -L -x $1 -w "$$tardir"\'\n- am__tar_=\'pax -L -x $1 -w "$tardir"\'\n- am__untar=\'pax -r\'\n- ;;\n- cpio)\n- am__tar=\'find "$$tardir" -print | cpio -o -H $1 -L\'\n- am__tar_=\'find "$tardir" -print | cpio -o -H $1 -L\'\n- am__untar=\'cpio -i -H $1 -d\'\n- ;;\n- none)\n- am__tar=false\n- am__tar_=false\n- am__untar=false\n- ;;\n- esac\n-\n- # If the value was cached, stop now. We just wanted to have am__tar\n- # and am__untar set.\n- test -n "${am_cv_prog_tar_$1}" && break\n-\n- # tar/untar a dummy directory, and stop if the command works.\n- rm -rf conftest.dir\n- mkdir conftest.dir\n- echo GrepMe > conftest.dir/file\n- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])\n- rm -rf conftest.dir\n- if test -s conftest.tar; then\n- AM_RUN_LOG([$am__untar <conftest.tar])\n- AM_RUN_LOG([cat conftest.dir/file])\n- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break\n- fi\n- done\n- rm -rf conftest.dir\n-\n- AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])\n- AC_MSG_RESULT([$am_cv_prog_tar_$1])])\n-\n-AC_SUBST([am__tar])\n-AC_SUBST([am__untar])\n-]) # _AM_PROG_TAR\n-\n-m4_include([m4/general.m4])\n-m4_include([m4/hpdf.m4])\n-m4_include([m4/java.m4])\n-m4_include([m4/lf_x11.m4])\n-m4_include([m4/libtool.m4])\n-m4_include([m4/ltoptions.m4])\n-m4_include([m4/ltsugar.m4])\n-m4_include([m4/ltversion.m4])\n-m4_include([m4/lt~obsolete.m4])\n-m4_include([m4/mysql.m4])\n-m4_include([m4/pngdriver.m4])\n-m4_include([m4/postgresql.m4])\n-m4_include([m4/sgi.m4])\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/compile
--- a/GEMBASSY-1.0.3/compile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,347 +0,0 @@
-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
-
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
-# Written by Tom Tromey <tromey@cygnus.com>.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake@gnu.org> or send patches to
-# <automake-patches@gnu.org>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" "" $nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
-  file=$1
-  case $file in
-    / | /[!/]*) # absolute file, and not a UNC file
-      if test -z "$file_conv"; then
- # lazily determine how to convert abs files
- case `uname -s` in
-   MINGW*)
-     file_conv=mingw
-     ;;
-   CYGWIN*)
-     file_conv=cygwin
-     ;;
-   *)
-     file_conv=wine
-     ;;
- esac
-      fi
-      case $file_conv/,$2, in
- *,$file_conv,*)
-   ;;
- mingw/*)
-   file=`cmd //C echo "$file " | sed -e 's/"$.*$ " *$/\1/'`
-   ;;
- cygwin/*)
-   file=`cygpath -m "$file" || echo "$file"`
-   ;;
- wine/*)
-   file=`winepath -w "$file" || echo "$file"`
-   ;;
-      esac
-      ;;
-  esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
-  func_file_conv "$1"
-  if test -z "$lib_path"; then
-    lib_path=$file
-  else
-    lib_path="$lib_path;$file"
-  fi
-  linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
-  lib=$1
-  found=no
-  save_IFS=$IFS
-  IFS=';'
-  for dir in $lib_path $LIB
-  do
-    IFS=$save_IFS
-    if $shared && test -f "$dir/$lib.dll.lib"; then
-      found=yes
-      lib=$dir/$lib.dll.lib
-      break
-    fi
-    if test -f "$dir/$lib.lib"; then
-      found=yes
-      lib=$dir/$lib.lib
-      break
-    fi
-    if test -f "$dir/lib$lib.a"; then
-      found=yes
-      lib=$dir/lib$lib.a
-      break
-    fi
-  done
-  IFS=$save_IFS
-
-  if test "$found" != yes; then
-    lib=$lib.lib
-  fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
-  # Assume a capable shell
-  lib_path=
-  shared=:
-  linker_opts=
-  for arg
-  do
-    if test -n "$eat"; then
-      eat=
-    else
-      case $1 in
- -o)
-   # configure might choose to run compile as 'compile cc -o foo foo.c'.
-   eat=1
-   case $2 in
-     *.o | *.[oO][bB][jJ])
-       func_file_conv "$2"
-       set x "$@" -Fo"$file"
-       shift
-       ;;
-     *)
-       func_file_conv "$2"
-       set x "$@" -Fe"$file"
-       shift
-       ;;
-   esac
-   ;;
- -I)
-   eat=1
-   func_file_conv "$2" mingw
-   set x "$@" -I"$file"
-   shift
-   ;;
- -I*)
-   func_file_conv "${1#-I}" mingw
-   set x "$@" -I"$file"
-   shift
-   ;;
- -l)
-   eat=1
-   func_cl_dashl "$2"
-   set x "$@" "$lib"
-   shift
-   ;;
- -l*)
-   func_cl_dashl "${1#-l}"
-   set x "$@" "$lib"
-   shift
-   ;;
- -L)
-   eat=1
-   func_cl_dashL "$2"
-   ;;
- -L*)
-   func_cl_dashL "${1#-L}"
-   ;;
- -static)
-   shared=false
-   ;;
- -Wl,*)
-   arg=${1#-Wl,}
-   save_ifs="$IFS"; IFS=','
-   for flag in $arg; do
-     IFS="$save_ifs"
-     linker_opts="$linker_opts $flag"
-   done
-   IFS="$save_ifs"
-   ;;
- -Xlinker)
-   eat=1
-   linker_opts="$linker_opts $2"
-   ;;
- -*)
-   set x "$@" "$1"
-   shift
-   ;;
- *.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
-   func_file_conv "$1"
-   set x "$@" -Tp"$file"
-   shift
-   ;;
- *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
-   func_file_conv "$1" mingw
-   set x "$@" "$file"
-   shift
-   ;;
- *)
-   set x "$@" "$1"
-   shift
-   ;;
-      esac
-    fi
-    shift
-  done
-  if test -n "$linker_opts"; then
-    linker_opts="-link$linker_opts"
-  fi
-  exec "$@" $linker_opts
-  exit 1
-}
-
-eat=
-
-case $1 in
-  '')
-     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
-     exit 1;
-     ;;
-  -h | --h*)
-    cat <<\EOF
-Usage: compile [--help] [--version] PROGRAM [ARGS]
-
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
-arguments, and rename the output as expected.
-
-If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <bug-automake@gnu.org>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "compile $scriptversion"
-    exit $?
-    ;;
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
-    func_cl_wrapper "$@"      # Doesn't return...
-    ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
-  if test -n "$eat"; then
-    eat=
-  else
-    case $1 in
-      -o)
- # configure might choose to run compile as 'compile cc -o foo foo.c'.
- # So we strip '-o arg' only if arg is an object.
- eat=1
- case $2 in
-   *.o | *.obj)
-     ofile=$2
-     ;;
-   *)
-     set x "$@" -o "$2"
-     shift
-     ;;
- esac
- ;;
-      *.c)
- cfile=$1
- set x "$@" "$1"
- shift
- ;;
-      *)
- set x "$@" "$1"
- shift
- ;;
-    esac
-  fi
-  shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
-  # If no '-o' option was seen then we might have been invoked from a
-  # pattern rule where we don't need one.  That is ok -- this is a
-  # normal compilation that the losing compiler can handle.  If no
-  # '.c' file was seen then we are probably linking.  That is also
-  # ok.
-  exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file.  Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
-  if mkdir "$lockdir" >/dev/null 2>&1; then
-    break
-  fi
-  sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
-  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
-  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/config.guess
--- a/GEMBASSY-1.0.3/config.guess Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1421 +0,0 @@\n-#! /bin/sh\n-# Attempt to guess a canonical system name.\n-# Copyright 1992-2014 Free Software Foundation, Inc.\n-\n-timestamp=\'2014-11-04\'\n-\n-# This file is free software; you can redistribute it and/or modify it\n-# under the terms of the GNU General Public License as published by\n-# the Free Software Foundation; either version 3 of the License, or\n-# (at your option) any later version.\n-#\n-# This program is distributed in the hope that it will be useful, but\n-# WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n-# General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program; if not, see <http://www.gnu.org/licenses/>.\n-#\n-# As a special exception to the GNU General Public License, if you\n-# distribute this file as part of a program that contains a\n-# configuration script generated by Autoconf, you may include it under\n-# the same distribution terms that you use for the rest of that\n-# program. This Exception is an additional permission under section 7\n-# of the GNU General Public License, version 3 ("GPLv3").\n-#\n-# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.\n-#\n-# You can get the latest version of this script from:\n-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD\n-#\n-# Please send patches to <config-patches@gnu.org>.\n-\n-\n-me=`echo "$0" | sed -e \'s,.*/,,\'`\n-\n-usage="\\\n-Usage: $0 [OPTION]\n-\n-Output the configuration name of the system \\`$me\' is run on.\n-\n-Operation modes:\n- -h, --help print this help, then exit\n- -t, --time-stamp print date of last modification, then exit\n- -v, --version print version number, then exit\n-\n-Report bugs and patches to <config-patches@gnu.org>."\n-\n-version="\\\n-GNU config.guess ($timestamp)\n-\n-Originally written by Per Bothner.\n-Copyright 1992-2014 Free Software Foundation, Inc.\n-\n-This is free software; see the source for copying conditions. There is NO\n-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."\n-\n-help="\n-Try \\`$me --help\' for more information."\n-\n-# Parse command line\n-while test $# -gt 0 ; do\n- case $1 in\n- --time-stamp | --time* | -t )\n- echo "$timestamp" ; exit ;;\n- --version | -v )\n- echo "$version" ; exit ;;\n- --help | --h* | -h )\n- echo "$usage"; exit ;;\n- -- ) # Stop option processing\n- shift; break ;;\n- - )\t# Use stdin as input.\n- break ;;\n- -* )\n- echo "$me: invalid option $1$help" >&2\n- exit 1 ;;\n- * )\n- break ;;\n- esac\n-done\n-\n-if test $# != 0; then\n- echo "$me: too many arguments$help" >&2\n- exit 1\n-fi\n-\n-trap \'exit 1\' 1 2 15\n-\n-# CC_FOR_BUILD -- compiler used by this script. Note that the use of a\n-# compiler to aid in system detection is discouraged as it requires\n-# temporary files to be created and, as you can see below, it is a\n-# headache to deal with in a portable fashion.\n-\n-# Historically, `CC_FOR_BUILD\' used to be named `HOST_CC\'. We still\n-# use `HOST_CC\' if defined, but it is deprecated.\n-\n-# Portable tmp directory creation inspired by the Autoconf team.\n-\n-set_cc_for_build=\'\n-trap "exitcode=\\$?; (rm -f \\$tmpfiles 2>/dev/null; rmdir \\$tmp 2>/dev/null) && exit \\$exitcode" 0 ;\n-trap "rm -f \\$tmpfiles 2>/dev/null; rmdir \\$tmp 2>/dev/null; exit 1" 1 2 13 15 ;\n-: ${TMPDIR=/tmp} ;\n- { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||\n- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||\n- { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||\n- { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;\n-dummy=$tmp/dummy ;\n-tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;\n-case $CC_FOR_BUILD,$HOST_CC,$CC in\n- ,,) echo "int x;" > $dummy.c ;\n-\tfor'..b'ces.\n-\t UNAME_PROCESSOR=x86_64\n-\tfi\n-\techo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}\n-\texit ;;\n- *:procnto*:*:* | *:QNX:[0123456789]*:*)\n-\tUNAME_PROCESSOR=`uname -p`\n-\tif test "$UNAME_PROCESSOR" = "x86"; then\n-\t\tUNAME_PROCESSOR=i386\n-\t\tUNAME_MACHINE=pc\n-\tfi\n-\techo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}\n-\texit ;;\n- *:QNX:*:4*)\n-\techo i386-pc-qnx\n-\texit ;;\n- NEO-?:NONSTOP_KERNEL:*:*)\n-\techo neo-tandem-nsk${UNAME_RELEASE}\n-\texit ;;\n- NSE-*:NONSTOP_KERNEL:*:*)\n-\techo nse-tandem-nsk${UNAME_RELEASE}\n-\texit ;;\n- NSR-?:NONSTOP_KERNEL:*:*)\n-\techo nsr-tandem-nsk${UNAME_RELEASE}\n-\texit ;;\n- *:NonStop-UX:*:*)\n-\techo mips-compaq-nonstopux\n-\texit ;;\n- BS2000:POSIX*:*:*)\n-\techo bs2000-siemens-sysv\n-\texit ;;\n- DS/*:UNIX_System_V:*:*)\n-\techo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}\n-\texit ;;\n- *:Plan9:*:*)\n-\t# "uname -m" is not consistent, so use $cputype instead. 386\n-\t# is converted to i386 for consistency with other x86\n-\t# operating systems.\n-\tif test "$cputype" = "386"; then\n-\t UNAME_MACHINE=i386\n-\telse\n-\t UNAME_MACHINE="$cputype"\n-\tfi\n-\techo ${UNAME_MACHINE}-unknown-plan9\n-\texit ;;\n- *:TOPS-10:*:*)\n-\techo pdp10-unknown-tops10\n-\texit ;;\n- *:TENEX:*:*)\n-\techo pdp10-unknown-tenex\n-\texit ;;\n- KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)\n-\techo pdp10-dec-tops20\n-\texit ;;\n- XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)\n-\techo pdp10-xkl-tops20\n-\texit ;;\n- *:TOPS-20:*:*)\n-\techo pdp10-unknown-tops20\n-\texit ;;\n- *:ITS:*:*)\n-\techo pdp10-unknown-its\n-\texit ;;\n- SEI:*:*:SEIUX)\n-\techo mips-sei-seiux${UNAME_RELEASE}\n-\texit ;;\n- *:DragonFly:*:*)\n-\techo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e \'s/[-(].*//\'`\n-\texit ;;\n- *:*VMS:*:*)\n-\tUNAME_MACHINE=`(uname -p) 2>/dev/null`\n-\tcase "${UNAME_MACHINE}" in\n-\t A*) echo alpha-dec-vms ; exit ;;\n-\t I*) echo ia64-dec-vms ; exit ;;\n-\t V*) echo vax-dec-vms ; exit ;;\n-\tesac ;;\n- *:XENIX:*:SysV)\n-\techo i386-pc-xenix\n-\texit ;;\n- i*86:skyos:*:*)\n-\techo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e \'s/ .*$//\'\n-\texit ;;\n- i*86:rdos:*:*)\n-\techo ${UNAME_MACHINE}-pc-rdos\n-\texit ;;\n- i*86:AROS:*:*)\n-\techo ${UNAME_MACHINE}-pc-aros\n-\texit ;;\n- x86_64:VMkernel:*:*)\n-\techo ${UNAME_MACHINE}-unknown-esx\n-\texit ;;\n-esac\n-\n-cat >&2 <<EOF\n-$0: unable to guess system type\n-\n-This script, last modified $timestamp, has failed to recognize\n-the operating system you are using. It is advised that you\n-download the most up to date version of the config scripts from\n-\n- http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD\n-and\n- http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD\n-\n-If the version you run ($0) is already up to date, please\n-send the following data and any information you think might be\n-pertinent to <config-patches@gnu.org> in order to provide the needed\n-information to handle your system.\n-\n-config.guess timestamp = $timestamp\n-\n-uname -m = `(uname -m) 2>/dev/null || echo unknown`\n-uname -r = `(uname -r) 2>/dev/null || echo unknown`\n-uname -s = `(uname -s) 2>/dev/null || echo unknown`\n-uname -v = `(uname -v) 2>/dev/null || echo unknown`\n-\n-/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`\n-/bin/uname -X = `(/bin/uname -X) 2>/dev/null`\n-\n-hostinfo = `(hostinfo) 2>/dev/null`\n-/bin/universe = `(/bin/universe) 2>/dev/null`\n-/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`\n-/bin/arch = `(/bin/arch) 2>/dev/null`\n-/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`\n-/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`\n-\n-UNAME_MACHINE = ${UNAME_MACHINE}\n-UNAME_RELEASE = ${UNAME_RELEASE}\n-UNAME_SYSTEM = ${UNAME_SYSTEM}\n-UNAME_VERSION = ${UNAME_VERSION}\n-EOF\n-\n-exit 1\n-\n-# Local variables:\n-# eval: (add-hook \'write-file-hooks \'time-stamp)\n-# time-stamp-start: "timestamp=\'"\n-# time-stamp-format: "%:y-%02m-%02d"\n-# time-stamp-end: "\'"\n-# End:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/config.sub
--- a/GEMBASSY-1.0.3/config.sub Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1807 +0,0 @@\n-#! /bin/sh\n-# Configuration validation subroutine script.\n-# Copyright 1992-2014 Free Software Foundation, Inc.\n-\n-timestamp=\'2014-12-03\'\n-\n-# This file is free software; you can redistribute it and/or modify it\n-# under the terms of the GNU General Public License as published by\n-# the Free Software Foundation; either version 3 of the License, or\n-# (at your option) any later version.\n-#\n-# This program is distributed in the hope that it will be useful, but\n-# WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n-# General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program; if not, see <http://www.gnu.org/licenses/>.\n-#\n-# As a special exception to the GNU General Public License, if you\n-# distribute this file as part of a program that contains a\n-# configuration script generated by Autoconf, you may include it under\n-# the same distribution terms that you use for the rest of that\n-# program. This Exception is an additional permission under section 7\n-# of the GNU General Public License, version 3 ("GPLv3").\n-\n-\n-# Please send patches to <config-patches@gnu.org>.\n-#\n-# Configuration subroutine to validate and canonicalize a configuration type.\n-# Supply the specified configuration type as an argument.\n-# If it is invalid, we print an error message on stderr and exit with code 1.\n-# Otherwise, we print the canonical config type on stdout and succeed.\n-\n-# You can get the latest version of this script from:\n-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD\n-\n-# This file is supposed to be the same for all GNU packages\n-# and recognize all the CPU types, system types and aliases\n-# that are meaningful with *any* GNU software.\n-# Each package is responsible for reporting which valid configurations\n-# it does not support. The user should be able to distinguish\n-# a failure to support a valid configuration from a meaningless\n-# configuration.\n-\n-# The goal of this file is to map all the various variations of a given\n-# machine specification into a single specification in the form:\n-#\tCPU_TYPE-MANUFACTURER-OPERATING_SYSTEM\n-# or in some cases, the newer four-part form:\n-#\tCPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM\n-# It is wrong to echo any other type of specification.\n-\n-me=`echo "$0" | sed -e \'s,.*/,,\'`\n-\n-usage="\\\n-Usage: $0 [OPTION] CPU-MFR-OPSYS\n- $0 [OPTION] ALIAS\n-\n-Canonicalize a configuration name.\n-\n-Operation modes:\n- -h, --help print this help, then exit\n- -t, --time-stamp print date of last modification, then exit\n- -v, --version print version number, then exit\n-\n-Report bugs and patches to <config-patches@gnu.org>."\n-\n-version="\\\n-GNU config.sub ($timestamp)\n-\n-Copyright 1992-2014 Free Software Foundation, Inc.\n-\n-This is free software; see the source for copying conditions. There is NO\n-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."\n-\n-help="\n-Try \\`$me --help\' for more information."\n-\n-# Parse command line\n-while test $# -gt 0 ; do\n- case $1 in\n- --time-stamp | --time* | -t )\n- echo "$timestamp" ; exit ;;\n- --version | -v )\n- echo "$version" ; exit ;;\n- --help | --h* | -h )\n- echo "$usage"; exit ;;\n- -- ) # Stop option processing\n- shift; break ;;\n- - )\t# Use stdin as input.\n- break ;;\n- -* )\n- echo "$me: invalid option $1$help"\n- exit 1 ;;\n-\n- *local*)\n- # First pass through any local machine types.\n- echo $1\n- exit ;;\n-\n- * )\n- break ;;\n- esac\n-done\n-\n-case $# in\n- 0) echo "$me: missing argument$help" >&2\n- exit 1;;\n- 1) ;;\n- *) echo "$me: too many arguments$help" >&2\n- exit 1;;\n-esac\n-\n-# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).\n-# Here we must recognize all the valid KERNEL-OS combinations.\n-maybe_os=`echo $1 '..b'`echo $os | sed \'s/[^-]*-//\'`\n-\t\techo Invalid configuration \\`$1\\\': system \\`$os\\\' not recognized 1>&2\n-\t\texit 1\n-\t\t;;\n-esac\n-else\n-\n-# Here we handle the default operating systems that come with various machines.\n-# The value should be what the vendor currently ships out the door with their\n-# machine or put another way, the most popular os provided with the machine.\n-\n-# Note that if you\'re going to try to match "-MANUFACTURER" here (say,\n-# "-sun"), then you have to tell the case statement up towards the top\n-# that MANUFACTURER isn\'t an operating system. Otherwise, code above\n-# will signal an error saying that MANUFACTURER isn\'t an operating\n-# system, and we\'ll never get to this point.\n-\n-case $basic_machine in\n-\tscore-*)\n-\t\tos=-elf\n-\t\t;;\n-\tspu-*)\n-\t\tos=-elf\n-\t\t;;\n-\t*-acorn)\n-\t\tos=-riscix1.2\n-\t\t;;\n-\tarm*-rebel)\n-\t\tos=-linux\n-\t\t;;\n-\tarm*-semi)\n-\t\tos=-aout\n-\t\t;;\n-\tc4x-* | tic4x-*)\n-\t\tos=-coff\n-\t\t;;\n-\tc8051-*)\n-\t\tos=-elf\n-\t\t;;\n-\thexagon-*)\n-\t\tos=-elf\n-\t\t;;\n-\ttic54x-*)\n-\t\tos=-coff\n-\t\t;;\n-\ttic55x-*)\n-\t\tos=-coff\n-\t\t;;\n-\ttic6x-*)\n-\t\tos=-coff\n-\t\t;;\n-\t# This must come before the *-dec entry.\n-\tpdp10-*)\n-\t\tos=-tops20\n-\t\t;;\n-\tpdp11-*)\n-\t\tos=-none\n-\t\t;;\n-\t*-dec | vax-*)\n-\t\tos=-ultrix4.2\n-\t\t;;\n-\tm68*-apollo)\n-\t\tos=-domain\n-\t\t;;\n-\ti386-sun)\n-\t\tos=-sunos4.0.2\n-\t\t;;\n-\tm68000-sun)\n-\t\tos=-sunos3\n-\t\t;;\n-\tm68*-cisco)\n-\t\tos=-aout\n-\t\t;;\n-\tmep-*)\n-\t\tos=-elf\n-\t\t;;\n-\tmips*-cisco)\n-\t\tos=-elf\n-\t\t;;\n-\tmips*-*)\n-\t\tos=-elf\n-\t\t;;\n-\tor32-*)\n-\t\tos=-coff\n-\t\t;;\n-\t*-tti)\t# must be before sparc entry or we get the wrong os.\n-\t\tos=-sysv3\n-\t\t;;\n-\tsparc-* | *-sun)\n-\t\tos=-sunos4.1.1\n-\t\t;;\n-\t*-be)\n-\t\tos=-beos\n-\t\t;;\n-\t*-haiku)\n-\t\tos=-haiku\n-\t\t;;\n-\t*-ibm)\n-\t\tos=-aix\n-\t\t;;\n-\t*-knuth)\n-\t\tos=-mmixware\n-\t\t;;\n-\t*-wec)\n-\t\tos=-proelf\n-\t\t;;\n-\t*-winbond)\n-\t\tos=-proelf\n-\t\t;;\n-\t*-oki)\n-\t\tos=-proelf\n-\t\t;;\n-\t*-hp)\n-\t\tos=-hpux\n-\t\t;;\n-\t*-hitachi)\n-\t\tos=-hiux\n-\t\t;;\n-\ti860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)\n-\t\tos=-sysv\n-\t\t;;\n-\t*-cbm)\n-\t\tos=-amigaos\n-\t\t;;\n-\t*-dg)\n-\t\tos=-dgux\n-\t\t;;\n-\t*-dolphin)\n-\t\tos=-sysv3\n-\t\t;;\n-\tm68k-ccur)\n-\t\tos=-rtu\n-\t\t;;\n-\tm88k-omron*)\n-\t\tos=-luna\n-\t\t;;\n-\t*-next )\n-\t\tos=-nextstep\n-\t\t;;\n-\t*-sequent)\n-\t\tos=-ptx\n-\t\t;;\n-\t*-crds)\n-\t\tos=-unos\n-\t\t;;\n-\t*-ns)\n-\t\tos=-genix\n-\t\t;;\n-\ti370-*)\n-\t\tos=-mvs\n-\t\t;;\n-\t*-next)\n-\t\tos=-nextstep3\n-\t\t;;\n-\t*-gould)\n-\t\tos=-sysv\n-\t\t;;\n-\t*-highlevel)\n-\t\tos=-bsd\n-\t\t;;\n-\t*-encore)\n-\t\tos=-bsd\n-\t\t;;\n-\t*-sgi)\n-\t\tos=-irix\n-\t\t;;\n-\t*-siemens)\n-\t\tos=-sysv4\n-\t\t;;\n-\t*-masscomp)\n-\t\tos=-rtu\n-\t\t;;\n-\tf30[01]-fujitsu | f700-fujitsu)\n-\t\tos=-uxpv\n-\t\t;;\n-\t*-rom68k)\n-\t\tos=-coff\n-\t\t;;\n-\t*-*bug)\n-\t\tos=-coff\n-\t\t;;\n-\t*-apple)\n-\t\tos=-macos\n-\t\t;;\n-\t*-atari*)\n-\t\tos=-mint\n-\t\t;;\n-\t*)\n-\t\tos=-none\n-\t\t;;\n-esac\n-fi\n-\n-# Here we handle the case where we know the os, and the CPU type, but not the\n-# manufacturer. We pick the logical manufacturer.\n-vendor=unknown\n-case $basic_machine in\n-\t*-unknown)\n-\t\tcase $os in\n-\t\t\t-riscix*)\n-\t\t\t\tvendor=acorn\n-\t\t\t\t;;\n-\t\t\t-sunos*)\n-\t\t\t\tvendor=sun\n-\t\t\t\t;;\n-\t\t\t-cnk*|-aix*)\n-\t\t\t\tvendor=ibm\n-\t\t\t\t;;\n-\t\t\t-beos*)\n-\t\t\t\tvendor=be\n-\t\t\t\t;;\n-\t\t\t-hpux*)\n-\t\t\t\tvendor=hp\n-\t\t\t\t;;\n-\t\t\t-mpeix*)\n-\t\t\t\tvendor=hp\n-\t\t\t\t;;\n-\t\t\t-hiux*)\n-\t\t\t\tvendor=hitachi\n-\t\t\t\t;;\n-\t\t\t-unos*)\n-\t\t\t\tvendor=crds\n-\t\t\t\t;;\n-\t\t\t-dgux*)\n-\t\t\t\tvendor=dg\n-\t\t\t\t;;\n-\t\t\t-luna*)\n-\t\t\t\tvendor=omron\n-\t\t\t\t;;\n-\t\t\t-genix*)\n-\t\t\t\tvendor=ns\n-\t\t\t\t;;\n-\t\t\t-mvs* | -opened*)\n-\t\t\t\tvendor=ibm\n-\t\t\t\t;;\n-\t\t\t-os400*)\n-\t\t\t\tvendor=ibm\n-\t\t\t\t;;\n-\t\t\t-ptx*)\n-\t\t\t\tvendor=sequent\n-\t\t\t\t;;\n-\t\t\t-tpf*)\n-\t\t\t\tvendor=ibm\n-\t\t\t\t;;\n-\t\t\t-vxsim* | -vxworks* | -windiss*)\n-\t\t\t\tvendor=wrs\n-\t\t\t\t;;\n-\t\t\t-aux*)\n-\t\t\t\tvendor=apple\n-\t\t\t\t;;\n-\t\t\t-hms*)\n-\t\t\t\tvendor=hitachi\n-\t\t\t\t;;\n-\t\t\t-mpw* | -macos*)\n-\t\t\t\tvendor=apple\n-\t\t\t\t;;\n-\t\t\t-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)\n-\t\t\t\tvendor=atari\n-\t\t\t\t;;\n-\t\t\t-vos*)\n-\t\t\t\tvendor=stratus\n-\t\t\t\t;;\n-\t\tesac\n-\t\tbasic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`\n-\t\t;;\n-esac\n-\n-echo $basic_machine$os\n-exit\n-\n-# Local variables:\n-# eval: (add-hook \'write-file-hooks \'time-stamp)\n-# time-stamp-start: "timestamp=\'"\n-# time-stamp-format: "%:y-%02m-%02d"\n-# time-stamp-end: "\'"\n-# End:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/configure
--- a/GEMBASSY-1.0.3/configure Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,22938 +0,0 @@\n-#! /bin/sh\n-# From configure.in Revision: 1.35 .\n-# Guess values for system-dependent variables and create Makefiles.\n-# Generated by GNU Autoconf 2.69 for GEMBASSY 1.0.3.\n-#\n-# Report bugs to <celery@g-language.org>.\n-#\n-#\n-# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.\n-#\n-#\n-# This configure script is free software; the Free Software Foundation\n-# gives unlimited permission to copy, distribute and modify it.\n-## -------------------- ##\n-## M4sh Initialization. ##\n-## -------------------- ##\n-\n-# Be more Bourne compatible\n-DUALCASE=1; export DUALCASE # for MKS sh\n-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :\n- emulate sh\n- NULLCMD=:\n- # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which\n- # is contrary to our usage. Disable this feature.\n- alias -g \'${1+"$@"}\'=\'"$@"\'\n- setopt NO_GLOB_SUBST\n-else\n- case `(set -o) 2>/dev/null` in #(\n- *posix*) :\n- set -o posix ;; #(\n- *) :\n- ;;\n-esac\n-fi\n-\n-\n-as_nl=\'\n-\'\n-export as_nl\n-# Printing a long string crashes Solaris 7 /usr/bin/printf.\n-as_echo=\'\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'\n-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo\n-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo\n-# Prefer a ksh shell builtin over an external printf program on Solaris,\n-# but without wasting forks for bash or zsh.\n-if test -z "$BASH_VERSION$ZSH_VERSION" \\\n- && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then\n- as_echo=\'print -r --\'\n- as_echo_n=\'print -rn --\'\n-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then\n- as_echo=\'printf %s\\n\'\n- as_echo_n=\'printf %s\'\n-else\n- if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then\n- as_echo_body=\'eval /usr/ucb/echo -n "$1$as_nl"\'\n- as_echo_n=\'/usr/ucb/echo -n\'\n- else\n- as_echo_body=\'eval expr "X$1" : "X\\\$.*\\\$"\'\n- as_echo_n_body=\'eval\n- arg=$1;\n- case $arg in #(\n- *"$as_nl"*)\n-\texpr "X$arg" : "X\\\$.*\\\$$as_nl";\n-\targ=`expr "X$arg" : ".*$as_nl\\\$.*\\\$"`;;\n- esac;\n- expr "X$arg" : "X\\\$.*\\\$" | tr -d "$as_nl"\n- \'\n- export as_echo_n_body\n- as_echo_n=\'sh -c $as_echo_n_body as_echo\'\n- fi\n- export as_echo_body\n- as_echo=\'sh -c $as_echo_body as_echo\'\n-fi\n-\n-# The user is always right.\n-if test "${PATH_SEPARATOR+set}" != set; then\n- PATH_SEPARATOR=:\n- (PATH=\'/bin;/bin\'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {\n- (PATH=\'/bin:/bin\'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||\n- PATH_SEPARATOR=\';\'\n- }\n-fi\n-\n-\n-# IFS\n-# We need space, tab and new line, in precisely that order. Quoting is\n-# there to prevent editors from complaining about space-tab.\n-# (If _AS_PATH_WALK were called with IFS unset, it would disable word\n-# splitting by setting IFS to empty value.)\n-IFS=" ""\t$as_nl"\n-\n-# Find who we are. Look in the path if we contain no directory separator.\n-as_myself=\n-case $0 in #((\n- *[\\\\/]* ) as_myself=$0 ;;\n- *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR\n-for as_dir in $PATH\n-do\n- IFS=$as_save_IFS\n- test -z "$as_dir" && as_dir=.\n- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break\n- done\n-IFS=$as_save_IFS\n-\n- ;;\n-esac\n-# We did not find ourselves, most probably we were run as `sh COMMAND\'\n-# in which case we are not to be found in the path.\n-if test "x$as_myself" = x; then\n- as_myself=$0\n-fi\n-if test ! -f "$as_myself"; then\n- $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2\n- exit 1\n-fi\n-\n-# Unset variables that we do not need and which cause bugs (e.g. in\n-# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"\n-# suppresses any "Segmentation fault" message there. \'((\' could\n-# trigger a bug in pdksh 5.2.14.\n-for as_var in BASH_ENV ENV MAIL MAILPATH\n-do eval test x\\${$as_var+set} = xset \\\n- && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :\n-done\n-PS1=\'$ \'\n-PS2=\'> \'\n-PS4=\'+ \'\n-\n-# NLS nui'..b'or_CXX\n-\n-# Set to "yes" if using DIR/libNAME\\$shared_ext during linking hardcodes\n-# DIR into the resulting binary.\n-hardcode_direct=$hardcode_direct_CXX\n-\n-# Set to "yes" if using DIR/libNAME\\$shared_ext during linking hardcodes\n-# DIR into the resulting binary and the resulting library dependency is\n-# "absolute",i.e impossible to change by setting \\$shlibpath_var if the\n-# library is relocated.\n-hardcode_direct_absolute=$hardcode_direct_absolute_CXX\n-\n-# Set to "yes" if using the -LDIR flag during linking hardcodes DIR\n-# into the resulting binary.\n-hardcode_minus_L=$hardcode_minus_L_CXX\n-\n-# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR\n-# into the resulting binary.\n-hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX\n-\n-# Set to "yes" if building a shared library automatically hardcodes DIR\n-# into the library and all subsequent libraries and executables linked\n-# against it.\n-hardcode_automatic=$hardcode_automatic_CXX\n-\n-# Set to yes if linker adds runtime paths of dependent libraries\n-# to runtime path list.\n-inherit_rpath=$inherit_rpath_CXX\n-\n-# Whether libtool must link a program against all its dependency libraries.\n-link_all_deplibs=$link_all_deplibs_CXX\n-\n-# Set to "yes" if exported symbols are required.\n-always_export_symbols=$always_export_symbols_CXX\n-\n-# The commands to list exported symbols.\n-export_symbols_cmds=$lt_export_symbols_cmds_CXX\n-\n-# Symbols that should not be listed in the preloaded symbols.\n-exclude_expsyms=$lt_exclude_expsyms_CXX\n-\n-# Symbols that must always be exported.\n-include_expsyms=$lt_include_expsyms_CXX\n-\n-# Commands necessary for linking programs (against libraries) with templates.\n-prelink_cmds=$lt_prelink_cmds_CXX\n-\n-# Commands necessary for finishing linking programs.\n-postlink_cmds=$lt_postlink_cmds_CXX\n-\n-# Specify filename containing input files.\n-file_list_spec=$lt_file_list_spec_CXX\n-\n-# How to hardcode a shared library path into an executable.\n-hardcode_action=$hardcode_action_CXX\n-\n-# The directories searched by this compiler when creating a shared library.\n-compiler_lib_search_dirs=$lt_compiler_lib_search_dirs_CXX\n-\n-# Dependencies to place before and after the objects being linked to\n-# create a shared library.\n-predep_objects=$lt_predep_objects_CXX\n-postdep_objects=$lt_postdep_objects_CXX\n-predeps=$lt_predeps_CXX\n-postdeps=$lt_postdeps_CXX\n-\n-# The library search path used internally by the compiler when linking\n-# a shared library.\n-compiler_lib_search_path=$lt_compiler_lib_search_path_CXX\n-\n-# ### END LIBTOOL TAG CONFIG: CXX\n-_LT_EOF\n-\n- ;;\n-\n- esac\n-done # for ac_tag\n-\n-\n-as_fn_exit 0\n-_ACEOF\n-ac_clean_files=$ac_clean_files_save\n-\n-test $ac_write_fail = 0 ||\n- as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5\n-\n-\n-# configure is writing to config.log, and then calls config.status.\n-# config.status does its own redirection, appending to config.log.\n-# Unfortunately, on DOS this fails, as config.log is still kept open\n-# by configure, so config.status won\'t be able to write to it; its\n-# output is simply discarded. So we exec the FD to /dev/null,\n-# effectively closing config.log, so it can be properly (re)opened and\n-# appended to by config.status. When coming back to configure, we\n-# need to make the FD available again.\n-if test "$no_create" != yes; then\n- ac_cs_success=:\n- ac_config_status_args=\n- test "$silent" = yes &&\n- ac_config_status_args="$ac_config_status_args --quiet"\n- exec 5>/dev/null\n- $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false\n- exec 5>>config.log\n- # Use ||, not &&, to avoid exiting from the if with $? = 1, which\n- # would make configure fail if this is the last instruction.\n- $ac_cs_success || as_fn_exit 1\n-fi\n-if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then\n- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5\n-$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}\n-fi\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/configure.in
--- a/GEMBASSY-1.0.3/configure.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1012 +0,0 @@\n-# -*- Autoconf -*-\n-# Configure template for the EMBOSS package.\n-# Process this file with autoconf to produce a configure script.\n-\n-AC_PREREQ([2.64])\n-AC_INIT([GEMBASSY],\n-[1.0.3],\n-[celery@g-language.org],\n-[GEMBASSY],\n-[http://www.g-language.org/gembassy/])\n-AC_REVISION([$Revision: 1.35 $])\n-AC_CONFIG_SRCDIR([src/ggcskew.c])\n-AC_CONFIG_HEADERS([src/config.h])\n-AC_CONFIG_MACRO_DIR([m4])\n-\n-# Make sure CFLAGS is defined to stop AC_PROG_CC adding -g.\n-CFLAGS="${CFLAGS} "\n-\n-# Checks for programs.\n-AC_PROG_AWK\n-AC_PROG_CC([icc gcc cc])\n-AC_PROG_CXX([icpc g++])\n-AC_PROG_CPP\n-AC_PROG_INSTALL\n-AC_PROG_LN_S\n-AC_PROG_MAKE_SET\n-AC_PROG_MKDIR_P\n-\n-AM_INIT_AUTOMAKE\n-\n-# Use libtool to make a shared library.\n-LT_INIT\n-\n-\n-\n-\n-# Check if 64 bit pointer support is required on 32 bit machines\n-# Disabled by default\n-\n-AC_ARG_ENABLE([64],\n-[AS_HELP_STRING([--enable-64], [64 bit pointers on 32 bit machines])])\n-\n-AS_IF([test "x${enable_64}" = "xyes"],\n-[\n- AC_MSG_CHECKING([for 64bit compilation support])\n-\n- AS_CASE([${host_os}],\n- [aix*],\n- [\n- CPPFLAGS="-DAJ_AIX64 ${CPPFLAGS}"\n- AS_CASE([${CC}],\n- [gcc],\n- [],\n- [\n- AS_VAR_APPEND([CC], [" -q64"])\n- ])\n- NM="nm -B -X 64"\n- AR="ar -X 64"\n- ],\n- [hpux*],\n- [\n- AS_CASE([${CC}],\n- [gcc],\n- [],\n- [\n- AS_VAR_APPEND([CC], [" +DD64"])\n- ])\n- AC_DEFINE([HPUX64PTRS], [1], [Set to 1 if HPUX 64bit ptrs on 32 bit m/c])\n- ])\n- AC_MSG_RESULT([done])\n-])\n-\n-\n-\n-\n-# Compiler optimisations\n-# The Solaris 64bit ptr check has to be done here owing to param order\n-\n-AC_ARG_WITH([optimisation],\n-[AS_HELP_STRING([--without-optimisation], [Disable compiler optimisation])])\n-\n-AS_IF([test "x${with_optimisation}" != "xno"],\n-[\n- AS_CASE([${CC}],\n- [gcc],\n- [\n- # Intel MacOSX requires reduced optimisation for PCRE code\n- # other OSs just use -O2\n- AS_CASE([${host_os}],\n- [darwin*],\n- [\n- AS_IF([test "x${host_cpu}" = "xi386"],\n- [AS_VAR_APPEND([CFLAGS], [" -O1"])],\n- [AS_VAR_APPEND([CFLAGS], [" -O2"])])\n- ],\n- [\n- AS_VAR_APPEND([CFLAGS], [" -O2"])\n- ])\n- ],\n- [\n- AS_CASE([${host_os}],\n- [aix*],\n- [\n- AS_VAR_APPEND([CFLAGS], [" -O3 -qstrict -qarch=auto -qtune=auto"])\n- ],\n- [irix*],\n- [\n- LD="/usr/bin/ld -IPA"\n- AS_VAR_APPEND([CFLAGS], [" -O3"])\n- ],\n- [hpux*],\n- [\n- AS_VAR_APPEND([CFLAGS], [" -fast"])\n- ],\n- [osf*],\n- [\n- AS_VAR_APPEND([CFLAGS], [" -fast -U_FASTMATH"])\n- ],\n- [solaris*],\n- [\n- AS_VAR_APPEND([CFLAGS], [" -O"])\n- # test for 64 bit ptr here (see Solaris 64bit above)\n- AS_IF([test "x${enable_64}" = "xyes"],\n- [AS_VAR_APPEND([CFLAGS], [" -xtarget=ultra -xarch=v9"])])\n- ],\n- [linux*],\n- [\n- # Default optimisation for non-gcc compilers under Linux\n- AS_VAR_APPEND([CFLAGS], [" -O2"])\n- ],\n- [freebsd*],\n- [\n- AS_VAR_APPEND([CFLAGS], [" -O2"])\n- ])\n- ])\n-])\n-\n-\n-\n-\n-# Compiler warning settings: --enable-warnings, defines WARN_CFLAGS\n-\n-AC_ARG_ENABLE([warnings],\n-[AS_HELP_STRING([--enable-warnings], [compiler warnings])])\n-\n-AS_IF([test "x${enable_warnings}" = "xyes"],\n-[\n- AS_CASE([${CC}],\n- [gcc],\n- [\n- # -Wall priovides:\n- # -Waddress\n- # -Warray-bounds (only with -O2)\n- # -Wc++0x-compat\n- # -Wchar-subscripts\n- # -Wenum-compare (in C/Objc; this is on by default in C++)\n- # -Wimplicit-int (C and Objective-C only)\n- # -Wimplicit-function-declaration (C and Objective-C only)\n- # -Wcomment\n- # -Wformat\n- # -Wmain (only for C/ObjC and unless -ffreestanding)\n- # -Wmissing-braces\n- # -Wnonnull\n- # -Wparentheses\n- # -Wpointer-sign\n- # -Wreorder\n- # -Wreturn-type\n- # -Wsequence-point\n- # -Wsign-compare (only in C++)\n- # -Wstrict-aliasing\n- # -Wstrict-overflow=1\n- # -Wswitch\n- # -Wtri'..b'PEND([CPPFLAGS], [" -DAJ_FreeBSDLF"])\n- ],\n- [solaris*],\n- [\n- AS_VAR_APPEND([CPPFLAGS], [" -DAJ_SolarisLF"])\n- AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"])\n- AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"])\n- ],\n- [osf*],\n- [\n- AS_VAR_APPEND([CPPFLAGS], [" -DAJ_OSF1LF"])\n- ],\n- [irix*],\n- [\n- AS_VAR_APPEND([CPPFLAGS], [" -DAJ_IRIXLF"])\n- AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE64_SOURCE"])\n- ],\n- [aix*],\n- [\n- AS_VAR_APPEND([CPPFLAGS], [" -DAJ_AIXLF"])\n- AS_VAR_APPEND([CPPFLAGS], [" -D_LARGE_FILES"])\n- ],\n- [hpux*],\n- [\n- AS_VAR_APPEND([CPPFLAGS], [" -DAJ_HPUXLF"])\n- AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"])\n- AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"])\n- ],\n- [darwin*],\n- [\n- AS_VAR_APPEND([CPPFLAGS], [" -DAJ_MACOSXLF"])\n- ])\n-\n- AC_MSG_RESULT([yes])\n-])\n-\n-\n-\n-\n-# Enable libraries provided by the system rather than EMBOSS:\n-# --enable-systemlibs, sets ESYSTEMLIBS\n-\n-AC_ARG_ENABLE([systemlibs],\n-[AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])\n-\n-AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])\n-\n-\n-\n-\n-# Enable the purify tool: --enable-purify, sets CC and LIBTOOL\n-\n-AC_ARG_ENABLE([purify],\n-[AS_HELP_STRING([--enable-purify], [purify])])\n-\n-AC_MSG_CHECKING([for purify])\n-\n-AS_IF([test "x${enable_purify}" = "xyes"],\n-[\n-dnl if(purify -version) < /dev/null > /dev/null 2>&1; then\n- CC="purify --chain-length=20 -best-effort -windows=yes gcc -g"\n- LIBTOOL="${LIBTOOL} --tag=CC"\n- AC_MSG_RESULT([yes])\n-dnl fi\n-],\n-[\n- AC_MSG_RESULT([no])\n-])\n-\n-\n-\n-\n-dnl Set extra needed compiler flags\n-if test "x${CC}" = "xcc"; then\n- case "${host}" in\n- alpha*-dec-osf*) CFLAGS="${CFLAGS} -ieee";;\n- esac\n-fi\n-\n-AM_CONDITIONAL([PURIFY], [test "x${enable_purify}" = "xyes"])\n-\n-\n-\n-\n-dnl Test for cygwin to set AM_LDFLAGS in library & apps Makefile.ams\n-dnl Replaces original version which used \'expr\' and so wasn\'t entirely\n-dnl portable.\n-platform_cygwin="no"\n-AC_MSG_CHECKING([for cygwin])\n-case "${host}" in\n- *-*-mingw*|*-*-cygwin*)\n- platform_cygwin="yes"\n- ;;\n- *)\n- platform_cygwin="no"\n- ;;\n-esac\n-AC_MSG_RESULT([${platform_cygwin}])\n-AM_CONDITIONAL([ISCYGWIN], [test "x${platform_cygwin}" = "xyes"])\n-\n-\n-\n-\n-dnl Tests for AIX\n-dnl If shared needs -Wl,-G in plplot,ajax,nucleus, -lX11 in plplot,\n-dnl and -Wl,brtl -Wl,-bdynamic in emboss\n-dnl We therefore need a static test as well\n-needajax="no"\n-\n-AS_CASE([${host_os}],\n-[aix*],\n-[AM_CONDITIONAL([ISAIXIA64], [true])],\n-[AM_CONDITIONAL([ISAIXIA64], [false])])\n-\n-AM_CONDITIONAL([ISSHARED], [test "x${enable_shared}" = "xyes"])\n-\n-AS_CASE([${host_os}],\n-[aix*],\n-[\n- AS_IF([test -d ajax/.libs],\n- [AS_ECHO(["AIX ajax/.libs exists"])], [mkdir ajax/.libs])\n-\n- AS_CASE([${host_os}],\n- [aix5*], [needajax="no"],\n- [aix4.3.3*], [needajax="yes"],\n- [needajax="no"])\n-])\n-\n-AM_CONDITIONAL([NEEDAJAX], [test "x${needajax}" = "xyes"])\n-\n-\n-\n-\n-# HP-UX needs -lsec for shadow passwords\n-\n-AS_CASE([${host_os}],\n-[hpux*],\n-[AS_VAR_APPEND([LDFLAGS], [" -lsec"])])\n-\n-\n-\n-\n-# GNU mcheck functions: --enable-mcheck, defines HAVE_MCHECK\n-\n-AC_ARG_ENABLE([mcheck],\n-[AS_HELP_STRING([--enable-mcheck],\n-[mcheck and mprobe memory allocation test])])\n-\n-AS_IF([test "x${enable_mcheck}" = "xyes"], [AC_CHECK_FUNCS([mcheck])])\n-\n-\n-\n-\n-# Collect AJAX statistics: --enable-savestats, defines AJ_SAVESTATS\n-\n-AC_ARG_ENABLE([savestats],\n-[AS_HELP_STRING([--enable-savestats],\n-[save AJAX statistics and print with debug output])])\n-\n-AC_MSG_CHECKING([for savestats])\n-\n-AS_IF([test "x${enable_savestats}" = "xyes"],\n-[\n- AC_DEFINE([AJ_SAVESTATS], [1],\n- [Define to 1 to collect AJAX library usage statistics.])\n- AC_MSG_RESULT([yes])\n-],\n-[\n- AC_MSG_RESULT([no])\n-])\n-\n-\n-\n-\n-AC_CONFIG_FILES([Makefile\n- src/Makefile\n- acd/Makefile\n- doc/Makefile\n- doc/html/Makefile\n- doc/text/Makefile\n-])\n-\n-AC_OUTPUT\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/data/ADH_HUMAN.fasta
--- a/GEMBASSY-1.0.3/data/ADH_HUMAN.fasta Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,8 +0,0 @@
->lcl|NM_000668.4_cdsid_NP_000659.2 [gene=ADH1B] [protein=alcohol dehydrogenase 1B] [protein_id=NP_000659.2] [location=85..1212]
-MSTAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICHTDDHVVSGNLVTPLPVILGHEA
-AGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRVCKNPESNYCLKNDLGNPRGTLQDGTRRFTCRGKPIHH
-FLGTSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVNVAKVTPGSTCAVFGLGGVGLSAVM
-GCKAAGAARIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTMMASL
-LCCHEACGTSVIVGVPPASQNLSINPMLLLTGRTWKGAVYGGFKSKEGIPKLVADFMAKKFSLDALITHV
-LPFEKINEGFDLLHSGKSIRTVLTF
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/data/accid.fasta
--- a/GEMBASSY-1.0.3/data/accid.fasta Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,77329 +0,0 @@\n->NC_000913 NC_000913.2 Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome.\n-agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtc\n-tgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttagg\n-tcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtac\n-acaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggt\n-aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcggg\n-ctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggt\n-acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc\n-aggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtg\n-gcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgccgaa\n-cgtatttttgccgaacttttgacgggactcgccgccgcccagccggggttcccgctggcg\n-caattgaaaactttcgtcgatcaggaatttgcccaaataaaacatgtcctgcatggcatt\n-agtttgttggggcagtgcccggatagcatcaacgctgcgctgatttgccgtggcgagaaa\n-atgtcgatcgccattatggccggcgtattagaagcgcgcggtcacaacgttactgttatc\n-gatccggtcgaaaaactgctggcagtggggcattacctcgaatctaccgtcgatattgct\n-gagtccacccgccgtattgcggcaagccgcattccggctgatcacatggtgctgatggca\n-ggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgcaacggttccgac\n-tactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggac\n-gttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcg\n-atgtcctaccaggaagcgatggagctttcctacttcggcgctaaagttcttcacccccgc\n-accattacccccatcgcccagttccagatcccttgcctgattaaaaataccggaaatcct\n-caagcaccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaagggc\n-atttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaagggatg\n-gtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgctg\n-attacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtg\n-cgagctgaacgggcaatgcaggaagagttctacctggaactgaaagaaggcttactggag\n-ccgctggcagtgacggaacggctggccattatctcggtggtaggtgatggtatgcgcacc\n-ttgcgtgggatctcggcgaaattctttgccgcactggcccgcgccaatatcaacattgtc\n-gccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgatgcg\n-accactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagtg\n-tttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaa\n-agctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggct\n-ctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgcaagcc\n-aaagagccgtttaatctcgggcgcttaattcgcctcgtgaaagaatatcatctgctgaac\n-ccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctg\n-cgcgaaggtttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgatggattac\n-taccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaac\n-gttggggctggattaccggttattgagaacctgcaaaatctgctcaatgcaggtgatgaa\n-ttgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagac\n-gaaggcatgagtttctccgaggcgaccacgctggcgcgggaaatgggttataccgaaccg\n-gacccgcgagatgatctttctggtatggatgtggcgcgtaaactattgattctcgctcgt\n-gaaacgggacgtgaactggagctggcggatattgaaattgaacctgtgctgcccgcagag\n-tttaacgccgagggtgatgttgccgcttttatggcgaatctgtcacaactcgacgatctc\n-tttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttggcaat\n-attgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctg\n-ttcaaagtgaaaaatggcgaaaacgccctggccttctatagccactattatcagccgctg\n-ccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgct\n-gatctgctacgtaccctctcatggaagttaggagtctgacatggttaaagtttatgcccc\n-ggcttccagtgccaatatgagcgtcgggtttgatgtgctcggggcggcggtgacacctgt\n-tgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctcaa\n-caacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatca\n-gtgctgggagcgtttttgccaggaactgggtaagcaaattccagtggcgatgaccctgga\n-aaagaatatgccgatcggttcgggcttaggctccagtgcctgttcggtggtcgcggcgct\n-gatggcgatgaatgaacactgcggcaagccgcttaatgacactcgtttgctggctttgat\n-gggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttt\n-tctcggtggtatgcagttgatgatcgaagaaaacgacatcatcagccagcaagtgccagg\n-gtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaagc\n-cagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatct\n-ggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaa\n-agatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggca\n-ggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgtt\n-cgctctgtgtgacaagccggaaaccgcccagcgcgttgccgactggttgggtaagaacta\n-cctgcaaaatcaggaaggttttgttcatatttgccggctggatacggcgggcgcacgagt\n-actggaaaactaaatgaaactctacaatctgaaagatca'..b'ctgaaccggcgttactggagcaggcgctgggaaat\n-ttactggataacgccatcgattttacccccgagagcggttgcatcacgctaagcgccgaa\n-gtggatcaggaacacgtcacgcttaaggtgctggataccggtagtggtattcctgactac\n-gcgctttcacgtatttttgaacgcttttactctttgcctcgtgcaaatgggcaaaaaagc\n-agcggtctggggttggcgttcgtcagtgaggtcgcccgtttgtttaacggcgaagtcacg\n-ctgcgcaacgtgcaggaaggtggcgtgctggcctcgcttcgacttcaccgtcacttcaca\n-tagcttcaaattcttcccacatagtcttcgtatcctgctgccattgcaaaggagaagact\n-atgttgaaatcccccctgttctggaaaatgactagcctgtttggtgcagtattgctgttg\n-ttgattccgataatgctgattcggcaggtgattgtcgaacgtgctgattaccgtagcgat\n-gtggaagatgcgattcgccaaagtaccagcgggccgcaaaaactcgttgggccgctcatc\n-gctattcctgtgaccgagctttatacggtgcaggaagaggataaaaccgtggagcggaaa\n-cgaagttttatccatttttggttacctgagtcattgatggttgatggcaatcagaacgtg\n-gaagaacgcaagatagggatttataccggtcaggtctggcacagtgatttaacgttaaaa\n-gccgatttcgatgtttcgcgtcttagcgaactcaacgcgccaaatatcaccttaggcaag\n-ccatttattgtgattagcgtcggggatgcgcgtggtattggtgtggtgaaagcgcctgaa\n-gttaacggaacggcgctgaccattgaacccggcaccgggttagagcaaggcgggcagggc\n-gtgcatatccctttacctgaaggggactggcggaagcagaacctgaagctgaatatggcc\n-ctgaatttaagcggtaccggcgatctttctgtggtgcctggcgggcgtaatagcgaaatg\n-accttaaccagcaactggccgcatcccagttttttaggtgattttctaccagccaaacgg\n-gaagttagcgagtcaggttttcaggcgcactggcaaagcagctggtttgctaataatctc\n-ggtgagcgttttgcttcaggcaatgataccggctgggaaaacttcccggcgtttagcgtc\n-gcagtaacgacgccagccgatcaataccaattaactgaccgggcgactaagtacgccatt\n-ctgctgattgcactgacttttatggcgttctttgtttttgaaacgctcaccgcgcaacgt\n-ttacacccaatgcaatatttgctggtggggctttcattggtgatgttttatttgctcttg\n-ctggcgctttctgaacataccggttttaccgtggcatggataatcgccagtctgattggg\n-gcgataatgaacggtatttatttgcaagcggtattgaaaggttggtgcaacagcatgttg\n-tttaccctcgcgctgttgttgctggatggtgtgatgtggggactgctcaactctgccgat\n-agcgcgctgttgttgggaaccagtgtgctggtggtggcgctggccggcatgatgtttgtg\n-acccgtaatatcgactggtatgcgttttcactgccgaaaatgaaagccagtaaagaagtt\n-acaacggacgatgagttacgtatctggaaataaggttgaaaaataaaaacggcgctaaaa\n-agcgccgttttttttgacggtggtaaagccgattaatcttccagatcaccgcagaagcga\n-taaccttcaccgtgaatggtggcgatgatttccggcgtatccggcgtagattcgaaatgt\n-ttacgaatacggcggatcgtcacgtctacagtacggtcgtgcggtttcagctcacggccg\n-gtcattttcttcagcagttcagcacgggactgaattttgcctgggttttcacagaagtga\n-agcatggcgcggaactcgctgcgcggcagcttgtactgctcgccatcagggccgatcaac\n-gaacggctgttgatgtccagttcccaaccattgaacttgtagctttcaacgctacgacgt\n-tcttcgctgacagtacccagattcatggtacgggacagtaggttgcgtgcacgaatcgtc\n-agttcacgcgggttgaacggtttggtgatgtagtcatctgcaccgatttcgaggccgaga\n-attttatcgacttcgttgtcacggccagtcaggaacatcaacgcaacattcgcctgctcg\n-cgcagttcacgcgctaacagaagaccgttcttacccggcagattgatatccatgatcacc\n-aggttgatgtcatattcagagaggatctgatgcatttccgcgccatctgtcgcttcgaaa\n-acatcatagccttccgcttcgaaaatacttttcaacgtgttgcgtgttaccaactcgtct\n-tcaacgataagaatgtgcggggtctgcatgtttgctacctaaattgccaactaaatcgaa\n-acaggaagtacaaaagtccctgacctgcctgatgcatgctgcaaattaacatgatcggcg\n-taacatgactaaagtacgtaattgcgttcttgatgcactttccatcaacgtcaacaacat\n-cattagcttggtcgtgggtactttccctcaggacccgacagtgtcaaaaacggctgtcat\n-cctaaccattttaacagcaacataacaggctaagaggggccggacacccaataaaactac\n-gcttcgttgacatatatcaagttcaattgtagcacgttaacagtttgatgaaatcatcgt\n-atctaaatgctagctttcgtcacattattttaataatccaactagttgcatcatacaact\n-aataaacgtggtgaatccaattgtcgagatttattttttataaaattatcctaagtaaac\n-agaaggatatgtagcattttttaacaactcaaccgttagtacagtcaggaaatagtttag\n-ccttttttaagctaagtaaagggctttttctgcgacttacgttaagaatttgtaaattcg\n-caccgcgtaataagttgacagtgatcacccggttcgcggttatttgatcaagaagagtgg\n-caatatgcgtataacgattattctggtcgcacccgccagagcagaaaatattggggcagc\n-ggcgcgggcaatgaaaacgatggggtttagcgatctgcggattgtcgatagtcaggcaca\n-cctggagccagccacccgctgggtcgcacatggatctggtgatattattgataatattaa\n-agttttcccgacattggctgaatcgttacacgatgtcgatttcactgtcgccaccactgc\n-gcgcagtcgggcgaaatatcattactacgccacgccagttgaactggtgccgctgttaga\n-ggaaaaatcttcatggatgagccatgccgcgctggtgtttggtcgcgaagattccgggtt\n-gactaacgaagagttagcgttggctgacgttcttactggtgtgccgatggtggcggatta\n-tccttcgctcaatctggggcaggcggtgatggtctattgctatcaattagcaacattaat\n-acaacaaccggcgaaaagtgatgcaacggcagaccaacatcaactgcaagctttacgcga\n-acgagccatgacattgctgacgactctggcagtggcagatgacataaaactggtcgactg\n-gttacaacaacgcctggggcttttagagcaacgagacacggcaatgttgcaccgtttgct\n-gcatgatattgaaaaaaatatcaccaaataaaaaacgccttagtaagtatttttc\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/data/consensus.fasta
--- a/GEMBASSY-1.0.3/data/consensus.fasta Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
->RS_000000
-agccaaccttagtcagggatcctctggtagaaagttataaatcagtttataggattcgatacgtccgtaaccttagccgattaacatctgtccaatggaaacagcataggtagaggctcccacaaacgtatttttcgagaactaaatccagacgtgatagtgcgccgccccgatgcagtgcgcttcagaaaactcccaaaaatggaattgtagcccacgtccgttggaaatatgatttgccgtgtaacgggtctatacgtcctcctgagcaattttgctgaagtcgggcaacgtcgagtttgcccatcctgcggcctcaacgtccgcgtaacggtaatatcctacataaatagcttggacgggtatgctcgaatacgacccggagacaagtaggttccaggctagggtttatgtgccaggactagtcctatggagggcaatttaaccagtacctcaatatgcccagttcttgcgccgcctatctctgtattaaggttaga
->RS_000001
-ttataaatcagtttataggattcgatacgtccgtaaccttagccgattaacatctgtccaatggaaacagcataggtagaggctcccacaaacgtatttttcgagaactaaatccagacgtgatagtgcgccgccccgatgcagtgcgcttcagaaaactcccaaaaatggaattgtagcccacgtccgttggaaatatgatttgccgtgtaacgggtctatacgtcctcctgagcaattttgctgaagtcgggcaacgtcgagtttgcccatcctgcggcctcaacgtccgcgtaacggtaatatcctacataaatagcttggacgggtatgctcgaatacgacccggagacaagtaggttccaggctagggtttatgtgccaggactagtcctatggagggcaatttaaccagtacctcaatatgcccagttcttgcgccgcctatctctgtattaaggttagacactggtatagggcgccgtcgcagggtgaattgc
->RS_000002
-acgtatttttcgagaactaaatccagacgtgatagtgcgccgccccgatgcagtgcgcttcagaaaactcccaaaaatggaattgtagcccacgtccgttggaaatatgatttgccgtgtaacgggtctatacgtcctcctgagcaattttgctgaagtcgggcaacgtcgagtttgcccatcctgcggcctcaacgtccgcgtaacggtaatatcctacataaatagcttggacgggtatgctcgaatacgacccggagacaagtaggttccaggctagggtttatgtgccaggactagtcctatggagggcaatttaaccagtacctcaatatgcccagttcttgcgccgcctatctctgtattaaggttagacactggtatagggcgccgtcgcagggtgaattgcactgcacactcattccacatctcgccgagcacatctgcattatccacccagtcacctgcaagggggttgacagggtttacgggagcgcagg
->RS_000003
-gcccacgtccgttggaaatatgatttgccgtgtaacgggtctatacgtcctcctgagcaattttgctgaagtcgggcaacgtcgagtttgcccatcctgcggcctcaacgtccgcgtaacggtaatatcctacataaatagcttggacgggtatgctcgaatacgacccggagacaagtaggttccaggctagggtttatgtgccaggactagtcctatggagggcaatttaaccagtacctcaatatgcccagttcttgcgccgcctatctctgtattaaggttagacactggtatagggcgccgtcgcagggtgaattgcactgcacactcattccacatctcgccgagcacatctgcattatccacccagtcacctgcaagggggttgacagggtttacgggagcgcaggcgggtagtttgcaataatgctaatacactgtatacgtggaaatagtcatcaaaatccttttgggtggttctcaatctatgatcccat
->RS_000004
-cctgcagtagccaaccttagtcagggatcctctggtagaaagttataaatcagtttataggattcgatacgtccgtaaccttagccgattaacatctgtccaatggaaacagcataggtagaggctcccacaaacgtatttttcgagaactaaatccagacgtgatagtgcgccgccccgatgcagtgcgcttcagaaaactcccaaaaatggaattgtagcccacgtccgttggaaatatgatttgccgtgtaacgggtctatacgtcctcctgagcaattttgctgaagtcgggcaacgtcgagtttgcccatcctgcggcctcaacgtccgcgtaacggtaatatcctacataaatagcttggacgggtatgctcgaatacgacccggagacaagtaggttccaggctagggtttatgtgccaggactagtcctatggagggcaatttaaccagtacctcaatatgcccagttcttgcgccgcctatctctgtatta
->RS_000005
-cgatagagagtctttagtgggggacgggcataggtagtgcgtagccgtcggtagggcttgcctcacaggccacagctgaccgccagcactgacaggcccactgcagtcatggtgatcatctcgtatacgaacatagactagccgtccaggagtgccgatcgcttgctaggatcagctatgtgaatggacctgcagtagccaaccttagtcagggatcctctggtagaaagttataaatcagtttataggattcgatacgtccgtaaccttagccgattaacatctgtccaatggaaacagcataggtagaggctcccacaaacgtatttttcgagaactaaatccagacgtgatagtgcgccgccccgatgcagtgcgcttcagaaaactcccaaaaatggaattgtagcccacgtccgttggaaatatgatttgccgtgtaacgggtctatacgtcctcctgagcaattttgctgaagtcgggcaacgtcgagtttgcc

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/depcomp
--- a/GEMBASSY-1.0.3/depcomp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,791 +0,0 @@\n-#! /bin/sh\n-# depcomp - compile a program generating dependencies as side-effects\n-\n-scriptversion=2013-05-30.07; # UTC\n-\n-# Copyright (C) 1999-2014 Free Software Foundation, Inc.\n-\n-# This program is free software; you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation; either version 2, or (at your option)\n-# any later version.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-# GNU General Public License for more details.\n-\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n-\n-# As a special exception to the GNU General Public License, if you\n-# distribute this file as part of a program that contains a\n-# configuration script generated by Autoconf, you may include it under\n-# the same distribution terms that you use for the rest of that program.\n-\n-# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.\n-\n-case $1 in\n- \'\')\n- echo "$0: No command. Try \'$0 --help\' for more information." 1>&2\n- exit 1;\n- ;;\n- -h | --h*)\n- cat <<\\EOF\n-Usage: depcomp [--help] [--version] PROGRAM [ARGS]\n-\n-Run PROGRAMS ARGS to compile a file, generating dependencies\n-as side-effects.\n-\n-Environment variables:\n- depmode Dependency tracking mode.\n- source Source file read by \'PROGRAMS ARGS\'.\n- object Object file output by \'PROGRAMS ARGS\'.\n- DEPDIR directory where to store dependencies.\n- depfile Dependency file to output.\n- tmpdepfile Temporary file to use when outputting dependencies.\n- libtool Whether libtool is used (yes/no).\n-\n-Report bugs to <bug-automake@gnu.org>.\n-EOF\n- exit $?\n- ;;\n- -v | --v*)\n- echo "depcomp $scriptversion"\n- exit $?\n- ;;\n-esac\n-\n-# Get the directory component of the given path, and save it in the\n-# global variables \'$dir\'. Note that this directory component will\n-# be either empty or ending with a \'/\' character. This is deliberate.\n-set_dir_from ()\n-{\n- case $1 in\n- */*) dir=`echo "$1" | sed -e \'s|/[^/]*$|/|\'`;;\n- *) dir=;;\n- esac\n-}\n-\n-# Get the suffix-stripped basename of the given path, and save it the\n-# global variable \'$base\'.\n-set_base_from ()\n-{\n- base=`echo "$1" | sed -e \'s|^.*/||\' -e \'s/\\.[^.]*$//\'`\n-}\n-\n-# If no dependency file was actually created by the compiler invocation,\n-# we still have to create a dummy depfile, to avoid errors with the\n-# Makefile "include basename.Plo" scheme.\n-make_dummy_depfile ()\n-{\n- echo "#dummy" > "$depfile"\n-}\n-\n-# Factor out some common post-processing of the generated depfile.\n-# Requires the auxiliary global variable \'$tmpdepfile\' to be set.\n-aix_post_process_depfile ()\n-{\n- # If the compiler actually managed to produce a dependency file,\n- # post-process it.\n- if test -f "$tmpdepfile"; then\n- # Each line is of the form \'foo.o: dependency.h\'.\n- # Do two passes, one to just change these to\n- # $object: dependency.h\n- # and one to simply output\n- # dependency.h:\n- # which is needed to avoid the deleted-header problem.\n- { sed -e "s,^.*\\.[$lower]*:,$object:," < "$tmpdepfile"\n- sed -e "s,^.*\\.[$lower]*:[$tab ]*,," -e \'s,$,:,\' < "$tmpdepfile"\n- } > "$depfile"\n- rm -f "$tmpdepfile"\n- else\n- make_dummy_depfile\n- fi\n-}\n-\n-# A tabulation character.\n-tab=\'\t\'\n-# A newline character.\n-nl=\'\n-\'\n-# Character ranges might be problematic outside the C locale.\n-# These definitions help.\n-upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ\n-lower=abcdefghijklmnopqrstuvwxyz\n-digits=0123456789\n-alpha=${upper}${lower}\n-\n-if test -z "$depmode" || test -z "$source" || test -z "$object"; then\n- echo "depcomp: Variables source, object and depmode must be set" 1>&2\n- exit 1\n-fi\n-\n-# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar'..b' 1\n- ;;\n-\n-makedepend)\n- "$@" || exit $?\n- # Remove any Libtool call\n- if test "$libtool" = yes; then\n- while test "X$1" != \'X--mode=compile\'; do\n- shift\n- done\n- shift\n- fi\n- # X makedepend\n- shift\n- cleared=no eat=no\n- for arg\n- do\n- case $cleared in\n- no)\n- set ""; shift\n- cleared=yes ;;\n- esac\n- if test $eat = yes; then\n- eat=no\n- continue\n- fi\n- case "$arg" in\n- -D*|-I*)\n- set fnord "$@" "$arg"; shift ;;\n- # Strip any option that makedepend may not understand. Remove\n- # the object too, otherwise makedepend will parse it as a source file.\n- -arch)\n- eat=yes ;;\n- -*|$object)\n- ;;\n- *)\n- set fnord "$@" "$arg"; shift ;;\n- esac\n- done\n- obj_suffix=`echo "$object" | sed \'s/^.*\\././\'`\n- touch "$tmpdepfile"\n- ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"\n- rm -f "$depfile"\n- # makedepend may prepend the VPATH from the source file name to the object.\n- # No need to regex-escape $object, excess matching of \'.\' is harmless.\n- sed "s|^.*\$$object *:\$|\\1|" "$tmpdepfile" > "$depfile"\n- # Some versions of the HPUX 10.20 sed can\'t process the last invocation\n- # correctly. Breaking it into two sed invocations is a workaround.\n- sed \'1,2d\' "$tmpdepfile" \\\n- | tr \' \' "$nl" \\\n- | sed -e \'s/^\\\\$//\' -e \'/^$/d\' -e \'/:$/d\' \\\n- | sed -e \'s/$/ :/\' >> "$depfile"\n- rm -f "$tmpdepfile" "$tmpdepfile".bak\n- ;;\n-\n-cpp)\n- # Important note: in order to support this mode, a compiler *must*\n- # always write the preprocessed file to stdout.\n- "$@" || exit $?\n-\n- # Remove the call to Libtool.\n- if test "$libtool" = yes; then\n- while test "X$1" != \'X--mode=compile\'; do\n- shift\n- done\n- shift\n- fi\n-\n- # Remove \'-o $object\'.\n- IFS=" "\n- for arg\n- do\n- case $arg in\n- -o)\n- shift\n- ;;\n- $object)\n- shift\n- ;;\n- *)\n- set fnord "$@" "$arg"\n- shift # fnord\n- shift # $arg\n- ;;\n- esac\n- done\n-\n- "$@" -E \\\n- | sed -n -e \'/^# [0-9][0-9]* "\$[^"]*\$".*/ s:: \\1 \\\\:p\' \\\n- -e \'/^#line [0-9][0-9]* "\$[^"]*\$".*/ s:: \\1 \\\\:p\' \\\n- | sed \'$ s: \\\\$::\' > "$tmpdepfile"\n- rm -f "$depfile"\n- echo "$object : \\\\" > "$depfile"\n- cat < "$tmpdepfile" >> "$depfile"\n- sed < "$tmpdepfile" \'/^$/d;s/^ //;s/ \\\\$//;s/$/ :/\' >> "$depfile"\n- rm -f "$tmpdepfile"\n- ;;\n-\n-msvisualcpp)\n- # Important note: in order to support this mode, a compiler *must*\n- # always write the preprocessed file to stdout.\n- "$@" || exit $?\n-\n- # Remove the call to Libtool.\n- if test "$libtool" = yes; then\n- while test "X$1" != \'X--mode=compile\'; do\n- shift\n- done\n- shift\n- fi\n-\n- IFS=" "\n- for arg\n- do\n- case "$arg" in\n- -o)\n- shift\n- ;;\n- $object)\n- shift\n- ;;\n- "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")\n- set fnord "$@"\n- shift\n- shift\n- ;;\n- *)\n- set fnord "$@" "$arg"\n- shift\n- shift\n- ;;\n- esac\n- done\n- "$@" -E 2>/dev/null |\n- sed -n \'/^#line [0-9][0-9]* "\$[^"]*\$"/ s::\\1:p\' | $cygpath_u | sort -u > "$tmpdepfile"\n- rm -f "$depfile"\n- echo "$object : \\\\" > "$depfile"\n- sed < "$tmpdepfile" -n -e \'s% %\\\\ %g\' -e \'/^\$.*\$$/ s::\'"$tab"\'\\1 \\\\:p\' >> "$depfile"\n- echo "$tab" >> "$depfile"\n- sed < "$tmpdepfile" -n -e \'s% %\\\\ %g\' -e \'/^\$.*\$$/ s::\\1\\::p\' >> "$depfile"\n- rm -f "$tmpdepfile"\n- ;;\n-\n-msvcmsys)\n- # This case exists only to let depend.m4 do its work. It works by\n- # looking at the text of this script. This case will never be run,\n- # since it is checked for above.\n- exit 1\n- ;;\n-\n-none)\n- exec "$@"\n- ;;\n-\n-*)\n- echo "Unknown depmode $depmode" 1>&2\n- exit 1\n- ;;\n-esac\n-\n-exit 0\n-\n-# Local Variables:\n-# mode: shell-script\n-# sh-indentation: 2\n-# eval: (add-hook \'write-file-hooks \'time-stamp)\n-# time-stamp-start: "scriptversion="\n-# time-stamp-format: "%:y-%02m-%02d.%02H"\n-# time-stamp-time-zone: "UTC"\n-# time-stamp-end: "; # UTC"\n-# End:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/Makefile
--- a/GEMBASSY-1.0.3/doc/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,659 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# doc/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgdatadir = $(datadir)/GEMBASSY\n-pkgincludedir = $(includedir)/GEMBASSY\n-pkglibdir = $(libdir)/GEMBASSY\n-pkglibexecdir = $(libexecdir)/GEMBASSY\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = x86_64-apple-darwin14.0.0\n-host_triplet = x86_64-apple-darwin14.0.0\n-subdir = doc\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_$(V))\n-am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_$(V))\n-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_$(V))\n-am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY)'..b'r" = .; then :; else \\\n-\t $(am__make_dryrun) \\\n-\t || test -d "$(distdir)/$$subdir" \\\n-\t || $(MKDIR_P) "$(distdir)/$$subdir" \\\n-\t || exit 1; \\\n-\t dir1=$$subdir; dir2="$(distdir)/$$subdir"; \\\n-\t $(am__relativize); \\\n-\t new_distdir=$$reldir; \\\n-\t dir1=$$subdir; dir2="$(top_distdir)"; \\\n-\t $(am__relativize); \\\n-\t new_top_distdir=$$reldir; \\\n-\t echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\\\"; \\\n-\t echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \\\n-\t ($(am__cd) $$subdir && \\\n-\t $(MAKE) $(AM_MAKEFLAGS) \\\n-\t top_distdir="$$new_top_distdir" \\\n-\t distdir="$$new_distdir" \\\n-\t\tam__remove_distdir=: \\\n-\t\tam__skip_length_check=: \\\n-\t\tam__skip_mode_fix=: \\\n-\t distdir) \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-recursive\n-all-am: Makefile\n-installdirs: installdirs-recursive\n-installdirs-am:\n-install: install-recursive\n-install-exec: install-exec-recursive\n-install-data: install-data-recursive\n-uninstall: uninstall-recursive\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-recursive\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-recursive\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-recursive\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic distclean-tags\n-\n-dvi: dvi-recursive\n-\n-dvi-am:\n-\n-html: html-recursive\n-\n-html-am:\n-\n-info: info-recursive\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-recursive\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-recursive\n-\n-install-html-am:\n-\n-install-info: install-info-recursive\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-recursive\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-recursive\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-recursive\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-recursive\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-recursive\n-\n-pdf-am:\n-\n-ps: ps-recursive\n-\n-ps-am:\n-\n-uninstall-am:\n-\n-.MAKE: $(am__recursive_targets) install-am install-strip\n-\n-.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am check \\\n-\tcheck-am clean clean-generic clean-libtool cscopelist-am ctags \\\n-\tctags-am distclean distclean-generic distclean-libtool \\\n-\tdistclean-tags distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-ps install-ps-am \\\n-\tinstall-strip installcheck installcheck-am installdirs \\\n-\tinstalldirs-am maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags tags-am uninstall uninstall-am\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/Makefile.am
--- a/GEMBASSY-1.0.3/doc/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-SUBDIRS = html text

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/Makefile.in
--- a/GEMBASSY-1.0.3/doc/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,659 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-VPATH = @srcdir@\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgdatadir = $(datadir)/@PACKAGE@\n-pkgincludedir = $(includedir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkglibexecdir = $(libexecdir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-subdir = doc\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_@AM_V@)\n-am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_@AM_V@)\n-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_@AM_V@)\n-am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)\n-am__v_at_0 = @\n-am__v_at_1 = \n-SOURCES =\n-DIST_SOURCES =\n-RECUR'..b'r" = .; then :; else \\\n-\t $(am__make_dryrun) \\\n-\t || test -d "$(distdir)/$$subdir" \\\n-\t || $(MKDIR_P) "$(distdir)/$$subdir" \\\n-\t || exit 1; \\\n-\t dir1=$$subdir; dir2="$(distdir)/$$subdir"; \\\n-\t $(am__relativize); \\\n-\t new_distdir=$$reldir; \\\n-\t dir1=$$subdir; dir2="$(top_distdir)"; \\\n-\t $(am__relativize); \\\n-\t new_top_distdir=$$reldir; \\\n-\t echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\\\"; \\\n-\t echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \\\n-\t ($(am__cd) $$subdir && \\\n-\t $(MAKE) $(AM_MAKEFLAGS) \\\n-\t top_distdir="$$new_top_distdir" \\\n-\t distdir="$$new_distdir" \\\n-\t\tam__remove_distdir=: \\\n-\t\tam__skip_length_check=: \\\n-\t\tam__skip_mode_fix=: \\\n-\t distdir) \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-recursive\n-all-am: Makefile\n-installdirs: installdirs-recursive\n-installdirs-am:\n-install: install-recursive\n-install-exec: install-exec-recursive\n-install-data: install-data-recursive\n-uninstall: uninstall-recursive\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-recursive\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-recursive\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-recursive\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic distclean-tags\n-\n-dvi: dvi-recursive\n-\n-dvi-am:\n-\n-html: html-recursive\n-\n-html-am:\n-\n-info: info-recursive\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-recursive\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-recursive\n-\n-install-html-am:\n-\n-install-info: install-info-recursive\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-recursive\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-recursive\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-recursive\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-recursive\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-recursive\n-\n-pdf-am:\n-\n-ps: ps-recursive\n-\n-ps-am:\n-\n-uninstall-am:\n-\n-.MAKE: $(am__recursive_targets) install-am install-strip\n-\n-.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am check \\\n-\tcheck-am clean clean-generic clean-libtool cscopelist-am ctags \\\n-\tctags-am distclean distclean-generic distclean-libtool \\\n-\tdistclean-tags distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-ps install-ps-am \\\n-\tinstall-strip installcheck installcheck-am installdirs \\\n-\tinstalldirs-am maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags tags-am uninstall uninstall-am\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/Makefile
--- a/GEMBASSY-1.0.3/doc/html/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,533 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# doc/html/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgincludedir = $(includedir)/GEMBASSY\n-pkglibdir = $(libdir)/GEMBASSY\n-pkglibexecdir = $(libexecdir)/GEMBASSY\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = x86_64-apple-darwin14.0.0\n-host_triplet = x86_64-apple-darwin14.0.0\n-subdir = doc/html\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_$(V))\n-am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_$(V))\n-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_$(V))\n-am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))\n-am__v_at_0 = @\n-am_'..b'-e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(DATA)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(pkgdatadir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am: install-pkgdataDATA\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-pkgdataDATA\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: all all-am check check-am clean clean-generic clean-libtool \\\n-\tcscopelist-am ctags-am distclean distclean-generic \\\n-\tdistclean-libtool distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-pkgdataDATA install-ps \\\n-\tinstall-ps-am install-strip installcheck installcheck-am \\\n-\tinstalldirs maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags-am uninstall uninstall-am uninstall-pkgdataDATA\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/Makefile.am
--- a/GEMBASSY-1.0.3/doc/html/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-pkgdata_DATA = *.html
-
-pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/gembassy
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/Makefile.in
--- a/GEMBASSY-1.0.3/doc/html/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,533 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-VPATH = @srcdir@\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgincludedir = $(includedir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkglibexecdir = $(libexecdir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-subdir = doc/html\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_@AM_V@)\n-am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_@AM_V@)\n-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_@AM_V@)\n-am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)\n-am__v_at_0 = @\n-am__v_at_1 = \n-SOURCES =\n-DIST_SOURCES =\n-am__can_run_installinfo = \\\n- ca'..b'-e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(DATA)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(pkgdatadir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am: install-pkgdataDATA\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-pkgdataDATA\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: all all-am check check-am clean clean-generic clean-libtool \\\n-\tcscopelist-am ctags-am distclean distclean-generic \\\n-\tdistclean-libtool distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-pkgdataDATA install-ps \\\n-\tinstall-ps-am install-strip installcheck installcheck-am \\\n-\tinstalldirs maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags-am uninstall uninstall-am uninstall-pkgdataDATA\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gaaui.html
--- a/GEMBASSY-1.0.3/doc/html/gaaui.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gaaui </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gaaui </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates various indece of amino acid usage  <H2>Description</H2> <p> gaaui calculates amino acid usage indices for proteins (excluding<br /> formylmethionine). Calculated indices are as follows,<br /> Laa: Length in amino acids<br /> ndaa: Number of different amino acids<br /> Haau: Entropy of amino acid usage<br /> mmw: Mean molecular weight<br /> gravy: Mean hydropathic indices of each amino acid<br /> aroma: Relative frequency of aromatic amino acids<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gaaui <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gaaui refseqn:NC_000913 Calculates various indece of amino acid usage AAINDEX entry output file [nc_000913.gaaui]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>AAINDEX entry output file</td> <td>Output file</td> <td><i><*></i>.gaaui</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gaaui reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gaaui is to a plain text file.<br /> <br /> File: nc_000913.gaaui<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> Laa,ndaa,Haau,mmw,gravy,aroma,gene<br /> 20,8,2.4842,117.48,+0.0150,0.0000,thrL<br /> 819,20,4.0887,126.65,+0.0328,0.0659,thrA<br /> 309,20,4.1228,126.35,+0.0181,0.0712,thrB<br /> 427,20,4.0806,128.00,-0.1014,0.0843,thrC<br /> 97,18,3.9165,133.54,-1.0268,0.0928,yaaX<br /> 257,19,4.0733,132.55,-0.4117,0.1089,yaaA<br /> 475,20,4.0413,126.46,+0.6781,0.1242,yaaJ<br /> 316,20,4.0395,128.99,-0.2165,0.0728,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 169,20,4.0001,124.90,+0.0231,0.0710,yjjX<br /> 214,20,3.9937,129.77,-0.3813,0.0374,ytjC<br /> 288,20,4.1421,132.58,-0.3628,0.1111,rob<br /> 156,20,4.0627,126.72,-0.0442,0.0705,creA<br /> 228,20,4.0471,131.94,-0.1408,0.0789,creB<br /> 473,20,4.0254,128.01,+0.0023,0.0677,creC<br /> 449,20,4.0871,128.66,+0.2082,0.0980,creD<br /> 237,20,4.0729,132.54,-0.4970,0.0675,arcA<br /> 45,15,3.5800,123.27,+0.7533,0.0222,yjjY<br /> 227,20,4.0283,128.63,-0.0031,0.0573,yjtD<br /> </td></tr></table> <br /> <br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga maritima J Mol Evol. 54(5):563-8. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gaminoinfo.html">gaminoinfo</a></td> <td>Prints out basic amino acid sequence statistics</td> </tr><tr> <td><a href="gcodoncompiler.html">gcodoncompiler</a></td> <td>Calculate various kinds of amino acid and codon usage data</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gaminoinfo.html
--- a/GEMBASSY-1.0.3/doc/html/gaminoinfo.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1 +0,0 @@\n-\r\r<HTML>\r<HEAD>\r <TITLE> EMBOSS: gaminoinfo </TITLE>\r</HEAD>\r<BODY BGCOLOR="#FFFFFF" text="#000000">\r\r\r\r<table align=center border=0 cellspacing=0 cellpadding=0>\r<tr><td valign=top>\r<A HREF="/" ONMOUSEOVER="self.status=\'Go to the EMBOSS home page\';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>\r</td>\r<td align=left valign=middle>\r<b><font size="+6">\rgaminoinfo\r</font></b>\r</td></tr>\r</table>\r<br> \r<p>\r\r\r\r\r\r\r\r\r\r<H2> Function </H2>\r Prints out basic amino acid sequence statistics\r\r\r\r\r\r<H2>Description</H2>\r<p>\r gaminoinfo prints out basic compositional statistics of the given amino<br />\r acid sequence in a human readble manner. The calculated values are molecular<br />\r weight, number of residues, average residue weight, charge, isoelectric<br />\r point, number/mole/Dayhoffstat of each amino acid, and percentage of<br />\r Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),<br />\r Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),<br />\r Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R), and<br />\r Acidic (B+D+E+Z) reidues.<br />\r <br />\r <br />\r G-language SOAP service is provided by the<br />\r Institute for Advanced Biosciences, Keio University.<br />\r The original web service is located at the following URL:<br />\r<br />\r http://www.g-language.org/wiki/soap<br />\r<br />\r WSDL(RPC/Encoded) file is located at:<br />\r<br />\r http://soap.g-language.org/g-language.wsdl<br />\r<br />\r Documentation on G-language Genome Analysis Environment methods are<br />\r provided at the Document Center<br />\r<br />\r http://ws.g-language.org/gdoc/<br />\r<br />\r\r</p>\r\r<H2>Usage</H2>\r\rHere is a sample session with gaminoinfo\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% gaminoinfo tsw:hbb_human\rPrints out basic amino acid sequence statistics\rAAINDEX entry output file [hbb_human.gaminoinfo]: \r\r</pre></td></tr></table>\r\rGo to the <a href="#input">input files</a> for this example<br>\rGo to the <a href="#output">output files</a> for this example<br><br>\r\r<h2>Command line arguments</h2>\r\r<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">\r<tr bgcolor="#FFFFCC">\r<th align="left">Qualifier</th>\r<th align="left">Type</th>\r<th align="left">Description</th>\r<th align="left">Allowed values</th>\r<th align="left">Default</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-sequence]<br>(Parameter 1)</td>\r<td>seqall</td>\r<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>\r<td>Readable sequence(s)</td>\r<td><b>Required</b></td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-outfile]<br>(Parameter 2)</td>\r<td>outfile</td>\r<td>AAINDEX entry output file</td>\r<td>Output file</td>\r<td><i><*></i>.gaminoinfo</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Additional (Optional) qualifiers</th>\r</tr>\r\r<tr>\r<td colspan=5>(none)</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>\r</tr>\r\r<tr>\r<td colspan=5>(none)</td>\r</tr>\r\r</table>\r\r\r<h2 id="input">Input file format</h2>\r\r<p>\r The database definitions for following commands are available at<br />\r http://soap.g-language.org/kbws/embossrc<br />\r<br />\r gaminoinfo reads one or more protein sequences.<br />\r<br />\r\r</p>\r\r<h2 id="output">Output file format</h2>\r\r<p>\r The output from gaminoinfo is to a plain text file.<br />\r<br />\r File: hbb_human.gaminoinfo<br />\r<br />\r<table width="90%"><tr><td bgcolor="#CCFFCC">\rSequence: P68871<br />\rAminoInfo of from 1 to 158<br />\r<br />\rMolecular weight = 19309.27 Residues = 158<br />\rAverage Weight = 122.21 Charge = 3.5<br />\rIsoelectric Point = 7.4065<br />\rResidue Number Mo'..b' = Ala 16 10.127 1.178<br />\rB = Asx 2 1.266 0.000<br />\rC = Cys 2 1.266 0.436<br />\rD = Asp 7 4.430 0.806<br />\rE = Glu 8 5.063 0.844<br />\rF = Phe 8 5.063 1.406<br />\rG = Gly 13 8.228 0.980<br />\rH = His 11 6.962 3.481<br />\rK = Lys 11 6.962 1.055<br />\rL = Leu 18 11.392 1.540<br />\rM = Met 3 1.899 1.117<br />\rN = Asn 7 4.430 1.030<br />\rP = Pro 7 4.430 0.852<br />\rQ = Gln 3 1.899 0.487<br />\rR = Arg 3 1.899 0.387<br />\rS = Ser 5 3.165 0.452<br />\rT = Thr 7 4.430 0.726<br />\rU = Sec 1 0.633 0.000<br />\rV = Val 18 11.392 1.726<br />\rW = Trp 2 1.266 0.974<br />\rY = Tyr 3 1.899 0.558<br />\r_ = 1 0.633 0.000<br />\r<br />\rProperty Residues Number Mole%<br />\rTiny (A+C+G+S+T) 43 27.215<br />\rSmall (A+B+C+D+G+N+P+S+T+V) 84 53.165<br />\rAliphatic (I+L+V) 36 22.785<br />\rAromatic (F+H+W+Y) 24 15.190<br />\rNon-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962<br />\rPolar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241<br />\rCharged (B+D+E+H+K+R+Z) 42 26.582<br />\rBasic (H+K+R) 25 15.823<br />\rAcidic (B+D+E+Z) 17 10.759<br />\r</pre></td></tr></table>\r\r</p>\r\r<h2>Data files</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Notes</h2>\r\r<p>\rNone.\r</p>\r\r<h2>References</h2>\r\r<pre>\r Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\r Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\r for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\r\r Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\r large-scale analysis of high-throughput omics data, J. Pest Sci.,\r 31, 7.\r\r Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\r Analysis Environment with REST and SOAP Web Service Interfaces,\r Nucleic Acids Res., 38, W700-W705.\r\r</pre>\r\r<h2>Warnings</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Diagnostic Error Messages</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Exit status</h2>\r\r<p>\rIt always exits with a status of 0.\r</p>\r\r<h2>Known bugs</h2>\r\r<p>\rNone.\r</p>\r\r<h2>See also</h2>\r\r<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>\r<th>Description</th></tr>\r\r<tr>\r<td><a href="gaaui.html">gaaui</a></td>\r<td>Calculates various indece of amino acid usage</td>\r</tr><tr>\r<td><a href="gcodoncompiler.html">gcodoncompiler</a></td>\r<td>Calculate various kinds of amino acid and codon usage data</td>\r</tr>\r\r</table>\r\r<h2>Author(s)</h2>\r\r<pre>\rHidetoshi Itaya (celery@g-language.org)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan\r\rKazuharu Arakawa (gaou@sfc.keio.ac.jp)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan</pre>\r\r<h2>History</h2>\r\r 2012 - Written by Hidetoshi Itaya\r\r<h2>Target users</h2>\r\r This program is intended to be used by everyone and everything, from\r naive users to embedded scrips.\r\r<h2>Comments</h2>\r\r None.\r\r\n\\ No newline at end of file\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gb1.html
--- a/GEMBASSY-1.0.3/doc/html/gb1.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gb1 </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gb1 </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate strand bias of bacterial genome using B1 index  <H2>Description</H2> <p> gb1 calculates the strand bias of bacterial genome using B1 index,<br /> first proposed by Lobry and Sueoka (2002), and further extended by<br /> Rocha et al. (2006). Basic idea of B1 index is to calculate the<br /> distance between the two strands, when the leading and lagging strands<br /> are plotted in a coordinate system with axes representing G/(G+C) and<br /> A/(A+T), using the third codon position of genes. This index measures the<br /> degree of replication-induced bias from Chargaff's second parity rule.<br /> Rocha et al. modified B1 index to only use >fourfold degenerate codons,<br /> and to use T/(A+T) in place of A/(A+T).<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gb1 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gb1 refseqn:NC_000913 Calculate strand bias of bacterial genome using B1 index Program compseq output file [nc_000913.gb1]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gb1</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-method</td> <td>selection</td> <td>Choose method of 'lobry' or 'rocha'</td> <td>Choose from selection list of values</td> <td>rocha</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gb1 reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gb1 is to a plain text file.<br /> <br /> File: nc_000913.gb1<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 B1: 0.0630702874711314<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in bacteria, Genome Biology, 3(10):0058 Rocha EPC et al. (2006) Similar compositional biases are caused by very different mutational effects, Genome Research, 16:1537-1547 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gb2.html">gb2</a></td> <td>Calculate strand bias of bacterial genome using B2 index</td> </tr><tr> <td><a href="gdeltagcskew.html">gdeltagcskew</a></td> <td>Calculate strand bias of bacterial genome using delta GC skew</td> </tr><tr> <td><a href="ggcsi.html">ggcsi</a></td> <td>GC Skew Index: an index for strand-specefic mutational bias</td> </tr><tr> <td><a href="gldabias.html">gldabias</a></td> <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gb2.html
--- a/GEMBASSY-1.0.3/doc/html/gb2.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gb2 </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gb2 </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate strand bias of bacterial genome using B2 index  <H2>Description</H2> <p> gb2 calculates strand bias of bacterial genome using B2 index,<br /> proposed by Lobry and Sueoka(2002). Basic idea of B2 index is to calculate<br /> the distance from neutral parity state (0.5, 0.5), when the bias of<br /> the coding regions is plotted in a coordinate system with axes representing<br /> G/(G+C) and A/(A+T), using the third codon position of genes. This index<br /> measures the degree of transcription- and translation-associated effects of<br /> bias from Chargaff's second parity rule.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gb2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gb2 refseqn:NC_000913 Calculate strand bias of bacterial genome using B2 index Program compseq output file [nc_000913.gb2]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gb2</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gb2 reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gb2 is to a plain text file.<br /> <br /> File: nc_000913.gb2<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 B2: 0.0919769585775651<br /> </td></tr></table> <br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in bacteria, Genome Biology, 3(10):0058 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gb1.html">gb1</a></td> <td>Calculate strand bias of bacterial genome using B1 index</td> </tr><tr> <td><a href="gdeltagcskew.html">gdeltagcskew</a></td> <td>Calculate strand bias of bacterial genome using delta GC skew</td> </tr><tr> <td><a href="ggcsi.html">ggcsi</a></td> <td>GC Skew Index: an index for strand-specefic mutational bias</td> </tr><tr> <td><a href="gldabias.html">gldabias</a></td> <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gbasecounter.html
--- a/GEMBASSY-1.0.3/doc/html/gbasecounter.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1 +0,0 @@\n-\r\r<HTML>\r<HEAD>\r <TITLE> EMBOSS: gbasecounter </TITLE>\r</HEAD>\r<BODY BGCOLOR="#FFFFFF" text="#000000">\r\r\r\r<table align=center border=0 cellspacing=0 cellpadding=0>\r<tr><td valign=top>\r<A HREF="/" ONMOUSEOVER="self.status=\'Go to the EMBOSS home page\';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>\r</td>\r<td align=left valign=middle>\r<b><font size="+6">\rgbasecounter\r</font></b>\r</td></tr>\r</table>\r<br> \r<p>\r\r\r\r\r\r\r\r\r\r<H2> Function </H2>\r Creates a position weight matrix of oligomers around start codon\r\r\r\r\r\r<H2>Description</H2>\r<p>\r This function creates a position weight matrix (PWM) of<br />\r oligomers of specified length around the start codon of all<br />\r genes in the given genome.<br />\r <br />\r G-language SOAP service is provided by the<br />\r Institute for Advanced Biosciences, Keio University.<br />\r The original web service is located at the following URL:<br />\r<br />\r http://www.g-language.org/wiki/soap<br />\r<br />\r WSDL(RPC/Encoded) file is located at:<br />\r<br />\r http://soap.g-language.org/g-language.wsdl<br />\r<br />\r Documentation on G-language Genome Analysis Environment methods are<br />\r provided at the Document Center<br />\r<br />\r http://ws.g-language.org/gdoc/<br />\r<br />\r\r</p>\r\r<H2>Usage</H2>\r\rHere is a sample session with gbasecounter\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% gbasecounter refseqn:NC_000913\rCreates a position weight matrix of oligomers around start codon\rWeight matrix output file [nc_000913.gbasecounter]: \r\r</pre></td></tr></table>\r\rGo to the <a href="#input">input files</a> for this example<br>\rGo to the <a href="#output">output files</a> for this example<br><br>\r\r<h2>Command line arguments</h2>\r\r<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">\r<tr bgcolor="#FFFFCC">\r<th align="left">Qualifier</th>\r<th align="left">Type</th>\r<th align="left">Description</th>\r<th align="left">Allowed values</th>\r<th align="left">Default</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-sequence]<br>(Parameter 1)</td>\r<td>seqall</td>\r<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>\r<td>Readable sequence(s)</td>\r<td><b>Required</b></td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-outfile]<br>(Parameter 2)</td>\r<td>outfile</td>\r<td>Weight matrix output file</td>\r<td>Output file</td>\r<td><i><*></i>.gbasecounter</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Additional (Optional) qualifiers</th>\r</tr>\r\r<tr>\r<td colspan=5>(none)</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-position</td>\r<td>selection</td>\r<td>Either \'start\' (around start codon) or \'end\' (around stop codon) to create the PWM</td>\r<td>Choose from selection list of values</td>\r<td>start</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-patlen</td>\r<td>integer</td>\r<td>Length of oligomer to count</td>\r<td>Any integer value</td>\r<td>3</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-upstream</td>\r<td>integer</td>\r<td>Length upstream of specified position to create PWM</td>\r<td>Any integer value</td>\r<td>30</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-downstream</td>\r<td>integer</td>\r<td>Length downstream of specified position to create PWM</td>\r<td>Any integer value</td>\r<td>30</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-[no]accid</td>\r<td>boolean</td>\r<td>Include to use sequence accession ID as query</td>\r<td>Boolean value Yes/No</td>\r<td>Yes</td>\r</tr>\r\r</table>\r\r\r<h2 id="input">Input file format</h2>\r\r<p>\r The database definitions for following commands are available at<br />\r http://soap.g-language.org/kbws/embossrc<br />\r<br />\r gbasecounter reads one or more nucleot'..b',0.671,1.343,1.713,1.621,1.482,0.810,0.834,0.718,0.301,0.463,0.509,0.509,0.741,0.579,0.509,0.625,0.486,0.509,0.625,0.625,0.533,0.857,0.996,0.718,1.968,1.042,0.880,1.760,0.671,0.949,1.459,0.556,0.787,0.903,0.718,0.695,1.273,0.533,0.440,0.648,0.880,0.417,0.718,0.648,0.278,0.625,0.463,0.440,0.486,0.116,0.023,11.021<br />\rtgt,0.023,0.880,0.023,0.533,1.135,0.301,0.440,0.602,0.417,0.208,0.232,0.185,0.185,0.278,0.370,0.440,0.533,0.556,0.648,0.764,0.509,0.926,0.579,0.718,0.880,0.695,0.718,0.741,0.741,0.579,0.625,0.278,1.158,0.857,0.278,0.972,0.718,0.324,0.926,0.695,0.463,1.111,0.834,0.162,1.482,0.787,0.278,1.065,0.695,0.278,1.042,0.695,0.208,0.903,0.718,0.139,0.857,0.232,0.093,0.023,7.340<br />\rtta,0.000,0.000,6.506,0.648,0.810,1.829,1.320,0.602,0.486,0.509,0.255,0.347,0.301,0.834,1.320,1.459,1.412,1.667,1.644,1.852,1.667,1.574,1.366,1.042,1.204,1.621,1.505,1.227,1.436,1.088,1.273,1.343,0.486,1.158,1.042,0.440,1.135,1.389,0.370,1.273,1.574,0.486,1.875,1.505,0.463,1.991,1.875,0.533,2.362,2.061,0.324,2.084,2.200,0.509,1.505,1.320,0.463,1.366,0.648,0.000,0.069<br />\rttc,0.000,0.000,0.000,0.648,0.417,0.695,0.764,0.347,0.301,0.278,0.208,0.023,0.232,0.533,0.718,0.718,0.903,1.042,1.158,0.880,1.158,1.065,0.903,0.834,1.343,0.996,0.926,0.810,0.741,0.834,1.042,0.926,0.579,1.088,0.695,0.695,1.297,0.741,0.741,1.111,0.926,0.787,1.366,0.695,0.857,1.412,0.648,0.834,1.111,0.440,0.602,1.250,1.019,1.135,0.787,0.440,0.880,0.509,0.370,0.000,0.000<br />\rttg,0.857,0.023,0.255,0.394,0.556,1.111,0.533,0.463,0.417,0.185,0.232,0.533,0.602,1.042,0.718,0.695,1.135,0.972,0.857,0.926,0.787,0.671,1.320,0.695,0.903,1.204,0.880,0.764,0.926,0.741,0.718,1.019,0.347,1.551,1.042,0.370,2.014,0.834,0.463,2.061,0.880,0.278,2.014,0.857,0.208,2.593,0.741,0.278,1.922,0.764,0.417,2.130,0.834,0.208,1.111,0.394,0.093,1.111,0.417,0.000,0.023<br />\rttt,0.023,0.440,0.093,1.598,1.181,1.320,1.829,1.343,0.648,0.370,0.394,0.278,0.185,0.440,1.135,1.574,1.667,1.945,2.315,2.362,2.431,2.501,2.107,2.362,1.806,2.014,2.292,2.014,1.598,1.760,1.829,1.389,1.505,1.042,1.343,1.297,0.926,1.528,1.574,1.227,1.482,1.737,1.389,1.667,1.922,1.389,1.945,1.922,1.343,1.806,1.760,1.389,2.014,1.760,1.065,0.949,1.111,0.625,1.227,0.023,0.023<br />\r</td></tr></table>\r\r</p>\r\r<h2>Data files</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Notes</h2>\r\r<p>\rNone.\r</p>\r\r<h2>References</h2>\r\r<pre>\r Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\r Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\r for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\r\r Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\r large-scale analysis of high-throughput omics data, J. Pest Sci.,\r 31, 7.\r\r Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\r Analysis Environment with REST and SOAP Web Service Interfaces,\r Nucleic Acids Res., 38, W700-W705.\r\r</pre>\r\r<h2>Warnings</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Diagnostic Error Messages</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Exit status</h2>\r\r<p>\rIt always exits with a status of 0.\r</p>\r\r<h2>Known bugs</h2>\r\r<p>\rNone.\r</p>\r\r<h2>See also</h2>\r\r<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>\r<th>Description</th></tr>\r\r<tr>\r<td><a href="gbasezvalue.html">gbasezvalue</a></td>\r<td>Extracts conserved oligomers per position using Z-score</td>\r</tr><tr>\r<td><a href="gviewcds.html">gviewcds</a></td>\r<td>Displays a graph of nucleotide contents around start and stop codons</td>\r</tr>\r\r</table>\r\r<h2>Author(s)</h2>\r\r<pre>\rHidetoshi Itaya (celery@g-language.org)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan\r\rKazuharu Arakawa (gaou@sfc.keio.ac.jp)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan</pre>\r\r<h2>History</h2>\r\r 2012 - Written by Hidetoshi Itaya\r\r<h2>Target users</h2>\r\r This program is intended to be used by everyone and everything, from\r naive users to embedded scrips.\r\r<h2>Comments</h2>\r\r None.\r\r</p>\r\r</BODY>\r</HTML>\n\\ No newline at end of file\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gbaseentropy.html
--- a/GEMBASSY-1.0.3/doc/html/gbaseentropy.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gbaseentropy </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gbaseentropy </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)  <H2>Description</H2> <p> This function calculates and graphs the sequence conservation in regions<br /> around the start/stop codons using Shanon uncertainty (entropy). Smaller<br /> values resemble higher conservation where the minumum value is 0 and the<br /> maximum value is 2. The entropy is typically the lowest around position 0<br /> (start/stop codon position).<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gbaseentropy <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbaseentropy refseqn:NC_000913 Calculates and graphs the sequence conservation using Shanon uncertainty (entropy) Program compseq output file (optional) [nc_000913.gbaseentropy]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbaseentropy refseqn:NC_000913 -plot -graph png Calculates and graphs the sequence conservation using Shanon uncertainty (entropy) Created gbaseentropy.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.gbaseentropy</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-position</td> <td>selection</td> <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td> <td>Choose from selection list of values</td> <td>start</td> </tr> <tr bgcolor="#FFFFCC"> <td>-patlen</td> <td>integer</td> <td>Length of oligomer to count</td> <td>Any integer value</td> <td>3</td> </tr> <tr bgcolor="#FFFFCC"> <td>-upstream</td> <td>integer</td> <td>Length upstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-downstream</td> <td>integer</td> <td>Length downstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gbaseentropy reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gbaseentropy is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.gbaseentropy<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> -30,1.98284<br /> -29,1.97873<br /> -28,1.97692<br /> -27,1.97595<br /> -26,1.97094<br /> -25,1.96777<br /> -24,1.96272<br /> -23,1.96288<br /> -22,1.95707<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 21,1.93528<br /> 22,1.94470<br /> 23,1.95204<br /> 25,1.93139<br /> 25,1.95640<br /> 26,1.95711<br /> 27,1.93785<br /> 28,1.96060<br /> 29,1.94316<br /> 30,1.92581<br /> </td></tr></table> </p> <h3>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gbaseinformationcontent.html">gbaseinformationcontent</a></td> <td>Calculates and graphs the sequence conservation using information content</td> </tr> <tr> <td><a href="gbaserelativeentropy.html">gbaserelativeentropy</a></td> <td>Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gbaseinformationcontent.html
--- a/GEMBASSY-1.0.3/doc/html/gbaseinformationcontent.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gbaseinformationcontent </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gbaseinformationcontent </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates and graphs the sequence conservation using information content  <H2>Description</H2> <p> This function calculates and graphs the sequence conservation in regions<br /> around the start/stop codons using information content. Values are obtained<br /> by subtracting the entropy for each positfion from the maximum possible value<br /> (which will be 2 in the case of nucleotide sequences). Information content<br /> will show the highest value when the frequency is most biased to a single<br /> alphabet.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gbaseinformationcontent <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbaseinformationcontent refseqn:NC_000913 Calculates and graphs the sequence conservation using information content Program compseq output file (optional) [nc_000913.gbaseinformationcontent]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbaseinformationcontent refseqn:NC_000913 -plot -graph png Calculates and graphs the sequence conservation using information content Created gbaseinformationcontent.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.gbaseinformationcontent</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-position</td> <td>selection</td> <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td> <td>Choose from selection list of values</td> <td>start</td> </tr> <tr bgcolor="#FFFFCC"> <td>-upstream</td> <td>integer</td> <td>Length upstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-downstream</td> <td>integer</td> <td>Length downstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-patlen</td> <td>integer</td> <td>Length of oligomer to count</td> <td>Any integer value</td> <td>3</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gbaseinformationcontent reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gbaseinformationcontent is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.gbaseinformationcontent<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> -30,2.42457<br /> -29,2.42811<br /> -28,2.43235<br /> -27,2.43116<br /> -26,2.44278<br /> -25,2.44236<br /> -24,2.44502<br /> -23,2.46097<br /> -22,2.46588<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 21,2.27547<br /> 22,2.46974<br /> 23,2.46342<br /> 24,2.32686<br /> 25,2.46245<br /> 26,2.46061<br /> 27,2.27664<br /> 28,2.45650<br /> 29,2.48206<br /> 30,2.29140<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gbaseentropy.html">gbaseentropy</a></td> <td>Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)</td> </tr><tr> <td><a href="gbaserelativeentropy.html">gbaserelativeentropy</a></td> <td>Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gbaserelativeentropy.html
--- a/GEMBASSY-1.0.3/doc/html/gbaserelativeentropy.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gbaserelativeentropy </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gbaserelativeentropy </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy)  <H2>Description</H2> <p> This function calculates and graphs the sequence conservation in regions<br /> around the start/stop codons using Kullback-Leibler divergence (relative<br /> entropy). In realistic conditions, as background nucleotide composition<br /> (e.g. G+C content) varies among species. Kullback-Leibler divergence<br /> calculates the entropy with reduced background noise.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gbaserelativeentropy <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbaserelativeentropy refseqn:NC_000913 Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy) Program compseq output file (optional) [nc_000913.gbaserelativeentropy]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbaserelativeentropy refseqn:NC_000913 -plot -graph png Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy) Created gbaserelativeentropy.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.gbaserelativeentropy</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-position</td> <td>selection</td> <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td> <td>Choose from selection list of values</td> <td>start</td> </tr> <tr bgcolor="#FFFFCC"> <td>-patlen</td> <td>integer</td> <td>Length of oligomer to count</td> <td>Any integer value</td> <td>3</td> </tr> <tr bgcolor="#FFFFCC"> <td>-upstream</td> <td>integer</td> <td>Length upstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-downstream</td> <td>integer</td> <td>Length downstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gbaserelativeentropy reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gbaserelativeentropy is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.gbaserelativeentropy<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> -30,-0.46682<br /> -29,-0.46265<br /> -28,-0.45732<br /> -27,-0.45704<br /> -26,-0.44692<br /> -25,-0.44396<br /> -24,-0.43528<br /> -23,-0.43419<br /> -22,-0.42518<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 21,-0.40010<br /> 22,-0.41772<br /> 23,-0.42503<br /> 24,-0.39675<br /> 25,-0.43091<br /> 26,-0.43196<br /> 27,-0.40576<br /> 28,-0.43387<br /> 29,-0.41228<br /> 30,-0.38869<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gbase_entropy.html">gbase_entropy</a></td> <td>Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)</td> </tr></td> </tr><tr> <td><a href="gbase_information_content.html">gbase_information_content</a></td> <td>Calculates and graphs the sequence conservation using information content</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gbasezvalue.html
--- a/GEMBASSY-1.0.3/doc/html/gbasezvalue.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gbasezvalue </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gbasezvalue </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Extracts conserved oligomers per position using Z-score  <H2>Description</H2> <p> This function calculates and extracts conserved oligomers per position using<br /> Z-score, in regions around the start/stop codons. The oligomers are returned<br /> in ranking order up to "-limit" number.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gbasezvalue <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbasezvalue refseqn:NC_000913 Extracts conserved oligomers per position using Z-score Program compseq output file (optional) [nc_000913.gbasezvalue]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.gbasezvalue</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-limit</td> <td>integer</td> <td>Rank threshold for showing the conserved oligomer</td> <td>Any integer value</td> <td>5</td> </tr> <tr bgcolor="#FFFFCC"> <td>-position</td> <td>selection</td> <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td> <td>Choose from selection list of values</td> <td>start</td> </tr> <tr bgcolor="#FFFFCC"> <td>-patlen</td> <td>integer</td> <td>Length of oligomer to count</td> <td>Any integer value</td> <td>3</td> </tr> <tr bgcolor="#FFFFCC"> <td>-upstream</td> <td>integer</td> <td>Length upstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-downstream</td> <td>integer</td> <td>Length downstream of specified position to create PWM</td> <td>Any integer value</td> <td>30</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gbasezvalue reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h3> <p> The output from gbasezvalue is to a plain text file.<br /> <br /> File: nc_000913.gbasezvalue<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> position:-30,1,taa,-0.76525<br /> 2,aga,-0.79101<br /> 3,tta,-1.14174<br /> 4,cta,-1.18831<br /> 5,aat,-1.86652<br /> position:-29,1,cta,-0.18368<br /> 2,aat,-0.71851<br /> 3,gac,-1.26182<br /> 4,taa,-1.39455<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> position:29,1,gct,1.66288<br /> 2,act,1.26637<br /> 3,tat,0.66721<br /> 4,cct,-0.43158<br /> 5,tgt,-0.59254<br /> position:30,1,ctg,3.12072<br /> 2,att,0.04193<br /> 3,ctc,-0.12416<br /> 4,cta,-0.38461<br /> 5,tta,-0.76413<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gbase_counter.html">gbase_counter</a></td> <td>Creates a position weight matrix of oligomers around start codon</td> </tr><tr> <td><a href="gview_cds.html">gview_cds</a></td> <td>Displays a graph of nucleotide contents around start and stop codons</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gbui.html
--- a/GEMBASSY-1.0.3/doc/html/gbui.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gbui </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gbui </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates base usage indices for protein-coding sequences  <H2>Description</H2> <p> gbui calculates base usage indices of protein-coding sequences (excluding<br /> start and stop codons) for each gene. Indices calculated are as follows,<br /> acgt: Total bumber of bases (A+T+G+C)<br /> ryr: Purine/Pyrimidine ratio (A+G)/(T+C)<br /> gcc: G+C content (G+C)/(A+T+G+C)<br /> Hgc: entropy of G+C content (G+C)/(A+T+G+C)<br /> gcs: GC skew (C-G)/(C+G)<br /> ats: AT skew (A-T)/(A+T)<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gbui <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbui refseqn:NC_000913 Calculates base usage indices for protein-coding sequences Program compseq output file [nc_000913.gbui]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gbui</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translating using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-position</td> <td>list</td> <td>Codon position</td> <td><table><tr><td>all</td> <td><i>(Assess overall base usage of the gene)</i></td></tr><tr><td>1</td> <td><i>(Assess base usage at 1st position of codons)</i></td></tr><tr><td>2</td> <td><i>(Assess base usage at 2nd position of codons)</i></td></tr><tr><td>3</td> <td><i>(Assess base usage at 3rd position of codons)</i></td></tr></table></td> <td>all</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gbui reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gbui is to a plain text file.<br /> <br /> File: nc_000913.gbui<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> acgt,ryr,gcc,Hgc,gcs,ats,gene<br /> 60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL<br /> 2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA<br /> 927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB<br /> 1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC<br /> 291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX<br /> 771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA<br /> 1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ<br /> 948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX<br /> 642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC<br /> 864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob<br /> 468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA<br /> 684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB<br /> 1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC<br /> 1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD<br /> 711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA<br /> 135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY<br /> 681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gdinuc.html">gdinuc</a></td> <td>Calculates dinucleotide usage</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gcai.html
--- a/GEMBASSY-1.0.3/doc/html/gcai.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gcai </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gcai </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate codon adaptation index for each gene  <H2>Description</H2> <p> gcai calculates codon adaptation index (CAI) for each gene. CAI is measure<br /> a of the relative adaptiveness of the codon usage of a gene towards the<br /> codon usage of highly expressed genes, ranging from 0 (no bias) to 1<br /> (maximum bias). CAI can be used as a 'universal' measure of codon usage<br /> bias as it is correlated with various gene features such as gene expression<br /> level, GC content, and GC skew.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gcai <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gcai refseqn:NC_000913 Calculate codon adaptation index for each gene Codon usage output file [nc_000913.gcai]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gcai</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translating using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-wabsent</td> <td>string</td> <td>W value of codons absent from a reference set to negative when excludes such codons from the calculation</td> <td>Any string</td> <td>-1</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gcai reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gcai is to a plain text file.<br /> <br /> File: nc_000913.gcai<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> cai,gene<br /> 0.7256,thrL<br /> 0.4831,thrA<br /> 0.4719,thrB<br /> 0.5178,thrC<br /> 0.4989,yaaX<br /> 0.4933,yaaA<br /> 0.4533,yaaJ<br /> 0.7074,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 0.4681,yjjX<br /> 0.4797,ytjC<br /> 0.5350,rob<br /> 0.4932,creA<br /> 0.3918,creB<br /> 0.4170,creC<br /> 0.4167,creD<br /> 0.6466,arcA<br /> 0.4236,yjjY<br /> 0.3913,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15(3):1281-95. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gp2.html">gp2</a></td> <td>Calculate the P2 index of each gene</td> </tr><tr> <td><a href="gphx.html">gphx</a></td> <td>Identify predicted highly expressed gene</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gcbi.html
--- a/GEMBASSY-1.0.3/doc/html/gcbi.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gcbi </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gcbi </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the codon bias index (CBI)  <H2>Description</H2> <p> gcbi calculates the codon bias index (CBI) for each gene af the given<br /> genome. CBI is a directional codon bias which measures the usage of<br /> optimal codons in a gene. CBI is similar to Fop, basically taking values<br /> from0 (no bias) and 1 (maximum bias) and can take negative values<br /> depending on the codon usage.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gcbi <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gcbi refseqn:NC_000913 Calculates the codon bias index (CBI) Codon usage output file [nc_000913.gcbi]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gcbi</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translating using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gcbi reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gcbi is to a plain text file.<br /> <br /> File: nc_000913.gcbi<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> cbi,gene<br /> 0.8716,thrL<br /> 0.3441,thrA<br /> 0.3462,thrB<br /> 0.4280,thrC<br /> 0.3868,yaaX<br /> 0.3908,yaaA<br /> 0.3521,yaaJ<br /> 0.5354,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 0.4005,yjjX<br /> 0.4388,ytjC<br /> 0.3934,rob<br /> 0.4645,creA<br /> 0.4266,creB<br /> 0.3435,creC<br /> 0.3796,creD<br /> 0.4980,arcA<br /> 0.5412,yjjY<br /> 0.4018,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability, J.Mol.Evo,. 37:273-280. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gdeltaenc.html">gdeltaenc</a></td> <td>Calculate the codon usage bias related to translation optimization (delta ENC)</td> </tr><tr> <td><a href="gicdi.html">gicdi</a></td> <td>Calculates the intrinsic codon deviation index (ICDI)</td> </tr><tr> <td><a href="gsvalue.html">gsvalue</a></td> <td>Calculate the strength of selected codon usage bias (S)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gcgr.html
--- a/GEMBASSY-1.0.3/doc/html/gcgr.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gcgr </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gcgr </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Create a Chaos Game Representation of a given sequence  <H2>Description</H2> <p> gcgr creates a Chaos Game Representation (CGR) image of a given sequence. CGR is generated by the following procedure:<br /> <br /> 1. Start from position (0,0) or the origin of two dimensional coordinate.<br /> Four nucleotides are located at the four corners:<br /> A: (-1, 1) upper left<br /> T: (1, -1) lower right<br /> G: (1, 1) upper right<br /> C: (-1, -1) lower left<br /> 2. For each nucleotide, move and mark the new location which is halfway<br /> between the current location and the nucleotide.<br /> For example, if the first letter is A, position is moved from (0,0) to<br /> midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).<br /> <br /> 3. Repeat this procedure for all nucleotides.<br /> CGR is a generalized scale-independent Markov probability table for the<br /> sequence, and oligomer tables can be deduced from CGR image.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gcgr <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gcgr refseqn:NC_000913 Create a Chaos Game Representation of a given sequence Created gcgr.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-width</td> <td>integer</td> <td>Width of image</td> <td>Any integer value</td> <td>1024</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>gcgr</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gcgr reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gcgr is to an image file. </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gseq2png.html">gseq2png</a></td> <td>Converts a sequence to PNG image</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gcircularmap.html
--- a/GEMBASSY-1.0.3/doc/html/gcircularmap.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gcircularmap </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gcircularmap </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Draws circular map of the genome  <H2>Description</H2> <p> gdnawalk creates a circular map of the genome using SVG, suitable for<br /> plasmids and circular bacterial chromosomes.<br /> From the outer ring inwards, genes on direct strand (pink), <br /> genes on complementary strand (yellow), tRNAs (green arrows), <br /> rRNAs (pink or orange stripes depending on the strand), <br /> GC content (brown lines), GC skew (yellow lines). Replication <br /> origin and terminus predicted from the GC skew shift points <br /> are also labeled. <br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gcircularmap <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gcircularmap refseqn:NC_000913 Draws circular map of the genome Created gcircularmap.1.svg </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>svg</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>gcircularmap</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gcircularmap reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gcircularmap is to an image file. </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gdnawalk.html">gdnawalk</a></td> <td>Draws DNA Walk map of the genome</td> </tr><tr> <td><a href="ggenomemap3.html">ggenomemap3</a></td> <td>Draws the map of the genome (version 3)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gcodoncompiler.html
--- a/GEMBASSY-1.0.3/doc/html/gcodoncompiler.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1 +0,0 @@\n-\r\r<HTML>\r<HEAD>\r <TITLE> EMBOSS: gcodoncompiler </TITLE>\r</HEAD>\r<BODY BGCOLOR="#FFFFFF" text="#000000">\r\r\r\r<table align=center border=0 cellspacing=0 cellpadding=0>\r<tr><td valign=top>\r<A HREF="/" ONMOUSEOVER="self.status=\'Go to the EMBOSS home page\';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>\r</td>\r<td align=left valign=middle>\r<b><font size="+6">\rgcodoncompiler\r</font></b>\r</td></tr>\r</table>\r<br> \r<p>\r\r\r\r\r\r\r\r\r\r<H2> Function </H2>\r Calculate various kinds of amino acid and codon usage data\r\r\r\r\r\r<H2>Description</H2>\r<p>\r gcodoncompiler calculates various kinds of amino acid and codon usage data.<br />\r The following values are calculable:<br />\r A0: Absolute amino acid frequency<br />\r A1: Relative amino acid frequency<br />\r C0: Absolute codon frequency<br />\r C1: Relative codon frequency in a complete sequence<br />\r C2: Relative codon frequency in each amino acid<br />\r C3: Relative synonymous codon usage<br />\r C4: Relative adaptiveness<br />\r C5: Maximum or minor codon<br />\r For amino acids unpresent in a gene, C2-C3 does not calculate the values.<br />\r By using R* in place, such values are hypothesized that alternative<br />\r synonymous codons are used with equal frequency.<br />\r <br />\r G-language SOAP service is provided by the<br />\r Institute for Advanced Biosciences, Keio University.<br />\r The original web service is located at the following URL:<br />\r<br />\r http://www.g-language.org/wiki/soap<br />\r<br />\r WSDL(RPC/Encoded) file is located at:<br />\r<br />\r http://soap.g-language.org/g-language.wsdl<br />\r<br />\r Documentation on G-language Genome Analysis Environment methods are<br />\r provided at the Document Center<br />\r<br />\r http://ws.g-language.org/gdoc/<br />\r<br />\r\r</p>\r\r<H2>Usage</H2>\r\rHere is a sample session with gcodoncompiler\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% gcodoncompiler refseqn:NC_000913\rCalculate various kinds of amino acid and codon usage data\rCodon usage output file [nc_000913.gcodoncompiler]: \r\r</pre></td></tr></table>\r\rGo to the <a href="#input">input files</a> for this example<br>\rGo to the <a href="#output">output files</a> for this example<br><br>\r\r<h2>Command line arguments</h2>\r\r<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">\r<tr bgcolor="#FFFFCC">\r<th align="left">Qualifier</th>\r<th align="left">Type</th>\r<th align="left">Description</th>\r<th align="left">Allowed values</th>\r<th align="left">Default</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-sequence]<br>(Parameter 1)</td>\r<td>seqall</td>\r<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>\r<td>Readable sequence(s)</td>\r<td><b>Required</b></td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-outfile]<br>(Parameter 2)</td>\r<td>outfile</td>\r<td>Codon usage output file</td>\r<td>Output file</td>\r<td><i><*></i>.gcodoncompiler</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Additional (Optional) qualifiers</th>\r</tr>\r\r<tr>\r<td colspan=5>(none)</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-translate</td>\r<td>boolean</td>\r<td>Include to translate using standard codon table</td>\r<td>Boolean value Yes/No</td>\r<td>No</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-startcodon</td>\r<td>boolean</td>\r<td>Include to include start codon</td>\r<td>Boolean value Yes/No</td>\r<td>No</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-stopcodon</td>\r<td>boolean</td>\r<td>Include to include stop codon</td>\r<td>Boolean value Yes/No</td>\r<td>No</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-delkey</td>\r<td>string</td>\r<td>Regula'..b'/i></td></tr><tr><td>C2</td> <td><i>(Relative codon frequency in each amino acid (\'RF\'))</i></td></tr><tr><td>C3</td> <td><i>(Relative synonymous codon usage (\'RSCU\'))</i></td></tr><tr><td>C4</td> <td><i>(Relative adaptiveness)</i></td></tr><tr><td>i.e., ratio to maximum of minor codon (\'W\') C5</td> <td><i>(Maximum (1) or minor (0) codon)</i></td></tr><tr><td>R0</td> <td><i>(Absolute codon frequency (\'AF\'))</i></td></tr><tr><td>R1</td> <td><i>(Relative codon frequency in a complete sequence)</i></td></tr><tr><td>R2</td> <td><i>(Relative codon frequency in each amino acid (\'RF\'))</i></td></tr><tr><td>R3</td> <td><i>(Relative synonymous codon usage (\'RSCU\'))</i></td></tr><tr><td>R4</td> <td><i>(Relative adaptiveness)</i></td></tr><tr><td>i.e., ratio to maximum of minor codon (\'W\') R5</td> <td><i>(Maximum (1) or minor (0) codon)</i></td></tr></table></td>\r<td>R0</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-[no]accid</td>\r<td>boolean</td>\r<td>Include to use sequence accession ID as query</td>\r<td>Boolean value Yes/No</td>\r<td>Yes</td>\r</tr>\r\r</table>\r\r\r<h2 id="input">Input file format</h2>\r\r<p>\r The database definitions for following commands are available at<br />\r http://soap.g-language.org/kbws/embossrc<br />\r<br />\r gcodoncompiler reads one or more nucleotide sequences.<br />\r<br />\r\r</p>\r\r<h2 id="output">Output file format</h2>\r\r<p>\r The output from gcodoncompiler is to a plain text file.<br />\r<br />\r File: nc_000913.gcodoncompiler<br />\r<br />\r<table width="90%"><tr><td bgcolor="#CCFFCC">\rSequence: NC_000913<br />\rAgca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag<br />\r26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,<br />\r</td></tr></table>\r\r</p>\r\r<h2>Data files</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Notes</h2>\r\r<p>\rNone.\r</p>\r\r<h2>References</h2>\r\r<pre>\r Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\r Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\r for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\r\r Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\r large-scale analysis of high-throughput omics data, J. Pest Sci.,\r 31, 7.\r\r Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\r Analysis Environment with REST and SOAP Web Service Interfaces,\r Nucleic Acids Res., 38, W700-W705.\r\r</pre>\r\r<h2>Warnings</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Diagnostic Error Messages</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Exit status</h2>\r\r<p>\rIt always exits with a status of 0.\r</p>\r\r<h2>Known bugs</h2>\r\r<p>\rNone.\r</p>\r\r<h2>See also</h2>\r\r<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>\r<th>Description</th></tr>\r\r<tr>\r<td><a href="gaminoinfo.html">gaminoinfo</a></td>\r<td>Prints out basic amino acid sequence statistics</td>\r</tr><tr>\r<td><a href="gaaui.html">gaaui</a></td>\r<td>Calculates various indece of amino acid usage</td>\r</tr>\r\r</table>\r\r<h2>Author(s)</h2>\r\r<pre>\r Hidetoshi Itaya (celery@g-language.org)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan\r\r Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan</pre>\r\r<h2>History</h2>\r\r 2012 - Written by Hidetoshi Itaya\r\r<h2>Target users</h2>\r\r This program is intended to be used by everyone and everything, from\r naive users to embedded scrips.\r\r<h2>Comments</h2>\r\r None.\r\r</BODY>\r</HTML>\r\n\\ No newline at end of file\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gconsensusz.html
--- a/GEMBASSY-1.0.3/doc/html/gconsensusz.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1 +0,0 @@\n-\r\r<HTML>\r<HEAD>\r <TITLE> EMBOSS: gconsensusz </TITLE>\r</HEAD>\r<BODY BGCOLOR="#FFFFFF" text="#000000">\r\r\r\r<table align=center border=0 cellspacing=0 cellpadding=0>\r<tr><td valign=top>\r<A HREF="/" ONMOUSEOVER="self.status=\'Go to the EMBOSS home page\';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>\r</td>\r<td align=left valign=middle>\r<b><font size="+6">\rgconsensusz\r</font></b>\r</td></tr>\r</table>\r<br> \r<p>\r\r\r\r\r\r\r\r\r\r<H2> Function </H2>\r Calculate consensus in given array of sequences\r\r\r\r\r\r<H2>Description</H2>\r<p>\r gconsensusz calculates the consensus of given list of sequences, using<br />\r Z-score. The Z-score will show higher values when the sequences are biased<br />\r to a single character within the list.<br />\r <br />\r G-language SOAP service is provided by the<br />\r Institute for Advanced Biosciences, Keio University.<br />\r The original web service is located at the following URL:<br />\r<br />\r http://www.g-language.org/wiki/soap<br />\r<br />\r WSDL(RPC/Encoded) file is located at:<br />\r<br />\r http://soap.g-language.org/g-language.wsdl<br />\r<br />\r Documentation on G-language Genome Analysis Environment methods are<br />\r provided at the Document Center<br />\r<br />\r http://ws.g-language.org/gdoc/<br />\r<br />\r\r</p>\r\r<H2>Usage</H2>\r\rHere is a sample session with gconsensusz\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% gconsensusz consensus.fasta\rCalculate consensus in given array of sequences\rProgram compseq output file (optional) [rs_000000.gconsensusz]: \r\r</pre></td></tr></table>\r\rGo to the <a href="#input">input files</a> for this example<br>\rGo to the <a href="#output">output files</a> for this example<br><br>\r\r Example 2\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% gconsensusz consensus.fasta -plot -graph png\rCalculate consensus in given array of sequences\rCreated gconsensusz.1.png\r\r</pre></td></tr></table>\r\rGo to the <a href="#input">input files</a> for this example<br>\rGo to the <a href="#output">output files</a> for this example<br><br>\r\r<h2>Command line arguments</h2>\r\r<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">\r<tr bgcolor="#FFFFCC">\r<th align="left">Qualifier</th>\r<th align="left">Type</th>\r<th align="left">Description</th>\r<th align="left">Allowed values</th>\r<th align="left">Default</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>[-sequence]<br>(Parameter 1)</td>\r<td>seqall</td>\r<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>\r<td>Readable sequence(s)</td>\r<td><b>Required</b></td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-graph</td>\r<td>xygraph</td>\r<td>Graph type</td>\r<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td>\r<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-outfile</td>\r<td>outfile</td>\r<td>Program compseq output file (optional)</td>\r<td>Output file</td>\r<td><i><*></i>.gconsensusz</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Additional (Optional) qualifiers</th>\r</tr>\r\r<tr>\r<td colspan=5>(none)</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-high</td>\r<td>integer</td>\r<td>Z value greater than which is significant</td>\r<td>Any integer value</td>\r<td>1</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-low</td>\r<td>float</td>\r<td>Z value less than which is insignificant</td>\r<td>Any numeric value</td>\r<td>0.2</td>\r</tr>\r\r<tr bgcolor="#FFFFCC">\r<td>-plot</td>\r<td>toggle</td>\r<td>Include to plot result</td>\r<td>Toggle value Yes/No</td>\r<td>No</td>\r</tr>\r\r</table>\r\r\r<h2 id="input">I'..b'.487923290212298,0.487923290212298,0.487923290212298,0.487923290212298,3.00732065791778,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,4.26701934177052,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,3.00732065791778,1.74762197406504,4.26701934177052,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,3.00732065791778,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,5.52671802562326,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,3.00732065791778,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,<br />\r</td></tr></table>\r\r</p>\r\r<h2>Data files</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Notes</h2>\r\r<p>\rNone.\r</p>\r\r<h2>References</h2>\r\r<pre>\r Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\r Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\r for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\r\r Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\r large-scale analysis of high-throughput omics data, J. Pest Sci.,\r 31, 7.\r\r Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\r Analysis Environment with REST and SOAP Web Service Interfaces,\r Nucleic Acids Res., 38, W700-W705.\r\r</pre>\r\r<h2>Warnings</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Diagnostic Error Messages</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Exit status</h2>\r\r<p>\rIt always exits with a status of 0.\r</p>\r\r<h2>Known bugs</h2>\r\r<p>\rNone.\r</p>\r\r<h2>See also</h2>\r\r<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>\r<th>Description</th></tr>\r\r<tr>\r<td><a href="gdistincc.html">gdistincc</a></td>\r<td>Calculates the distance between two loci in circular chromosomes</td>\r</tr><tr>\r<td><a href="gpalindrome.html">gpalindrome</a></td>\r<td>Searches palindrome sequences</td>\r</tr><tr>\r<td><a href="gseqinfo.html">gseqinfo</a></td>\r<td>Prints out basic nucleotide sequence statistics</td>\r</tr>\r\r</table>\r\r<h2>Author(s)</h2>\r\r<pre>\rHidetoshi Itaya (celery@g-language.org)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan\r\rKazuharu Arakawa (gaou@sfc.keio.ac.jp)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan</pre>\r\r<h2>History</h2>\r\r 2012 - Written by Hidetoshi Itaya\r\r<h2>Target users</h2>\r\r This program is intended to be used by everyone and everything, from\r naive users to embedded scrips.\r\r<h2>Comments</h2>\r\r None.\r\r</BODY>\r</HTML>\n\\ No newline at end of file\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gdeltaenc.html
--- a/GEMBASSY-1.0.3/doc/html/gdeltaenc.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gdeltaenc </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gdeltaenc </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the codon usage bias related to translation optimization (delta ENC)  <H2>Description</H2> <p> gdeltaenc calculates the codon usage bias related to translation<br /> optimization (delta ENC) described in Rocha (2004). The basic idea is to<br /> calculate the Effective Number of Codons (ENC) for highly-expressed genes<br /> (ribosomal genes) and weakly-expressed genes (all genes), and taking the<br /> relative difference between them. ENC assigns a gene a number between 20 to<br /> 61 where 20 indicates that one codon is used for each aminoacid and 61<br /> indicates that each codon is used equally throughout the protein sequence.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gdeltaenc <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gdeltaenc refseqn:NC_000913 Calculate the codon usage bias related to translation optimization (delta ENC) Program compseq output file [nc_000913.gdeltaenc]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gdeltaenc</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gdeltaenc reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gdeltaenc is to a plain text file.<br /> <br /> File: nc_000913.gdeltaenc<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 DELTA-ENC 0.255663430420712<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization, Genome Research, 14(11):2279-2286 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcbi.html">gcbi</a></td> <td>Calculates the codon bias index (CBI)</td> </tr><tr> <td><a href="gicdi.html">gicdi</a></td> <td>Calculates the intrinsic codon deviation index (ICDI)</td> </tr><tr> <td><a href="gsvalue.html">gsvalue</a></td> <td>Calculate the strength of selected codon usage bias (S)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gdeltagcskew.html
--- a/GEMBASSY-1.0.3/doc/html/gdeltagcskew.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gdeltagcskew </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gdeltagcskew </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate strand bias of bacterial genome using delta GC skew index  <H2>Description</H2> <p> gdeltagcskew calculates strand bias of bacterial genome using delta GC skew<br /> index, first proposed by Rocha et al. (2001), and further extended in 2006.<br /> Basic idea of delta GC skew index is to calculate the difference of GC skew<br /> in coding regions residing in leading and lagging strands. Rocha et al.<br /> (2001) calculates delta GC skew index using the third codon position of<br /> genes, and Rocha et al. (2006) modified to only use >fourfold degenerate<br /> codons.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gdeltagcskew <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gdeltagcskew refseqn:NC_000913 Calculate strand bias of bacterial genome using delta GC skew index Program compseq output file [nc_000913.gdeltagcskew]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gdeltagcskew</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-at</td> <td>boolean</td> <td>Include when observing AT skew instead of GC skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-purine</td> <td>boolean</td> <td>Include when observing purine (AG/TC) skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-keto</td> <td>boolean</td> <td>Include when observing keto (TG/AC) skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-method</td> <td>selection</td> <td>Choose the nucleotides to use 'degenerate', 'gc3', or 'all'</td> <td>Choose from selection list of values</td> <td>degenerate</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gdeltagcskew reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gdeltagcskew is to a plain text file.<br /> <br /> File: nc_000913.gdeltagcskew<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 DELTA-GCskew -0.108937<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial Genomes, Molecular Biology and Evolution, 18(9):1789-1799 Rocha EPC et al. (2006) Similar compositional biases are caused by very different mutational effects, Genome Research, 16:1537-1547 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gb1.html">gb1</a></td> <td>Calculate strand bias of bacterial genome using B1 index</td> </tr><tr> <td><a href="gb2.html">gb2</a></td> <td>Calculate strand bias of bacterial genome using B2 index</td> </tr><tr> <td><a href="ggcsi.html">ggcsi</a></td> <td>GC Skew Index: an index for strand-specefic mutational bias</td> </tr><tr> <td><a href="gldabias.html">glda_bias</a></td> <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gdinuc.html
--- a/GEMBASSY-1.0.3/doc/html/gdinuc.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gdinuc </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gdinuc </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates dinucleotide usage  <H2>Description</H2> <p> gdinuc calculates dinucleotide usage indices for protein-coding sequences<br /> (excluding start and stop codons). Dinucleotide usage is computed as the<br /> ratio of observed (O) to expected (E) dinucleotide frequencies within the<br /> given sequence. Dinucleotides are known to have consistent patterns within<br /> the genome (signatures) and tend to have certain periodicities.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gdinuc <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gdinuc refseqn:NC_000913 Calculates dinucleotide usage Program compseq output file [nc_000913.gdinuc]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gdinuc</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translates using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-position</td> <td>list</td> <td>Codon position or reading frame</td> <td><table><tr><td>all</td> <td><i>(Assess all codon positions)</i></td></tr><tr><td>12</td> <td><i>(Assess the reading frame 1-2)</i></td></tr><tr><td>23</td> <td><i>(Assess the reading frame 2-3)</i></td></tr><tr><td>31</td> <td><i>(Assess the reading frame 3-1)</i></td></tr></table></td> <td>all</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gdinuc reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gdinuc is to a plain text file.<br /> <br /> File: nc_000913.gdinuc<br /> <br /> Sequence: NC_000913<br /> <br />?<table width="90%"><tr><td bgcolor="#CCFFCC"> keys,aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,gene,<br /> All,1.293,0.921,0.720,1.108,1.022,0.868,1.166,0.925,0.958,1.285,0.897,0.867,0.729,0.891,1.228,1.123,<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Yew et al. (2004) Base usage and dinucleotide frequency of infectious bursal disease virus, Virus Genes, 28:1,41-53. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gbui.html">gbui</a></td> <td>Calculates base usage indices for protein-coding sequences</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gdistincc.html
--- a/GEMBASSY-1.0.3/doc/html/gdistincc.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gdistincc </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gdistincc </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the distance between two loci in circular chromosomes  <H2>Description</H2> <p> gdistincc calculates the distance between two loci in circular<br /> chromosomes. It is mostly useful to calculate the distance from the<br /> replication origin.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gdistincc <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gdistincc refseqn:NC_000913 1234 Calculates the distance between two loci in circular chromosomes Output file [nc_000913.gdistincc]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-first]<br>(Parameter 2)</td> <td>integer</td> <td>Position to find the distance</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 3)</td> <td>outfile</td> <td>Output file name</td> <td>Output file</td> <td><i><*></i>.gdistincc</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-second</td> <td>integer</td> <td>If the second position is negative, position of replication origin is used</td> <td>Any integer value</td> <td>-1</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gdistincc reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gdistincc is to a plain text file.<br /> <br /> File: nc_000913.gdistincc<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Position1: 1234 Distance 1169193600<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gconsensusz.html">gconsensusz</a></td> <td>Calculate consensus in given array of sequences</td> </tr><tr> <td><a href="gpalindrome.html">gpalindrome</a></td> <td>Searches palindrome sequences</td> </tr><tr> <td><a href="gseqinfo.html">gseqinfo</a></td> <td>Prints out basic nucleotide sequence statistics</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gdnawalk.html
--- a/GEMBASSY-1.0.3/doc/html/gdnawalk.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gdnawalk </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gdnawalk </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Draws DNA Walk map of the genome  <H2>Description</H2> <p> gdnawalk draws the DNA Walk map of the given genome. DNA Walk is drawn by<br /> moving a single pixel per nucleotide, in the direction specified for each<br /> base. Here A is moved upward, T downward, G to the right, and C to the<br /> left. Position zero (first letter of the genome) is indicated by the<br /> crossing of thin axes.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gdnawalk <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gdnawalk refseqn:NC_000913 Draws DNA Walk map of the genome Created gdnawalk.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>gdnawalk</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gdnawalk reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gdnawalk is to an image file.<br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcircularmap.html">gcircularmap</a></td> <td>Draws circular map of the genome</td> </tr><tr> <td><a href="ggenomemap3.html">ggenomemap3</a></td> <td>Draws the map of the genome (version 3)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/genc.html
--- a/GEMBASSY-1.0.3/doc/html/genc.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: genc </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> genc </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the effective number of codons (Nc)  <H2>Description</H2> <p> genc calculates the effective number of codons (ENC|Nc). ENC is a measure<br /> for species-independent codon usage bias. Some measures including CAI are<br /> species-dependent as optimal codons differ. ENC assigns a gene a number<br /> between 20 to 61 where 20 indicates that one codon is used for each amino<br /> acid and 61 indicates that each codon is used equally throughout the<br /> protein sequence.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with genc <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genc refseqn:NC_000913 Calculate the effective number of codons (Nc) Codon usage output file [nc_000913.genc]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.genc</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translates using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> genc reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from genc is to a plain text file.<br /> <br /> File: nc_000913.genc<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> enc,gene<br /> ,thrL<br /> 48.41,thrA<br /> 54.13,thrB<br /> 46.18,thrC<br /> 51.65,yaaX<br /> 45.71,yaaA<br /> 48.54,yaaJ<br /> 36.83,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 51.43,yjjX<br /> 46.61,ytjC<br /> 49.83,rob<br /> 47.74,creA<br /> 50.63,creB<br /> 51.39,creC<br /> 48.42,creD<br /> 41.53,arcA<br /> 61,yjjY<br /> 53.63,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Wright F. (1990) The 'effective number of codons' used in a gene, Gene, 87:23-29. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gew.html">gew</a></td> <td>Calculate a measure of synonymous codon usage evenness (Ew)</td> </tr><tr> <td><a href="gfop.html">gfop</a></td> <td>Calculate the frequency of optimal codons (Fop)</td> </tr><tr> <td><a href="gscs.html">gscs</a></td> <td>Calculates the scaled chi-square</td> </tr><tr> <td><a href="gwvalue.html">gwvalue</a></td> <td>Calculate the 'relative adaptiveness of each codon' (W)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/genret.html
--- a/GEMBASSY-1.0.3/doc/html/genret.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,17 +0,0 @@\n-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"\n- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n-<html xmlns=\'http://www.w3.org/1999/xhtml\' xml:lang=\'en\' lang=\'en\'>\n- <head>\n- <title>EMBOSS: genret manual</title>\n- <link rel=\'stylesheet\' type=\'text/css\' href=\'/gembassy/emboss_explorer/style/emboss.css\' />\n- \n- </head>\n- <body>\n- <div id=\'manual\'>\n- \n- \r\r\r\r<table align=center border=0 cellspacing=0 cellpadding=0>\r<tr><td valign=top>\r<A HREF="/" ONMOUSEOVER="self.status=\'Go to the EMBOSS home page\';return true"><img border=0 src="/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>\r</td>\r<td align=left valign=middle>\r<b><font size="+6">\rgenret\r</font></b>\r</td></tr>\r</table>\r<br> \r<p>\r\r\r\r\r\r\r\r\r\r<H2> Function </H2>\r Retrieves various gene related information from genome flatfile\r\r\r\r\r\r<H2>Description</H2>\r<p>\r genret reads in one or more genome flatfiles and retrieves various data from<br />\r the input file. It is a wrapper program to the G-language REST service,<br />\r where a method is specified by giving a string to the "method" qualifier. By<br />\r default, genret will parse the input file to retrieve the accession ID<br />\r (or name) of the genome to query G-language REST service. By setting the<br />\r "accid" qualifier to false (or 0), genret will instead parse the sequence<br />\r and features of the genome to create a GenBank formatted flatfile and upload<br />\r the file to the G-language web server. Using the file uploaded, genret will<br />\r execute the method provided.<br />\r<br />\r genret is able to perform a variety of tasks, incluing the retrieval of<br />\r sequence upstream, downstream, or around the start or stop codon,<br />\r translated gene sequences search of gene data by keyword.<br />\r<br />\r Details on G-language REST service is available from the wiki page<br />\r<br />\r http://www.g-language.org/wiki/rest<br />\r<br />\r Documentation on G-language Genome Analysis Environment methods are<br />\r provided at the Document Center<br />\r<br />\r http://ws.g-language.org/gdoc/<br />\r<br />\r\r</p>\r\r<H2>Usage</H2>\r\rHere is a sample session with genret<br><br>\r\rRetrieving sequences upstream, downstream, or around the start/stop codons.\rThe following example shows the retrieval of sequence around the start\rcodons of all genes.<br><br>\r\rGenes to access are specified by regular expression. \'*\' stands for every\rgene.<br><br>\r\rAvailable methods are:<br>\r after_startcodon<br>\r after_stopcodon<br>\r around_startcodon<br>\r around_stopcodon<br>\r before_startcodon<br>\r before_stopcodon<br><br>\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% genret\rRetrieves various gene related information from genome flatfile\rInput nucleotide sequence(s): refseqn:NC_000913\rGene name(s) to lookup [*]:\rFeature to access: around_startcodon\rFull text output file [nc_000913.around_startcodon]:\r\r</pre></td></tr></table>\r\rGo to the <a href="#input">input files</a> for this example<br>\rGo to the <a href="#output">output files</a> for this example<br><br>\r\rExample 2<br><br>\r\rUsing flat text as target genes. The names can be split with with a space, comma, or vertical bar.<br><br>\r\r<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>\r\r% genret\rRetrieves various gene related information from genome flatfile\rInput nucleotide sequence(s): refseqn:NC_000913\rList of gene name(s) to report [*]: recA,recB\rName of gene feature to access: translation\rSequence output file [nc_000913.translation.genret]: stdout\r>recA\rMAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR\rIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT\rGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL\rKQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR\rVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN\r'..b'006203; GHMP_knse_ATP-bd_CS."<br />\r /rs_xr="InterPro; IPR000870; Homoserine_kin."<br />\r /rs_xr="InterPro; IPR020568; Ribosomal_S5_D2-typ_fold."<br />\r /rs_xr="InterPro; IPR014721;<br />\r Ribosomal_S5_D2-typ_fold_subgr."<br />\r /rs_xr="Gene3D; G3DSA:3.30.230.10;<br />\r Ribosomal_S5_D2-type_fold; 1."<br />\r /rs_xr="Pfam; PF08544; GHMP_kinases_C; 1."<br />\r /rs_xr="Pfam; PF00288; GHMP_kinases_N; 1."<br />\r /rs_xr="PIRSF; PIRSF000676; Homoser_kin; 1."<br />\r /rs_xr="PRINTS; PR00958; HOMSERKINASE."<br />\r /rs_xr="SUPFAM; SSF54211; Ribosomal_S5_D2-typ_fold; 1."<br />\r /rs_xr="TIGRFAMs; TIGR00191; thrB; 1."<br />\r /rs_xr="PROSITE; PS00627; GHMP_KINASES_ATP; 1."<br />\r /transl_table="11"<br />\r /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETF<br />\r SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS<br />\r VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI<br />\r ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQ<br />\r PELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETA<br />\r QRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"<br />\r<br />\r<font color="red">[Part of this file has been deleted for brevity]</font><br />\r<br />\r 4639201 gcgcagtcgg gcgaaatatc attactacgc cacgccagtt gaactggtgc cgctgttaga<br />\r 4639261 ggaaaaatct tcatggatga gccatgccgc gctggtgttt ggtcgcgaag attccgggtt<br />\r 4639321 gactaacgaa gagttagcgt tggctgacgt tcttactggt gtgccgatgg tggcggatta<br />\r 4639381 tccttcgctc aatctggggc aggcggtgat ggtctattgc tatcaattag caacattaat<br />\r 4639441 acaacaaccg gcgaaaagtg atgcaacggc agaccaacat caactgcaag ctttacgcga<br />\r 4639501 acgagccatg acattgctga cgactctggc agtggcagat gacataaaac tggtcgactg<br />\r 4639561 gttacaacaa cgcctggggc ttttagagca acgagacacg gcaatgttgc accgtttgct<br />\r 4639621 gcatgatatt gaaaaaaata tcaccaaata aaaaacgcct tagtaagtat ttttc<br />\r//<br />\r</td></tr></table>\r\r</p>\r\r<h2>Data files</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Notes</h2>\r\r<p>\rNone.\r</p>\r\r<h2>References</h2>\r\r<pre>\r Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\r Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\r for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\r\r Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\r large-scale analysis of high-throughput omics data, J. Pest Sci.,\r 31, 7.\r\r Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\r Analysis Environment with REST and SOAP Web Service Interfaces,\r Nucleic Acids Res., 38, W700-W705.\r\r</pre>\r\r<h2>Warnings</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Diagnostic Error Messages</h2>\r\r<p>\rNone.\r</p>\r\r<h2>Exit status</h2>\r\r<p>\rIt always exits with a status of 0.\r</p>\r\r<h2>Known bugs</h2>\r\r<p>\rNone.\r</p>\r\r<h2>See also</h2>\r\r<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>\r<th>Description</th></tr>\r\r<tr>\r<td><a href="entret">entret</a></td>\r<td>Retrieve sequence entries from flatfile databases and files</td>\r</tr><tr>\r<td><a href="seqret">seqret</a></td>\r<td>Read and write (return) sequences</td>\r</tr>\r\r</table>\r\r<h2>Author(s)</h2>\r\r<pre>\rHidetoshi Itaya (celery@g-language.org)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan\r\rKazuharu Arakawa (gaou@sfc.keio.ac.jp)\r Institute for Advanced Biosciences, Keio University\r 252-0882 Japan</pre>\r\r<h2>History</h2>\r\r 2012 - Written by Hidetoshi Itaya\r\r<h2>Target users</h2>\r\r This program is intended to be used by everyone and everything, from\r naive users to embedded scrips.\r\r<h2>Comments</h2>\r\r None.\r\r\r</HTML>\r\n-\n- \n- </div>\n- </body>\n-</html>\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gentrez.html
--- a/GEMBASSY-1.0.3/doc/html/gentrez.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gentrez </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gentrez </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Search NCBI Entrez  <H2>Description</H2> <p> gentrez searches NCBI Entrez with keyword through EUtilities. <br /> This is intended for quick lookup through the command line<br /> so only top ten hits are reported.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gentrez <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gentrez genome 'Escherichia coli' Search NCBI Entrez ASCII text output file [genome.Escherichia coli.gentrez]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-database]<br>(Parameter 1)</td> <td>string</td> <td>NCBI database to search</td> <td>Any string</td> <td>pubmed</td> </tr> <tr bgcolor="#FFFFCC"> <td>[-query]<br>(Parameter 2)</td> <td>string</td> <td>Query to search</td> <td>Any string</td> <td> </td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 3)</td> <td>outfile</td> <td>ASCII text output file</td> <td>Output file</td> <td>$(database).$(query).gentrez</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gentrez reads no file input.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gentrez is to a plain text file.<br /> <br /> File: genome.Escherichia coli.gentrez<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> 53 entries found in NUCLEOTIDE: (Showing up to 10 hits)<br /> <br /> 1. Accession Number: NZ_AKBV01000001<br /> Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome<br /> <br /> 2. Accession Number: NC_018658<br /> Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome<br /> <br /> 3. Accession Number: NC_012971<br /> Escherichia coli BL21(DE3) chromosome, complete genome<br /> <br /> 4. Accession Number: NC_017635<br /> Escherichia coli W chromosome, complete genome<br /> <br /> 5. Accession Number: NC_018650<br /> Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome<br /> <br /> 6. Accession Number: NC_018661<br /> Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome<br /> <br /> 7. Accession Number: NC_017906<br /> Escherichia coli Xuzhou21 chromosome, complete genome<br /> <br /> 8. Accession Number: NC_017634<br /> Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome<br /> <br /> 9. Accession Number: NC_017656<br /> Escherichia coli O55:H7 str. RM12579 chromosome, complete genome<br /> <br /> 10. Accession Number: NC_017664<br /> Escherichia coli W chromosome, complete genome<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gew.html
--- a/GEMBASSY-1.0.3/doc/html/gew.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gew </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gew </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate a measure of synonymous codon usage evenness (Ew)  <H2>Description</H2> <p> gew calculates the 'weighted sum of relative entropy' (Ew) as a measure <br /> of synonymous codon usage evenness for each gene. This index takes all <br /> three aspects of amino acid usage (number of distinct amino acids, <br /> relatieve frequencies, and degree of codon degeneracy) into account.<br /> The values range from 0 (no bias) to 1 (maximum bias).<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gew <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gew refseqn:NC_000913 Calculate a measure of synonymous codon usage evenness (Ew) Codon usage output file [nc_000913.gew]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gew</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translates using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gew reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gew is to a plain text file.<br /> <br /> File: nc_000913.gew<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> Ew,gene<br /> 0.2800,thrL<br /> 0.8458,thrA<br /> 0.8292,thrB<br /> 0.7937,thrC<br /> 0.7032,yaaX<br /> 0.7922,yaaA<br /> 0.8100,yaaJ<br /> 0.6685,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 0.7943,yjjX<br /> 0.7265,ytjC<br /> 0.7932,rob<br /> 0.7498,creA<br /> 0.7967,creB<br /> 0.8490,creC<br /> 0.7979,creD<br /> 0.6826,arcA<br /> 0.6475,yjjY<br /> 0.7729,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Suzuki H. et al. (2004) The 'weighted sum of relative entropy': a new index for synonymous codon usage bias, Gene, 23;335:19-23. Suzuki H. et al. (2007) Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria, EURASIP J Bioinform Syst Biol, 2007:61374. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="genc.html">genc</a></td> <td>Calculate the effective number of codons (Nc)</td> </tr><tr> <td><a href="gfop.html">gfop</a></td> <td>Calculate the frequency of optimal codons (Fop)</td> </tr><tr> <td><a href="gscs.html">gscs</a></td> <td>Calculates the scaled chi-square</td> </tr><tr> <td><a href="gwvalue.html">gwvalue</a></td> <td>Calculate the 'relative adaptiveness of each codon' (W)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gfindoriter.html
--- a/GEMBASSY-1.0.3/doc/html/gfindoriter.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gfindoriter </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gfindoriter </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Predict the replication origin and terminus in bacterial genomes  <H2>Description</H2> <p> gfindoriter predicts the replicational origin and terminus in circular<br /> bacterial genomes, by taking the vertices of cumulative skew graphs (GC,<br /> d keto, or purine). See Frank and Lobry (2000) for the basic idea behind<br /> this algorithm (but also note that this algorithm is different from that<br /> of Oriloc, which uses GC3 of genes). <br /> Terminus of replication can be more accurate by using noise-reduction <br /> filtering using Fourier spectrum of the GC skew. This low-pass filtering<br /> can be applied using -filter option. See Arakawa et al. (2007) for details.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gfindoriter <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gfindoriter refseqn:NC_000913 Predict the replication origin and terminus in bacterial genomes Output file [nc_000913.gfindoriter]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Output file name</td> <td>Output file</td> <td><i><*></i>.gfindoriter</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Number of windows to use for Fat Fourier Transform. Only active when -lowpass option is specified. Value must be the power of two</td> <td>Any integer value</td> <td>4096</td> </tr> <tr bgcolor="#FFFFCC"> <td>-purine</td> <td>boolean</td> <td>Use purine skew for calculation</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-keto</td> <td>boolean</td> <td>Use keto skew for calculation</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-lowpass</td> <td>integer</td> <td>Lowpass filter strength in percent. Typically 95 or 99 works best</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gfindoriter reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gfindoriter is to a plain text file.<br /> <br /> File: nc_000913.gfindoriter<br /> <br />?<table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Origin: 3922946 Terminus: 1550274<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes, Bioinformatics, 16:566-567. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="greporiter.html">greporiter</a></td> <td>Gets the positions of replication origin and terminus</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scripts. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gfop.html
--- a/GEMBASSY-1.0.3/doc/html/gfop.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gfop </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gfop </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the frequency of optimal codons (Fop)  <H2>Description</H2> <p> gfop calculates the frequency of optimal codons (Fop).Fop is an index to <br /> show the optimization level of synonymous codon usage choice. It is<br /> basically a ratio of optimal codons against all codons used. The value<br /> of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal<br /> codons are used).<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gfop <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gfop refseqn:NC_000913 Calculate the frequency of optimal codons (Fop) Codon usage output file [nc_000913.gfop]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gfop</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translates using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gfop reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gfop is to a plain text file.<br /> <br /> File: nc_000913.gfop<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> Laa,Lc,fop,gene<br /> 20,5,0.4000,thrL<br /> 819,133,0.4361,thrA<br /> 309,46,0.4783,thrB<br /> 427,69,0.5217,thrC<br /> 97,7,0.2857,yaaX<br /> 257,56,0.4643,yaaA<br /> 475,96,0.3958,yaaJ<br /> 316,56,0.6964,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 169,27,0.2593,yjjX<br /> 214,23,0.5652,ytjC<br /> 288,49,0.4082,rob<br /> 156,23,0.3478,creA<br /> 228,26,0.3462,creB<br /> 473,69,0.3478,creC<br /> 449,70,0.3286,creD<br /> 237,46,0.6957,arcA<br /> 45,10,0.7000,yjjY<br /> 227,24,0.2500,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Ikemura, T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, J.Mol.Biol, 151:389-409. Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular organisms, Mol.Biol.Evol, 2(1):13-34. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="genc.html">genc</a></td> <td>Calculate the effective number of codons (Nc)</td> </tr><tr> <td><a href="gew.html">gew</a></td> <td>Calculate a measure of synonymous codon usage evenness (Ew)</td> </tr><tr> <td><a href="gscs.html">gscs</a></td> <td>Calculates the scaled chi-square</td> </tr><tr> <td><a href="gwvalue.html">gwvalue</a></td> <td>Calculate the 'relative adaptiveness of each codon' (W)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/ggcsi.html
--- a/GEMBASSY-1.0.3/doc/html/ggcsi.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: ggcsi </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> ggcsi </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> GC Skew Index: an index for strand-specific mutational bias  <H2>Description</H2> <p> ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial<br /> genome. GCSI quantifies the degree of GC Skew. In other words, this index<br /> represents the degree of strand-specific mutational bias in bacterial<br /> genomes, caused by replicational selection. <br /> GCSI is calculated by the following formula:<br /> <br /> GCSI = sqrt((SA/6000) * (dist/600))<br /> <br /> where SA is the spectral amplitude of Fourier power spectrum at 1Hz,<br /> and dist is the normalized Euclidean distance between the vertices of <br /> cumulative GC skew.<br /> <br /> GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal<br /> genomes that have multiple replication origins and therefore have no<br /> observable skew mostly have GCSI below 0.05. Escherichia coli genome has<br /> values around 0.10.<br /> <br /> Version 1 of GCSI required fixed number of windows (4096), but the new GCSI<br /> version 2 (also known as generalized GCSI: gGCSI) is invariant of the number<br /> of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed<br /> to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise<br /> ratio of 1Hz power spectrum) and dist.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggcsi <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggcsi refseqn:NC_000913 GC Skew Index: an index for strand-specific mutational bias Program compseq output file [nc_000913.ggcsi]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.ggcsi</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-gcsi</td> <td>selection</td> <td>GCSI version to use</td> <td>Choose from selection list of values</td> <td>2</td> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Number of windows. Must be a power of 2</td> <td>Any integer value</td> <td>4096</td> </tr> <tr bgcolor="#FFFFCC"> <td>-purine</td> <td>boolean</td> <td>Use purine skew for calculation</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-keto</td> <td>boolean</td> <td>Use keto skew for calculation</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-at</td> <td>boolean</td> <td>Use AT skew for calculation</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-pval</td> <td>boolean</td> <td>Calculate p-value when GCSI version 2 is selected</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2>Input file format</h2> <p id="input"> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggcsi reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from ggcsi is to a plain text file.<br /> <br /> File: nc_000913.ggcsi<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gb1.html">gb1</a></td> <td>Calculate strand bias of bacterial genome using B1 index</td> </tr><tr> <td><a href="gb2.html">gb2</a></td> <td>Calculate strand bias of bacterial genome using B2 index</td> </tr><tr> <td><a href="gdeltagcskew.html">gdeltagcskew</a></td> <td>Calculate strand bias of bacterial genome using delta GC skew</td> </tr><tr> <td><a href="gldabias.html">gldabias</a></td> <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/ggcskew.html
--- a/GEMBASSY-1.0.3/doc/html/ggcskew.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: ggcskew </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> ggcskew </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the GC skew of the input sequence  <H2>Description</H2> <p> ggcskew calculates and plots the GC skew of the given sequence. The "skew"<br /> of a sequence is calculated as (C-G)/(C+G) in GC skew. The program can<br /> alternatively calculate AT skew, purine skew, and keto skew, as well as<br /> cumulative skew. GC skew is used to observe various biological aspects<br /> such as prediction of replication origin and terminus in bacteria.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggcskew <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggcskew refseqn:NC_000913 Calculates the GC skew of the input sequence Program compseq output file (optional) [nc_000913.ggcskew]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggcskew refseqn:NC_000913 -plot -graph png Calculates the GC skew of the input sequence Created ggcskew.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.ggcskew</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Window size to observe</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-slide</td> <td>integer</td> <td>Window slide size</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-cumulative</td> <td>boolean</td> <td>Include to calculate cumulative skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-at</td> <td>boolean</td> <td>Include for observing AT skew instead of GC skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-purine</td> <td>boolean</td> <td>Include for observing purine (AG/TC) skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-keto</td> <td>boolean</td> <td>Include for observing keto (TG/AC) skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggcskew reads one or more nucleotide sequences.<br /> <br /> </p> <h2 output="output">Output file format</h2> <p> The output from ggcskew is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.ggcskew<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> location,GC skew<br /> 0,-0.035529<br /> 10000,-0.039648<br /> 20000,-0.049791<br /> 30000,0.005072<br /> 40000,-0.063483<br /> 50000,-0.030256<br /> 60000,0.011875<br /> 70000,-0.029478<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 4530000,-0.017164<br /> 4540000,-0.036140<br /> 4550000,-0.028166<br /> 4560000,0.012166<br /> 4570000,-0.040486<br /> 4580000,-0.020692<br /> 4590000,-0.043920<br /> 4600000,-0.026363<br /> 4610000,-0.022778<br /> 4620000,-0.049396<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="ggcwin.html">ggcwin</a></td> <td>Calculates the GC content along the given genome</td> </tr><tr> <td><a href="ggeneskew.html">ggeneskew</a></td> <td>Calculate the gene strand bias of the given genome</td> </tr><tr> <td><a href="ggenomicskew.html">ggenomicskew</a></td> <td>Calculates the GC skew in different regions of the given genome</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/ggcwin.html
--- a/GEMBASSY-1.0.3/doc/html/ggcwin.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: ggcwin </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> ggcwin </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the GC content along the given genome  <H2>Description</H2> <p> ggcwin calculates and plots the GC content of the given sequence.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggcwin <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggcwin refseqn:NC_000913 Calculates the GC content along the given genome Program compseq output file (optional) [nc_000913.ggcwin]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFCC"> % ggcwin refseqn:NC_000913 -plot -graph png Calculates the GC content along the given genome Created ggcwin.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.ggcwin</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Window size to observe</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-at</td> <td>boolean</td> <td>Include for observing AT skew instead of GC skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-purine</td> <td>boolean</td> <td>Include for observing purine (AG/TC) skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-keto</td> <td>boolean</td> <td>Include for observing keto (TG/AC) skew default: "0</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggcwin reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from ggcwin is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.ggcwin<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> location,GC content<br /> 0,0.520700<br /> 10000,0.499400<br /> 20000,0.526200<br /> 30000,0.532300<br /> 40000,0.527700<br /> 50000,0.515600<br /> 60000,0.555800<br /> 70000,0.536000<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 4530000,0.442800<br /> 4540000,0.487000<br /> 4550000,0.507700<br /> 4560000,0.509600<br /> 4570000,0.444600<br /> 4580000,0.531600<br /> 4590000,0.512300<br /> 4600000,0.504500<br /> 4610000,0.535600<br /> 4620000,0.546600<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="ggcskew.html">ggcskew</a></td> <td>Calculates the GC skew of the input sequence</td> </tr><tr> <td><a href="ggeneskew.html">ggeneskew</a></td> <td>Calculate the gene strand bias of the given genome</td> </tr><tr> <td><a href="ggenomicskew.html">ggenomicskew</a></td> <td>Calculates the GC skew in different regions of the given genome</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/ggeneskew.html
--- a/GEMBASSY-1.0.3/doc/html/ggeneskew.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: ggeneskew </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> ggeneskew </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the gene strand bias of the given genome  <H2>Description</H2> <p> ggeneskew calculates and plots the strand bias of genes (or the GC skew<br /> within them). By default, this program visualizes the gene strand preference<br /> (1 for direct, -1 for complement strand), but by specifying -base option<br /> option, GC/AT/Purine/Keto skews of the coding regions or more specifically<br /> in the GC3 (third codon position) with -gctri option can be calculated.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggeneskew <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggeneskew refseqn:NC_000913 Calculate the gene strand bias of the given genome Program compseq output file (optional) [nc_000913.ggeneskew]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggeneskew refseqn:NC_000913 -plot -graph png Calculate the gene strand bias of the given genome Created ggeneskew.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.ggeneskew</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Window size to observe</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-slide</td> <td>integer</td> <td>Window slide size</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-cumulative</td> <td>boolean</td> <td>Input 1 to calculate cumulative skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-base</td> <td>selection</td> <td>Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews</td> <td>Choose from selection list of values</td> <td>none</td> </tr> <tr bgcolor="#FFFFCC"> <td>-gctri</td> <td>boolean</td> <td>Include to use only the third codon positions</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggeneskew reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from ggeneskew is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.ggeneskew<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> location,gene None skew<br /> 190,0.294118<br /> 337,-0.058914<br /> 2801,-0.120000<br /> 3734,-0.070588<br /> 5234,0.037500<br /> 5683,0.020725<br /> 6529,0.032765<br /> 8238,-0.028226<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 4631820,-0.093407<br /> 4632464,-0.006479<br /> 4633544,-0.120690<br /> 4634030,-0.060367<br /> 4634719,-0.104167<br /> 4636201,-0.144560<br /> 4637613,0.010929<br /> 4638425,0.200000<br /> 4638965,-0.081871<br /> ,<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="ggcskew.html">ggcskew</a></td> <td>Calculates the GC skew of the input sequence</td> </tr><tr> <td><a href="ggcwin.html">ggcwin</a></td> <td>Calculates the GC content along the given genome</td> </tr><tr> <td><a href="ggenomicskew.html">ggenomicskew</a></td> <td>Calculates the GC skew in different regions of the given genome</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/ggenomemap3.html
--- a/GEMBASSY-1.0.3/doc/html/ggenomemap3.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: ggenomemap3 </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> ggenomemap3 </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Draws the map of the genome (version 3)  <H2>Description</H2> <p> ggenomemap3 creates a map of the genome, showing the local nucleotide<br /> contents and positions of genes. A is shown in red, T is shown in green, <br /> G is shown in yellow, and C is shown in blue.<br /> Created image has a resolution of 8192x8192 and is suited for conversion<br /> to SVG, which can be performed by specifying the -format option. The formats<br /> available are dependent to the "convert" command from ImageMagick.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggenomemap3 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggenomemap3 refseqn:NC_000913 Draws the map of the genome (version 3) Created ggenomemap3.1.png </pre></td></tr></table> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-width</td> <td>integer</td> <td>Image width</td> <td>Any integer value</td> <td>8192</td> </tr> <tr bgcolor="#FFFFCC"> <td>-height</td> <td>integer</td> <td>Image height</td> <td>Any integer value</td> <td>8192</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>ggenomemap3</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggenomemap3 reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from ggenomemap3 is to an image file.<br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcircularmap.html">gcircular_map</a></td> <td>Draws circular map of the genome</td> </tr><tr> <td><a href="gdnawalk.html">gdnawalk</a></td> <td>Draws DNA Walk map of the genome</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/ggenomicskew.html
--- a/GEMBASSY-1.0.3/doc/html/ggenomicskew.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: ggenomicskew </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> ggenomicskew </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the GC skew in different regions of the given genome  <H2>Description</H2> <p> ggenomicskew calculates and plots the GC skew for the whole genome, coding<br /> regions, intergenic regions, and the third codon. This program is useful in<br /> visualizing various base composition bias within the genome. AT skew can be<br /> calculated instead of GC skew by toggling the -at qualifier.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggenomicskew <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggenomicskew refseqn:NC_000913 Calculates the GC skew in different regions of the given genome Program compseq output file (optional) [nc_000913.ggenomicskew]: </pre></td></tr></table>? Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggenomicskew refseqn:NC_000913 -plot -graph png Calculates the GC skew in different regions of the given genome Created ggenomicskew.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.ggenomicskew</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-divide</td> <td>integer</td> <td>Window to divide into</td> <td>Any integer value</td> <td>250</td> </tr> <tr bgcolor="#FFFFCC"> <td>-at</td> <td>boolean</td> <td>Input 1 when observing AT skew instead of GC skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggenomicskew reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.ggenomicskew<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> location,GC skew,coding,intergenic,third codon<br /> 0,-0.036259,-0.040085,-0.034707,-0.141888,<br /> 1,-0.031167,-0.035657,0.047953,-0.175758,<br /> 2,-0.028670,-0.031139,-0.049143,-0.018466,<br /> 3,-0.016647,-0.004656,-0.102616,0.086181,<br /> 4,-0.041985,-0.029846,-0.088670,0.015291,<br /> 5,-0.097093,-0.103813,-0.067275,-0.247401,<br /> 6,-0.028028,-0.016363,-0.048806,-0.047332,<br /> 7,-0.055805,-0.059329,-0.020071,-0.123271,<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 241,0.000772,-0.012151,-0.063786,0.069585,<br /> 242,-0.025787,-0.000384,-0.049143,0.029431,<br /> 243,0.010516,0.008217,-0.030600,0.128657,<br /> 244,-0.037115,-0.015134,0.017500,0.035398,<br /> 245,-0.000317,0.006021,-0.047170,0.091549,<br /> 246,-0.025417,-0.015190,-0.116608,0.044619,<br /> 247,-0.038404,-0.035676,-0.135714,0.015375,<br /> 248,-0.026246,-0.024240,-0.037190,-0.130118,<br /> 249,-0.053371,-0.057225,-0.022472,-0.082167,<br /> 250,-0.026316,0.166667,-0.151515,0.000000,<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="ggcskew.html">ggcskew</a></td> <td>Calculates the GC skew of the input sequence</td> </tr><tr> <td><a href="ggcwin.html">ggcwin</a></td> <td>Calculates the GC content along the given genome</td> </tr><tr> <td><a href="ggeneskew.html">ggeneskew</a></td> <td>Calculate the gene strand bias of the given genome</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gicdi.html
--- a/GEMBASSY-1.0.3/doc/html/gicdi.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gicdi </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gicdi </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the intrinsic codon deviation index (ICDI)  <H2>Description</H2> <p> gphx calculates codon usage differences between gene classes for identifying<br /> Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is<br /> identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's<br /> nature. PHX genes are known to generally have favorable codon usage, strong<br /> SD sequences, and probably stronger conservation of promoter sequences.<br /> A gene is idenfitied as PA if BgC and BgH is greater than the median of<br /> BgC for every gene with a length close to the gene.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gicdi <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gicdi refseqn:NC_000913 Calculates the intrinsic codon deviation index (ICDI) Codon usage output file [nc_000913.gicdi]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gicdi</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translating using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gicdi reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gicdi is to a plain text file.<br /> <br /> File: nc_000913.gicdi<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> icdi,gene<br /> 0.8192,thrL<br /> 0.1258,thrA<br /> 0.1127,thrB<br /> 0.1689,thrC<br /> 0.3099,yaaX<br /> 0.2030,yaaA<br /> 0.1600,yaaJ<br /> 0.3533,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 0.2203,yjjX<br /> 0.2719,ytjC<br /> 0.1377,rob<br /> 0.2647,creA<br /> 0.1944,creB<br /> 0.1733,creC<br /> 0.1926,creD<br /> 0.2728,arcA<br /> 0.5171,yjjY<br /> 0.2434,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes, Gene, 139:43-49. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcbi.html">gcbi</a></td> <td>Calculates the codon bias index (CBI)</td> </tr><tr> <td><a href="gdeltaenc.html">gdelta_enc</a></td> <td>Calculate the codon usage bias related to translation optimization (delta ENC)</td> </tr><tr> <td><a href="gsvalue.html">gs_value</a></td> <td>Calculate the strength of selected codon usage bias (S)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gkmertable.html
--- a/GEMBASSY-1.0.3/doc/html/gkmertable.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gkmertable </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gkmertable </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Create an image showing all k-mer abundance within a sequence  <H2>Description</H2> <p> gkmertable creates an image showing the abundance of all k-mers<br /> (oligonucleotides of length k) in a given sequence. For example, for<br /> tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each<br /> representing an oligomer. Oligomer name and abundance is written within<br /> these boxes, and abundance is also visualized with the box color, from<br /> white (none) to black (highly frequent).<br /> This k-mer table is alternatively known as the FCGR (frequency matrices<br /> extracted from Chaos Game Representation).<br /> Position of the oligomers can be recursively located as follows:<br /> For each letter in an oligomer, a box is subdivided into four quadrants, <br /> where A is upper left, T is lower right, G is upper right, and C is lower<br /> left.<br /> Therefore, oligomer ATGC is in the <br /> A = upper left quadrant<br /> T = lower right within the above quadrant<br /> G = upper right within the above quadrant<br /> C = lower left within the above quadrant<br /> More detailed documentation is available at <br /> http://www.g-language.org/wiki/cgr<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> Here is a sample session with gkmertable % gkmertable refseqn:NC_000913 Create an image showing all k-mer abundance within a sequence Created gkmertable.1.png Go to the input files for this example Go to the output files for this example </pre></td></tr></table> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-k</td> <td>integer</td> <td>Length of oligomer</td> <td>Any integer value</td> <td>6</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>gkmertable</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gkmertable reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gkmertable is to an image file.<br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td> <td>Checks the periodicity of certain oligonucleotides</td> </tr><tr> <td><a href="goligomercounter.html">goligomercounter</a></td> <td>Counts the number of given oligomers in a sequence</td> </tr><tr> <td><a href="goligomersearch.html">goligomersearch</a></td> <td>Searches oligomers in given sequence</td> </tr><tr> <td><a href="gsignature.html">gsignature</a></td> <td>Calculate oligonucleotide usage (genomic signature)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gldabias.html
--- a/GEMBASSY-1.0.3/doc/html/gldabias.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gldabias </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gldabias </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate strand bias of bacterial genome using linear discriminant  <H2>Description</H2> <p> gldabias calculates strand bias of bacterial genome using linear<br /> discriminant analysis (LDA), as proposed in Reference 1. The basic idea is<br /> to use composition data of genes to train and predict the strand of genes<br /> residing either on the leading or the lagging strand. For computational<br /> efficiency, this method trans and predicts the strands at putative<br /> replication origin as reported by the rep_ori_ter() method. This usually<br /> results in maximum predictability of LDA within bacterial genomes.<br /> Data to use for LDA can be chosen from "base", "codonbase", "codon", and<br /> "amino", with -variable option.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gldabias <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gldabias refseqn:NC_000913 Calculate strand bias of bacterial genome using linear discriminant analysis (LDA) Program compseq output file [nc_000913.gldabias]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gldabias</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-coefficients</td> <td>integer</td> <td>Show LDA coefficients</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>-variable</td> <td>selection</td> <td>Data to use for LDA. Either 'base', 'codonbase', 'codon', or 'amino'</td> <td>Choose from selection list of values</td> <td>codon</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gldabias reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gldabias is to a plain text file.<br /> <br /> File: nc_000913.gldabias<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 LDA-BIAS: 0.742533<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Rocha EPC et al. (1999) "Universal replication biases in bacteria", Molecular Microbiology, 32(1):11-16 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gb1.html">gb1</a></td> <td>Calculate strand bias of bacterial genome using B1 index</td> </tr><tr> <td><a href="gb2.html">gb2</a></td> <td>Calculate strand bias of bacterial genome using B2 index</td> </tr><tr> <td><a href="gdeltagcskew.html">gdeltagcskew</a></td> <td>Calculate strand bias of bacterial genome using delta GC skew</td> </tr><tr> <td><a href="ggcsi.html">ggcsi</a></td> <td>GC Skew Index: an index for strand-specefic mutational bias</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gnucleotideperiodicity.html
--- a/GEMBASSY-1.0.3/doc/html/gnucleotideperiodicity.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gnucleotideperiodicity </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gnucleotideperiodicity </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Checks the periodicity of certain oligonucleotides  <H2>Description</H2> <p> gnucleotideperiodicity checks the periodicity of certain nucleotide<br> (best known with AA dinucleotide). Bacteria and archaebacteria are<br> known to show periodicity of ApA dinucleotides at about 11bp and 10bp.<br> Lower eukaryotes also show periodicity but higher eukaryotes do not.<br> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gnucleotideperiodicity <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gnucleotideperiodicity refseqn:NC_000913 Checks the periodicity of certain oligonucleotides Program compseq output file (optional) [nc_000913.gnucleotideperiodicity]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>? % gnucleotideperiodicity refseqn:NC_000913 -plot -graph png Checks the periodicity of certain oligonucleotides Created gnucleotideperiodicity.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.gnucleotideperiodicity</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Window size to seek periodicity</td> <td>Any integer value</td> <td>50</td> </tr> <tr bgcolor="#FFFFCC"> <td>-nucleotide</td> <td>string</td> <td>Nucleotide to search</td> <td>Any string</td> <td>aa</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gnucleotideperiodicity reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gnucleotideperiodicity is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.gnucleotideperiodicity<br /> <br /></td></tr></table> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> window,value<br /> 0,35134<br /> 1,30121<br /> 2,25409<br /> 3,23508<br /> 4,25830<br /> 5,25136<br /> 6,25658<br /> 7,28279<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 40,28042<br /> 41,25892<br /> 42,25968<br /> 43,28240<br /> 44,25841<br /> 45,25591<br /> 46,27788<br /> 47,25832<br /> 48,25427<br /> 49,0<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gkmertable.html">gkmertable</a></td> <td>Create an image showing all k-mer abundance within a sequence</td> </tr><tr> <td><a href="goligomercounter.html">goligomercounter</a></td> <td>Counts the number of given oligomers in a sequence</td> </tr><tr> <td><a href="goligomersearch.html">goligomersearch</a></td> <td>Searches oligomers in given sequence</td> </tr><tr> <td><a href="gsignature.html">gsignature</a></td> <td>Calculate oligonucleotide usage (genomic signature)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/goligomercounter.html
--- a/GEMBASSY-1.0.3/doc/html/goligomercounter.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: goligomercounter </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> goligomercounter </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Counts the number of given oligomers in a sequence  <H2>Description</H2> <p> goligomercounter counts the number of oligomers in a sequence (by windows<br /> optionally). Oligomer can be specified using degenerate nucleotide alphabet,<br /> or by regular expressions. k-mers can be counted by specifying the "-length"<br /> qualifier.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with goligomercounter <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % goligomercounter refseqn:NC_000913 atgcatgc Counts the number of given oligomers in a sequence Program compseq output file [nc_000913.goligomercounter]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-oligomer]<br>(Parameter 2)</td> <td>string</td> <td>Oligomer to count</td> <td>Any string</td> <td> </td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 3)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.goligomercounter</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Int window size</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> goligomercounter reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from goligomercounter is to a plain text file.<br /> <br /> File: nc_000913.goligomercounter<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Oligomer: atgcatgc Number: 27<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gkmertable.html">gkmertable</a></td> <td>Create an image showing all k-mer abundance within a sequence</td> </tr><tr> <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td> <td>Checks the periodicity of certain oligonucleotides</td> </tr><tr> <td><a href="goligomersearch.html">goligomersearch</a></td> <td>Searches oligomers in given sequence</td> </tr><tr> <td><a href="gsignature.html">gsignature</a></td> <td>Calculate oligonucleotide usage (genomic signature)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/goligomersearch.html
--- a/GEMBASSY-1.0.3/doc/html/goligomersearch.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: goligomersearch </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> goligomersearch </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Searches oligomers in given sequence  <H2>Description</H2> <p> goligomersearch searches for the given oligomer in given sequence. Oligomer<br /> can be specified using degenerate nucleotide alphabet, or by regular<br /> expressions. Performance is optimized for fast searching.<br /> This method changes the returning value according to the given options.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with goligomersearch <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % goligomersearch refseqn:NC_000913 atgcatgc Searches oligomers in given sequence Program compseq output file [nc_000913.goligomersearch]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-oligomer]<br>(Parameter 2)</td> <td>string</td> <td>Oligomer to search</td> <td>Any string</td> <td> </td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 3)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.goligomersearch</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-return</td> <td>selection</td> <td>'position' to return list of positions where oligomers are found, 'oligo' to return list of oligomers found ordered by positions, 'both' to return a hash with positions as keys and oligomers as values, 'distribution' to return four values about the distribution of given oligomer</td> <td>Choose from selection list of values</td> <td>position</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> goligomersearch reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from goligomersearch is to a plain text file.<br /> <br /> File: nc_000913.goligomersearch<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gkmertable.html">gkmertable</a></td> <td>Create an image showing all k-mer abundance within a sequence</td> </tr><tr> <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td> <td>Checks the periodicity of certain oligonucleotides</td> </tr><tr> <td><a href="goligomercounter.html">goligomercounter</a></td> <td>Counts the number of given oligomers in a sequence</td> </tr><tr> <td><a href="gsignature.html">gsignature</a></td> <td>Calculate oligonucleotide usage (genomic signature)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gp2.html
--- a/GEMBASSY-1.0.3/doc/html/gp2.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gp2 </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gp2 </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the P2 index of each gene  <H2>Description</H2> <p> gp2 calculates the P2 index for each gene. This index describes<br /> the proportion of codons conforming to the intermediate strength of<br /> codon-anticodon interaction energy rule of Grosjean and Fiers:<br /> P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.<br /> It indicates the efficiency of the codon-anticodon interaction, and has<br /> been used as an indicator of the presence of translational selection.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gp2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gp2 refseqn:NC_000913 Calculate the P2 index of each gene Codon usage output file [nc_000913.gp2]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gp2</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gp2 reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gp2 is to a plain text file.<br /> <br /> File: nc_000913.gp2<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> P2,gene<br /> 0.4444,thrL<br /> 0.4234,thrA<br /> 0.4565,thrB<br /> 0.5156,thrC<br /> 0.4074,yaaX<br /> 0.4494,yaaA<br /> 0.3621,yaaJ<br /> 0.6832,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 0.3692,yjjX<br /> 0.4912,ytjC<br /> 0.4271,rob<br /> 0.4318,creA<br /> 0.3065,creB<br /> 0.3851,creC<br /> 0.4320,creD<br /> 0.6395,arcA<br /> 0.7857,yjjY<br /> 0.3333,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Res, 10(22):7055-74. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcai.html">gcai</a></td> <td>Calculate codon adaptation index for each gene</td> </tr><tr> <td><a href="gphx.html">gphx</a></td> <td>Identify predicted highly expressed gene</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gpalindrome.html
--- a/GEMBASSY-1.0.3/doc/html/gpalindrome.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gpalindrome </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gpalindrome </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Searches palindrome sequences  <H2>Description</H2> <p> gpalindrome searches for palindrome sequences in the genome.<br /> Search parameters can be changed for more efficient searches, and g-t<br /> matching can be specified by passing the "-gtmatch" qualifier.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gpalindrome <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gpalindrome refseqn:NC_000913 Searches palindrome sequences Program compseq output file [nc_000913.gpalindrome]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gpalindrome</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-shortest</td> <td>integer</td> <td>Shortest palindrome to search</td> <td>Any integer value</td> <td>4</td> </tr> <tr bgcolor="#FFFFCC"> <td>-loop</td> <td>integer</td> <td>Longest stem loop to allow</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>-gtmatch</td> <td>boolean</td> <td>If 1, allows g-t match</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gpalindrome reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gpalindrome is to a plain text file.<br /> <br /> File: nc_000913.gpalindrome<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> Length, start, end, sequence<br /> 4,16,18,tg ca<br /> 4,27,29,at at<br /> 4,44,46,tt aa<br /> 4,67,69,ag ct<br /> 4,97,99,aa tt<br /> 4,99,101,tt aa<br /> 10,100,108,taaaa tttta<br /> 4,132,134,tt aa<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 4,4639484,4639486,tg ca<br /> 6,4639487,4639491,aag ctt<br /> 4,4639495,4639497,cg cg<br /> 4,4639506,4639508,ca tg<br /> 6,4639552,4639556,gtc gac<br /> 4,4639607,4639609,tg ca<br /> 4,4639619,4639621,tg ca<br /> 4,4639621,4639623,ca tg<br /> 4,4639625,4639627,at at<br /> 4,4639637,4639639,at at<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gconsensusz.html">gconsensusz</a></td> <td>Calculate consensus in given array of sequences</td> </tr><tr> <td><a href="gdistincc.html">gdistincc</a></td> <td>Calculates the distance between two loci in circular chromosomes</td> </tr><tr> <td><a href="gseqinfo.html">gseqinfo</a></td> <td>Prints out basic nucleotide sequence statistics</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gphx.html
--- a/GEMBASSY-1.0.3/doc/html/gphx.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gphx </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gphx </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Identify predicted highly expressed gene  <H2>Description</H2> <p> gphx calculates codon usage differences between gene classes for identifying<br /> Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is<br /> identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's<br /> nature. PHX genes are known to generally have favorable codon usage, strong<br /> SD sequences, and probably stronger conservation of promoter sequences.<br /> A gene is idenfitied as PA if BgC and BgH is greater than the median of<br /> BgC for every gene with a length close to the gene.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gphx <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gphx refseqn:NC_000913 Identify predicted highly expressed gene Codon usage output file [nc_000913.gphx]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gphx</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translating using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gphx reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gphx is to a plain text file.<br /> <br /> File: nc_000913.gphx<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> BgC,BgH,E_g,phx,pa,gene<br /> 0.8070,0.8977,0.8990,0,1,thrL<br /> 0.1857,0.5958,0.3116,0,0,thrA<br /> 0.2323,0.5964,0.3896,0,0,thrB<br /> 0.2353,0.6064,0.3881,0,0,thrC<br /> 0.4353,0.6020,0.7231,0,1,yaaX<br /> 0.2961,0.6790,0.4361,0,0,yaaA<br /> 0.2233,0.7009,0.3186,0,0,yaaJ<br /> 0.4149,0.3071,1.3511,1,0,talB<br /> <br /> [Part of this file has been deleted for brevity]<br /> <br /> 0.3255,0.7038,0.4625,0,0,yjjX<br /> 0.3531,0.5906,0.5979,0,0,ytjC<br /> 0.2257,0.5235,0.4311,0,0,rob<br /> 0.3584,0.6809,0.5264,0,0,creA<br /> 0.3455,0.7950,0.4346,0,0,creB<br /> 0.2298,0.7154,0.3212,0,0,creC<br /> 0.3299,0.7916,0.4167,0,0,creD<br /> 0.3543,0.3786,0.9357,0,0,arcA<br /> 0.7295,0.8286,0.8804,0,1,yjjY<br /> 0.4028,0.8401,0.4795,0,0,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm Henry I., Sharp PM. (2007) Predicting gene expression level from codon usage bias Mol Biol Evol, 24(1):10-2. Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse prokaryotic genomes J.Bacteriol, 182(18):5238-5250. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcai.html">gcai</a></td> <td>Calculate codon adaptation index for each gene</td> </tr><tr> <td><a href="gp2.html">gp2</a></td> <td>Calculate the P2 index of each gene</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gqueryarm.html
--- a/GEMBASSY-1.0.3/doc/html/gqueryarm.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gqueryarm </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gqueryarm </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Get the replication arm name (left or right) from the given position  <H2>Description</H2> <p> gqueryarm returns whether the given position is in the left or right arm of<br /> a circular chromosome.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gqueryarm <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gqueryarm refseqn:NC_000913 1234 Get the replication arm name (left or right) from the given position Output file [nc_000913.gqueryarm]: </pre></td></tr></table> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-position]<br>(Parameter 2)</td> <td>integer</td> <td>Position to query</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 3)</td> <td>outfile</td> <td>Output file name</td> <td>Output file</td> <td><i><*></i>.gqueryarm</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gqueryarm reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gqueryarm is to a plain text file.<br /> <br /> File: nc_000913.gqueryarm<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Arm: right<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gquerystrand.html">gquerystrand</a></td> <td>Get the strand name (leading or lagging) from the given</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharua Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gquerystrand.html
--- a/GEMBASSY-1.0.3/doc/html/gquerystrand.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gquerystrand </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gquerystrand </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Get the strand name (leading or lagging) from the given position  <H2>Description</H2> <p> gquerystrand returns whether the given position is in the leading or lagging<br /> strand of a circular chromosome.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gquerystrand <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gquerystrand refseqn:NC_000913 1234 Get the strand name (leading or lagging) from the given position Output file [nc_000913.gquerystrand]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-position]<br>(Parameter 2)</td> <td>integer</td> <td>Position to query</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 3)</td> <td>outfile</td> <td>Output file name</td> <td>Output file</td> <td><i><*></i>.gquerystrand</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-direction</td> <td>selection</td> <td>Strand of the querying position either 'direct' or 'complement'</td> <td>Choose from selection list of values</td> <td>direct</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gquerystrand reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gquerystrand is to a plain text file.<br /> <br /> File: nc_000913.gquerystrand<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Strand: leading<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gqueryarm.html">gqueryarm</a></td> <td>Get the replication arm name (left or right) from the given</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/greporiter.html
--- a/GEMBASSY-1.0.3/doc/html/greporiter.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: greporiter </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> greporiter </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Get the positions of replication origin and terminus  <H2>Description</H2> <p> greporiter returns the positions of replication origin and terminus<br /> in bacterial genomes by several means. <br /> <br /> 1. Use of databases<br /> By default, grep_ori_ter tries to retrieve the position of replication<br /> origin in DoriC Gao and Zhang (2007) database, and the position of<br /> replication terminus from the supplemental data provided in<br /> Kono et al. (2011).<br /> If the position of origin cannot be found in the database, but "rep_origin" <br /> feature is available, center position within this feature is used for<br /> origin. <br /> <br /> 2. Oriloc<br /> Using -orilocoption, you can predict the replication origin and <br /> terminus using the popular Oriloc program developed by Lobry et al. <br /> available as part of the SeqinR package Frank and Lobry (2000).<br /> <br /> 3. Use GC skew shift-point<br /> If the positions of origin or terminus cannot be found in the databases,<br /> grep_ori_ter automatically calls find_ori_ter() method to predict the <br /> positions using GC skew shift-points at one-base-pair resolution.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with greporiter <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % greporiter refseqn:NC_000913 Get the positions of replication origin and terminus Output file [nc_000913.greporiter]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Output file name</td> <td>Output file</td> <td><i><*></i>.greporiter</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-oriloc</td> <td>boolean</td> <td>Include Oriloc for prediction</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-gcskew</td> <td>boolean</td> <td>Include to use GC skew shift-point for prediction</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-difthreshold</td> <td>integer</td> <td>Distance between the GC skew shift point and predicted dif site expressed as the precentage of genome size, used as a threshold to retrieve dif sequence from the database</td> <td>Any integer value</td> <td>0</td> </tr> <tr bgcolor="#FFFFCC"> <td>-dbonly</td> <td>boolean</td> <td>Include to only use values available in databases and to suppress prediction</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> greporiter reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from greporiter is to a plain text file.<br /> <br /> File: nc_000913.greporiter<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 Origin: 3923881 Terminus: 1550412<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial genomes, Bioinformatics, 23(14):1866-1867 Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes, BMC Genomics, 12(1):19 Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gfindoriter.html">gfindoriter</a></td> <td>Predicts the replication origin and terminus in bacterial</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gscs.html
--- a/GEMBASSY-1.0.3/doc/html/gscs.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gscs </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gscs </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculates the scaled chi-square  <H2>Description</H2> <p> gscs calculates the Scaled Chi Square (SCS) of each gene. Values of SCS<br /> are calculated using completely synonymous codon usage as the expectation<br /> and then scaled by dividing the value by the number of codons in the gene<br /> excluding Trp and Met.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gscs <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gscs refseqn:NC_000913 Calculates the scaled chi-square Codon usage output file [nc_000913.gscs]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gscs</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-translate</td> <td>boolean</td> <td>Include when translates using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gscs reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gscs is to a plain text file.<br /> <br /> File: nc_000913.gscs<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> scs,gene<br /> 1.4458,thrL<br /> 0.3122,thrA<br /> 0.2551,thrB<br /> 0.4104,thrC<br /> 0.3084,yaaX<br /> 0.3230,yaaA<br /> 0.2957,yaaJ<br /> 0.7101,talB<br /> <br /> [Part of this file has been deleted for brevity]<br /> <br /> 0.3054,yjjX<br /> 0.4076,ytjC<br /> 0.4231,rob<br /> 0.3903,creA<br /> 0.3472,creB<br /> 0.2695,creC<br /> 0.3500,creD<br /> 0.5077,arcA<br /> 0.4576,yjjY<br /> 0.2926,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Comeron JM., Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Shields DC, Sharp PM. (1987) Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases, 15(19):8023-40. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="genc.html">genc</a></td> <td>Calculate the effective number of codons (Nc)</td> </tr><tr> <td><a href="gew.html">gew</a></td> <td>Calculate a measure of synonymous codon usage evenness (Ew)</td> </tr><tr> <td><a href="gfop.html">gfop</a></td> <td>Calculate the frequency of optimal codons (Fop)</td> </tr><tr> <td><a href="gwvalue.html">gwvalue</a></td> <td>Calculate the 'relative adaptiveness of each codon' (W)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gseq2png.html
--- a/GEMBASSY-1.0.3/doc/html/gseq2png.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gseq2png </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gseq2png </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Converts a sequence to PNG image  <H2>Description</H2> <p> gseq2png converts a sequence to a png image, by representing nucleotide<br /> sequences with representative pixels. A is shown in red, T is shown in<br /> green, G is shown in yellow, and C is shown in blue.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gseq2png <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gseq2png refseqn:NC_000913 Converts a sequence to PNG image Created gseq2png.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-width</td> <td>integer</td> <td>Width of the image</td> <td>Any integer value</td> <td>640</td> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Window size of a sequence to represent each pixel</td> <td>Any integer value</td> <td>20</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>gcgr</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gseq2png reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gseq2png is to an image file.<br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcgr.html">gcgr</a></td> <td>Create a Chaos Game Representation of a given sequence</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gseqinfo.html
--- a/GEMBASSY-1.0.3/doc/html/gseqinfo.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gseqinfo </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gseqinfo </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Prints out basic nucleotide sequence statistics  <H2>Description</H2> <p> gseqinfo prints out basic nucleotide sequence statistics of the given<br /> nucleotide sequence. It returns the number of A, T, G, and C bases.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gseqinfo <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gseqinfo refseqn:NC_000913 Prints out basic nucleotide sequence statistics Program compseq output file [nc_000913.gseqinfo]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gseqinfo</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gseqinfo reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gseqinfo is to a plain text file.<br /> <br /> File: nc_000913.gseqinfo<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 A: 1142228 T: 1140970 G: 1176923 C: 1179555<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gconsensusz.html">gconsensusz</a></td> <td>Calculate consensus in given array of sequences</td> </tr><tr> <td><a href="gdistincc.html">gdistincc</a></td> <td>Calculates the distance between two loci in circular chromosomes</td> </tr><tr> <td><a href="gpalindrome.html">gpalindrome</a></td> <td>Searches palindrome sequences</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gshuffleseq.html
--- a/GEMBASSY-1.0.3/doc/html/gshuffleseq.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gshuffleseq </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gshuffleseq </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Create randomized sequence with conserved k-mer composition  <H2>Description</H2> <p> gshuffleseq shuffles and randomizes the given sequence, conserving the<br /> nucleotide/peptide k-mer content of the original sequence.<br /> <br /> For k=1, i.e. shuffling sequencing preserving single nucleotide composition,<br /> Fisher-Yates Algorithm is employed.<br /> For k>1, shuffling preserves all k-mers (all k where k=1~k). For example,<br /> k=3 preserves all triplet, doublet, and single nucleotide composition.<br /> Algorithm for k-mer preserved shuffling is non-trivial, which is solved<br /> by graph theoretical approach with Eulerian random walks in the graph of<br /> k-1-mers. See Jiang et al., Kandel et al., and Propp et al., for details<br /> of this algorithm.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gshuffleseq <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gshuffleseq tsw:hbb_human Create randomized sequence with conserved k-mer composition output sequence [hbb_human.fasta]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outseq]<br>(Parameter 2)</td> <td>seqout</td> <td>Sequence filename and optional format (output USA)</td> <td>Writeable sequence</td> <td><i><*></i>.<i>format</i></td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-k</td> <td>integer</td> <td>Sequence k-mer to preserve composition</td> <td>Any integer value</td> <td>1</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gshuffleseq reads one or more nucleotide or protein sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gshuffleseq is to .<br /> <br /> File: hbb_human.fasta<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> >HBB_HUMAN P68871 Hemoglobin subunit beta (Beta-globin) (Hemoglobin beta chain) (LVV-hemorphin-7)<br /> KGWLDLVAGAAHFVRRLKMLLEVDWAAHEERVGTSNPNNALKNEAADVEVHSPTHVNPTQ<br /> LVLVQVGFGTLHLQGVECPKPKPGGVALKPVAHLLAMKECTLVALGSDFYVDHGSDGEDK<br /> GFKAYVLATSFFAYTNFLHGKVKHVLF<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Fisher R.A. and Yates F. (1938) "Example 12", Statistical Tables, London Durstenfeld R. (1964) "Algorithm 235: Random permutation", CACM 7(7):420 Jiang M., Anderson J., Gillespie J., and Mayne M. (2008) "uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts", BMC Bioinformatics 9:192 Kandel D., Matias Y., Unver R., and Winker P. (1996) "Shuffling biological sequences", Discrete Applied Mathematics 71(1-3):171-185 Propp J.G. and Wilson D.B. (1998) "How to get a perfectly random sample from a generic Markov chain and generate a random spanning tree of a directed graph", Journal of Algorithms 27(2):170-217 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="shuffleseq.html">shuffleseq</a></td> <td>Shuffles a set of sequences maintaining composition</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gsignature.html
--- a/GEMBASSY-1.0.3/doc/html/gsignature.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gsignature </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gsignature </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate oligonucleotide usage (genomic signature)  <H2>Description</H2> <p> gsignature calculates short oligonuleotide usage (genomic signture),<br /> defined as the ratio of observed (O) to expected (E) oligonucleotide<br /> frequencies. It is known that the genomic signature stays constant<br /> throughout the genome.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gsignature <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gsignature refseqn:NC_000913 Calculate oligonucleotide usage (genomic signature) Program compseq output file [nc_000913.gsignature]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gsignature</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-wordlength</td> <td>integer</td> <td>Word length</td> <td>Any integer value</td> <td>2</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]bothstrand</td> <td>boolean</td> <td>Include to use both strands direct used otherwise</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]oe</td> <td>boolean</td> <td>Include to use O/E value observed values used otherwise</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2>Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gsignature reads one or more nucleotide sequences.<br /> <br /> </p> <h2>Output file format</h2> <p> The output from gsignature is to a plain text file.<br /> <br /> File: nc_000913.gsignature<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,memo<br /> 1.206,0.884,0.817,1.103,1.117,0.905,1.159,0.817,0.922,1.283,0.905,0.884,0.755,0.922,1.117,1.206,<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Campbell A et al. (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA, Proc Natl Acad Sci U S A. 96(16):9184-9. Karlin S. (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes, Trends Microbiol. 9(7):335-43. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gkmertable.html">gkmertable</a></td> <td>Create an image showing all k-mer abundance within a sequence</td> </tr><tr> <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td> <td>Checks the periodicity of certain oligonucleotides</td> </tr><tr> <td><a href="goligomercounter.html">goligomercounter</a></td> <td>Counts the number of given oligomers in a sequence</td> </tr><tr> <td><a href="goligomersearch.html">goligomersearch</a></td> <td>Searches oligomers in given sequence</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gsvalue.html
--- a/GEMBASSY-1.0.3/doc/html/gsvalue.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gsvalue </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gsvalue </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the strength of selected codon usage bias (S)  <H2>Description</H2> <p> gsvalue calculates the strength of selected codon usage bias (S), also<br /> known as Sharp's S index. Using four codon pairs that are recognized by the<br /> same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and<br /> UAU), and Asn(AAC and AAU), since the former in each of the pairs has<br /> stronger Watson-Crick pairing, selection towards the former codon can be<br /> observed for highly expressed genes. S index is therefore the weighted<br /> average of such bias, giving an over-all value for a genome, indicating its<br /> strength of selected codon usage bias. See Sharp et al. (2005) for details.<br /> Sharp originally defined 40 genes as the highly expressed gene group, with<br /> tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton<br /> of these genes is not convenient for computational automation, by default,<br /> this method uses ribosomal proteins as the highly expressed gene group,<br /> as used by Viera-silva and Rocha (2010).<br /> However, Sharp's gene group can be optionally used with -sharp option.<br /> With this option, all of the 40 genes must be named accordingly in the given<br /> genome file.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> Here is a sample session with gsvalue % gsvalue refseqn:NC_000913 Calculate the strength of selected codon usage bias (S) Codon usage output file [nc_000913.gsvalue]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gsvalue</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-sharp</td> <td>boolean</td> <td>Include to use the 40 genes used by Sharp instead of ribosomal proteins</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gsvalue reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gsvalue is to a plain text file.<br /> <br /> File: nc_000913.gsvalue<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 S-value: 1.23467100598485<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Sharp PM et al. (2005) "Variation in the strength of selected codon usage bias among bacteria", Nucleic Acids Research, 33(4):1141-1153 Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gcbi.html">gcbi</a></td> <td>Calculates the codon bias index (CBI)</td> </tr><tr> <td><a href="gdeltaenc.html">gdeltaenc</a></td> <td>Calculate the codon usage bias related to translation optimization (delta ENC)</td> </tr><tr> <td><a href="gicdi.html">gicdi</a></td> <td>Calculates the intrinsic codon deviation index (ICDI)</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gviewcds.html
--- a/GEMBASSY-1.0.3/doc/html/gviewcds.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gviewcds </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gviewcds </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Displays a graph of nucleotide contents around start and stop codons  <H2>Description</H2> <p> gviewcds creates a graph showing the average A,T,G,C contents<br /> around start/stop codons. This is useful to view consensus around<br /> start/stop codons and to find characteristic pattern in CDS.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> Here is a sample session with gviewcds % gviewcds refseqn:NC_000913 Displays a graph of nucleotide contents around start and stop codons Program compseq output file (optional) [nc_000913.gviewcds]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFCC"> % gviewcds refseqn:NC_000913 -plot -graph png Displays a graph of nucleotide contents around start and stop codons Created gviewcds.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.gviewcds</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-length</td> <td>integer</td> <td>Length in bases to show around start/stop codons</td> <td>Any integer value</td> <td>100</td> </tr> <tr bgcolor="#FFFFCC"> <td>-gap</td> <td>integer</td> <td>Gap shown in graph in between start/stop codon neighbors</td> <td>Any integer value</td> <td>3</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gviewcds reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gviewcds is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.gviewcds<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> position,A,T,G,C<br /> 1,28.20,27.60,22.18,22.02<br /> 2,26.05,26.81,23.06,24.08<br /> 3,27.34,27.37,23.94,21.35<br /> 4,26.28,28.83,23.01,21.88<br /> 5,26.72,28.22,22.18,22.88<br /> 6,26.42,26.72,24.96,21.90<br /> 7,27.21,28.66,21.95,22.18<br /> 8,25.47,28.39,23.06,23.08<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 400,26.60,27.44,22.67,23.27<br /> 401,24.38,26.63,25.05,23.92<br /> 402,25.03,26.37,23.71,24.87<br /> 403,25.96,27.53,22.53,23.96<br /> 404,26.63,25.52,24.17,23.66<br /> 405,25.68,26.26,23.50,24.54<br /> 406,24.94,26.86,23.92,24.26<br /> 407,25.54,26.28,23.73,24.43<br /> 408,25.28,26.93,24.38,23.39<br /> 409,26.63,26.46,22.32,24.57<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="gbasecounter.html">gbasecounter</a></td> <td>Creates a position weight matrix of oligomers around start codon</td> </tr><tr> <td><a href="gbasezvalue.html">gbasezvalue</a></td> <td>Extracts conserved oligomers per position using Z-score</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/html/gwvalue.html
--- a/GEMBASSY-1.0.3/doc/html/gwvalue.html Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
- <HTML> <HEAD> <TITLE> EMBOSS: gwvalue </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> gwvalue </font></b> </td></tr> </table> <br>  <p>  <H2> Function </H2> Calculate the 'relative adaptiveness of each codon' (W)  <H2>Description</H2> <p> gwvalue calculates the 'relative adaptiveness of each codon' (W value)<br /> which is essential in CAI analysis. W value is calculated by setting the<br /> best codon to 1 and calculating the proportion of the other codons.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with gwvalue <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gwvalue refseqn:NC_000913 Calculate the 'relative adaptiveness of each codon' (W) Codon usage output file [nc_000913.gwvalue]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Codon usage output file</td> <td>Output file</td> <td><i><*></i>.gwvalue</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-include</td> <td>string</td> <td>Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al.</td> <td>Any string</td> <td>ribosomal.*protein</td> </tr> <tr bgcolor="#FFFFCC"> <td>-exclude</td> <td>string</td> <td>Regular expression to exclude genes from a reference set</td> <td>Any string</td> <td>[Mm]itochondrial</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2>Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> gwvalue reads one or more nucleotide sequences.<br /> <br /> </p> <h2>Output file format</h2> <p> The output from gwvalue is to a plain text file.<br /> <br /> File: nc_000913.gwvalue<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> Reference set of highly expressed genes<br /> product<br /> 30S ribosomal subunit protein S20<br /> 30S ribosomal subunit protein S2<br /> ribosomal protein S12 methylthiotransferase; radical SAM superfamily<br /> ribosomal protein S6 modification protein<br /> 30S ribosomal subunit protein S1<br /> ribosomal-protein-S5-alanine N-acetyltransferase<br /> 50S ribosomal subunit protein L32<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> T,acc,1.0000<br /> T,acg,0.2234<br /> T,act,0.9734<br /> V,gta,0.4960<br /> V,gtc,0.2281<br /> V,gtg,0.3422<br /> V,gtt,1.0000<br /> W,tgg,1.0000<br /> Y,tac,1.0000<br /> Y,tat,0.5310<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Sharp PM et al. (2005) Variation in the strength of selected codon usage bias among bacteria, Nucleic Acids Res. 33(4):1141-1153 Sakai et al. (2001) Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170. Nakamura and Tabata (1997) Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes, Microb.Comp.Genomics 2:299-312. Sharp and Li (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res. 15:1281-1295. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="genc.html">genc</a></td> <td>Calculate the effective number of codons (Nc)</td> </tr><tr> <td><a href="gew.html">gew</a></td> <td>Calculate a measure of synonymous codon usage evenness (Ew)</td> </tr><tr> <td><a href="gfop.html">gfop</a></td> <td>Calculate the frequency of optimal codons (Fop)</td> </tr><tr> <td><a href="gscs.html">gscs</a></td> <td>Calculates the scaled chi-square</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </BODY> </HTML>
\ No newline at end of file

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/Makefile
--- a/GEMBASSY-1.0.3/doc/text/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,533 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# doc/text/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgincludedir = $(includedir)/GEMBASSY\n-pkglibdir = $(libdir)/GEMBASSY\n-pkglibexecdir = $(libexecdir)/GEMBASSY\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = x86_64-apple-darwin14.0.0\n-host_triplet = x86_64-apple-darwin14.0.0\n-subdir = doc/text\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_$(V))\n-am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_$(V))\n-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_$(V))\n-am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))\n-am__v_at_0 = @\n-am_'..b'-e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(DATA)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(pkgdatadir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am: install-pkgdataDATA\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-pkgdataDATA\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: all all-am check check-am clean clean-generic clean-libtool \\\n-\tcscopelist-am ctags-am distclean distclean-generic \\\n-\tdistclean-libtool distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-pkgdataDATA install-ps \\\n-\tinstall-ps-am install-strip installcheck installcheck-am \\\n-\tinstalldirs maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags-am uninstall uninstall-am uninstall-pkgdataDATA\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/Makefile.am
--- a/GEMBASSY-1.0.3/doc/text/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-pkgdata_DATA = *.txt
-
-pkgdatadir=$(prefix)/share/EMBOSS/doc/programs/text
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/Makefile.in
--- a/GEMBASSY-1.0.3/doc/text/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,533 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-VPATH = @srcdir@\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgincludedir = $(includedir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkglibexecdir = $(libexecdir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-subdir = doc/text\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/general.m4 \\\n-\t$(top_srcdir)/m4/hpdf.m4 $(top_srcdir)/m4/java.m4 \\\n-\t$(top_srcdir)/m4/lf_x11.m4 $(top_srcdir)/m4/libtool.m4 \\\n-\t$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \\\n-\t$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \\\n-\t$(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \\\n-\t$(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \\\n-\t$(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-AM_V_P = $(am__v_P_@AM_V@)\n-am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_@AM_V@)\n-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_@AM_V@)\n-am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)\n-am__v_at_0 = @\n-am__v_at_1 = \n-SOURCES =\n-DIST_SOURCES =\n-am__can_run_installinfo = \\\n- ca'..b'-e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(DATA)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(pkgdatadir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-generic\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am: install-pkgdataDATA\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-generic mostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-pkgdataDATA\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: all all-am check check-am clean clean-generic clean-libtool \\\n-\tcscopelist-am ctags-am distclean distclean-generic \\\n-\tdistclean-libtool distdir dvi dvi-am html html-am info info-am \\\n-\tinstall install-am install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-pkgdataDATA install-ps \\\n-\tinstall-ps-am install-strip installcheck installcheck-am \\\n-\tinstalldirs maintainer-clean maintainer-clean-generic \\\n-\tmostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \\\n-\tps ps-am tags-am uninstall uninstall-am uninstall-pkgdataDATA\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/copydesc.pl
--- a/GEMBASSY-1.0.3/doc/text/copydesc.pl Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,36 +0,0 @@
-use strict;
-use warnings;
-
-my @progs = split "\n", `wossname -showembassy GEMBASSY -auto | cut -d ' ' -f 1| grep ^g | sort`;
-
-copy($_) foreach @progs;
-
-sub copy {
-    my $prog = shift;
-
-    print STDERR "\r\e[K$prog";
-
-    open my $rdr, "<", "old/$prog.txt";
-    open my $wtr, ">", "final/$prog.txt";
-    open my $tmp, "<", "new/$prog.txt";
-
-    my $out = join "", <$tmp>;
-
-    my $progdesc;
-
-    while(my $line = readline $rdr) {
-        if($line =~ /^Description/) {
-            readline $rdr;
-            while($line !~ /SOAP/) {
-                $line = readline $rdr;
-                last if $line =~ /SOAP/;
-                $progdesc .= $line;
-            }
-        $progdesc =~ s/\n+$//smg;
-        }
-    }
-
-    $out =~ s/\[ProgDef\]\n/$progdesc/smg;
-
-    print $wtr $out;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gaaui.txt
--- a/GEMBASSY-1.0.3/doc/text/gaaui.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,208 +0,0 @@
-                                     gaaui
-Function
-
-   Calculates various indece of amino acid usage
-
-Description
-
-   gaaui calculates amino acid usage indices for proteins (excluding
-   formylmethionine). Calculated indices are as follows,
-      Laa:   Length in amino acids
-      ndaa:  Number of different amino acids
-      Haau:  Entropy of amino acid usage
-      mmw:   Mean molecular weight
-      gravy: Mean hydropathic indices of each amino acid
-      aroma: Relative frequency of aromatic amino acids
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gaaui
-
-% gaaui refseqn:NC_000913
-Calculates various indece of amino acid usage
-AAINDEX entry output file [nc_000913.gaaui]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gaaui] AAINDEX entry output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gaaui reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gaaui is to a plain text file.
-
-   File: nc_000913.gaaui
-
-Sequence: NC_000913
-Laa,ndaa,Haau,mmw,gravy,aroma,gene
-20,8,2.4842,117.48,+0.0150,0.0000,thrL
-819,20,4.0887,126.65,+0.0328,0.0659,thrA
-309,20,4.1228,126.35,+0.0181,0.0712,thrB
-427,20,4.0806,128.00,-0.1014,0.0843,thrC
-97,18,3.9165,133.54,-1.0268,0.0928,yaaX
-257,19,4.0733,132.55,-0.4117,0.1089,yaaA
-475,20,4.0413,126.46,+0.6781,0.1242,yaaJ
-316,20,4.0395,128.99,-0.2165,0.0728,talB
-
-   [Part of this file has been deleted for brevity]
-
-169,20,4.0001,124.90,+0.0231,0.0710,yjjX
-214,20,3.9937,129.77,-0.3813,0.0374,ytjC
-288,20,4.1421,132.58,-0.3628,0.1111,rob
-156,20,4.0627,126.72,-0.0442,0.0705,creA
-228,20,4.0471,131.94,-0.1408,0.0789,creB
-473,20,4.0254,128.01,+0.0023,0.0677,creC
-449,20,4.0871,128.66,+0.2082,0.0980,creD
-237,20,4.0729,132.54,-0.4970,0.0675,arcA
-45,15,3.5800,123.27,+0.7533,0.0222,yjjY
-227,20,4.0283,128.63,-0.0031,0.0573,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and
-      aromaticity are the major trends of amino-acid usage in 999 Escherichia
-      coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a
-
-   Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga
-      maritima J Mol Evol. 54(5):563-8.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gaminoinfo     Prints out basic amino acid sequence statistics
-   gbui           Calculates base usage indeces for protein-codin sequences
-   gcodoncompiler Calculates various kinds of amino acid and codon usage data
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gaminoinfo.txt
--- a/GEMBASSY-1.0.3/doc/text/gaminoinfo.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,219 +0,0 @@\n- gaminoinfo\n-Function\n-\n- Prints out basic amino acid sequence statistics\n-\n-Description\n-\n- gaminoinfo prints out basic compositional statistics of the given amino\n- acid sequence in a human readble manner. The calculated values are molecular\n- weight, number of residues, average residue weight, charge, isoelectric\n- point, number/mole/Dayhoffstat of each amino acid, and percentage of\n- Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),\n- Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),\n- Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R), and\n- Acidic (B+D+E+Z) reidues.\n- \n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gaminoinfo\n-\n-% gaminoinfo tsw:hbb_human\n-Prints out basic amino acid sequence statistics\n-AAINDEX entry output file [hbb_human.gaminoinfo]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n- Standard (Mandatory) qualifiers:\n- [-sequence] seqall Protein sequence(s) filename and optional\n- format, or reference (input USA)\n- [-outfile] outfile [*.gaminoinfo] AAINDEX entry output file\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers: (none)\n- Associated qualifiers:\n-\n- "-sequence" associated qualifiers\n- -sbegin1 integer Start of each sequence to be used\n- -send1 integer End of each sequence to be used\n- -sreverse1 boolean Reverse (if DNA)\n- -sask1 boolean Ask for begin/end/reverse\n- -snucleotide1 boolean Sequence is nucleotide\n- -sprotein1 boolean Sequence is protein\n- -slower1 boolean Make lower case\n- -supper1 boolean Make upper case\n- -scircular1 boolean Sequence is circular\n- -sformat1 string Input sequence format\n- -iquery1 string Input query fields or ID list\n- -ioffset1 integer Input start position offset\n- -sdbname1 string Database name\n- -sid1 string Entryname\n- -ufo1 string UFO features\n- -fformat1 string Features format\n- -fopenfile1 string Features file name\n-\n- "-outfile" associated qualifiers\n- -odirectory2 string Output directory\n-\n- General qualifiers:\n- -auto boolean Turn off prompts\n- -stdout boolean Write first file to standard output\n- -filter boolean Read first file from standard input, write\n- first file to standard output\n- -options boolean Prompt for standard and additional values\n- -debug boolean Write debug output to program.dbg\n- -verbose boolean Report some/full command line options\n- -help boolean Report command line options and exit. More\n- information on associated and general\n- qualifiers can be found with -help -verbose\n- -warning boolean Report warnings\n- -error boolean Report errors\n- -fatal boolean Report fatal errors\n- -die boolean Report dying program messages\n- -version boolean Report version number and exit\n-\n-Input file format\n-\n- The database definitions for following'..b'tein sequences.\n-\n-Output file format\n-\n- The output from gaminoinfo is to a plain text file.\n-\n- File: hbb_human.gaminoinfo\n-\n-Sequence: P68871\n-AminoInfo of from 1 to 158\n-\n-Molecular weight = 19309.27 Residues = 158\n-Average Weight = 122.21 Charge = 3.5\n-Isoelectric Point = 7.4065\n-Residue Number Mole% DayhoffStat\n-\n- = 1 0.633 0.000\n-> = 1 0.633 0.000\n-A = Ala 16 10.127 1.178\n-B = Asx 2 1.266 0.000\n-C = Cys 2 1.266 0.436\n-D = Asp 7 4.430 0.806\n-E = Glu 8 5.063 0.844\n-F = Phe 8 5.063 1.406\n-G = Gly 13 8.228 0.980\n-H = His 11 6.962 3.481\n-K = Lys 11 6.962 1.055\n-L = Leu 18 11.392 1.540\n-M = Met 3 1.899 1.117\n-N = Asn 7 4.430 1.030\n-P = Pro 7 4.430 0.852\n-Q = Gln 3 1.899 0.487\n-R = Arg 3 1.899 0.387\n-S = Ser 5 3.165 0.452\n-T = Thr 7 4.430 0.726\n-U = Sec 1 0.633 0.000\n-V = Val 18 11.392 1.726\n-W = Trp 2 1.266 0.974\n-Y = Tyr 3 1.899 0.558\n-_ = 1 0.633 0.000\n-\n-Property Residues Number Mole%\n-Tiny (A+C+G+S+T) 43 27.215\n-Small (A+B+C+D+G+N+P+S+T+V) 84 53.165\n-Aliphatic (I+L+V) 36 22.785\n-Aromatic (F+H+W+Y) 24 15.190\n-Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962\n-Polar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241\n-Charged (B+D+E+H+K+R+Z) 42 26.582\n-Basic (H+K+R) 25 15.823\n-Acidic (B+D+E+Z) 17 10.759\n-\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gaaui Calculates various indece of amino acid usage\n- gcodoncompiler Calculate various kinds of amino acid and codon usage data\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gb1.txt
--- a/GEMBASSY-1.0.3/doc/text/gb1.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,190 +0,0 @@
-                                      gb1
-Function
-
-   Calculate strand bias of bacterial genome using B1 index
-
-Description
-
-   gb1 calculates the strand bias of bacterial genome using B1 index,
-   first proposed by Lobry and Sueoka (2002), and further extended by
-   Rocha et al. (2006). Basic idea of B1 index is to calculate the
-   distance between the two strands, when the leading and lagging strands
-   are plotted in a coordinate system with axes representing G/(G+C) and
-   A/(A+T), using the third codon position of genes. This index measures the
-   degree of replication-induced bias from Chargaff's second parity rule.
-   Rocha et al. modified B1 index to only use >fourfold degenerate codons,
-   and to use T/(A+T) in place of A/(A+T).
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gb1
-
-% gb1 refseqn:NC_000913
-Calculate strand bias of bacterial genome using B1 index
-Program compseq output file [nc_000913.gb1]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gb1] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -method             selection  [rocha] Choose method of 'lobry' or 'rocha'
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gb1 reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gb1 is to a plain text file.
-
-   File: nc_000913.gb1
-
-Sequence: NC_000913 B1: 0.0630702874711314
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
-      bacteria, Genome Biology, 3(10):0058
-
-   Rocha EPC et al. (2006) Similar compositional biases are caused by very
-      different mutational effects, Genome Research, 16:1537-1547
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gb2          Calculate strand bias of bacterial genome using B2 index
-   gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
-                index
-   ggcsi        GC Skew Index: an index for strand-specefic mutational bias
-   gldabias     Calculate strand bias of bacterial genome using linear
-                discriminant analysis (LDA)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gb2.txt
--- a/GEMBASSY-1.0.3/doc/text/gb2.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,184 +0,0 @@
-                                      gb2
-Function
-
-   Calculate strand bias of bacterial genome using B2 index
-
-Description
-
-   gb2 calculates strand bias of bacterial genome using B2 index,
-   proposed by Lobry and Sueoka(2002). Basic idea of B2 index is to calculate
-   the distance from neutral parity state (0.5, 0.5), when the bias of
-   the coding regions is plotted in a coordinate system with axes representing
-   G/(G+C) and A/(A+T), using the third codon position of genes. This index
-   measures the degree of transcription- and translation-associated effects of
-   bias from Chargaff's second parity rule.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gb2
-
-% gb2 refseqn:NC_000913
-Calculate strand bias of bacterial genome using B2 index
-Program compseq output file [nc_000913.gb2]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gb2] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gb2 reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gb2 is to a plain text file.
-
-   File: nc_000913.gb2
-
-Sequence: NC_000913 B2: 0.0919769585775651
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
-      bacteria, Genome Biology, 3(10):0058
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gb1          Calculate strand bias of bacterial genome using B1 index
-   gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
-                index
-   ggcsi        GC Skew Index: an index for strand-specefic mutational bias
-   gldabias     Calculate strand bias of bacterial genome using linear
-                discriminant analysis (LDA)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gbasecounter.txt
--- a/GEMBASSY-1.0.3/doc/text/gbasecounter.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,205 +0,0 @@\n- gbasecounter\n-Function\n-\n- Creates a position weight matrix of oligomers around start codon\n-\n-Description\n-\n- This function creates a position weight matrix (PWM) of\n- oligomers of specified length around the start codon of all\n- genes in the given genome.\n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gbasecounter\n-\n-% gbasecounter refseqn:NC_000913\n-Creates a position weight matrix of oligomers around start codon\n-Weight matrix output file [nc_000913.gbasecounter]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n- Standard (Mandatory) qualifiers:\n- [-sequence] seqall Nucleotide sequence(s) filename and optional\n- format, or reference (input USA)\n- [-outfile] outfile [*.gbasecounter] Weight matrix output file\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers:\n- -position selection [start] Either \'start\' (around start codon)\n- or \'end\' (around stop codon) to create the\n- PWM\n- -patlen integer [3] Length of oligomer to count (Any integer\n- value)\n- -upstream integer [30] Length upstream of specified position\n- to create PWM (Any integer value)\n- -downstream integer [30] Length downstream of specified position\n- to create PWM (Any integer value)\n- -[no]accid boolean [Y] Include to use sequence accession ID as\n- query\n-\n- Associated qualifiers:\n-\n- "-sequence" associated qualifiers\n- -sbegin1 integer Start of each sequence to be used\n- -send1 integer End of each sequence to be used\n- -sreverse1 boolean Reverse (if DNA)\n- -sask1 boolean Ask for begin/end/reverse\n- -snucleotide1 boolean Sequence is nucleotide\n- -sprotein1 boolean Sequence is protein\n- -slower1 boolean Make lower case\n- -supper1 boolean Make upper case\n- -scircular1 boolean Sequence is circular\n- -sformat1 string Input sequence format\n- -iquery1 string Input query fields or ID list\n- -ioffset1 integer Input start position offset\n- -sdbname1 string Database name\n- -sid1 string Entryname\n- -ufo1 string UFO features\n- -fformat1 string Features format\n- -fopenfile1 string Features file name\n-\n- "-outfile" associated qualifiers\n- -odirectory2 string Output directory\n-\n- General qualifiers:\n- -auto boolean Turn off prompts\n- -stdout boolean Write first file to standard output\n- -filter boolean Read first file from standard input, write\n- first file to standard output\n- -options boolean Prompt for standard and additional values\n- -debug boolean Write debug output to program.dbg\n- -verbose boolean Report some/full command line options\n- -help boolean Report command line options and exit. More\n- information on associated and general\n- qualifi'..b'8,0.116,0.278,0.324,0.394,0.834,0.486,0.394,0.718,0.556,0.509,0.857,0.509,0.625,0.810,0.741,0.695,0.834,0.625,0.787,1.158,0.347,1.158,1.621,0.394,1.667,1.204,0.347,1.551,1.320,0.417,1.088,1.065,0.232,1.320,1.042,0.139,1.204,0.996,0.208,0.996,0.602,0.139,0.648,0.764,0.069,0.857,0.394,0.023,0.000,7.803\n-tgg,0.000,0.023,0.069,0.208,0.370,0.509,0.486,0.417,0.394,0.671,1.343,1.713,1.621,1.482,0.810,0.834,0.718,0.301,0.463,0.509,0.509,0.741,0.579,0.509,0.625,0.486,0.509,0.625,0.625,0.533,0.857,0.996,0.718,1.968,1.042,0.880,1.760,0.671,0.949,1.459,0.556,0.787,0.903,0.718,0.695,1.273,0.533,0.440,0.648,0.880,0.417,0.718,0.648,0.278,0.625,0.463,0.440,0.486,0.116,0.023,11.021\n-tgt,0.023,0.880,0.023,0.533,1.135,0.301,0.440,0.602,0.417,0.208,0.232,0.185,0.185,0.278,0.370,0.440,0.533,0.556,0.648,0.764,0.509,0.926,0.579,0.718,0.880,0.695,0.718,0.741,0.741,0.579,0.625,0.278,1.158,0.857,0.278,0.972,0.718,0.324,0.926,0.695,0.463,1.111,0.834,0.162,1.482,0.787,0.278,1.065,0.695,0.278,1.042,0.695,0.208,0.903,0.718,0.139,0.857,0.232,0.093,0.023,7.340\n-tta,0.000,0.000,6.506,0.648,0.810,1.829,1.320,0.602,0.486,0.509,0.255,0.347,0.301,0.834,1.320,1.459,1.412,1.667,1.644,1.852,1.667,1.574,1.366,1.042,1.204,1.621,1.505,1.227,1.436,1.088,1.273,1.343,0.486,1.158,1.042,0.440,1.135,1.389,0.370,1.273,1.574,0.486,1.875,1.505,0.463,1.991,1.875,0.533,2.362,2.061,0.324,2.084,2.200,0.509,1.505,1.320,0.463,1.366,0.648,0.000,0.069\n-ttc,0.000,0.000,0.000,0.648,0.417,0.695,0.764,0.347,0.301,0.278,0.208,0.023,0.232,0.533,0.718,0.718,0.903,1.042,1.158,0.880,1.158,1.065,0.903,0.834,1.343,0.996,0.926,0.810,0.741,0.834,1.042,0.926,0.579,1.088,0.695,0.695,1.297,0.741,0.741,1.111,0.926,0.787,1.366,0.695,0.857,1.412,0.648,0.834,1.111,0.440,0.602,1.250,1.019,1.135,0.787,0.440,0.880,0.509,0.370,0.000,0.000\n-ttg,0.857,0.023,0.255,0.394,0.556,1.111,0.533,0.463,0.417,0.185,0.232,0.533,0.602,1.042,0.718,0.695,1.135,0.972,0.857,0.926,0.787,0.671,1.320,0.695,0.903,1.204,0.880,0.764,0.926,0.741,0.718,1.019,0.347,1.551,1.042,0.370,2.014,0.834,0.463,2.061,0.880,0.278,2.014,0.857,0.208,2.593,0.741,0.278,1.922,0.764,0.417,2.130,0.834,0.208,1.111,0.394,0.093,1.111,0.417,0.000,0.023\n-ttt,0.023,0.440,0.093,1.598,1.181,1.320,1.829,1.343,0.648,0.370,0.394,0.278,0.185,0.440,1.135,1.574,1.667,1.945,2.315,2.362,2.431,2.501,2.107,2.362,1.806,2.014,2.292,2.014,1.598,1.760,1.829,1.389,1.505,1.042,1.343,1.297,0.926,1.528,1.574,1.227,1.482,1.737,1.389,1.667,1.922,1.389,1.945,1.922,1.343,1.806,1.760,1.389,2.014,1.760,1.065,0.949,1.111,0.625,1.227,0.023,0.023\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gbasezvalue Extracts conserved oligomers per position using Z-score\n- gviewcds Displays a graph of nucleotide contents around start and stop\n- codons\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gbaseentropy.txt
--- a/GEMBASSY-1.0.3/doc/text/gbaseentropy.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,243 +0,0 @@\n- gbaseentropy\n-Function\n-\n- Calculates and graphs the sequence conservation using Shanon uncertainty\n-\n-Description\n-\n- This function calculates and graphs the sequence conservation in regions\n- around the start/stop codons using Shanon uncertainty (entropy). Smaller\n- values resemble higher conservation where the minumum value is 0 and the\n- maximum value is 2. The entropy is typically the lowest around position 0\n- (start/stop codon position).\n-\n- The entropy H at position i with distribution P(i) is calculated as follows:\n- H(P(i)) = -sum(P(i,j) * log(2,P(i,j)))\n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gbaseentropy\n-\n-% gbaseentropy refseqn:NC_000913\n-Calculates and graphs the sequence conservation using Shanon uncertainty\n-(entropy)\n-Program compseq output file (optional) [nc_000913.gbaseentropy]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n- Example 2\n-\n-% gbaseentropy refseqn:NC_000913 -plot -graph png\n-Calculates and graphs the sequence conservation using Shanon uncertainty\n-(entropy)\n-Created gbaseentropy.1.png\n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n-Calculates and graphs the sequence conservation using Shanon uncertainty\n-(entropy)\n-Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1\n-\n- Standard (Mandatory) qualifiers (* if not always prompted):\n- [-sequence] seqall Nucleotide sequence(s) filename and optional\n- format, or reference (input USA)\n-* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type\n- (ps, hpgl, hp7470, hp7580, meta, cps, x11,\n- tek, tekt, none, data, xterm, png, gif, svg)\n-* -outfile outfile [*.gbaseentropy] Program compseq output file\n- (optional)\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers:\n- -position selection [start] Either \'start\' (around start codon)\n- or \'end\' (around stop codon) to create the\n- PWM\n- -patlen integer [3] Length of oligomer to count (Any integer\n- value)\n- -upstream integer [30] Length upstream of specified position\n- to create PWM (Any integer value)\n- -downstream integer [30] Length downstream of specified position\n- to create PWM (Any integer value)\n- -[no]accid boolean [Y] Include to use sequence accession ID as\n- query\n- -plot toggle [N] Include to plot result\n-\n- Associated qualifiers:\n-\n- "-sequence" associated qualifiers\n- -sbegin1 integer Start of each sequence to be used\n- -send1 integer End of each sequence to be used\n- -sreverse1 boolean Reverse (if DNA)\n- -sask1 boolean Ask for begin/end/reverse\n- -snucleotide1 boolean Sequence is nucleotide\n- -sprotein1 boolean Sequence is protein\n- -slower1 boolean Make lower case\n- -supper1 boolean Make upper case\n- -scircular1 boolean Sequence is circular\n- -sformat1 string Input sequence format\n- -iquery1 string Input quer'..b' string UFO features\n- -fformat1 string Features format\n- -fopenfile1 string Features file name\n-\n- "-graph" associated qualifiers\n- -gprompt boolean Graph prompting\n- -gdesc string Graph description\n- -gtitle string Graph title\n- -gsubtitle string Graph subtitle\n- -gxtitle string Graph x axis title\n- -gytitle string Graph y axis title\n- -goutfile string Output file for non interactive displays\n- -gdirectory string Output directory\n-\n- "-outfile" associated qualifiers\n- -odirectory string Output directory\n-\n- General qualifiers:\n- -auto boolean Turn off prompts\n- -stdout boolean Write first file to standard output\n- -filter boolean Read first file from standard input, write\n- first file to standard output\n- -options boolean Prompt for standard and additional values\n- -debug boolean Write debug output to program.dbg\n- -verbose boolean Report some/full command line options\n- -help boolean Report command line options and exit. More\n- information on associated and general\n- qualifiers can be found with -help -verbose\n- -warning boolean Report warnings\n- -error boolean Report errors\n- -fatal boolean Report fatal errors\n- -die boolean Report dying program messages\n- -version boolean Report version number and exit\n-\n-Input file format\n-\n- The database definitions for following commands are available at\n- http://soap.g-language.org/kbws/embossrc\n-\n- gbaseentropy reads one or more nucleotide sequences.\n-\n-Output file format\n-\n- The output from gbaseentropy is to a plain text file or the EMBOSS\n- graphics device.\n-\n- File: nc_000913.gbaseentropy\n-\n-Sequence: NC_000913\n--30,1.98284\n--29,1.97873\n--28,1.97692\n--27,1.97595\n--26,1.97094\n--25,1.96777\n--24,1.96272\n--23,1.96288\n--22,1.95707\n-\n- [Part of this file has been deleted for brevity]\n-\n-21,1.93528\n-22,1.94470\n-23,1.95204\n-24,1.93139\n-25,1.95640\n-26,1.95711\n-27,1.93785\n-28,1.96060\n-29,1.94316\n-30,1.92581\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gbaseinformationcontent Calculates and graphs the sequence conservation\n- using information content\n- gbaserelativeentropy Calculates and graphs the sequence conservation\n- using Kullback-Leibler divergence (relative\n- entropy)\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gbaseinformationcontent.txt
--- a/GEMBASSY-1.0.3/doc/text/gbaseinformationcontent.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,239 +0,0 @@\n- gbaseinformationcontent\n-Function\n-\n- Calculates and graphs the sequence conservation using information content\n-\n-Description\n-\n- This function calculates and graphs the sequence conservation in regions\n- around the start/stop codons using information content. Values are obtained\n- by subtracting the entropy for each positfion from the maximum possible\n- value (which will be 2 in the case of nucleotide sequences). Information\n- content will show the highest value when the frequency is most biased to a\n- single alphabet.\n-\n- Information content I is obtained by subtracting the entropy H from the\n- maximum uncertainty log(2,|M|):\n- I(P(i)) = log(2,|M|) - (-sum(P(i,j) * log(2,P(i,j))))\n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gbaseinformationcontent\n-\n-% gbaseinformationcontent refseqn:NC_000913\n-Calculates and graphs the sequence conservation using information content\n-Program compseq output file (optional) [nc_000913.gbaseinformationcontent]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n- Example 2\n-\n-% gbaseinformationcontent refseqn:NC_000913 -plot -graph png\n-Calculates and graphs the sequence conservation using information content\n-Created gbaseinformationcontent.1.png\n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n- Standard (Mandatory) qualifiers (* if not always prompted):\n- [-sequence] seqall Nucleotide sequence(s) filename and optional\n- format, or reference (input USA)\n-* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type\n- (ps, hpgl, hp7470, hp7580, meta, cps, x11,\n- tek, tekt, none, data, xterm, png, gif, svg)\n-* -outfile outfile [*.gbaseinformationcontent] Program compseq\n- output file (optional)\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers:\n- -position selection [start] Either \'start\' (around start codon)\n- or \'end\' (around stop codon) to create the\n- PWM\n- -upstream integer [30] Length upstream of specified position\n- to create PWM (Any integer value)\n- -downstream integer [30] Length downstream of specified position\n- to create PWM (Any integer value)\n- -patlen integer [3] Length of oligomer to count (Any integer\n- value)\n- -[no]accid boolean [Y] Include to use sequence accession ID as\n- query\n- -plot toggle [N] Include to plot result\n-\n- Associated qualifiers:\n-\n- "-sequence" associated qualifiers\n- -sbegin1 integer Start of each sequence to be used\n- -send1 integer End of each sequence to be used\n- -sreverse1 boolean Reverse (if DNA)\n- -sask1 boolean Ask for begin/end/reverse\n- -snucleotide1 boolean Sequence is nucleotide\n- -sprotein1 boolean Sequence is protein\n- -slower1 boolean Make lower case\n- -supper1 boolean Make upper case\n- -scircular1 boolean Sequence is circular\n- -sformat1 string Input sequence format\n- -i'..b' string Features format\n- -fopenfile1 string Features file name\n-\n- "-graph" associated qualifiers\n- -gprompt boolean Graph prompting\n- -gdesc string Graph description\n- -gtitle string Graph title\n- -gsubtitle string Graph subtitle\n- -gxtitle string Graph x axis title\n- -gytitle string Graph y axis title\n- -goutfile string Output file for non interactive displays\n- -gdirectory string Output directory\n-\n- "-outfile" associated qualifiers\n- -odirectory string Output directory\n-\n- General qualifiers:\n- -auto boolean Turn off prompts\n- -stdout boolean Write first file to standard output\n- -filter boolean Read first file from standard input, write\n- first file to standard output\n- -options boolean Prompt for standard and additional values\n- -debug boolean Write debug output to program.dbg\n- -verbose boolean Report some/full command line options\n- -help boolean Report command line options and exit. More\n- information on associated and general\n- qualifiers can be found with -help -verbose\n- -warning boolean Report warnings\n- -error boolean Report errors\n- -fatal boolean Report fatal errors\n- -die boolean Report dying program messages\n- -version boolean Report version number and exit\n-\n-Input file format\n-\n- The database definitions for following commands are available at\n- http://soap.g-language.org/kbws/embossrc\n-\n- gbaseinformationcontent reads one or more nucleotide sequences.\n-\n-Output file format\n-\n- The output from gbaseinformationcontent is to a plain text file or the\n- EMBOSS graphics device.\n-\n- File: nc_000913.gbaseinformationcontent\n-\n-Sequence: NC_000913\n--30,2.42457\n--29,2.42811\n--28,2.43235\n--27,2.43116\n--26,2.44278\n--25,2.44236\n--24,2.44502\n--23,2.46097\n--22,2.46588\n-\n- [Part of this file has been deleted for brevity]\n-\n-21,2.27547\n-22,2.46974\n-23,2.46342\n-24,2.32686\n-25,2.46245\n-26,2.46061\n-27,2.27664\n-28,2.45650\n-29,2.48206\n-30,2.29140\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gbaseentropy Calculates and graphs the sequence conservation\n- using Shanon uncertainty (entropy)\n- gbaserelativeentropy Calculates and graphs the sequence conservation\n- using Kullback-Leibler divergence (relative\n- entropy)\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gbaserelativeentropy.txt
--- a/GEMBASSY-1.0.3/doc/text/gbaserelativeentropy.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,243 +0,0 @@\n- gbaserelativeentropy\n-Function\n-\n- Calculates and graphs the sequence conservation using Kullback-Leibler\n-\n-Description\n-\n- This function calculates and graphs the sequence conservation in regions\n- around the start/stop codons using Kullback-Leibler divergence (relative\n- entropy). In realistic conditions, as background nucleotide composition\n- (e.g. G+C content) varies among species. Kullback-Leibler divergence\n- calculates the entropy with reduced background noise.\n-\n- The relative entropy H at position i with distribution P(i) is calculated\n- as follows:\n- H(P(i)||pi) = sum(P(i,j) * log(2, P(i,j)/pi(j)))\n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gbaserelativeentropy\n-\n-% gbaserelativeentropy refseqn:NC_000913\n-Calculates and graphs the sequence conservation using Kullback-Leibler\n-divergence (relative entropy)\n-Program compseq output file (optional) [nc_000913.gbaserelativeentropy]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n- Example 2\n-\n-% gbaserelativeentropy refseqn:NC_000913 -plot -graph png\n-Calculates and graphs the sequence conservation using Kullback-Leibler\n-divergence (relative entropy)\n-Created gbaserelativeentropy.1.png\n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n-Calculates and graphs the sequence conservation using Kullback-Leibler\n-divergence (relative entropy)\n-Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1\n-\n- Standard (Mandatory) qualifiers (* if not always prompted):\n- [-sequence] seqall Nucleotide sequence(s) filename and optional\n- format, or reference (input USA)\n-* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type\n- (ps, hpgl, hp7470, hp7580, meta, cps, x11,\n- tek, tekt, none, data, xterm, png, gif, svg)\n-* -outfile outfile [*.gbaserelativeentropy] Program compseq\n- output file (optional)\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers:\n- -position selection [start] Either \'start\' (around start codon)\n- or \'end\' (around stop codon) to create the\n- PWM\n- -patlen integer [3] Length of oligomer to count (Any integer\n- value)\n- -upstream integer [30] Length upstream of specified position\n- to create PWM (Any integer value)\n- -downstream integer [30] Length downstream of specified position\n- to create PWM (Any integer value)\n- -[no]accid boolean [Y] Include to use sequence accession ID as\n- query\n- -plot toggle [N] Include to plot result\n-\n- Associated qualifiers:\n-\n- "-sequence" associated qualifiers\n- -sbegin1 integer Start of each sequence to be used\n- -send1 integer End of each sequence to be used\n- -sreverse1 boolean Reverse (if DNA)\n- -sask1 boolean Ask for begin/end/reverse\n- -snucleotide1 boolean Sequence is nucleotide\n- -sprotein1 boolean Sequence is protein\n- -slower1 boolean Make lower case\n- -supper1 boolean Make upper case\n- -scircul'..b'ing UFO features\n- -fformat1 string Features format\n- -fopenfile1 string Features file name\n-\n- "-graph" associated qualifiers\n- -gprompt boolean Graph prompting\n- -gdesc string Graph description\n- -gtitle string Graph title\n- -gsubtitle string Graph subtitle\n- -gxtitle string Graph x axis title\n- -gytitle string Graph y axis title\n- -goutfile string Output file for non interactive displays\n- -gdirectory string Output directory\n-\n- "-outfile" associated qualifiers\n- -odirectory string Output directory\n-\n- General qualifiers:\n- -auto boolean Turn off prompts\n- -stdout boolean Write first file to standard output\n- -filter boolean Read first file from standard input, write\n- first file to standard output\n- -options boolean Prompt for standard and additional values\n- -debug boolean Write debug output to program.dbg\n- -verbose boolean Report some/full command line options\n- -help boolean Report command line options and exit. More\n- information on associated and general\n- qualifiers can be found with -help -verbose\n- -warning boolean Report warnings\n- -error boolean Report errors\n- -fatal boolean Report fatal errors\n- -die boolean Report dying program messages\n- -version boolean Report version number and exit\n-\n-Input file format\n-\n- The database definitions for following commands are available at\n- http://soap.g-language.org/kbws/embossrc\n-\n- gbaserelativeentropy reads one or more nucleotide sequences.\n-\n-Output file format\n-\n- The output from gbaserelativeentropy is to a plain text file or the\n- EMBOSS graphics device.\n-\n- File: nc_000913.gbaserelativeentropy\n-\n-Sequence: NC_000913\n--30,-0.46682\n--29,-0.46265\n--28,-0.45732\n--27,-0.45704\n--26,-0.44692\n--25,-0.44396\n--24,-0.43528\n--23,-0.43419\n--22,-0.42518\n-\n- [Part of this file has been deleted for brevity]\n-\n-21,-0.40010\n-22,-0.41772\n-23,-0.42503\n-24,-0.39675\n-25,-0.43091\n-26,-0.43196\n-27,-0.40576\n-28,-0.43387\n-29,-0.41228\n-30,-0.38869\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gbase_entropy Calculates and graphs the sequence conservation\n- using Shanon uncertainty (entropy)\n- gbase_information_content Calculates and graphs the sequence conservation\n- using information content\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gbasezvalue.txt
--- a/GEMBASSY-1.0.3/doc/text/gbasezvalue.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,214 +0,0 @@
-                                  gbasezvalue
-Function
-
-   Extracts conserved oligomers per position using Z-score
-
-Description
-
-   This function calculates and extracts conserved oligomers per position using
-   Z-score, in regions around the start/stop codons. The oligomers are returned
-   in ranking order up to "-limit" number.
-
-   The Z-score for mean m and standard error SE is calculated as follows:
-   z = (x - m) / SE
-   where SE for standard deviation s and number of samples s is as follows:
-   SE = s/sqrt(n)
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gbasezvalue
-
-% gbasezvalue refseqn:NC_000913
-Extracts conserved oligomers per position using Z-score
-Program compseq output file (optional) [nc_000913.gbasezvalue]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gbasezvalue] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -limit              integer    [5] Rank threshold for showing the conserved
-                                  oligomer (Any integer value)
-   -position           selection  [start] Either 'start' (around start codon)
-                                  or 'end' (around stop codon) to create the
-                                  PWM
-   -patlen             integer    [3] Length of oligomer to count (Any integer
-                                  value)
-   -upstream           integer    [30] Length upstream of specified position
-                                  to create PWM (Any integer value)
-   -downstream         integer    [30] Length downstream of specified position
-                                  to create PWM (Any integer value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gbasezvalue reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gbasezvalue is to a plain text file.
-
-   File: nc_000913.gbasezvalue
-
-Sequence: NC_000913
-position:-30,1,taa,-0.76525
-2,aga,-0.79101
-3,tta,-1.14174
-4,cta,-1.18831
-5,aat,-1.86652
-position:-29,1,cta,-0.18368
-2,aat,-0.71851
-3,gac,-1.26182
-4,taa,-1.39455
-
-   [Part of this file has been deleted for brevity]
-
-position:29,1,gct,1.66288
-2,act,1.26637
-3,tat,0.66721
-4,cct,-0.43158
-5,tgt,-0.59254
-position:30,1,ctg,3.12072
-2,att,0.04193
-3,ctc,-0.12416
-4,cta,-0.38461
-5,tta,-0.76413
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gbasecounter Creates a position weight matrix of oligomers around start
-                codon
-   gviewcds     Displays a graph of nucleotide contents around start and stop
-                codons
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gbui.txt
--- a/GEMBASSY-1.0.3/doc/text/gbui.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,209 +0,0 @@
-                                      gbui
-Function
-
-   Calculates base usage indices for protein-coding sequences
-
-Description
-
-   gbui calculates base usage indices of protein-coding sequences (excluding
-   start and stop codons) for each gene. Indices calculated are as follows,
-      acgt: Total bumber of bases (A+T+G+C)
-      ryr:  Purine/Pyrimidine ratio (A+G)/(T+C)
-      gcc:  G+C content (G+C)/(A+T+G+C)
-      Hgc:  entropy of G+C content (G+C)/(A+T+G+C)
-      gcs:  GC skew (C-G)/(C+G)
-      ats:  AT skew (A-T)/(A+T)
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gbui
-
-% gbui refseqn:NC_000913
-Calculates base usage indices for protein-coding sequences
-Program compseq output file [nc_000913.gbui]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gbui] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translating using standard
-                                  codon table
-   -position           menu       [all] Codon position (Values: all (Assess
-                                  overall base usage of the gene); 1 (Assess
-                                  base usage at 1st position of codons); 2
-                                  (Assess base usage at 2nd position of
-                                  codons); 3 (Assess base usage at 3rd
-                                  position of codons))
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gbui reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gbui is to a plain text file.
-
-   File: nc_000913.gbui
-
-Sequence: NC_000913
-acgt,ryr,gcc,Hgc,gcs,ats,gene
-60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL
-2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA
-927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB
-1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC
-291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX
-771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA
-1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ
-948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB
-
-   [Part of this file has been deleted for brevity]
-
-507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX
-642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC
-864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob
-468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA
-684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB
-1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC
-1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD
-711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA
-135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY
-681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gdinuc Calculates dinucleotide usage
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gcai.txt
--- a/GEMBASSY-1.0.3/doc/text/gcai.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,212 +0,0 @@
-                                      gcai
-Function
-
-   Calculate codon adaptation index for each gene
-
-Description
-
-   gcai calculates codon adaptation index (CAI) for each gene. CAI is measure
-   a of the relative adaptiveness of the codon usage of a gene towards the
-   codon usage of highly expressed genes, ranging from 0 (no bias) to 1
-   (maximum bias). CAI can be used as a 'universal' measure of codon usage
-   bias as it is correlated with various gene features such as gene expression
-   level, GC content, and GC skew.
-
-   The CAI for a gene where A(i) is the amino acid at position i and W(A) is
-   the W value corresponding to the amino acid is calculated as follows:
-
-   CAI = sum(log(e,W(A(i))))
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gcai
-
-% gcai refseqn:NC_000913
-Calculate codon adaptation index for each gene
-Codon usage output file [nc_000913.gcai]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gcai] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translating using standard
-                                  codon table
-   -wabsent            string     [-1] W value of codons absent from a
-                                  reference set to negative when excludes such
-                                  codons from the calculation (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gcai reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gcai is to a plain text file.
-
-   File: nc_000913.gcai
-
-Sequence: NC_000913
-cai,gene
-0.7256,thrL
-0.4831,thrA
-0.4719,thrB
-0.5178,thrC
-0.4989,yaaX
-0.4933,yaaA
-0.4533,yaaJ
-0.7074,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.4681,yjjX
-0.4797,ytjC
-0.5350,rob
-0.4932,creA
-0.3918,creB
-0.4170,creC
-0.4167,creD
-0.6466,arcA
-0.4236,yjjY
-0.3913,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional
-      synonymous codon usage bias, and its potential applications.
-      Nucleic Acids Res. 15(3):1281-95.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gp2  Calculate the P2 index of each gene
-   gphx Identify predicted highly expressed gene
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gcbi.txt
--- a/GEMBASSY-1.0.3/doc/text/gcbi.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,209 +0,0 @@
-                                      gcbi
-Function
-
-   Calculates the codon bias index (CBI)
-
-Description
-
-   gcbi calculates the codon bias index (CBI) for each gene af the given
-   genome. CBI is a directional codon bias which measures the usage of
-   optimal codons in a gene. CBI is similar to Fop, basically taking values
-   from 0 (no bias) and 1 (maximum bias) and can take negative values
-   depending on the codon usage.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gcbi
-
-% gcbi refseqn:NC_000913
-Calculates the codon bias index (CBI)
-Codon usage output file [nc_000913.gcbi]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gcbi] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translating using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gcbi reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gcbi is to a plain text file.
-
-   File: nc_000913.gcbi
-
-Sequence: NC_000913
-cbi,gene
-0.8716,thrL
-0.3441,thrA
-0.3462,thrB
-0.4280,thrC
-0.3868,yaaX
-0.3908,yaaA
-0.3521,yaaJ
-0.5354,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.4005,yjjX
-0.4388,ytjC
-0.3934,rob
-0.4645,creA
-0.4266,creB
-0.3435,creC
-0.3796,creD
-0.4980,arcA
-0.5412,yjjY
-0.4018,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
-      usage bias, J Mol Evol, 47(3):268-74.
-
-   Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the
-      psb A locus based on tRNA availability, J.Mol.Evo,. 37:273-280.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gdeltaenc Calculate the codon usage bias related to translation optimization
-             (delta ENC)
-   gicdi     Calculates the intrinsic codon deviation index (ICDI)
-   gsvalue   Calculate the strength of selected codon usage bias (S)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gcgr.txt
--- a/GEMBASSY-1.0.3/doc/text/gcgr.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,180 +0,0 @@
-                                      gcgr
-Function
-
-   Create a Chaos Game Representation of a given sequence
-
-Description
-
-   gcgr creates a Chaos Game Representation (CGR) image of a given sequence.
-   CGR is generated by the following procedure:
-
-   1. Start from position (0,0) or the origin of two dimensional coordinate.
-   Four nucleotides are located at the four corners:
-      A: (-1, 1)  upper left
-      T: (1, -1)  lower right
-      G: (1, 1)   upper right
-      C: (-1, -1) lower left
-   2. For each nucleotide, move and mark the new location which is halfway
-   between the current location and the nucleotide.
-   For example, if the first letter is A, position is moved from (0,0) to
-   midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).
-
-   3. Repeat this procedure for all nucleotides.
-   CGR is a generalized scale-independent Markov probability table for the
-   sequence, and oligomer tables can be deduced from CGR image.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gcgr
-
-% gcgr refseqn:NC_000913
-Create a Chaos Game Representation of a given sequence
-Created gcgr.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [png] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -width              integer    [1024] Width of image (Any integer value)
-   -goutfile           string     [gcgr] Output file for non interactive
-                                  displays (Any string)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gcgr reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gcgr is to an image file.
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gseq2png Converts a sequence to PNG image
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gcircularmap.txt
--- a/GEMBASSY-1.0.3/doc/text/gcircularmap.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,174 +0,0 @@
-                                  gcircularmap
-Function
-
-   Draws circular map of the genome
-
-Description
-
-   gdnawalk creates a circular map of the genome using SVG, suitable for
-   plasmids and circular bacterial chromosomes.
-
-   From the outer ring inwards, genes on direct strand (pink),
-   genes on complementary strand (yellow), tRNAs (green arrows),
-   rRNAs (pink or orange stripes depending on the strand),
-   GC content (brown lines), GC skew (yellow lines). Replication
-   origin and terminus predicted from the GC skew shift points
-   are also labeled.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gcircularmap
-
-% gcircularmap refseqn:NC_000913
-Draws circular map of the genome
-Created gcircularmap.1.svg
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [svg] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -goutfile           string     [gcircularmap] Output file for non
-                                  interactive displays (Any string)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gcircularmap reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gcircularmap is to an image file.
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gdnawalk     Draws DNA Walk map of the genome
-   ggenomemap3  Draws the map of the genome (version 3)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gcodoncompiler.txt
--- a/GEMBASSY-1.0.3/doc/text/gcodoncompiler.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b"@@ -1,213 +0,0 @@\n- gcodoncompiler\n-Function\n-\n- Calculate various kinds of amino acid and codon usage data\n-\n-Description\n-\n- gcodoncompiler calculates various kinds of amino acid and codon usage data.\n- The following values are calculable:\n- A0: Absolute amino acid frequency\n- A1: Relative amino acid frequency\n- C0: Absolute codon frequency\n- C1: Relative codon frequency in a complete sequence\n- C2: Relative codon frequency in each amino acid\n- C3: Relative synonymous codon usage\n- C4: Relative adaptiveness\n- C5: Maximum or minor codon\n-\n- For amino acids unpresent in a gene, C2-C3 does not calculate the values.\n- By using R* in place, such values are hypothesized that alternative\n- synonymous codons are used with equal frequency.\n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gcodoncompiler\n-\n-% gcodoncompiler refseqn:NC_000913\n-Calculate various kinds of amino acid and codon usage data\n-Codon usage output file [nc_000913.gcodoncompiler]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n- Standard (Mandatory) qualifiers:\n- [-sequence] seqall Nucleotide sequence(s) filename and optional\n- format, or reference (input USA)\n- [-outfile] outfile [*.gcodoncompiler] Codon usage output file\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers:\n- -translate boolean [N] Include to translate using standard\n- codon table\n- -startcodon boolean [N] Include to include start codon\n- -stopcodon boolean [N] Include to include stop codon\n- -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular\n- expression to delete key (i.e. amino acids\n- and nucleotides) (Any string)\n- -data menu [R0] Kinds of codon usage data. R*\n- hypothesizes amino acids which are not\n- present in the gene (Values: A0 (Absolute\n- amino acid frequency ('AA')); A1 (Relative\n- amino acid frequency ('RAAU')); C0 (Absolute\n- codon frequency ('AF')); C1 (Relative codon\n- frequency in a complete sequence); C2\n- (Relative codon frequency in each amino acid\n- ('RF')); C3 (Relative synonymous codon\n- usage ('RSCU')); C4 (Relative adaptiveness);\n- i.e., ratio to maximum of minor codon ('W')\n- C5 (Maximum (1) or minor (0) codon); R0\n- (Absolute codon frequency ('AF')); R1\n- (Relative codon frequency in a complete\n- sequence); R2 (Relative codon frequency in\n- each amino acid ('RF')); R3 (Relative\n- synonymous codon usage ('RSCU')); R4\n- (Relative adaptiveness); i.e., ratio to\n- maximum of minor codon ('W') R5 (Maximum (1)\n- or minor (0) codon))\n- -[no]accid boolean [Y] Include to use sequence ac"..b'rcular\n- -sformat1 string Input sequence format\n- -iquery1 string Input query fields or ID list\n- -ioffset1 integer Input start position offset\n- -sdbname1 string Database name\n- -sid1 string Entryname\n- -ufo1 string UFO features\n- -fformat1 string Features format\n- -fopenfile1 string Features file name\n-\n- "-outfile" associated qualifiers\n- -odirectory2 string Output directory\n-\n- General qualifiers:\n- -auto boolean Turn off prompts\n- -stdout boolean Write first file to standard output\n- -filter boolean Read first file from standard input, write\n- first file to standard output\n- -options boolean Prompt for standard and additional values\n- -debug boolean Write debug output to program.dbg\n- -verbose boolean Report some/full command line options\n- -help boolean Report command line options and exit. More\n- information on associated and general\n- qualifiers can be found with -help -verbose\n- -warning boolean Report warnings\n- -error boolean Report errors\n- -fatal boolean Report fatal errors\n- -die boolean Report dying program messages\n- -version boolean Report version number and exit\n-\n-Input file format\n-\n- The database definitions for following commands are available at\n- http://soap.g-language.org/kbws/embossrc\n-\n- gcodoncompiler reads one or more nucleotide sequences.\n-\n-Output file format\n-\n- The output from gcodoncompiler is to a plain text file.\n-\n- File: nc_000913.gcodoncompiler\n-\n-Sequence: NC_000913\n-Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag\n-26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gaminoinfo Prints out basic amino acid sequence statistics\n- gaaui Calculates various indece of amino acid usage\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gconsensusz.txt
--- a/GEMBASSY-1.0.3/doc/text/gconsensusz.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,205 +0,0 @@\n- gconsensusz\n-Function\n-\n- Calculate consensus in given array of sequences\n-\n-Description\n-\n- gconsensusz calculates the consensus of given list of sequences, using\n- Z-score. The Z-score will show higher values when the sequences are biased\n- to a single character within the list.\n-\n- The Z-score for mean m and standard error SE is calculated as follows:\n- z = (x - m) / SE\n- where SE for standard deviation s and number of samples s is as follows:\n- SE = s/sqrt(n)\n- \n- G-language SOAP service is provided by the\n- Institute for Advanced Biosciences, Keio University.\n- The original web service is located at the following URL:\n-\n- http://www.g-language.org/wiki/soap\n-\n- WSDL(RPC/Encoded) file is located at:\n-\n- http://soap.g-language.org/g-language.wsdl\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n-Here is a sample session with gconsensusz\n-\n-% gconsensusz consensus.fasta\n-Calculate consensus in given array of sequences\n-Program compseq output file (optional) [rs_000000.gconsensusz]: \n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n- Example 2\n-\n-% gconsensusz consensus.fasta -plot -graph png\n-Calculate consensus in given array of sequences\n-Created gconsensusz.1.png\n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n-Command line arguments\n-\n- Standard (Mandatory) qualifiers (* if not always prompted):\n- [-sequence] seqall Nucleotide sequence(s) filename and optional\n- format, or reference (input USA)\n-* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type\n- (ps, hpgl, hp7470, hp7580, meta, cps, x11,\n- tek, tekt, none, data, xterm, png, gif, svg)\n-* -outfile outfile [*.gconsensusz] Program compseq output file\n- (optional)\n-\n- Additional (Optional) qualifiers: (none)\n- Advanced (Unprompted) qualifiers:\n- -high integer [1] Z value greater than which is\n- significant (Any integer value)\n- -low float [0.2] Z value less than which is\n- insignificant (Any numeric value)\n- -plot toggle [N] Include to plot result\n-\n- Associated qualifiers:\n-\n- "-sequence" associated qualifiers\n- -sbegin1 integer Start of each sequence to be used\n- -send1 integer End of each sequence to be used\n- -sreverse1 boolean Reverse (if DNA)\n- -sask1 boolean Ask for begin/end/reverse\n- -snucleotide1 boolean Sequence is nucleotide\n- -sprotein1 boolean Sequence is protein\n- -slower1 boolean Make lower case\n- -supper1 boolean Make upper case\n- -scircular1 boolean Sequence is circular\n- -sformat1 string Input sequence format\n- -iquery1 string Input query fields or ID list\n- -ioffset1 integer Input start position offset\n- -sdbname1 string Database name\n- -sid1 string Entryname\n- -ufo1 string UFO features\n- -fformat1 string Features format\n- -fopenfile1 string Features file name\n-\n- "-graph" associated qualifiers\n- -gprompt boolean Graph prompting\n- -gdesc string Graph description\n- -gtitle string Graph title\n- -gsubtitle string Graph subtitle\n- -gxtitle string Graph x axis title\n- -gytitle string Graph y axis title\n- -goutfile string Output file for non interactive displays\n- -gdirectory '..b'0212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,0.487923290212298,3.00732065791778,3.00732065791778,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,0.487923290212298,3.00732065791778,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,4.26701934177052,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,3.00732065791778,1.74762197406504,4.26701934177052,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,3.00732065791778,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,5.52671802562326,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,3.00732065791778,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,\n-\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- gdistincc Calculates the distance between two loci in circular chromosomes\n- gpalindrome Searches palindrome sequences\n- gseqinfo Prints out basic nucleotide sequence statistics\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n- 2013 - Fixed by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gdeltaenc.txt
--- a/GEMBASSY-1.0.3/doc/text/gdeltaenc.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,186 +0,0 @@
-                                   gdeltaenc
-Function
-
-   Calculate the codon usage bias related to translation optimization
-   (delta ENC)
-
-Description
-
-   gdeltaenc calculates the codon usage bias related to translation
-   optimization (delta ENC) described in Rocha (2004). The basic idea is to
-   calculate the Effective Number of Codons (ENC) for highly-expressed genes
-   (ribosomal genes) and weakly-expressed genes (all genes), and taking the
-   relative difference between them. ENC assigns a gene a number between 20 to
-   61 where 20 indicates that one codon is used for each aminoacid and 61
-   indicates that each codon is used equally throughout the protein sequence.
-
-   ENC is calculated as follows:
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gdeltaenc
-
-% gdeltaenc refseqn:NC_000913
-Calculate the codon usage bias related to translation optimization (delta
-ENC)
-Program compseq output file [nc_000913.gdeltaenc]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gdeltaenc] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gdeltaenc reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gdeltaenc is to a plain text file.
-
-   File: nc_000913.gdeltaenc
-
-Sequence: NC_000913 DELTA-ENC 0.255663430420712
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy,
-      specialization, and efficient decoding for translation optimization,
-      Genome Research, 14(11):2279-2286
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcbi    Calculates the codon bias index (CBI)
-   gicdi   Calculates the intrinsic codon deviation index (ICDI)
-   gsvalue Calculate the strength of selected codon usage bias (S)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gdeltagcskew.txt
--- a/GEMBASSY-1.0.3/doc/text/gdeltagcskew.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,193 +0,0 @@
-                                  gdeltagcskew
-Function
-
-   Calculate strand bias of bacterial genome using delta GC skew index
-
-Description
-
-   gdeltagcskew calculates strand bias of bacterial genome using delta GC skew
-   index, first proposed by Rocha et al. (2001), and further extended in 2006.
-   Basic idea of delta GC skew index is to calculate the difference of GC skew
-   in coding regions residing in leading and lagging strands. Rocha et al.
-   (2001) calculates delta GC skew index using the third codon position of
-   genes, and Rocha et al. (2006)  modified to only use >fourfold degenerate
-   codons.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gdeltagcskew
-
-% gdeltagcskew refseqn:NC_000913
-Calculate strand bias of bacterial genome using delta GC skew index
-Program compseq output file [nc_000913.gdeltagcskew]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gdeltagcskew] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -at                 boolean    [N] Include when observing AT skew instead
-                                  of GC skew
-   -purine             boolean    [N] Include when observing purine (AG/TC)
-                                  skew
-   -keto               boolean    [N] Include when observing keto (TG/AC) skew
-   -method             selection  [degenerate] Choose the nucleotides to use
-                                  'degenerate', 'gc3', or 'all'
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gdeltagcskew reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gdeltagcskew is to a plain text file.
-
-   File: nc_000913.gdeltagcskew
-
-Sequence: NC_000913 DELTA-GCskew -0.108937
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial
-      Genomes, Molecular Biology and Evolution, 18(9):1789-1799
-
-   Rocha EPC et al. (2006) Similar compositional biases are caused by very
-      different mutational effects, Genome Research, 16:1537-1547
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gb1      Calculate strand bias of bacterial genome using B1 index
-   gb2      Calculate strand bias of bacterial genome using B2 index
-   ggcsi    GC Skew Index: an index for strand-specefic mutational bias
-   gldabias Calculate strand bias of bacterial genome using linear
-            discriminant analysis (LDA)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gdinuc.txt
--- a/GEMBASSY-1.0.3/doc/text/gdinuc.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,190 +0,0 @@
-                                     gdinuc
-Function
-
-   Calculates dinucleotide usage
-
-Description
-
-   gdinuc calculates dinucleotide usage indices for protein-coding sequences
-   (excluding start and stop codons). Dinucleotide usage is computed as the
-   ratio of observed (O) to expected (E) dinucleotide frequencies within the
-   given sequence. Dinucleotides are known to have consistent patterns within
-   the genome (signatures) and tend to have certain periodicities.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gdinuc
-
-% gdinuc refseqn:NC_000913
-Calculates dinucleotide usage
-Program compseq output file [nc_000913.gdinuc]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gdinuc] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translates using standard
-                                  codon table
-   -position           menu       [all] Codon position or reading frame
-                                  (Values: all (Assess all codon positions);
-                                  12 (Assess the reading frame 1-2); 23
-                                  (Assess the reading frame 2-3); 31 (Assess
-                                  the reading frame 3-1))
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (i.e. amino acids
-                                  and nucleotides) (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gdinuc reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gdinuc is to a plain text file.
-
-   File: nc_000913.gdinuc
-
-Sequence: NC_000913
-
-keys,aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,gene,
-All,1.293,0.921,0.720,1.108,1.022,0.868,1.166,0.925,0.958,1.285,0.897,0.867,0.729,0.891,1.228,1.123,
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Yew et al. (2004) Base usage and dinucleotide frequency of infectious
-      bursal disease virus, Virus Genes, 28:1,41-53.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gbui Calculates base usage indices for protein-coding sequences
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gdistincc.txt
--- a/GEMBASSY-1.0.3/doc/text/gdistincc.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,179 +0,0 @@
-                                   gdistincc
-Function
-
-   Calculates the distance between two loci in circular chromosomes
-
-Description
-
-   gdistincc calculates the distance between two loci in circular
-   chromosomes. It is mostly useful to calculate the distance from the
-   replication origin.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gdistincc
-
-% gdistincc refseqn:NC_000913 1234
-Calculates the distance between two loci in circular chromosomes
-Output file [nc_000913.gdistincc]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-first]             integer    [0] Position to find the distance (Any
-                                  integer value)
-  [-outfile]           outfile    [*.gdistincc] Output file name
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -second             integer    [-1] If the second position is negative,
-                                  position of replication origin is used (Any
-                                  integer value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory3        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gdistincc reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gdistincc is to a plain text file.
-
-   File: nc_000913.gdistincc
-
-Sequence: NC_000913 Position1: 1234 Distance 1169193600
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gconsensus_z Calculate consensus in given array of sequences
-   gpalindrome  Searches palindrome sequences
-   gseqinfo     Prints out basic nucleotide sequence statistics
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gdnawalk.txt
--- a/GEMBASSY-1.0.3/doc/text/gdnawalk.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,170 +0,0 @@
-                                    gdnawalk
-Function
-
-   Draws DNA Walk map of the genome
-
-Description
-
-   gdnawalk draws the DNA Walk map of the given genome. DNA Walk is drawn by
-   moving a single pixel per nucleotide, in the direction specified for each
-   base. Here A is moved upward, T downward, G to the right, and C to the
-   left. Position zero (first letter of the genome) is indicated by the
-   crossing of thin axes.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gdnawalk
-
-% gdnawalk refseqn:NC_000913
-Draws DNA Walk map of the genome
-Created gdnawalk.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [png] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -goutfile           string     [gdnawalk] Output file for non interactive
-                                  displays (Any string)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gdnawalk reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gdnawalk is to an image file.
-
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcircularmap Draws circular map of the genome
-   ggenomemap3  Draws the map of the genome (version 3)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/genc.txt
--- a/GEMBASSY-1.0.3/doc/text/genc.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,211 +0,0 @@
-                                      genc
-Function
-
-   Calculate the effective number of codons (Nc)
-
-Description
-
-   genc calculates the effective number of codons (ENC|Nc). ENC is a measure
-   for species-independent codon usage bias. Some measures including CAI are
-   species-dependent as optimal codons differ. ENC assigns a gene a number
-   between 20 to 61 where 20 indicates that one codon is used for each amino
-   acid and 61 indicates that each codon is used equally throughout the
-   protein sequence.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with genc
-
-% genc refseqn:NC_000913
-Calculate the effective number of codons (Nc)
-Codon usage output file [nc_000913.genc]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.genc] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translates using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (i.e. amino acids
-                                  and nucleotides) (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   genc reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from genc is to a plain text file.
-
-   File: nc_000913.genc
-
-Sequence: NC_000913
-enc,gene
-,thrL
-48.41,thrA
-54.13,thrB
-46.18,thrC
-51.65,yaaX
-45.71,yaaA
-48.54,yaaJ
-36.83,talB
-
-   [Part of this file has been deleted for brevity]
-
-51.43,yjjX
-46.61,ytjC
-49.83,rob
-47.74,creA
-50.63,creB
-51.39,creC
-48.42,creD
-41.53,arcA
-61,yjjY
-53.63,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
-      usage bias, J Mol Evol, 47(3):268-74.
-
-   Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
-      87:23-29.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gew     Calculate a measure of synonymous codon usage evenness (Ew)
-   gfop    Calculate the frequency of optimal codons (Fop)
-   gscs    Calculates the scaled chi-square
-   gwvalue Calculate the 'relative adaptiveness of each codon' (W)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/genret.txt
--- a/GEMBASSY-1.0.3/doc/text/genret.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,451 +0,0 @@\n- genret\n-Function\n-\n- Retrieves various gene related information from genome flatfile\n-\n-Description\n-\n- genret reads in one or more genome flatfiles and retrieves various data from\n- the input file. It is a wrapper program to the G-language REST service,\n- where a method is specified by giving a string to the "method" qualifier. By\n- default, genret will parse the input file to retrieve the accession ID\n- (or name) of the genome to query G-language REST service. By setting the\n- "accid" qualifier to false (or 0), genret will instead parse the sequence\n- and features of the genome to create a GenBank formatted flatfile and upload\n- the file to the G-language web server. Using the file uploaded, genret will\n- execute the method provided.\n-\n- genret is able to perform a variety of tasks, incluing the retrieval of\n- sequence upstream, downstream, or around the start or stop codon,\n- translated gene sequences search of gene data by keyword, and re-annotation\n- and retrieval of genome flatfiles. The set of genes can be given as flat\n- text, regular expression, or a file containing the list of genes.\n-\n- Details on G-language REST service is available from the wiki page\n-\n- http://www.g-language.org/wiki/rest\n-\n- Documentation on G-language Genome Analysis Environment methods are\n- provided at the Document Center\n-\n- http://ws.g-language.org/gdoc/\n-\n-Usage\n-\n- Here is a sample session with genret\n-\n- Retrieving sequences upstream, downstream, or around the start/stop codons. \n- The following example shows the retrieval of sequence around the start\n- codons of all genes.\n-\n- Genes to access are specified by regular expression. \'*\' stands for every\n- gene.\n-\n- Available methods are:\n- after_startcodon\n- after_stopcodon\n- around_startcodon\n- around_stopcodon\n- before_startcodon\n- before_stopcodon\n-\n-% genret\n-Retrieves various gene related information from genome flatfile\n-Input nucleotide sequence(s): refseqn:NC_000913\n-Gene name(s) to lookup [*]:\n-Feature to access: around_startcodon\n-Full text output file [nc_000913.around_startcodon]:\n-\n- Go to the input files for this example\n- Go to the output files for this example\n-\n- Example 2\n-\n- Using flat text as target genes. The names can be split with with a space,\n- comma, or vertical bar.\n-\n-% genret\n-Retrieves various gene related information from genome flatfile\n-Input nucleotide sequence(s): refseqn:NC_000913\n-List of gene name(s) to report [*]: recA,recB\n-Name of gene feature to access: translation\n-Sequence output file [nc_000913.translation.genret]: stdout\n->recA\n-MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR\n-IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT\n-GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL\n-KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR\n-VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN\n-ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF\n->recB\n-MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLV\n-VTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEIDDKAQAAQWLLLAERQMD\n-EAAVFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLRYQACADFWRRHCYPLPREIAQVV\n-FETWKGPQALLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELD\n-ALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGETP\n-RHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSES\n-GEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQAIYAFRGADI\n-FTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAFMFREIPFIPVKSAGKNQALR\n-FVFKGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPV\n-RASDISVLVRSRQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPEREN\n-TLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMSARNIA\n-ENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQMRLESD\n-KHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAE\n-RLAEDLRLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLR\n-TCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTL'..b' IEA:UniProtKB-SubCell."\n- /rs_xr="GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW."\n- /rs_xr="GO; GO:0004413; F:homoserine kinase activity;\n- IEA:EC."\n- /rs_xr="GO; GO:0009088; P:threonine biosynthetic process;\n- IEA:UniProtKB-KW."\n- /rs_xr="HAMAP; MF_00384; Homoser_kinase; 1; -."\n- /rs_xr="InterPro; IPR006204; GHMP_kinase."\n- /rs_xr="InterPro; IPR013750; GHMP_kinase_C."\n- /rs_xr="InterPro; IPR006203; GHMP_knse_ATP-bd_CS."\n- /rs_xr="InterPro; IPR000870; Homoserine_kin."\n- /rs_xr="InterPro; IPR020568; Ribosomal_S5_D2-typ_fold."\n- /rs_xr="InterPro; IPR014721;\n- Ribosomal_S5_D2-typ_fold_subgr."\n- /rs_xr="Gene3D; G3DSA:3.30.230.10;\n- Ribosomal_S5_D2-type_fold; 1."\n- /rs_xr="Pfam; PF08544; GHMP_kinases_C; 1."\n- /rs_xr="Pfam; PF00288; GHMP_kinases_N; 1."\n- /rs_xr="PIRSF; PIRSF000676; Homoser_kin; 1."\n- /rs_xr="PRINTS; PR00958; HOMSERKINASE."\n- /rs_xr="SUPFAM; SSF54211; Ribosomal_S5_D2-typ_fold; 1."\n- /rs_xr="TIGRFAMs; TIGR00191; thrB; 1."\n- /rs_xr="PROSITE; PS00627; GHMP_KINASES_ATP; 1."\n- /transl_table="11"\n- /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETF\n- SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS\n- VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI\n- ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQ\n- PELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETA\n- QRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"\n-\n- [Part of this file has been deleted for brevity]\n-\n- 4639201 gcgcagtcgg gcgaaatatc attactacgc cacgccagtt gaactggtgc cgctgttaga\n- 4639261 ggaaaaatct tcatggatga gccatgccgc gctggtgttt ggtcgcgaag attccgggtt\n- 4639321 gactaacgaa gagttagcgt tggctgacgt tcttactggt gtgccgatgg tggcggatta\n- 4639381 tccttcgctc aatctggggc aggcggtgat ggtctattgc tatcaattag caacattaat\n- 4639441 acaacaaccg gcgaaaagtg atgcaacggc agaccaacat caactgcaag ctttacgcga\n- 4639501 acgagccatg acattgctga cgactctggc agtggcagat gacataaaac tggtcgactg\n- 4639561 gttacaacaa cgcctggggc ttttagagca acgagacacg gcaatgttgc accgtttgct\n- 4639621 gcatgatatt gaaaaaaata tcaccaaata aaaaacgcct tagtaagtat ttttc\n-//\n-\n-Data files\n-\n- None.\n-\n-Notes\n-\n- None.\n-\n-References\n-\n- Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and\n- Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench\n- for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.\n-\n- Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for\n- large-scale analysis of high-throughput omics data, J. Pest Sci.,\n- 31, 7.\n-\n- Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome\n- Analysis Environment with REST and SOAP Web Service Interfaces,\n- Nucleic Acids Res., 38, W700-W705.\n-\n-Warnings\n-\n- None.\n-\n-Diagnostic Error Messages\n-\n- None.\n-\n-Exit status\n-\n- It always exits with a status of 0.\n-\n-Known bugs\n-\n- None.\n-\n-See also\n-\n- entret Retrieve sequence entries from flatfile databases and files\n- seqret Read and write (return) sequences\n-\n-Author(s)\n-\n- Hidetoshi Itaya (celery@g-language.org)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n- Kazuharu Arakawa (gaou@sfc.keio.ac.jp)\n- Institute for Advanced Biosciences, Keio University\n- 252-0882 Japan\n-\n-History\n-\n- 2012 - Written by Hidetoshi Itaya\n-\n-Target users\n-\n- This program is intended to be used by everyone and everything, from\n- naive users to embedded scripts.\n-\n-Comments\n-\n- None.\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gentrez.txt
--- a/GEMBASSY-1.0.3/doc/text/gentrez.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,182 +0,0 @@
-                                    gentrez
-Function
-
-   Search NCBI Entrez
-
-Description
-
-   gentrez searches NCBI Entrez with keyword through EUtilities.
-   This is intended for quick lookup through the command line
-   so only top ten hits are reported.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gentrez
-
-% gentrez genome 'Escherichia coli'
-Search NCBI Entrez
-ASCII text output file [genome.Escherichia coli.gentrez]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-database]          string     [pubmed] NCBI database to search (Any
-                                  string)
-  [-query]             string     Query to search (Any string)
-  [-outfile]           outfile    [$(database).$(query).gentrez] ASCII text
-                                  output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers: (none)
-   Associated qualifiers:
-
-   "-outfile" associated qualifiers
-   -odirectory3        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gentrez reads no file input.
-
-Output file format
-
-   The output from gentrez is to a plain text file.
-
-   File: genome.Escherichia coli.gentrez
-
-    53 entries found in NUCLEOTIDE: (Showing up to 10 hits)
-
-     1. Accession Number:   NZ_AKBV01000001
-        Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome
-
-     2. Accession Number:   NC_018658
-        Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome
-
-     3. Accession Number:   NC_012971
-        Escherichia coli BL21(DE3) chromosome, complete genome
-
-     4. Accession Number:   NC_017635
-        Escherichia coli W chromosome, complete genome
-
-     5. Accession Number:   NC_018650
-        Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome
-
-     6. Accession Number:   NC_018661
-        Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome
-
-     7. Accession Number:   NC_017906
-        Escherichia coli Xuzhou21 chromosome, complete genome
-
-     8. Accession Number:   NC_017634
-        Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome
-
-     9. Accession Number:   NC_017656
-        Escherichia coli O55:H7 str. RM12579 chromosome, complete genome
-
-    10. Accession Number:   NC_017664
-        Escherichia coli W chromosome, complete genome
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   None.
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gew.txt
--- a/GEMBASSY-1.0.3/doc/text/gew.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,211 +0,0 @@
-                                      gew
-Function
-
-   Calculate a measure of synonymous codon usage evenness (Ew)
-
-Description
-
-   gew calculates the 'weighted sum of relative entropy' (Ew) as a measure
-   of synonymous codon usage evenness for each gene. This index takes all
-   three aspects of amino acid usage (number of distinct amino acids,
-   relatieve frequencies, and degree of codon degeneracy) into account.
-   The values range from 0 (no bias) to 1 (maximum bias).
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gew
-
-% gew refseqn:NC_000913
-Calculate a measure of synonymous codon usage evenness (Ew)
-Codon usage output file [nc_000913.gew]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gew] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translates using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (i.e. amino acids
-                                  and nucleotides) (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gew reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gew is to a plain text file.
-
-   File: nc_000913.gew
-
-Sequence: NC_000913
-Ew,gene
-0.2800,thrL
-0.8458,thrA
-0.8292,thrB
-0.7937,thrC
-0.7032,yaaX
-0.7922,yaaA
-0.8100,yaaJ
-0.6685,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.7943,yjjX
-0.7265,ytjC
-0.7932,rob
-0.7498,creA
-0.7967,creB
-0.8490,creC
-0.7979,creD
-0.6826,arcA
-0.6475,yjjY
-0.7729,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Suzuki H. et al. (2004) The 'weighted sum of relative entropy': a new
-      index for synonymous codon usage bias, Gene, 23;335:19-23.
-
-   Suzuki H. et al. (2007) Variation in the correlation of G + C composition
-      with synonymous codon usage bias among bacteria, EURASIP J Bioinform
-      Syst Biol, 2007:61374.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   genc    Calculate the effective number of codons (Nc)
-   gfop    Calculate the frequency of optimal codons (Fop)
-   gscs    Calculates the scaled chi-square
-   gwvalue Calculate the 'relative adaptiveness of each codon' (W)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gfindoriter.txt
--- a/GEMBASSY-1.0.3/doc/text/gfindoriter.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,189 +0,0 @@
-                                  gfindoriter
-Function
-
-   Predict the replication origin and terminus in bacterial genomes
-
-Description
-
-   gfindoriter predicts the replicational origin and terminus in circular
-   bacterial genomes, by taking the vertices of cumulative skew graphs (GC,
-   d keto, or purine). See Frank and Lobry (2000) for the basic idea behind
-   this algorithm (but also note that this algorithm is different from that
-   of Oriloc, which uses GC3 of genes).
-   Terminus of replication can be more accurate by using noise-reduction
-   filtering using Fourier spectrum of the GC skew. This low-pass filtering
-   can be applied using -filter option. See Arakawa et al. (2007) for details.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gfindoriter
-
-% gfindoriter refseqn:NC_000913
-Predict the replication origin and terminus in bacterial genomes
-Output file [nc_000913.gfindoriter]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gfindoriter] Output file name
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -window             integer    [4096] Number of windows to use for Fat
-                                  Fourier Transform. Only active when -lowpass
-                                  option is specified. Value must be the
-                                  power of two (Any integer value)
-   -purine             boolean    [N] Use purine skew for calculation
-   -keto               boolean    [N] Use keto skew for calculation
-   -lowpass            integer    [0] Lowpass filter strength in percent.
-                                  Typically 95 or 99 works best (Any integer
-                                  value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gfindoriter reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gfindoriter is to a plain text file.
-
-   File: nc_000913.gfindoriter
-
-Sequence: NC_000913 Origin: 3922946 Terminus: 1550274
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in
-      unannotated bacterial chromosomes, Bioinformatics, 16:566-567.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   greporiter Gets the positions of replication origin and terminus
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gfop.txt
--- a/GEMBASSY-1.0.3/doc/text/gfop.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,209 +0,0 @@
-                                      gfop
-Function
-
-   Calculate the frequency of optimal codons (Fop)
-
-Description
-
-   gfop calculates the frequency of optimal codons (Fop).Fop is an index to
-   show the optimization level of synonymous codon usage choice. It is
-   basically a ratio of optimal codons against all codons used. The value
-   of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal
-   codons are used).
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gfop
-
-% gfop refseqn:NC_000913
-Calculate the frequency of optimal codons (Fop)
-Codon usage output file [nc_000913.gfop]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gfop] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translates using standard
-                                  codon table
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gfop reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gfop is to a plain text file.
-
-   File: nc_000913.gfop
-
-Sequence: NC_000913
-Laa,Lc,fop,gene
-20,5,0.4000,thrL
-819,133,0.4361,thrA
-309,46,0.4783,thrB
-427,69,0.5217,thrC
-97,7,0.2857,yaaX
-257,56,0.4643,yaaA
-475,96,0.3958,yaaJ
-316,56,0.6964,talB
-
-   [Part of this file has been deleted for brevity]
-
-169,27,0.2593,yjjX
-214,23,0.5652,ytjC
-288,49,0.4082,rob
-156,23,0.3478,creA
-228,26,0.3462,creB
-473,69,0.3478,creC
-449,70,0.3286,creD
-237,46,0.6957,arcA
-45,10,0.7000,yjjY
-227,24,0.2500,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
-      transfer RNAs and the occurrence of the respective codons in its protein
-      genes: a proposal for a synonymous codon choice that is optimal for the
-      E. coli translational system, J.Mol.Biol, 151:389-409.
-
-   Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
-      organisms, Mol.Biol.Evol, 2(1):13-34.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   genc    Calculate the effective number of codons (Nc)
-   gew     Calculate a measure of synonymous codon usage evenness (Ew)
-   gscs    Calculates the scaled chi-square
-   gwvalue Calculate the 'relative adaptiveness of each codon' (W)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/ggcsi.txt
--- a/GEMBASSY-1.0.3/doc/text/ggcsi.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,204 +0,0 @@
-                                     ggcsi
-Function
-
-   GC Skew Index: an index for strand-specific mutational bias
-
-Description
-
-   ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial
-   genome. GCSI quantifies the degree of GC Skew. In other words, this index
-   represents the degree of strand-specific mutational bias in bacterial
-   genomes, caused by replicational selection.
-   GCSI is calculated by the following formula:
-
-      GCSI = sqrt((SA/6000) * (dist/600))
-
-   where SA is the spectral amplitude of Fourier power spectrum at 1Hz,
-   and dist is the normalized Euclidean distance between the vertices of
-   cumulative GC skew.
-
-   GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal
-   genomes that have multiple replication origins and therefore have no
-   observable skew mostly have GCSI below 0.05. Escherichia coli genome has
-   values around 0.10.
-
-   Version 1 of GCSI required fixed number of windows (4096), but the new GCSI
-   version 2 (also known as generalized GCSI: gGCSI) is invariant of the number
-   of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed
-   to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise
-   ratio of 1Hz power spectrum) and dist.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with ggcsi
-
-% ggcsi refseqn:NC_000913
-GC Skew Index: an index for strand-specific mutational bias
-Program compseq output file [nc_000913.ggcsi]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.ggcsi] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -gcsi               selection  [2] GCSI version to use
-   -window             integer    [4096] Number of windows. Must be a power of
-                                  2 (Any integer value)
-   -purine             boolean    [N] Use purine skew for calculation
-   -keto               boolean    [N] Use keto skew for calculation
-   -at                 boolean    [N] Use AT skew for calculation
-   -pval               boolean    [N] Calculate p-value when GCSI version 2 is
-                                  selected
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   ggcsi reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggcsi is to a plain text file.
-
-   File: nc_000913.ggcsi
-
-Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gb1          Calculate strand bias of bacterial genome using B1 index
-   gb2          Calculate strand bias of bacterial genome using B2 index
-   gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
-                index
-   gldabias     Calculate strand bias of bacterial genome using linear
-                discriminant analysis (LDA)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/ggcskew.txt
--- a/GEMBASSY-1.0.3/doc/text/ggcskew.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,231 +0,0 @@
-                                    ggcskew
-Function
-
-   Calculates the GC skew of the input sequence
-
-Description
-
-   ggcskew calculates and plots the GC skew of the given sequence. The "skew"
-   of a sequence is calculated as (C-G)/(C+G) in GC skew. The program can
-   alternatively calculate AT skew, purine skew, and keto skew, as well as
-   cumulative skew. GC skew is used to observe various biological aspects
-   such as prediction of replication origin and terminus in bacteria.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with ggcskew
-
-% ggcskew refseqn:NC_000913
-Calculates the GC skew of the input sequence
-Program compseq output file (optional) [nc_000913.ggcskew]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% ggcskew refseqn:NC_000913 -plot -graph png
-Calculates the GC skew of the input sequence
-Created ggcskew.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.ggcskew] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -window             integer    [10000] Window size to observe (Any integer
-                                  value)
-   -slide              integer    [10000] Window slide size (Any integer
-                                  value)
-   -cumulative         boolean    [N] Include to calculate cumulative skew
-   -at                 boolean    [N] Include for observing AT skew instead of
-                                  GC skew
-   -purine             boolean    [N] Include for observing purine (AG/TC)
-                                  skew
-   -keto               boolean    [N] Include for observing keto (TG/AC) skew
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   ggcskew reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggcskew is to a plain text file or the EMBOSS graphics
-   device.
-
-   File: nc_000913.ggcskew
-
-Sequence: NC_000913
-location,GC skew
-0,-0.035529
-10000,-0.039648
-20000,-0.049791
-30000,0.005072
-40000,-0.063483
-50000,-0.030256
-60000,0.011875
-70000,-0.029478
-
-   [Part of this file has been deleted for brevity]
-
-4530000,-0.017164
-4540000,-0.036140
-4550000,-0.028166
-4560000,0.012166
-4570000,-0.040486
-4580000,-0.020692
-4590000,-0.043920
-4600000,-0.026363
-4610000,-0.022778
-4620000,-0.049396
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   ggcwin       Calculates the GC content along the given genome
-   ggeneskew    Calculate the gene strand bias of the given genome
-   ggenomicskew Calculates the GC skew in different regions of the given genom
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/ggcwin.txt
--- a/GEMBASSY-1.0.3/doc/text/ggcwin.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,224 +0,0 @@
-                                     ggcwin
-Function
-
-   Calculates the GC content along the given genome
-
-Description
-
-   ggcwin calculates and plots the GC content of the given sequence.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with ggcwin
-
-% ggcwin refseqn:NC_000913
-Calculates the GC content along the given genome
-Program compseq output file (optional) [nc_000913.ggcwin]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% ggcwin refseqn:NC_000913 -plot -graph png
-Calculates the GC content along the given genome
-Created ggcwin.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.ggcwin] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -window             integer    [10000] Window size to observe (Any integer
-                                  value)
-   -at                 boolean    [N] Include for observing AT skew instead of
-                                  GC skew
-   -purine             boolean    [N] Include for observing purine (AG/TC)
-                                  skew
-   -keto               boolean    [N] Include for observing keto (TG/AC) skew
-                                  default: "0
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   ggcwin reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggcwin is to a plain text file or the EMBOSS graphics device.
-
-   File: nc_000913.ggcwin
-
-Sequence: NC_000913
-location,GC content
-0,0.520700
-10000,0.499400
-20000,0.526200
-30000,0.532300
-40000,0.527700
-50000,0.515600
-60000,0.555800
-70000,0.536000
-
-   [Part of this file has been deleted for brevity]
-
-4530000,0.442800
-4540000,0.487000
-4550000,0.507700
-4560000,0.509600
-4570000,0.444600
-4580000,0.531600
-4590000,0.512300
-4600000,0.504500
-4610000,0.535600
-4620000,0.546600
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   ggcskew      Calculates the GC skew of the input sequence
-   ggeneskew    Calculate the gene strand bias of the given genome
-   ggenomicskew Calculates the GC skew in different regions of the given genom
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/ggeneskew.txt
--- a/GEMBASSY-1.0.3/doc/text/ggeneskew.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,232 +0,0 @@
-                                   ggeneskew
-Function
-
-   Calculate the gene strand bias of the given genome
-
-Description
-
-   ggeneskew calculates and plots the strand bias of genes (or the GC skew
-   within them). By default, this program visualizes the gene strand preference
-   (1 for direct, -1 for complement strand), but by specifying -base option
-   option, GC/AT/Purine/Keto skews of the coding regions or more specifically
-   in the GC3 (third codon position) with -gctri option can be calculated.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with ggeneskew
-
-% ggeneskew refseqn:NC_000913
-Calculate the gene strand bias of the given genome
-Program compseq output file (optional) [nc_000913.ggeneskew]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% ggeneskew refseqn:NC_000913 -plot -graph png
-Calculate the gene strand bias of the given genome
-Created ggeneskew.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.ggeneskew] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -window             integer    [10000] Window size to observe (Any integer
-                                  value)
-   -slide              integer    [10000] Window slide size (Any integer
-                                  value)
-   -cumulative         boolean    [N] Input 1 to calculate cumulative skew
-   -base               selection  [none] Input 'gc', 'at', 'purine', or 'keto'
-                                  for observing GC/AT/Purine/Keto skews
-   -gctri              boolean    [N] Include to use only the third codon
-                                  positions
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   ggeneskew reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggeneskew is to a plain text file or the EMBOSS graphics
-   device.
-
-   File: nc_000913.ggeneskew
-
-Sequence: NC_000913
-location,gene None skew
-190,0.294118
-337,-0.058914
-2801,-0.120000
-3734,-0.070588
-5234,0.037500
-5683,0.020725
-6529,0.032765
-8238,-0.028226
-
-   [Part of this file has been deleted for brevity]
-
-4631820,-0.093407
-4632464,-0.006479
-4633544,-0.120690
-4634030,-0.060367
-4634719,-0.104167
-4636201,-0.144560
-4637613,0.010929
-4638425,0.200000
-4638965,-0.081871
-,
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   ggcskew      Calculates the GC skew of the input sequence
-   ggcwin       Calculates the GC content along the given genome
-   ggenomicskew Calculates the GC skew in different regions of the given genom
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/ggenomemap3.txt
--- a/GEMBASSY-1.0.3/doc/text/ggenomemap3.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,173 +0,0 @@
-                                  ggenomemap3
-Function
-
-   Draws the map of the genome (version 3)
-
-Description
-
-   ggenomemap3 creates a map of the genome, showing the local nucleotide
-   contents and positions of genes. A is shown in red, T is shown in green,
-   G is shown in yellow, and C is shown in blue.
-   Created image has a resolution of 8192x8192 and is suited for conversion
-   to SVG, which can be performed by specifying the -format option. The formats
-   available are dependent to the "convert" command from ImageMagick.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with ggenomemap3
-
-% ggenomemap3 refseqn:NC_000913
-Draws the map of the genome (version 3)
-Created ggenomemap3.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [png] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -width              integer    [8192] Image width (Any integer value)
-   -height             integer    [8192] Image height (Any integer value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -goutfile           string     [ggenomemap3] Output file for non
-                                  interactive displays (Any string)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   ggenomemap3 reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggenomemap3 is to an image file.
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcircularmap Draws circular map of the genome
-   gdnawalk     Draws DNA Walk map of the genome
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/ggenomicskew.txt
--- a/GEMBASSY-1.0.3/doc/text/ggenomicskew.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,225 +0,0 @@
-                                  ggenomicskew
-Function
-
-   Calculates the GC skew in different regions of the given genome
-
-Description
-
-   ggenomicskew calculates and plots the GC skew for the whole genome, coding
-   regions, intergenic regions, and the third codon. This program is useful in
-   visualizing various base composition bias within the genome. AT skew can be
-   calculated instead of GC skew by toggling the -at qualifier.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with ggenomicskew
-
-% ggenomicskew refseqn:NC_000913
-Calculates the GC skew in different regions of the given genome
-Program compseq output file (optional) [nc_000913.ggenomicskew]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% ggenomicskew refseqn:NC_000913 -plot -graph png
-Calculates the GC skew in different regions of the given genome
-Created ggenomicskew.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.ggenomicskew] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -divide             integer    [250] Window to divide into (Any integer
-                                  value)
-   -at                 boolean    [N] Input 1 when observing AT skew instead
-                                  of GC skew
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   ggenomicskew reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.
-
-   File: nc_000913.ggenomicskew
-
-Sequence: NC_000913
-location,GC skew,coding,intergenic,third codon
-0,-0.036259,-0.040085,-0.034707,-0.141888,
-1,-0.031167,-0.035657,0.047953,-0.175758,
-2,-0.028670,-0.031139,-0.049143,-0.018466,
-3,-0.016647,-0.004656,-0.102616,0.086181,
-4,-0.041985,-0.029846,-0.088670,0.015291,
-5,-0.097093,-0.103813,-0.067275,-0.247401,
-6,-0.028028,-0.016363,-0.048806,-0.047332,
-7,-0.055805,-0.059329,-0.020071,-0.123271,
-
-   [Part of this file has been deleted for brevity]
-
-241,0.000772,-0.012151,-0.063786,0.069585,
-242,-0.025787,-0.000384,-0.049143,0.029431,
-243,0.010516,0.008217,-0.030600,0.128657,
-244,-0.037115,-0.015134,0.017500,0.035398,
-245,-0.000317,0.006021,-0.047170,0.091549,
-246,-0.025417,-0.015190,-0.116608,0.044619,
-247,-0.038404,-0.035676,-0.135714,0.015375,
-248,-0.026246,-0.024240,-0.037190,-0.130118,
-249,-0.053371,-0.057225,-0.022472,-0.082167,
-250,-0.026316,0.166667,-0.151515,0.000000,
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   ggcskew   Calculates the GC skew of the input sequence
-   ggcwin    Calculates the GC content along the given genome
-   ggeneskew Calculate the gene strand bias of the given genome
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gicdi.txt
--- a/GEMBASSY-1.0.3/doc/text/gicdi.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,210 +0,0 @@
-                                     gicdi
-Function
-
-   Calculates the intrinsic codon deviation index (ICDI)
-
-Description
-
-   gicdi calculates the intrinsic codon deviation index (ICDI). ICDI is a
-   measure to estimate codon bias of genes from species in which optimal
-   codons are not known. It is known to show high correlation with other
-   indices such as CBI and ENC. A gene using only one codon for each amino
-   acid will have an ICDI of 1, and a gene using every codon equally for
-   each amino acid will have an ICDI of 0.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gicdi
-
-% gicdi refseqn:NC_000913
-Calculates the intrinsic codon deviation index (ICDI)
-Codon usage output file [nc_000913.gicdi]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gicdi] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translating using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gicdi reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gicdi is to a plain text file.
-
-   File: nc_000913.gicdi
-
-Sequence: NC_000913
-icdi,gene
-0.8192,thrL
-0.1258,thrA
-0.1127,thrB
-0.1689,thrC
-0.3099,yaaX
-0.2030,yaaA
-0.1600,yaaJ
-0.3533,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.2203,yjjX
-0.2719,ytjC
-0.1377,rob
-0.2647,creA
-0.1944,creB
-0.1733,creC
-0.1926,creD
-0.2728,arcA
-0.5171,yjjY
-0.2434,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
-      usage bias, J Mol Evol, 47(3):268-74.
-
-   Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in
-      yeast cytochrome c-encoding genes, Gene, 139:43-49.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcbi      Calculates the codon bias index (CBI)
-   gdeltaenc Calculate the codon usage bias related to translation optimization
-             (delta ENC)
-   gsvalue   Calculate the strength of selected codon usage bias (S)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gkmertable.txt
--- a/GEMBASSY-1.0.3/doc/text/gkmertable.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,187 +0,0 @@
-                                   gkmertable
-Function
-
-   Create an image showing all k-mer abundance within a sequence
-
-Description
-
-   gkmertable creates an image showing the abundance of all k-mers
-   (oligonucleotides of length k) in a given sequence. For example, for
-   tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each
-   representing an oligomer. Oligomer name and abundance is written within
-   these boxes, and abundance is also visualized with the box color, from
-   white (none) to black (highly frequent).
-
-   This k-mer table is alternatively known as the FCGR (frequency matrices
-   extracted from Chaos Game Representation).
-   Position of the oligomers can be recursively located as follows:
-   For each letter in an oligomer, a box is subdivided into four quadrants,
-   where A is upper left, T is lower right, G is upper right, and C is lower
-   left.
-
-   Therefore, oligomer ATGC is in the
-   A = upper left quadrant
-   T = lower right within the above quadrant
-   G = upper right within the above quadrant
-   C = lower left within the above quadrant
-   More detailed documentation is available at
-   http://www.g-language.org/wiki/cgr
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gkmertable
-
-% gkmertable refseqn:NC_000913
-Create an image showing all k-mer abundance within a sequence
-Created gkmertable.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [png] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -k                  integer    [6] Length of oligomer (Any integer value)
-   -goutfile           string     [gkmertable] Output file for non interactive
-                                  displays (Any string)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gkmertable reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gkmertable is to an image file.
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
-   goligomercounter       Counts the number of given oligomers in a sequence
-   goligomersearch        Searches oligomers in given sequence
-   gsignature             Calculate oligonucleotide usage (genomic signature)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gldabias.txt
--- a/GEMBASSY-1.0.3/doc/text/gldabias.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,194 +0,0 @@
-                                    gldabias
-Function
-
-   Calculate strand bias of bacterial genome using linear discriminant
-
-Description
-
-   gldabias calculates strand bias of bacterial genome using linear
-   discriminant analysis (LDA), as proposed in Reference 1. The basic idea is
-   to use composition data of genes to train and predict the strand of genes
-   residing either on the leading or the lagging strand. For computational
-   efficiency, this method trans and predicts the strands at putative
-   replication origin as reported by the rep_ori_ter() method. This usually
-   results in maximum predictability of LDA within bacterial genomes.
-   Data to use for LDA can be chosen from "base", "codonbase", "codon", and
-   "amino", with -variable option.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gldabias
-
-% gldabias refseqn:NC_000913
-Calculate strand bias of bacterial genome using linear discriminant
-analysis (LDA)
-Program compseq output file [nc_000913.gldabias]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-Calculate strand bias of bacterial genome using linear discriminant
-analysis (LDA)
-Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gldabias] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -coefficients       integer    [0] Show LDA coefficients (Any integer
-                                  value)
-   -variable           selection  [codon] Data to use for LDA. Either 'base',
-                                  'codonbase', 'codon', or 'amino'
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gldabias reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gldabias is to a plain text file.
-
-   File: nc_000913.gldabias
-
-Sequence: NC_000913 LDA-BIAS: 0.742533
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Rocha EPC et al. (1999) "Universal replication biases in bacteria",
-      Molecular Microbiology, 32(1):11-16
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gb1          Calculate strand bias of bacterial genome using B1 index
-   gb2          Calculate strand bias of bacterial genome using B2 index
-   gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
-                index
-   ggcsi        GC Skew Index: an index for strand-specefic mutational bias
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gnucleotideperiodicity.txt
--- a/GEMBASSY-1.0.3/doc/text/gnucleotideperiodicity.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,228 +0,0 @@
-                             gnucleotideperiodicity
-Function
-
-   Checks the periodicity of certain oligonucleotides
-
-Description
-
-   gnucleotideperiodicity checks the periodicity of certain nucleotide
-   (best known with AA dinucleotide). Bacteria and archaebacteria are
-   known to show periodicity of ApA dinucleotides at about 11bp and 10bp.
-   Lower eukaryotes also show periodicity but higher eukaryotes do not.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gnucleotideperiodicity
-
-% gnucleotideperiodicity refseqn:NC_000913
-Checks the periodicity of certain oligonucleotides
-Program compseq output file (optional) [nc_000913.gnucleotideperiodicity]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% gnucleotideperiodicity refseqn:NC_000913 -plot -graph png
-Checks the periodicity of certain oligonucleotides
-Created gnucleotideperiodicity.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.gnucleotideperiodicity] Program compseq
-                                  output file (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [png] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -window             integer    [50] Window size to seek periodicity (Any
-                                  integer value)
-   -nucleotide         string     [aa] Nucleotide to search (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gnucleotideperiodicity reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gnucleotideperiodicity is to a plain text file or the EMBOSS graphics device.
-
-   File: nc_000913.gnucleotideperiodicity
-
-Sequence: NC_000913
-window,value
-0,35134
-1,30121
-2,25409
-3,23508
-4,25830
-5,25136
-6,25658
-7,28279
-
-   [Part of this file has been deleted for brevity]
-
-40,28042
-41,25892
-42,25968
-43,28240
-44,25841
-45,25591
-46,27788
-47,25832
-48,25427
-49,0
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gkmertable       Create an image showing all k-mer abundance within a
-                    sequence
-   goligomercounter Counts the number of given oligomers in a sequence
-   goligomersearch  Searches oligomers in given sequence
-   gsignature       Calculate oligonucleotide usage (genomic signature)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/goligomercounter.txt
--- a/GEMBASSY-1.0.3/doc/text/goligomercounter.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,180 +0,0 @@
-                                goligomercounter
-Function
-
-   Counts the number of given oligomers in a sequence
-
-Description
-
-   goligomercounter counts the number of oligomers in a sequence (by windows
-   optionally). Oligomer can be specified using degenerate nucleotide alphabet,
-   or by regular expressions. k-mers can be counted by specifying the "-length"
-   qualifier.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with goligomercounter
-
-% goligomercounter refseqn:NC_000913 atgcatgc
-Counts the number of given oligomers in a sequence
-Program compseq output file [nc_000913.goligomercounter]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-oligomer]          string     Oligomer to count (Any string)
-  [-outfile]           outfile    [*.goligomercounter] Program compseq output
-                                  file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -window             integer    [0] Int window size (Any integer value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory3        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   goligomercounter reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from goligomercounter is to a plain text file.
-
-   File: nc_000913.goligomercounter
-
-Sequence: NC_000913 Oligomer: atgcatgc Number: 27
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gkmertable             Create an image showing all k-mer abundance within a
-                          sequence
-   gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
-   goligomersearch        Searches oligomers in given sequence
-   gsignature             Calculate oligonucleotide usage (genomic signature)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/goligomersearch.txt
--- a/GEMBASSY-1.0.3/doc/text/goligomersearch.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,186 +0,0 @@
-                                goligomersearch
-Function
-
-   Searches oligomers in given sequence
-
-Description
-
-   goligomersearch searches for the given oligomer in given sequence. Oligomer
-   can be specified using degenerate nucleotide alphabet, or by regular
-   expressions. Performance is optimized for fast searching.
-   This method changes the returning value according to the given options.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with goligomersearch
-
-% goligomersearch refseqn:NC_000913 atgcatgc
-Searches oligomers in given sequence
-Program compseq output file [nc_000913.goligomersearch]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-oligomer]          string     Oligomer to search (Any string)
-  [-outfile]           outfile    [*.goligomersearch] Program compseq output
-                                  file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -return             selection  [position] 'position' to return list of
-                                  positions where oligomers are found, 'oligo'
-                                  to return list of oligomers found ordered
-                                  by positions, 'both' to return a hash with
-                                  positions as keys and oligomers as values,
-                                  'distribution' to return four values about
-                                  the distribution of given oligomer
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory3        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   goligomersearch reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from goligomersearch is to a plain text file.
-
-   File: nc_000913.goligomersearch
-
-Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gkmertable             Create an image showing all k-mer abundance within a
-                          sequence
-   gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
-   goligomercounter       Counts the number of given oligomers in a sequence
-   gsignature             Calculate oligonucleotide usage (genomic signature)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gp2.txt
--- a/GEMBASSY-1.0.3/doc/text/gp2.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,201 +0,0 @@
-                                      gp2
-Function
-
-   Calculate the P2 index of each gene
-
-Description
-
-   gp2 calculates the P2 index for each gene. This index describes
-   the proportion of codons conforming to the intermediate strength of
-   codon-anticodon interaction energy rule of Grosjean and Fiers:
-   P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.
-   It indicates the efficiency of the codon-anticodon interaction, and has
-   been used as an indicator of the presence of translational selection.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gp2
-
-% gp2 refseqn:NC_000913
-Calculate the P2 index of each gene
-Codon usage output file [nc_000913.gp2]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gp2] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gp2 reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gp2 is to a plain text file.
-
-   File: nc_000913.gp2
-
-Sequence: NC_000913
-P2,gene
-0.4444,thrL
-0.4234,thrA
-0.4565,thrB
-0.5156,thrC
-0.4074,yaaX
-0.4494,yaaA
-0.3621,yaaJ
-0.6832,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.3692,yjjX
-0.4912,ytjC
-0.4271,rob
-0.4318,creA
-0.3065,creB
-0.3851,creC
-0.4320,creD
-0.6395,arcA
-0.7857,yjjY
-0.3333,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene
-      expressivity, Nucleic Acids Res, 10(22):7055-74.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcai Calculate codon adaptation index for each gene
-   gphx Identify predicted highly expressed gene
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gpalindrome.txt
--- a/GEMBASSY-1.0.3/doc/text/gpalindrome.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,201 +0,0 @@
-                                  gpalindrome
-Function
-
-   Searches palindrome sequences
-
-Description
-
-   gpalindrome searches for palindrome sequences in the genome.
-   Search parameters can be changed for more efficient searches, and g-t
-   matching can be specified by passing the "-gtmatch" qualifier.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gpalindrome
-
-% gpalindrome refseqn:NC_000913
-Searches palindrome sequences
-Program compseq output file [nc_000913.gpalindrome]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gpalindrome] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -shortest           integer    [4] Shortest palindrome to search (Any
-                                  integer value)
-   -loop               integer    [0] Longest stem loop to allow (Any integer
-                                  value)
-   -gtmatch            boolean    [0] If 1, allows g-t match
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gpalindrome reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gpalindrome is to a plain text file.
-
-   File: nc_000913.gpalindrome
-
-Sequence: NC_000913
-Length, start, end, sequence
-4,16,18,tg  ca
-4,27,29,at  at
-4,44,46,tt  aa
-4,67,69,ag  ct
-4,97,99,aa  tt
-4,99,101,tt  aa
-10,100,108,taaaa  tttta
-4,132,134,tt  aa
-
-   [Part of this file has been deleted for brevity]
-
-4,4639484,4639486,tg  ca
-6,4639487,4639491,aag  ctt
-4,4639495,4639497,cg  cg
-4,4639506,4639508,ca  tg
-6,4639552,4639556,gtc  gac
-4,4639607,4639609,tg  ca
-4,4639619,4639621,tg  ca
-4,4639621,4639623,ca  tg
-4,4639625,4639627,at  at
-4,4639637,4639639,at  at
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gconsensus_z Calculate consensus in given array of sequences
-   gdist_in_cc  Calculates the distance between two loci in circular chromosomes
-   gseqinfo     Prints out basic nucleotide sequence statistics
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gphx.txt
--- a/GEMBASSY-1.0.3/doc/text/gphx.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,211 +0,0 @@
-                                      gphx
-Function
-
-   Identify predicted highly expressed gene
-
-Description
-
-   gphx calculates codon usage differences between gene classes for identifying
-   Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is
-   identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's
-   nature. PHX genes are known to generally have favorable codon usage, strong
-   SD sequences, and probably stronger conservation of promoter sequences.
-   A gene is idenfitied as PA if BgC and BgH is greater than the median of
-   BgC for every gene with a length close to the gene.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gphx
-
-% gphx refseqn:NC_000913
-Identify predicted highly expressed gene
-Codon usage output file [nc_000913.gphx]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gphx] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translating using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gphx reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gphx is to a plain text file.
-
-   File: nc_000913.gphx
-
-Sequence: NC_000913
-BgC,BgH,E_g,phx,pa,gene
-0.8070,0.8977,0.8990,0,1,thrL
-0.1857,0.5958,0.3116,0,0,thrA
-0.2323,0.5964,0.3896,0,0,thrB
-0.2353,0.6064,0.3881,0,0,thrC
-0.4353,0.6020,0.7231,0,1,yaaX
-0.2961,0.6790,0.4361,0,0,yaaA
-0.2233,0.7009,0.3186,0,0,yaaJ
-0.4149,0.3071,1.3511,1,0,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.3255,0.7038,0.4625,0,0,yjjX
-0.3531,0.5906,0.5979,0,0,ytjC
-0.2257,0.5235,0.4311,0,0,rob
-0.3584,0.6809,0.5264,0,0,creA
-0.3455,0.7950,0.4346,0,0,creB
-0.2298,0.7154,0.3212,0,0,creC
-0.3299,0.7916,0.4167,0,0,creD
-0.3543,0.3786,0.9357,0,0,arcA
-0.7295,0.8286,0.8804,0,1,yjjY
-0.4028,0.8401,0.4795,0,0,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm
-
-   Henry I., Sharp PM. (2007) Predicting gene expression level from codon
-      usage bias Mol Biol Evol, 24(1):10-2.
-
-   Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse
-      prokaryotic genomes J.Bacteriol, 182(18):5238-5250.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcai Calculate codon adaptation index for each gene
-   gp2  Calculate the P2 index of each gene
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gqueryarm.txt
--- a/GEMBASSY-1.0.3/doc/text/gqueryarm.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,173 +0,0 @@
-                                   gqueryarm
-Function
-
-   Get the replication arm name (left or right) from the given position
-
-Description
-
-   gqueryarm returns whether the given position is in the left or right arm of
-   a circular chromosome.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gqueryarm
-
-% gqueryarm refseqn:NC_000913 1234
-Get the replication arm name (left or right) from the given position
-Output file [nc_000913.gqueryarm]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-position]          integer    [0] Position to query (Any integer value)
-  [-outfile]           outfile    [*.gqueryarm] Output file name
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory3        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gqueryarm reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gqueryarm is to a plain text file.
-
-   File: nc_000913.gqueryarm
-
-Sequence: NC_000913 Arm: right
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gquery_strand Get the strand name (leading or lagging) from the given
-                 position
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gquerystrand.txt
--- a/GEMBASSY-1.0.3/doc/text/gquerystrand.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,175 +0,0 @@
-                                  gquerystrand
-Function
-
-   Get the strand name (leading or lagging) from the given position
-
-Description
-
-   gquerystrand returns whether the given position is in the leading or lagging
-   strand of a circular chromosome.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gquerystrand
-
-% gquerystrand refseqn:NC_000913 1234
-Get the strand name (leading or lagging) from the given position
-Output file [nc_000913.gquerystrand]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-position]          integer    [0] Position to query (Any integer value)
-  [-outfile]           outfile    [*.gquerystrand] Output file name
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -direction          selection  [direct] Strand of the querying position
-                                  either 'direct' or 'complement'
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory3        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gquerystrand reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gquerystrand is to a plain text file.
-
-   File: nc_000913.gquerystrand
-
-Sequence: NC_000913 Strand: leading
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gquery_arm    Get the replication arm name (left or right) from the given
-                 position
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/greporiter.txt
--- a/GEMBASSY-1.0.3/doc/text/greporiter.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,210 +0,0 @@
-                                   greporiter
-Function
-
-   Get the positions of replication origin and terminus
-
-Description
-
-   greporiter returns the positions of replication origin and terminus
-   in bacterial genomes by several means.
-
-   1. Use of databases
-   By default, grep_ori_ter tries to retrieve the position of replication
-   origin in DoriC Gao and Zhang (2007) database, and the position of
-   replication terminus from the supplemental data provided in
-   Kono et al. (2011).
-   If the position of origin cannot be found in the database, but "rep_origin"
-   feature is available, center position within this feature is used for
-   origin.
-
-   2. Oriloc
-   Using -orilocoption, you can predict the replication origin and
-   terminus using the popular Oriloc program developed by Lobry et al.
-   available as part of the SeqinR package Frank and Lobry (2000).
-
-   3. Use GC skew shift-point
-   If the positions of origin or terminus cannot be found in the databases,
-   grep_ori_ter automatically calls find_ori_ter() method to predict the
-   positions using GC skew shift-points at one-base-pair resolution.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with greporiter
-
-% greporiter refseqn:NC_000913
-Get the positions of replication origin and terminus
-Output file [nc_000913.greporiter]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.greporiter] Output file name
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -oriloc             boolean    [N] Include Oriloc for prediction
-   -gcskew             boolean    [N] Include to use GC skew shift-point for
-                                  prediction
-   -difthreshold       integer    [0] Distance between the GC skew shift point
-                                  and predicted dif site expressed as the
-                                  precentage of genome size, used as a
-                                  threshold to retrieve dif sequence from the
-                                  database (Any integer value)
-   -dbonly             boolean    [N] Include to only use values available in
-                                  databases and to suppress prediction
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   greporiter reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from greporiter is to a plain text file.
-
-   File: nc_000913.greporiter
-
-Sequence: NC_000913 Origin: 3923881 Terminus: 1550412
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial
-      genomes, Bioinformatics, 23(14):1866-1867
-
-   Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution
-      sites in bacterial genomes, BMC Genomics, 12(1):19
-
-   Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries
-      in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gfindoriter Predicts the replication origin and terminus in bacterial
-               genomes
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gscs.txt
--- a/GEMBASSY-1.0.3/doc/text/gscs.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,211 +0,0 @@
-                                      gscs
-Function
-
-   Calculates the scaled chi-square
-
-
-Description
-
-   gscs calculates the Scaled Chi Square (SCS) of each gene. Values of SCS
-   are calculated using completely synonymous codon usage as the expectation
-   and then scaled by dividing the value by the number of codons in the gene
-   excluding Trp and Met.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gscs
-
-% gscs refseqn:NC_000913
-Calculates the scaled chi-square
-Codon usage output file [nc_000913.gscs]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gscs] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translates using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (i.e. amino acids
-                                  and nucleotides) (Any string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gscs reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gscs is to a plain text file.
-
-   File: nc_000913.gscs
-
-Sequence: NC_000913
-scs,gene
-1.4458,thrL
-0.3122,thrA
-0.2551,thrB
-0.4104,thrC
-0.3084,yaaX
-0.3230,yaaA
-0.2957,yaaJ
-0.7101,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.3054,yjjX
-0.4076,ytjC
-0.4231,rob
-0.3903,creA
-0.3472,creB
-0.2695,creC
-0.3500,creD
-0.5077,arcA
-0.4576,yjjY
-0.2926,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Comeron JM., Aguade M. (1998) An evaluation of measures of synonymous
-      codon usage bias, J Mol Evol, 47(3):268-74.
-
-   Shields DC, Sharp PM. (1987) Synonymous codon usage in Bacillus subtilis
-      reflects both translational selection and mutational biases,
-      15(19):8023-40.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   genc     Calculate the effective number of codons (Nc)
-   gew      Calculate a measure of synonymous codon usage evenness (Ew)
-   gfop     Calculate the frequency of optimal codons (Fop)
-   gw_value Calculate the 'relative adaptiveness of each codon' (W)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gseq2png.txt
--- a/GEMBASSY-1.0.3/doc/text/gseq2png.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,170 +0,0 @@
-                                    gseq2png
-Function
-
-   Converts a sequence to PNG image
-
-Description
-
-   gseq2png converts a sequence to a png image, by representing nucleotide
-   sequences with representative pixels. A is shown in red, T is shown in
-   green, G is shown in yellow, and C is shown in blue.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gseq2png
-
-% gseq2png refseqn:NC_000913
-Converts a sequence to PNG image
-Created gseq2png.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -format             string     [png] Output file format. Dependent on
-                                  'convert' command (Any string)
-   -width              integer    [640] Width of the image (Any integer value)
-   -window             integer    [20] Window size of a sequence to represent
-                                  each pixel (Any integer value)
-   -goutfile           string     [gcgr] Output file for non interactive
-                                  displays (Any string)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gseq2png reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gseq2png is to an image file.
-
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcgr Create a Chaos Game Representation of a given sequence
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gseqinfo.txt
--- a/GEMBASSY-1.0.3/doc/text/gseqinfo.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,170 +0,0 @@
-                                    gseqinfo
-Function
-
-   Prints out basic nucleotide sequence statistics
-
-Description
-
-   gseqinfo prints out basic nucleotide sequence statistics of the given
-   nucleotide sequence. It returns the number of A, T, G, and C bases.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gseqinfo
-
-% gseqinfo refseqn:NC_000913
-Prints out basic nucleotide sequence statistics
-Program compseq output file [nc_000913.gseqinfo]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gseqinfo] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers: (none)
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gseqinfo reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gseqinfo is to a plain text file.
-
-   File: nc_000913.gseqinfo
-
-Sequence: NC_000913 A: 1142228 T: 1140970 G: 1176923 C: 1179555
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gconsensus_z Calculate consensus in given array of sequences
-   gdist_in_cc  Calculates the distance between two loci in circular chromosomes
-   gpalindrome  Searches palindrome sequences
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gshuffleseq.txt
--- a/GEMBASSY-1.0.3/doc/text/gshuffleseq.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,208 +0,0 @@
-                                  gshuffleseq
-Function
-
-   Create randomized sequence with conserved k-mer composition
-
-Description
-
-   gshuffleseq shuffles and randomizes the given sequence, conserving the
-   nucleotide/peptide k-mer content of the original sequence.
-
-   For k=1, i.e. shuffling sequencing preserving single nucleotide composition,
-   Fisher-Yates Algorithm is employed.
-   For k>1, shuffling preserves all k-mers (all k where k=1~k). For example,
-   k=3 preserves all triplet, doublet, and single nucleotide composition.
-   Algorithm for k-mer preserved shuffling is non-trivial, which is solved
-   by graph theoretical approach with Eulerian random walks in the graph of
-   k-1-mers. See Jiang et al., Kandel et al., and Propp et al., for details
-   of this algorithm.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gshuffleseq
-
-% gshuffleseq tsw:hbb_human
-Create randomized sequence with conserved k-mer composition
-output sequence [hbb_human.fasta]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Sequence(s) filename and optional format, or
-                                  reference (input USA)
-  [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
-                                  optional format (output USA)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -k                  integer    [1] Sequence k-mer to preserve composition
-                                  (Any integer value)
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outseq" associated qualifiers
-   -osformat2          string     Output seq format
-   -osextension2       string     File name extension
-   -osname2            string     Base file name
-   -osdirectory2       string     Output directory
-   -osdbname2          string     Database name to add
-   -ossingle2          boolean    Separate file for each entry
-   -oufo2              string     UFO features
-   -offormat2          string     Features format
-   -ofname2            string     Features file name
-   -ofdirectory2       string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gshuffleseq reads one or more nucleotide or protein sequences.
-
-Output file format
-
-   The output from gshuffleseq is to .
-
-   File: hbb_human.fasta
-
->HBB_HUMAN P68871 Hemoglobin subunit beta (Beta-globin) (Hemoglobin beta chain) (LVV-hemorphin-7)
-KGWLDLVAGAAHFVRRLKMLLEVDWAAHEERVGTSNPNNALKNEAADVEVHSPTHVNPTQ
-LVLVQVGFGTLHLQGVECPKPKPGGVALKPVAHLLAMKECTLVALGSDFYVDHGSDGEDK
-GFKAYVLATSFFAYTNFLHGKVKHVLF
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Fisher R.A. and Yates F. (1938) "Example 12", Statistical Tables, London
-
-   Durstenfeld R. (1964) "Algorithm 235: Random permutation", CACM 7(7):420
-
-   Jiang M., Anderson J., Gillespie J., and Mayne M. (2008) "uShuffle:
-      a useful tool for shuffling biological sequences while preserving the
-      k-let counts", BMC Bioinformatics 9:192
-
-   Kandel D., Matias Y., Unver R., and Winker P. (1996) "Shuffling biological
-      sequences", Discrete Applied Mathematics 71(1-3):171-185
-
-   Propp J.G. and Wilson D.B. (1998) "How to get a perfectly random sample
-      from a generic Markov chain and generate a random spanning tree of a
-      directed graph", Journal of Algorithms 27(2):170-217
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   shuffleseq Shuffles a set of sequences maintaining composition
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gsignature.txt
--- a/GEMBASSY-1.0.3/doc/text/gsignature.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,188 +0,0 @@
-                                   gsignature
-Function
-
-   Calculate oligonucleotide usage (genomic signature)
-
-Description
-
-   gsignature calculates short oligonuleotide usage (genomic signture),
-   defined as the ratio of observed (O) to expected (E) oligonucleotide
-   frequencies. It is known that the genomic signature stays constant
-   throughout the genome.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gsignature
-
-% gsignature refseqn:NC_000913
-Calculate oligonucleotide usage (genomic signature)
-Program compseq output file [nc_000913.gsignature]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gsignature] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -wordlength         integer    [2] Word length (Any integer value)
-   -[no]bothstrand     boolean    [Y] Include to use both strands direct used
-                                  otherwise
-   -[no]oe             boolean    [Y] Include to use O/E value observed values
-                                  used otherwise
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gsignature reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gsignature is to a plain text file.
-
-   File: nc_000913.gsignature
-
-Sequence: NC_000913
-aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,memo
-1.206,0.884,0.817,1.103,1.117,0.905,1.159,0.817,0.922,1.283,0.905,0.884,0.755,0.922,1.117,1.206,
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Campbell A et al. (1999) Genome signature comparisons among prokaryote,
-      plasmid, and mitochondrial DNA, Proc Natl Acad Sci U S A. 96(16):9184-9.
-
-   Karlin S. (2001) Detecting anomalous gene clusters and pathogenicity islands
-      in diverse bacterial genomes, Trends Microbiol. 9(7):335-43.
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gkmer_table             Create an image showing all k-mer abundance within a                            sequence
-   gnucleotide_periodicity Checks the periodicity of certain oligonucleotides
-   goligomer_counter       Counts the number of given oligomers in a sequence
-   goligomer_search        Searches oligomers in given sequence
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gsvalue.txt
--- a/GEMBASSY-1.0.3/doc/text/gsvalue.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,195 +0,0 @@
-                                    gsvalue
-Function
-
-   Calculate the strength of selected codon usage bias (S)
-
-Description
-
-   gsvalue calculates the strength of selected codon usage bias (S), also
-   known as Sharp's S index. Using four codon pairs that are recognized by the
-   same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and
-   UAU), and Asn(AAC and AAU), since the former in each of the pairs has
-   stronger Watson-Crick pairing, selection towards the former codon can be
-   observed for highly expressed genes. S index is therefore the weighted
-   average of such bias, giving an over-all value for a genome, indicating its
-   strength of selected codon usage bias. See Sharp et al. (2005) for details.
-   Sharp originally defined 40 genes as the highly expressed gene group, with
-   tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton
-   of these genes is not convenient for computational automation, by default,
-   this method uses ribosomal proteins as the highly expressed gene group,
-   as used by Viera-silva and Rocha (2010).
-   However, Sharp's gene group can be optionally used with -sharp option.
-   With this option, all of the 40 genes must be named accordingly in the given
-   genome file.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gsvalue
-
-% gsvalue refseqn:NC_000913
-Calculate the strength of selected codon usage bias (S)
-Codon usage output file [nc_000913.gsvalue]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gsvalue] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -sharp              boolean    [N] Include to use the 40 genes used by
-                                  Sharp instead of ribosomal proteins
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gsvalue reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gsvalue is to a plain text file.
-
-   File: nc_000913.gsvalue
-
-Sequence: NC_000913 S-value: 1.23467100598485
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Sharp PM et al. (2005) "Variation in the strength of selected codon usage
-      bias among bacteria", Nucleic Acids Research, 33(4):1141-1153
-
-   Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its
-      uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gcbi       Calculates the codon bias index (CBI)
-   gdelta_enc Calculate the codon usage bias related to translation optimization              (delta ENC)
-   gicdi      Calculates the intrinsic codon deviation index (ICDI)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gviewcds.txt
--- a/GEMBASSY-1.0.3/doc/text/gviewcds.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,223 +0,0 @@
-                                    gviewcds
-Function
-
-   Displays a graph of nucleotide contents around start and stop codons
-
-Description
-
-   gviewcds creates a graph showing the average A,T,G,C contents
-   around start/stop codons. This is useful to view consensus around
-   start/stop codons and to find characteristic pattern in CDS.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gviewcds
-
-% gviewcds refseqn:NC_000913
-Displays a graph of nucleotide contents around start and stop codons
-Program compseq output file (optional) [nc_000913.gviewcds]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% gviewcds refseqn:NC_000913 -plot -graph png
-Displays a graph of nucleotide contents around start and stop codons
-Created gviewcds.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.gviewcds] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -length             integer    [100] Length in bases to show around
-                                  start/stop codons (Any integer value)
-   -gap                integer    [3] Gap shown in graph in between start/stop
-                                  codon neighbors (Any integer value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gviewcds reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gviewcds is to a plain text file or the EMBOSS graphics device.
-
-   File: nc_000913.gviewcds
-
-Sequence: NC_000913
-position,A,T,G,C
-1,28.20,27.60,22.18,22.02
-2,26.05,26.81,23.06,24.08
-3,27.34,27.37,23.94,21.35
-4,26.28,28.83,23.01,21.88
-5,26.72,28.22,22.18,22.88
-6,26.42,26.72,24.96,21.90
-7,27.21,28.66,21.95,22.18
-8,25.47,28.39,23.06,23.08
-
-   [Part of this file has been deleted for brevity]
-
-400,26.60,27.44,22.67,23.27
-401,24.38,26.63,25.05,23.92
-402,25.03,26.37,23.71,24.87
-403,25.96,27.53,22.53,23.96
-404,26.63,25.52,24.17,23.66
-405,25.68,26.26,23.50,24.54
-406,24.94,26.86,23.92,24.26
-407,25.54,26.28,23.73,24.43
-408,25.28,26.93,24.38,23.39
-409,26.63,26.46,22.32,24.57
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gbase_counter Creates a position weight matrix of oligomers around start                  codon
-   gbase_z_value Extracts conserved oligomers per position using Z-score
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/doc/text/gwvalue.txt
--- a/GEMBASSY-1.0.3/doc/text/gwvalue.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,219 +0,0 @@
-                                    gwvalue
-Function
-
-   Calculate the 'relative adaptiveness of each codon' (W)
-
-Description
-
-   gwvalue calculates the 'relative adaptiveness of each codon' (W value)
-   which is essential in CAI analysis. W value is calculated by setting the
-   best codon to 1 and calculating the proportion of the other codons.
-
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gwvalue
-
-% gwvalue refseqn:NC_000913
-Calculate the 'relative adaptiveness of each codon' (W)
-Codon usage output file [nc_000913.gwvalue]:
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.gwvalue] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -include            string     [ribosomal.*protein] Regular expression to
-                                  include genes in a reference set a reference
-                                  set in several studies are in-built 1:
-                                  Nakamura and Tabata, 2: Sharp and Li, 3:
-                                  Sakai et al. (Any string)
-   -exclude            string     [[Mm]itochondrial] Regular expression to
-                                  exclude genes from a reference set (Any
-                                  string)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-outfile" associated qualifiers
-   -odirectory2        string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gwvalue reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gwvalue is to a plain text file.
-
-   File: nc_000913.gwvalue
-
-Sequence: NC_000913
-Reference set of highly expressed genes
-product
-30S ribosomal subunit protein S20
-30S ribosomal subunit protein S2
-ribosomal protein S12 methylthiotransferase; radical SAM superfamily
-ribosomal protein S6 modification protein
-30S ribosomal subunit protein S1
-ribosomal-protein-S5-alanine N-acetyltransferase
-50S ribosomal subunit protein L32
-
-   [Part of this file has been deleted for brevity]
-
-T,acc,1.0000
-T,acg,0.2234
-T,act,0.9734
-V,gta,0.4960
-V,gtc,0.2281
-V,gtg,0.3422
-V,gtt,1.0000
-W,tgg,1.0000
-Y,tac,1.0000
-Y,tat,0.5310
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Sharp PM et al. (2005) Variation in the strength of selected codon usage
-      bias among bacteria, Nucleic Acids Res. 33(4):1141-1153
-
-   Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
-      conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.
-
-   Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
-      codon usage trends in seven microbial genomes, Microb.Comp.Genomics
-      2:299-312.
-
-   Sharp and Li (1987) The codon Adaptation Index--a measure of directional
-      synonymous codon usage bias, and its potential applications, Nucleic
-      Acids Res. 15:1281-1295.
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   genc Calculate the effective number of codons (Nc)
-   gew  Calculate a measure of synonymous codon usage evenness (Ew)
-   gfop Calculate the frequency of optimal codons (Fop)
-   gscs Calculates the scaled chi-square
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoap___a-dom_cpp.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoap___a-dom_cpp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,586 +0,0 @@\n-libgsoap___a-dom_cpp.o: dom_cpp.cpp stdsoap2.h ../config.h \\\n- /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \\\n- /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdarg.h \\\n- /usr/include/time.h /usr/include/_structs.h \\\n- /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \\\n- /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \\\n- /usr/include/_wctype.h /usr/include/_types/_wctype_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDef'..b'de.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/pthread.h:\n-\n-/usr/include/pthread_impl.h:\n-\n-/usr/include/sched.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_mach_port_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03:\n-\n-/usr/include/locale.h:\n-\n-/usr/include/_locale.h:\n-\n-/usr/include/xlocale.h:\n-\n-/usr/include/_xlocale.h:\n-\n-/usr/include/xlocale/_ctype.h:\n-\n-/usr/include/xlocale/__wctype.h:\n-\n-/usr/include/xlocale/_stdio.h:\n-\n-/usr/include/xlocale/_stdlib.h:\n-\n-/usr/include/xlocale/_string.h:\n-\n-/usr/include/xlocale/_time.h:\n-\n-/usr/include/xlocale/_wchar.h:\n-\n-/usr/include/xlocale/_wctype.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/streambuf:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/istream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ostream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/locale:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdlib:\n-\n-/usr/include/nl_types.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/_types/_nl_item.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/bitset:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n-\n-/usr/include/xlocale/_inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoap___a-stdsoap2_cpp.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoap___a-stdsoap2_cpp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,586 +0,0 @@\n-libgsoap___a-stdsoap2_cpp.o: stdsoap2_cpp.cpp stdsoap2.h ../config.h \\\n- /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \\\n- /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdarg.h \\\n- /usr/include/time.h /usr/include/_structs.h \\\n- /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \\\n- /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \\\n- /usr/include/_wctype.h /usr/include/_types/_wctype_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \\\n- /Applications/Xcode.app/Contents/Developer/Toolchain'..b'de.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/pthread.h:\n-\n-/usr/include/pthread_impl.h:\n-\n-/usr/include/sched.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_mach_port_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03:\n-\n-/usr/include/locale.h:\n-\n-/usr/include/_locale.h:\n-\n-/usr/include/xlocale.h:\n-\n-/usr/include/_xlocale.h:\n-\n-/usr/include/xlocale/_ctype.h:\n-\n-/usr/include/xlocale/__wctype.h:\n-\n-/usr/include/xlocale/_stdio.h:\n-\n-/usr/include/xlocale/_stdlib.h:\n-\n-/usr/include/xlocale/_string.h:\n-\n-/usr/include/xlocale/_time.h:\n-\n-/usr/include/xlocale/_wchar.h:\n-\n-/usr/include/xlocale/_wctype.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/streambuf:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/istream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ostream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/locale:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdlib:\n-\n-/usr/include/nl_types.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/_types/_nl_item.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/bitset:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n-\n-/usr/include/xlocale/_inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoap_a-dom.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoap_a-dom.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,381 +0,0 @@\n-libgsoap_a-dom.o: dom.c stdsoap2.h ../config.h /usr/include/stdlib.h \\\n- /usr/include/Availability.h /usr/include/AvailabilityInternal.h \\\n- /usr/include/_types.h /usr/include/sys/_types.h \\\n- /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \\\n- /usr/include/secure/_common.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/secure/_string.h \\\n- /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h /usr/include/errno.h /usr/include/sys/errno.h \\\n- /usr/include/sys/types.h /usr/include/sys/_types/_blkcnt_t.h \\\n- /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \\\n- /usr/include/sys/_types/_in_addr_t.h \\\n- /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \\\n- /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \\\n- /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \\\n- /usr/include/sys/_types/_time_t.h \\\n- /usr/include/sys/_types/_useconds_t.h \\\n- /usr/include/sys/_types/_suseconds_t.h \\\n- /usr/include/sys/_types/_fd_def.h \\\n- /usr/include/sys/_types/_fd_setsize.h \\\n- /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \\\n- /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \\\n- /usr/include/sys/_types/_fd_copy.h \\\n- /usr/include/sys/_types/_pthread_cond_t.h \\\n- /usr/include/sys/_types/_pthread_condattr_t.h \\\n- /usr/include/sys/_types/_pthread_mutex_t.h \\\n- /usr/include/sys/_types/_pthread_mutexattr_t.h \\\n- /usr/include/sys/_types/_pthread_once_t.h \\\n- /usr/inc'..b'64_t.h:\n-\n-/usr/include/sys/_types/_intptr_t.h:\n-\n-/usr/include/sys/_types/_uintptr_t.h:\n-\n-/usr/include/_types/_intmax_t.h:\n-\n-/usr/include/_types/_uintmax_t.h:\n-\n-/usr/include/sys/_types/_timeval.h:\n-\n-/usr/include/machine/endian.h:\n-\n-/usr/include/i386/endian.h:\n-\n-/usr/include/sys/_endian.h:\n-\n-/usr/include/libkern/_OSByteOrder.h:\n-\n-/usr/include/libkern/i386/_OSByteOrder.h:\n-\n-/usr/include/alloca.h:\n-\n-/usr/include/sys/_types/_ct_rune_t.h:\n-\n-/usr/include/sys/_types/_rune_t.h:\n-\n-/usr/include/sys/_types/_wchar_t.h:\n-\n-/usr/include/sys/_types/_null.h:\n-\n-/usr/include/machine/types.h:\n-\n-/usr/include/i386/types.h:\n-\n-/usr/include/sys/_types/___offsetof.h:\n-\n-/usr/include/sys/_types/_dev_t.h:\n-\n-/usr/include/sys/_types/_mode_t.h:\n-\n-/usr/include/stdio.h:\n-\n-/usr/include/sys/_types/_va_list.h:\n-\n-/usr/include/sys/_types/_off_t.h:\n-\n-/usr/include/sys/_types/_ssize_t.h:\n-\n-/usr/include/secure/_stdio.h:\n-\n-/usr/include/secure/_common.h:\n-\n-/usr/include/string.h:\n-\n-/usr/include/sys/_types/_rsize_t.h:\n-\n-/usr/include/sys/_types/_errno_t.h:\n-\n-/usr/include/strings.h:\n-\n-/usr/include/secure/_string.h:\n-\n-/usr/include/ctype.h:\n-\n-/usr/include/runetype.h:\n-\n-/usr/include/sys/_types/_wint_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h:\n-\n-/usr/include/limits.h:\n-\n-/usr/include/machine/limits.h:\n-\n-/usr/include/i386/limits.h:\n-\n-/usr/include/i386/_limits.h:\n-\n-/usr/include/sys/syslimits.h:\n-\n-/usr/include/poll.h:\n-\n-/usr/include/sys/poll.h:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_clock_t.h:\n-\n-/usr/include/sys/_types/_time_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/time.h:\n-\n-/usr/include/_structs.h:\n-\n-/usr/include/sys/_structs.h:\n-\n-/usr/include/sys/_types/_timespec.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoap_a-stdsoap2.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoap_a-stdsoap2.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,382 +0,0 @@\n-libgsoap_a-stdsoap2.o: stdsoap2.c stdsoap2.h ../config.h \\\n- /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \\\n- /usr/include/secure/_common.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/secure/_string.h \\\n- /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h /usr/include/errno.h /usr/include/sys/errno.h \\\n- /usr/include/sys/types.h /usr/include/sys/_types/_blkcnt_t.h \\\n- /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \\\n- /usr/include/sys/_types/_in_addr_t.h \\\n- /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \\\n- /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \\\n- /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \\\n- /usr/include/sys/_types/_time_t.h \\\n- /usr/include/sys/_types/_useconds_t.h \\\n- /usr/include/sys/_types/_suseconds_t.h \\\n- /usr/include/sys/_types/_fd_def.h \\\n- /usr/include/sys/_types/_fd_setsize.h \\\n- /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \\\n- /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \\\n- /usr/include/sys/_types/_fd_copy.h \\\n- /usr/include/sys/_types/_pthread_cond_t.h \\\n- /usr/include/sys/_types/_pthread_condattr_t.h \\\n- /usr/include/sys/_types/_pthread_mutex_t.h \\\n- /usr/include/sys/_types/_pthread_mutexattr_t.h \\\n- /usr/include/sys/_types/_pthread_once_t.'..b'64_t.h:\n-\n-/usr/include/sys/_types/_intptr_t.h:\n-\n-/usr/include/sys/_types/_uintptr_t.h:\n-\n-/usr/include/_types/_intmax_t.h:\n-\n-/usr/include/_types/_uintmax_t.h:\n-\n-/usr/include/sys/_types/_timeval.h:\n-\n-/usr/include/machine/endian.h:\n-\n-/usr/include/i386/endian.h:\n-\n-/usr/include/sys/_endian.h:\n-\n-/usr/include/libkern/_OSByteOrder.h:\n-\n-/usr/include/libkern/i386/_OSByteOrder.h:\n-\n-/usr/include/alloca.h:\n-\n-/usr/include/sys/_types/_ct_rune_t.h:\n-\n-/usr/include/sys/_types/_rune_t.h:\n-\n-/usr/include/sys/_types/_wchar_t.h:\n-\n-/usr/include/sys/_types/_null.h:\n-\n-/usr/include/machine/types.h:\n-\n-/usr/include/i386/types.h:\n-\n-/usr/include/sys/_types/___offsetof.h:\n-\n-/usr/include/sys/_types/_dev_t.h:\n-\n-/usr/include/sys/_types/_mode_t.h:\n-\n-/usr/include/stdio.h:\n-\n-/usr/include/sys/_types/_va_list.h:\n-\n-/usr/include/sys/_types/_off_t.h:\n-\n-/usr/include/sys/_types/_ssize_t.h:\n-\n-/usr/include/secure/_stdio.h:\n-\n-/usr/include/secure/_common.h:\n-\n-/usr/include/string.h:\n-\n-/usr/include/sys/_types/_rsize_t.h:\n-\n-/usr/include/sys/_types/_errno_t.h:\n-\n-/usr/include/strings.h:\n-\n-/usr/include/secure/_string.h:\n-\n-/usr/include/ctype.h:\n-\n-/usr/include/runetype.h:\n-\n-/usr/include/sys/_types/_wint_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h:\n-\n-/usr/include/limits.h:\n-\n-/usr/include/machine/limits.h:\n-\n-/usr/include/i386/limits.h:\n-\n-/usr/include/i386/_limits.h:\n-\n-/usr/include/sys/syslimits.h:\n-\n-/usr/include/poll.h:\n-\n-/usr/include/sys/poll.h:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_clock_t.h:\n-\n-/usr/include/sys/_types/_time_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/time.h:\n-\n-/usr/include/_structs.h:\n-\n-/usr/include/sys/_structs.h:\n-\n-/usr/include/sys/_types/_timespec.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapck___a-dom_cpp.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapck___a-dom_cpp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,586 +0,0 @@\n-libgsoapck___a-dom_cpp.o: dom_cpp.cpp stdsoap2.h ../config.h \\\n- /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \\\n- /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdarg.h \\\n- /usr/include/time.h /usr/include/_structs.h \\\n- /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \\\n- /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \\\n- /usr/include/_wctype.h /usr/include/_types/_wctype_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeD'..b'de.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/pthread.h:\n-\n-/usr/include/pthread_impl.h:\n-\n-/usr/include/sched.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_mach_port_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03:\n-\n-/usr/include/locale.h:\n-\n-/usr/include/_locale.h:\n-\n-/usr/include/xlocale.h:\n-\n-/usr/include/_xlocale.h:\n-\n-/usr/include/xlocale/_ctype.h:\n-\n-/usr/include/xlocale/__wctype.h:\n-\n-/usr/include/xlocale/_stdio.h:\n-\n-/usr/include/xlocale/_stdlib.h:\n-\n-/usr/include/xlocale/_string.h:\n-\n-/usr/include/xlocale/_time.h:\n-\n-/usr/include/xlocale/_wchar.h:\n-\n-/usr/include/xlocale/_wctype.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/streambuf:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/istream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ostream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/locale:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdlib:\n-\n-/usr/include/nl_types.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/_types/_nl_item.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/bitset:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n-\n-/usr/include/xlocale/_inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapck___a-stdsoap2_ck_cpp.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapck___a-stdsoap2_ck_cpp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,586 +0,0 @@\n-libgsoapck___a-stdsoap2_ck_cpp.o: stdsoap2_ck_cpp.cpp stdsoap2.h \\\n- ../config.h /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd \\\n- /usr/include/wchar.h /usr/include/sys/_types/_mbstate_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdarg.h \\\n- /usr/include/time.h /usr/include/_structs.h \\\n- /usr/include/sys/_structs.h /usr/include/sys/_types/_timespec.h \\\n- /usr/include/sys/_types/_clock_t.h /usr/include/sys/_types/_time_t.h \\\n- /usr/include/_wctype.h /usr/include/_types/_wctype_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstring \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdio \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cwchar \\\n- /Applications/Xcode.app/Contents/Developer/T'..b'de.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cerrno:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/pthread.h:\n-\n-/usr/include/pthread_impl.h:\n-\n-/usr/include/sched.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_mach_port_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/functional:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__functional_03:\n-\n-/usr/include/locale.h:\n-\n-/usr/include/_locale.h:\n-\n-/usr/include/xlocale.h:\n-\n-/usr/include/_xlocale.h:\n-\n-/usr/include/xlocale/_ctype.h:\n-\n-/usr/include/xlocale/__wctype.h:\n-\n-/usr/include/xlocale/_stdio.h:\n-\n-/usr/include/xlocale/_stdlib.h:\n-\n-/usr/include/xlocale/_string.h:\n-\n-/usr/include/xlocale/_time.h:\n-\n-/usr/include/xlocale/_wchar.h:\n-\n-/usr/include/xlocale/_wctype.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/streambuf:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/istream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ostream:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/locale:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstdlib:\n-\n-/usr/include/nl_types.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/_types/_nl_item.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/bitset:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n-\n-/usr/include/xlocale/_inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapck_a-dom.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapck_a-dom.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,381 +0,0 @@\n-libgsoapck_a-dom.o: dom.c stdsoap2.h ../config.h /usr/include/stdlib.h \\\n- /usr/include/Availability.h /usr/include/AvailabilityInternal.h \\\n- /usr/include/_types.h /usr/include/sys/_types.h \\\n- /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \\\n- /usr/include/secure/_common.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/secure/_string.h \\\n- /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h /usr/include/errno.h /usr/include/sys/errno.h \\\n- /usr/include/sys/types.h /usr/include/sys/_types/_blkcnt_t.h \\\n- /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \\\n- /usr/include/sys/_types/_in_addr_t.h \\\n- /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \\\n- /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \\\n- /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \\\n- /usr/include/sys/_types/_time_t.h \\\n- /usr/include/sys/_types/_useconds_t.h \\\n- /usr/include/sys/_types/_suseconds_t.h \\\n- /usr/include/sys/_types/_fd_def.h \\\n- /usr/include/sys/_types/_fd_setsize.h \\\n- /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \\\n- /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \\\n- /usr/include/sys/_types/_fd_copy.h \\\n- /usr/include/sys/_types/_pthread_cond_t.h \\\n- /usr/include/sys/_types/_pthread_condattr_t.h \\\n- /usr/include/sys/_types/_pthread_mutex_t.h \\\n- /usr/include/sys/_types/_pthread_mutexattr_t.h \\\n- /usr/include/sys/_types/_pthread_once_t.h \\\n- /usr/i'..b'64_t.h:\n-\n-/usr/include/sys/_types/_intptr_t.h:\n-\n-/usr/include/sys/_types/_uintptr_t.h:\n-\n-/usr/include/_types/_intmax_t.h:\n-\n-/usr/include/_types/_uintmax_t.h:\n-\n-/usr/include/sys/_types/_timeval.h:\n-\n-/usr/include/machine/endian.h:\n-\n-/usr/include/i386/endian.h:\n-\n-/usr/include/sys/_endian.h:\n-\n-/usr/include/libkern/_OSByteOrder.h:\n-\n-/usr/include/libkern/i386/_OSByteOrder.h:\n-\n-/usr/include/alloca.h:\n-\n-/usr/include/sys/_types/_ct_rune_t.h:\n-\n-/usr/include/sys/_types/_rune_t.h:\n-\n-/usr/include/sys/_types/_wchar_t.h:\n-\n-/usr/include/sys/_types/_null.h:\n-\n-/usr/include/machine/types.h:\n-\n-/usr/include/i386/types.h:\n-\n-/usr/include/sys/_types/___offsetof.h:\n-\n-/usr/include/sys/_types/_dev_t.h:\n-\n-/usr/include/sys/_types/_mode_t.h:\n-\n-/usr/include/stdio.h:\n-\n-/usr/include/sys/_types/_va_list.h:\n-\n-/usr/include/sys/_types/_off_t.h:\n-\n-/usr/include/sys/_types/_ssize_t.h:\n-\n-/usr/include/secure/_stdio.h:\n-\n-/usr/include/secure/_common.h:\n-\n-/usr/include/string.h:\n-\n-/usr/include/sys/_types/_rsize_t.h:\n-\n-/usr/include/sys/_types/_errno_t.h:\n-\n-/usr/include/strings.h:\n-\n-/usr/include/secure/_string.h:\n-\n-/usr/include/ctype.h:\n-\n-/usr/include/runetype.h:\n-\n-/usr/include/sys/_types/_wint_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h:\n-\n-/usr/include/limits.h:\n-\n-/usr/include/machine/limits.h:\n-\n-/usr/include/i386/limits.h:\n-\n-/usr/include/i386/_limits.h:\n-\n-/usr/include/sys/syslimits.h:\n-\n-/usr/include/poll.h:\n-\n-/usr/include/sys/poll.h:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_clock_t.h:\n-\n-/usr/include/sys/_types/_time_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/time.h:\n-\n-/usr/include/_structs.h:\n-\n-/usr/include/sys/_structs.h:\n-\n-/usr/include/sys/_types/_timespec.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapck_a-stdsoap2_ck.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapck_a-stdsoap2_ck.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,382 +0,0 @@\n-libgsoapck_a-stdsoap2_ck.o: stdsoap2_ck.c stdsoap2.h ../config.h \\\n- /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \\\n- /usr/include/secure/_common.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/secure/_string.h \\\n- /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h /usr/include/errno.h /usr/include/sys/errno.h \\\n- /usr/include/sys/types.h /usr/include/sys/_types/_blkcnt_t.h \\\n- /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \\\n- /usr/include/sys/_types/_in_addr_t.h \\\n- /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \\\n- /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \\\n- /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \\\n- /usr/include/sys/_types/_time_t.h \\\n- /usr/include/sys/_types/_useconds_t.h \\\n- /usr/include/sys/_types/_suseconds_t.h \\\n- /usr/include/sys/_types/_fd_def.h \\\n- /usr/include/sys/_types/_fd_setsize.h \\\n- /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \\\n- /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \\\n- /usr/include/sys/_types/_fd_copy.h \\\n- /usr/include/sys/_types/_pthread_cond_t.h \\\n- /usr/include/sys/_types/_pthread_condattr_t.h \\\n- /usr/include/sys/_types/_pthread_mutex_t.h \\\n- /usr/include/sys/_types/_pthread_mutexattr_t.h \\\n- /usr/include/sys/_types/_pthread'..b'64_t.h:\n-\n-/usr/include/sys/_types/_intptr_t.h:\n-\n-/usr/include/sys/_types/_uintptr_t.h:\n-\n-/usr/include/_types/_intmax_t.h:\n-\n-/usr/include/_types/_uintmax_t.h:\n-\n-/usr/include/sys/_types/_timeval.h:\n-\n-/usr/include/machine/endian.h:\n-\n-/usr/include/i386/endian.h:\n-\n-/usr/include/sys/_endian.h:\n-\n-/usr/include/libkern/_OSByteOrder.h:\n-\n-/usr/include/libkern/i386/_OSByteOrder.h:\n-\n-/usr/include/alloca.h:\n-\n-/usr/include/sys/_types/_ct_rune_t.h:\n-\n-/usr/include/sys/_types/_rune_t.h:\n-\n-/usr/include/sys/_types/_wchar_t.h:\n-\n-/usr/include/sys/_types/_null.h:\n-\n-/usr/include/machine/types.h:\n-\n-/usr/include/i386/types.h:\n-\n-/usr/include/sys/_types/___offsetof.h:\n-\n-/usr/include/sys/_types/_dev_t.h:\n-\n-/usr/include/sys/_types/_mode_t.h:\n-\n-/usr/include/stdio.h:\n-\n-/usr/include/sys/_types/_va_list.h:\n-\n-/usr/include/sys/_types/_off_t.h:\n-\n-/usr/include/sys/_types/_ssize_t.h:\n-\n-/usr/include/secure/_stdio.h:\n-\n-/usr/include/secure/_common.h:\n-\n-/usr/include/string.h:\n-\n-/usr/include/sys/_types/_rsize_t.h:\n-\n-/usr/include/sys/_types/_errno_t.h:\n-\n-/usr/include/strings.h:\n-\n-/usr/include/secure/_string.h:\n-\n-/usr/include/ctype.h:\n-\n-/usr/include/runetype.h:\n-\n-/usr/include/sys/_types/_wint_t.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h:\n-\n-/usr/include/limits.h:\n-\n-/usr/include/machine/limits.h:\n-\n-/usr/include/i386/limits.h:\n-\n-/usr/include/i386/_limits.h:\n-\n-/usr/include/sys/syslimits.h:\n-\n-/usr/include/poll.h:\n-\n-/usr/include/sys/poll.h:\n-\n-/usr/include/errno.h:\n-\n-/usr/include/sys/errno.h:\n-\n-/usr/include/sys/types.h:\n-\n-/usr/include/sys/_types/_blkcnt_t.h:\n-\n-/usr/include/sys/_types/_blksize_t.h:\n-\n-/usr/include/sys/_types/_gid_t.h:\n-\n-/usr/include/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_clock_t.h:\n-\n-/usr/include/sys/_types/_time_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/time.h:\n-\n-/usr/include/_structs.h:\n-\n-/usr/include/sys/_structs.h:\n-\n-/usr/include/sys/_types/_timespec.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl___a-dom_cpp.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl___a-dom_cpp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl___a-stdsoap2_ssl_cpp.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl___a-stdsoap2_ssl_cpp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl_a-dom.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl_a-dom.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,502 +0,0 @@\n-libgsoapssl_a-dom.o: dom.c stdsoap2.h ../config.h /usr/include/stdlib.h \\\n- /usr/include/Availability.h /usr/include/AvailabilityInternal.h \\\n- /usr/include/_types.h /usr/include/sys/_types.h \\\n- /usr/include/sys/cdefs.h /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \\\n- /usr/include/secure/_common.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/secure/_string.h \\\n- /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h /usr/include/errno.h /usr/include/sys/errno.h \\\n- /usr/include/sys/types.h /usr/include/sys/_types/_blkcnt_t.h \\\n- /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \\\n- /usr/include/sys/_types/_in_addr_t.h \\\n- /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \\\n- /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \\\n- /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \\\n- /usr/include/sys/_types/_time_t.h \\\n- /usr/include/sys/_types/_useconds_t.h \\\n- /usr/include/sys/_types/_suseconds_t.h \\\n- /usr/include/sys/_types/_fd_def.h \\\n- /usr/include/sys/_types/_fd_setsize.h \\\n- /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \\\n- /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \\\n- /usr/include/sys/_types/_fd_copy.h \\\n- /usr/include/sys/_types/_pthread_cond_t.h \\\n- /usr/include/sys/_types/_pthread_condattr_t.h \\\n- /usr/include/sys/_types/_pthread_mutex_t.h \\\n- /usr/include/sys/_types/_pthread_mutexattr_t.h \\\n- /usr/include/sys/_types/_pthread_once_t.h \\\n- /usr/'..b'e/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_clock_t.h:\n-\n-/usr/include/sys/_types/_time_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/time.h:\n-\n-/usr/include/_structs.h:\n-\n-/usr/include/sys/_structs.h:\n-\n-/usr/include/sys/_types/_timespec.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/openssl/bio.h:\n-\n-/usr/include/AvailabilityMacros.h:\n-\n-/usr/include/openssl/e_os2.h:\n-\n-/usr/include/openssl/opensslconf.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdarg.h:\n-\n-/usr/include/openssl/crypto.h:\n-\n-/usr/include/openssl/stack.h:\n-\n-/usr/include/openssl/safestack.h:\n-\n-/usr/include/openssl/opensslv.h:\n-\n-/usr/include/openssl/ossl_typ.h:\n-\n-/usr/include/openssl/symhacks.h:\n-\n-/usr/include/openssl/err.h:\n-\n-/usr/include/openssl/lhash.h:\n-\n-/usr/include/openssl/rand.h:\n-\n-/usr/include/openssl/ssl.h:\n-\n-/usr/include/openssl/comp.h:\n-\n-/usr/include/openssl/x509.h:\n-\n-/usr/include/openssl/buffer.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stddef.h:\n-\n-/usr/include/openssl/evp.h:\n-\n-/usr/include/openssl/objects.h:\n-\n-/usr/include/openssl/obj_mac.h:\n-\n-/usr/include/openssl/asn1.h:\n-\n-/usr/include/openssl/bn.h:\n-\n-/usr/include/openssl/ec.h:\n-\n-/usr/include/openssl/ecdsa.h:\n-\n-/usr/include/openssl/ecdh.h:\n-\n-/usr/include/openssl/rsa.h:\n-\n-/usr/include/openssl/dsa.h:\n-\n-/usr/include/openssl/dh.h:\n-\n-/usr/include/openssl/sha.h:\n-\n-/usr/include/openssl/x509_vfy.h:\n-\n-/usr/include/openssl/pkcs7.h:\n-\n-/usr/include/openssl/pem.h:\n-\n-/usr/include/openssl/pem2.h:\n-\n-/usr/include/openssl/hmac.h:\n-\n-/usr/include/openssl/kssl.h:\n-\n-/usr/include/openssl/ssl2.h:\n-\n-/usr/include/openssl/ssl3.h:\n-\n-/usr/include/openssl/pq_compat.h:\n-\n-/usr/include/openssl/tls1.h:\n-\n-/usr/include/openssl/dtls1.h:\n-\n-/usr/include/openssl/pqueue.h:\n-\n-/usr/include/openssl/ssl23.h:\n-\n-/usr/include/openssl/x509v3.h:\n-\n-/usr/include/openssl/conf.h:\n-\n-/usr/include/zlib.h:\n-\n-/usr/include/zconf.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl_a-stdsoap2_ssl.Po
--- a/GEMBASSY-1.0.3/gsoap/.deps/libgsoapssl_a-stdsoap2_ssl.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,503 +0,0 @@\n-libgsoapssl_a-stdsoap2_ssl.o: stdsoap2_ssl.c stdsoap2.h ../config.h \\\n- /usr/include/stdlib.h /usr/include/Availability.h \\\n- /usr/include/AvailabilityInternal.h /usr/include/_types.h \\\n- /usr/include/sys/_types.h /usr/include/sys/cdefs.h \\\n- /usr/include/sys/_symbol_aliasing.h \\\n- /usr/include/sys/_posix_availability.h /usr/include/machine/_types.h \\\n- /usr/include/i386/_types.h /usr/include/sys/wait.h \\\n- /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \\\n- /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \\\n- /usr/include/machine/signal.h /usr/include/i386/signal.h \\\n- /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \\\n- /usr/include/mach/i386/_structs.h \\\n- /usr/include/sys/_types/_sigaltstack.h \\\n- /usr/include/sys/_types/_ucontext.h \\\n- /usr/include/sys/_types/_pthread_attr_t.h \\\n- /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_size_t.h \\\n- /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdint.h \\\n- /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \\\n- /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \\\n- /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \\\n- /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \\\n- /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \\\n- /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \\\n- /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \\\n- /usr/include/machine/endian.h /usr/include/i386/endian.h \\\n- /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \\\n- /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \\\n- /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \\\n- /usr/include/sys/_types/_wchar_t.h /usr/include/sys/_types/_null.h \\\n- /usr/include/machine/types.h /usr/include/i386/types.h \\\n- /usr/include/sys/_types/___offsetof.h /usr/include/sys/_types/_dev_t.h \\\n- /usr/include/sys/_types/_mode_t.h /usr/include/stdio.h \\\n- /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_off_t.h \\\n- /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h \\\n- /usr/include/secure/_common.h /usr/include/string.h \\\n- /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h \\\n- /usr/include/strings.h /usr/include/secure/_string.h \\\n- /usr/include/ctype.h /usr/include/runetype.h \\\n- /usr/include/sys/_types/_wint_t.h \\\n- /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h \\\n- /usr/include/limits.h /usr/include/machine/limits.h \\\n- /usr/include/i386/limits.h /usr/include/i386/_limits.h \\\n- /usr/include/sys/syslimits.h /usr/include/poll.h \\\n- /usr/include/sys/poll.h /usr/include/errno.h /usr/include/sys/errno.h \\\n- /usr/include/sys/types.h /usr/include/sys/_types/_blkcnt_t.h \\\n- /usr/include/sys/_types/_blksize_t.h /usr/include/sys/_types/_gid_t.h \\\n- /usr/include/sys/_types/_in_addr_t.h \\\n- /usr/include/sys/_types/_in_port_t.h /usr/include/sys/_types/_ino_t.h \\\n- /usr/include/sys/_types/_ino64_t.h /usr/include/sys/_types/_key_t.h \\\n- /usr/include/sys/_types/_nlink_t.h /usr/include/sys/_types/_clock_t.h \\\n- /usr/include/sys/_types/_time_t.h \\\n- /usr/include/sys/_types/_useconds_t.h \\\n- /usr/include/sys/_types/_suseconds_t.h \\\n- /usr/include/sys/_types/_fd_def.h \\\n- /usr/include/sys/_types/_fd_setsize.h \\\n- /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h \\\n- /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_isset.h \\\n- /usr/include/sys/_types/_fd_copy.h \\\n- /usr/include/sys/_types/_pthread_cond_t.h \\\n- /usr/include/sys/_types/_pthread_condattr_t.h \\\n- /usr/include/sys/_types/_pthread_mutex_t.h \\\n- /usr/include/sys/_types/_pthread_mutexattr_t.h \\\n- /usr/include/sys/_types/_pthr'..b'e/sys/_types/_in_addr_t.h:\n-\n-/usr/include/sys/_types/_in_port_t.h:\n-\n-/usr/include/sys/_types/_ino_t.h:\n-\n-/usr/include/sys/_types/_ino64_t.h:\n-\n-/usr/include/sys/_types/_key_t.h:\n-\n-/usr/include/sys/_types/_nlink_t.h:\n-\n-/usr/include/sys/_types/_clock_t.h:\n-\n-/usr/include/sys/_types/_time_t.h:\n-\n-/usr/include/sys/_types/_useconds_t.h:\n-\n-/usr/include/sys/_types/_suseconds_t.h:\n-\n-/usr/include/sys/_types/_fd_def.h:\n-\n-/usr/include/sys/_types/_fd_setsize.h:\n-\n-/usr/include/sys/_types/_fd_set.h:\n-\n-/usr/include/sys/_types/_fd_clr.h:\n-\n-/usr/include/sys/_types/_fd_zero.h:\n-\n-/usr/include/sys/_types/_fd_isset.h:\n-\n-/usr/include/sys/_types/_fd_copy.h:\n-\n-/usr/include/sys/_types/_pthread_cond_t.h:\n-\n-/usr/include/sys/_types/_pthread_condattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutex_t.h:\n-\n-/usr/include/sys/_types/_pthread_mutexattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_once_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlock_t.h:\n-\n-/usr/include/sys/_types/_pthread_rwlockattr_t.h:\n-\n-/usr/include/sys/_types/_pthread_t.h:\n-\n-/usr/include/sys/_types/_pthread_key_t.h:\n-\n-/usr/include/sys/_types/_fsblkcnt_t.h:\n-\n-/usr/include/sys/_types/_fsfilcnt_t.h:\n-\n-/usr/include/sys/timeb.h:\n-\n-/usr/include/time.h:\n-\n-/usr/include/_structs.h:\n-\n-/usr/include/sys/_structs.h:\n-\n-/usr/include/sys/_types/_timespec.h:\n-\n-/usr/include/sys/socket.h:\n-\n-/usr/include/machine/_param.h:\n-\n-/usr/include/i386/_param.h:\n-\n-/usr/include/sys/_types/_sa_family_t.h:\n-\n-/usr/include/sys/_types/_socklen_t.h:\n-\n-/usr/include/sys/_types/_iovec_t.h:\n-\n-/usr/include/sys/time.h:\n-\n-/usr/include/sys/_select.h:\n-\n-/usr/include/netinet/in.h:\n-\n-/usr/include/netinet6/in6.h:\n-\n-/usr/include/netinet/tcp.h:\n-\n-/usr/include/arpa/inet.h:\n-\n-/usr/include/netdb.h:\n-\n-/usr/include/unistd.h:\n-\n-/usr/include/sys/unistd.h:\n-\n-/usr/include/sys/_types/_posix_vdisable.h:\n-\n-/usr/include/sys/_types/_seek_set.h:\n-\n-/usr/include/sys/select.h:\n-\n-/usr/include/sys/_types/_uuid_t.h:\n-\n-/usr/include/gethostuuid.h:\n-\n-/usr/include/fcntl.h:\n-\n-/usr/include/sys/fcntl.h:\n-\n-/usr/include/sys/_types/_o_sync.h:\n-\n-/usr/include/sys/_types/_o_dsync.h:\n-\n-/usr/include/sys/_types/_s_ifmt.h:\n-\n-/usr/include/sys/_types/_filesec_t.h:\n-\n-/usr/include/openssl/bio.h:\n-\n-/usr/include/AvailabilityMacros.h:\n-\n-/usr/include/openssl/e_os2.h:\n-\n-/usr/include/openssl/opensslconf.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stdarg.h:\n-\n-/usr/include/openssl/crypto.h:\n-\n-/usr/include/openssl/stack.h:\n-\n-/usr/include/openssl/safestack.h:\n-\n-/usr/include/openssl/opensslv.h:\n-\n-/usr/include/openssl/ossl_typ.h:\n-\n-/usr/include/openssl/symhacks.h:\n-\n-/usr/include/openssl/err.h:\n-\n-/usr/include/openssl/lhash.h:\n-\n-/usr/include/openssl/rand.h:\n-\n-/usr/include/openssl/ssl.h:\n-\n-/usr/include/openssl/comp.h:\n-\n-/usr/include/openssl/x509.h:\n-\n-/usr/include/openssl/buffer.h:\n-\n-/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/stddef.h:\n-\n-/usr/include/openssl/evp.h:\n-\n-/usr/include/openssl/objects.h:\n-\n-/usr/include/openssl/obj_mac.h:\n-\n-/usr/include/openssl/asn1.h:\n-\n-/usr/include/openssl/bn.h:\n-\n-/usr/include/openssl/ec.h:\n-\n-/usr/include/openssl/ecdsa.h:\n-\n-/usr/include/openssl/ecdh.h:\n-\n-/usr/include/openssl/rsa.h:\n-\n-/usr/include/openssl/dsa.h:\n-\n-/usr/include/openssl/dh.h:\n-\n-/usr/include/openssl/sha.h:\n-\n-/usr/include/openssl/x509_vfy.h:\n-\n-/usr/include/openssl/pkcs7.h:\n-\n-/usr/include/openssl/pem.h:\n-\n-/usr/include/openssl/pem2.h:\n-\n-/usr/include/openssl/hmac.h:\n-\n-/usr/include/openssl/kssl.h:\n-\n-/usr/include/openssl/ssl2.h:\n-\n-/usr/include/openssl/ssl3.h:\n-\n-/usr/include/openssl/pq_compat.h:\n-\n-/usr/include/openssl/tls1.h:\n-\n-/usr/include/openssl/dtls1.h:\n-\n-/usr/include/openssl/pqueue.h:\n-\n-/usr/include/openssl/ssl23.h:\n-\n-/usr/include/openssl/x509v3.h:\n-\n-/usr/include/openssl/conf.h:\n-\n-/usr/include/zlib.h:\n-\n-/usr/include/zconf.h:\n-\n-/usr/include/math.h:\n-\n-/usr/include/inttypes.h:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/Makefile
--- a/GEMBASSY-1.0.3/gsoap/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,920 +0,0 @@\n-# Makefile.in generated by automake 1.10 from Makefile.am.\n-# gsoap/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,\n-# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-\n-\n-\n-pkgdatadir = $(datadir)/gsoap\n-pkglibdir = $(libdir)/gsoap\n-pkgincludedir = $(includedir)/gsoap\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = i386-apple-darwin13.1.0\n-host_triplet = i386-apple-darwin13.1.0\n-subdir = gsoap\n-DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \\\n-\t$(srcdir)/Makefile.in\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs\n-CONFIG_HEADER = $(top_builddir)/config.h\n-CONFIG_CLEAN_FILES =\n-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed \'s|.|.|g\'`;\n-am__vpath_adj = case $$p in \\\n- $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \\\n- *) f=$$p;; \\\n- esac;\n-am__strip_dir = `echo $$p | sed -e \'s|^.*/||\'`;\n-am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgdatadir)" \\\n-\t"$(DESTDIR)$(includedir)"\n-libLIBRARIES_INSTALL = $(INSTALL_DATA)\n-LIBRARIES = $(lib_LIBRARIES)\n-AR = ar\n-ARFLAGS = cru\n-libgsoap___a_AR = $(AR) $(ARFLAGS)\n-libgsoap___a_LIBADD =\n-am_libgsoap___a_OBJECTS = libgsoap___a-stdsoap2_cpp.$(OBJEXT) \\\n-\tlibgsoap___a-dom_cpp.$(OBJEXT)\n-libgsoap___a_OBJECTS = $(am_libgsoap___a_OBJECTS)\n-libgsoap_a_AR = $(AR) $(ARFLAGS)\n-libgsoap_a_LIBADD =\n-am_libgsoap_a_OBJECTS = libgsoap_a-stdsoap2.$(OBJEXT) \\\n-\tlibgsoap_a-dom.$(OBJEXT)\n-libgsoap_a_OBJECTS = $(am_libgsoap_a_OBJECTS)\n-libgsoapck___a_AR = $(AR) $(ARFLAGS)\n-libgsoapck___a_LIBADD =\n-am_libgsoapck___a_OBJECTS = libgsoapck___a-stdsoap2_ck_cpp.$(OBJEXT) \\\n-\tlibgsoapck___a-dom_cpp.$(OBJEXT)\n-libgsoapck___a_OBJECTS = $(am_libgsoapck___a_OBJECTS)\n-libgsoapck_a_AR = $(AR) $(ARFLAGS)\n-libgsoapck_a_LIBADD =\n-am_libgsoapck_a_OBJECTS = libgsoapck_a-stdsoap2_ck.$(OBJEXT) \\\n-\tlibgsoapck_a-dom.$(OBJEXT)\n-libgsoapck_a_OBJECTS = $(am_libgsoapck_a_OBJECTS)\n-libgsoapssl___a_AR = $(AR) $(ARFLAGS)\n-libgsoapssl___a_LIBADD =\n-am_libgsoapssl___a_OBJECTS = \\\n-\tlibgsoapssl___a-stdsoap2_ssl_cpp.$(OBJEXT) \\\n-\tlibgsoapssl___a-dom_cpp.$(OBJEXT)\n-libgsoapssl___a_OBJECTS = $(am_libgsoapssl___a_OBJECTS)\n-libgsoapssl_a_AR = $(AR) $(ARFLAGS)\n-libgsoapssl_a_LIBADD =\n-am_libgsoapssl_a_OBJECTS = libgsoapssl_a-stdsoap2_ssl.$(OBJEXT) \\\n-\tlibgsoapssl_a-dom.$(OBJEXT)\n-libgsoapssl_a_OBJECTS = $(am_libgsoapssl_a_OBJECTS)\n-DEFAULT_INCLUDES = -I. -I$(top_builddir)\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \\\n-\t$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)\n-CCLD = $(CC)\n-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@\n-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \\\n-\t$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)\n-CXXLD = $(CXX)\n-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \\\n-\t-o $@\n-SOURCES = $(libgsoap___a_SOURCES) $(libgsoap_a_SOURCES) \\\n-\t$(libgsoapck___a_SOURCES) $(libgsoapck_a_SOURCES) \\\n-\t$(lib'..b'AKE) $(AM_MAKEFLAGS) install-recursive\n-install-exec: install-exec-recursive\n-install-data: install-data-recursive\n-uninstall: uninstall-recursive\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-recursive\n-install-strip:\n-\t$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t `test -z \'$(STRIP)\' || \\\n-\t echo "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'"` install\n-mostlyclean-generic:\n-\n-clean-generic:\n-\t-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-\t-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)\n-clean: clean-recursive\n-\n-clean-am: clean-generic clean-libLIBRARIES mostlyclean-am\n-\n-distclean: distclean-recursive\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-recursive\n-\n-dvi-am:\n-\n-html: html-recursive\n-\n-info: info-recursive\n-\n-info-am:\n-\n-install-data-am: install-includeHEADERS install-nobase_pkgdataDATA\n-\t@$(NORMAL_INSTALL)\n-\t$(MAKE) $(AM_MAKEFLAGS) install-data-hook\n-\n-install-dvi: install-dvi-recursive\n-\n-install-exec-am: install-libLIBRARIES\n-\n-install-html: install-html-recursive\n-\n-install-info: install-info-recursive\n-\n-install-man:\n-\n-install-pdf: install-pdf-recursive\n-\n-install-ps: install-ps-recursive\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-recursive\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-recursive\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic\n-\n-pdf: pdf-recursive\n-\n-pdf-am:\n-\n-ps: ps-recursive\n-\n-ps-am:\n-\n-uninstall-am: uninstall-includeHEADERS uninstall-libLIBRARIES \\\n-\tuninstall-nobase_pkgdataDATA\n-\n-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \\\n-\tinstall-data-am install-strip\n-\n-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \\\n-\tall all-am check check-am clean clean-generic \\\n-\tclean-libLIBRARIES ctags ctags-recursive distclean \\\n-\tdistclean-compile distclean-generic distclean-tags distdir dvi \\\n-\tdvi-am html html-am info info-am install install-am \\\n-\tinstall-data install-data-am install-data-hook install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-includeHEADERS install-info \\\n-\tinstall-info-am install-libLIBRARIES install-man \\\n-\tinstall-nobase_pkgdataDATA install-pdf install-pdf-am \\\n-\tinstall-ps install-ps-am install-strip installcheck \\\n-\tinstallcheck-am installdirs installdirs-am maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \\\n-\tuninstall uninstall-am uninstall-includeHEADERS \\\n-\tuninstall-libLIBRARIES uninstall-nobase_pkgdataDATA\n-\n-\n-stdsoap2_ck.c: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ck.c\n-\n-stdsoap2_cpp.cpp: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_cpp.cpp\n-\n-stdsoap2_ck_cpp.cpp: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ck_cpp.cpp\n-\n-stdsoap2_ssl.c: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ssl.c\n-\n-stdsoap2_ssl_cpp.cpp: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ssl_cpp.cpp\n-dom_cpp.cpp: dom.cpp\n-\t$(LN_S) -f $(srcdir)/dom.cpp dom_cpp.cpp\n-\n-install-data-hook:\n-\t$(LN_S) -f $(top_builddir)/gsoap/src/soapcpp2 $(top_builddir)/gsoap/soapcpp2 || echo "ok, link already exists".\n-\t$(LN_S) -f $(top_builddir)/gsoap/wsdl/wsdl2h $(top_builddir)/gsoap/wsdl2h || echo "ok, link already exists".\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/Makefile.am
--- a/GEMBASSY-1.0.3/gsoap/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,59 +0,0 @@
-## This is the input file for automake, which will generate Makefile.in ##
-## not a GNU package. You can remove this line, if
-## you have all needed files, that a GNU package needs
-AUTOMAKE_OPTIONS = foreign 1.4
-
-SUBDIRS = . src wsdl @SAMPLE_DIRS@
-CLEANFILES = soapcpp2 wsdl2h stdsoap2_cpp.cpp stdsoap2_ck.c stdsoap2_ck_cpp.cpp stdsoap2_ssl.c stdsoap2_ssl_cpp.cpp dom_cpp.cpp
-
-## *~ *.req.xml *.res.xml *.nsmap *.wsdl *.xsd *Proxy.h \
-## *.o soapH.h soapStub.h soapC.cpp soapC.c soapClient.cpp soapClient.c soapServer.cpp soapServer.c
-
-AM_CXXFLAGS = $(SOAPCPP2_DEBUG) -D$(platform)
-AM_CFLAGS = $(SOAPCPP2_DEBUG) -D$(platform)
-
-# Install all soapcpp2 and wsdl2h files into ${prefix}/share/gsoap
-nobase_pkgdata_DATA = $(srcdir)/import/* $(srcdir)/plugin/* $(srcdir)/WS/* $(srcdir)/custom/* $(srcdir)/extras/*
-
-## we cannot build stdsoap2.o from 2 different sources (stdsoap2.cpp and stdsoap2.c), so we need an intermediate target:
-stdsoap2_ck.c: stdsoap2.cpp
- $(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ck.c
-
-stdsoap2_cpp.cpp: stdsoap2.cpp
- $(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_cpp.cpp
-
-stdsoap2_ck_cpp.cpp: stdsoap2.cpp
- $(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ck_cpp.cpp
-
-stdsoap2_ssl.c: stdsoap2.cpp
- $(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ssl.c
-
-stdsoap2_ssl_cpp.cpp: stdsoap2.cpp
- $(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ssl_cpp.cpp
-## do the same fo dom.cpp since we want to link it into the cpp libs and dom.c into the c libs
-dom_cpp.cpp: dom.cpp
- $(LN_S) -f $(srcdir)/dom.cpp dom_cpp.cpp
-
-lib_LIBRARIES = libgsoap.a libgsoap++.a libgsoapck.a libgsoapck++.a libgsoapssl.a libgsoapssl++.a
-
-libgsoap_a_SOURCES = stdsoap2.c dom.c
-libgsoap_a_CFLAGS = $(SOAPCPP2_DEBUG) $(SOAPCPP2_NONAMESPACES) $(SOAPCPP2_IPV6) -D$(platform)
-libgsoap___a_SOURCES = stdsoap2_cpp.cpp dom_cpp.cpp
-libgsoap___a_CXXFLAGS = $(SOAPCPP2_DEBUG) $(SOAPCPP2_NONAMESPACES) $(SOAPCPP2_IPV6) -D$(platform)
-libgsoapck_a_SOURCES = stdsoap2_ck.c dom.c
-libgsoapck_a_CFLAGS = $(SOAPCPP2_DEBUG) $(SOAPCPP2_NONAMESPACES) $(SOAPCPP2_IPV6) -D$(platform) -DWITH_COOKIES
-libgsoapck___a_SOURCES = stdsoap2_ck_cpp.cpp dom_cpp.cpp
-libgsoapck___a_CXXFLAGS = $(SOAPCPP2_DEBUG) $(SOAPCPP2_NONAMESPACES) $(SOAPCPP2_IPV6) -D$(platform) -DWITH_COOKIES
-libgsoapssl_a_SOURCES = stdsoap2_ssl.c dom.c
-libgsoapssl_a_CFLAGS = $(SOAPCPP2_DEBUG) $(SOAPCPP2_NONAMESPACES) $(SOAPCPP2_IPV6) -D$(platform) $(WSDL2H_EXTRA_FLAGS) -DWITH_DOM
-libgsoapssl___a_SOURCES = stdsoap2_ssl_cpp.cpp dom_cpp.cpp
-libgsoapssl___a_CXXFLAGS = $(SOAPCPP2_DEBUG) $(SOAPCPP2_NONAMESPACES) $(SOAPCPP2_IPV6) -D$(platform) $(WSDL2H_EXTRA_FLAGS) -DWITH_DOM
-
-BUILT_SOURCES = stdsoap2_cpp.cpp dom_cpp.cpp $(lib_LIBRARIES)
-
-include_HEADERS = stdsoap2.h
-
-install-data-hook:
- $(LN_S) -f $(top_builddir)/gsoap/src/soapcpp2 $(top_builddir)/gsoap/soapcpp2 || echo "ok, link already exists".
- $(LN_S) -f $(top_builddir)/gsoap/wsdl/wsdl2h $(top_builddir)/gsoap/wsdl2h || echo "ok, link already exists".
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/Makefile.in
--- a/GEMBASSY-1.0.3/gsoap/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,920 +0,0 @@\n-# Makefile.in generated by automake 1.10 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,\n-# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-\n-\n-VPATH = @srcdir@\n-pkgdatadir = $(datadir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkgincludedir = $(includedir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-subdir = gsoap\n-DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \\\n-\t$(srcdir)/Makefile.in\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs\n-CONFIG_HEADER = $(top_builddir)/config.h\n-CONFIG_CLEAN_FILES =\n-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed \'s|.|.|g\'`;\n-am__vpath_adj = case $$p in \\\n- $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \\\n- *) f=$$p;; \\\n- esac;\n-am__strip_dir = `echo $$p | sed -e \'s|^.*/||\'`;\n-am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgdatadir)" \\\n-\t"$(DESTDIR)$(includedir)"\n-libLIBRARIES_INSTALL = $(INSTALL_DATA)\n-LIBRARIES = $(lib_LIBRARIES)\n-AR = ar\n-ARFLAGS = cru\n-libgsoap___a_AR = $(AR) $(ARFLAGS)\n-libgsoap___a_LIBADD =\n-am_libgsoap___a_OBJECTS = libgsoap___a-stdsoap2_cpp.$(OBJEXT) \\\n-\tlibgsoap___a-dom_cpp.$(OBJEXT)\n-libgsoap___a_OBJECTS = $(am_libgsoap___a_OBJECTS)\n-libgsoap_a_AR = $(AR) $(ARFLAGS)\n-libgsoap_a_LIBADD =\n-am_libgsoap_a_OBJECTS = libgsoap_a-stdsoap2.$(OBJEXT) \\\n-\tlibgsoap_a-dom.$(OBJEXT)\n-libgsoap_a_OBJECTS = $(am_libgsoap_a_OBJECTS)\n-libgsoapck___a_AR = $(AR) $(ARFLAGS)\n-libgsoapck___a_LIBADD =\n-am_libgsoapck___a_OBJECTS = libgsoapck___a-stdsoap2_ck_cpp.$(OBJEXT) \\\n-\tlibgsoapck___a-dom_cpp.$(OBJEXT)\n-libgsoapck___a_OBJECTS = $(am_libgsoapck___a_OBJECTS)\n-libgsoapck_a_AR = $(AR) $(ARFLAGS)\n-libgsoapck_a_LIBADD =\n-am_libgsoapck_a_OBJECTS = libgsoapck_a-stdsoap2_ck.$(OBJEXT) \\\n-\tlibgsoapck_a-dom.$(OBJEXT)\n-libgsoapck_a_OBJECTS = $(am_libgsoapck_a_OBJECTS)\n-libgsoapssl___a_AR = $(AR) $(ARFLAGS)\n-libgsoapssl___a_LIBADD =\n-am_libgsoapssl___a_OBJECTS = \\\n-\tlibgsoapssl___a-stdsoap2_ssl_cpp.$(OBJEXT) \\\n-\tlibgsoapssl___a-dom_cpp.$(OBJEXT)\n-libgsoapssl___a_OBJECTS = $(am_libgsoapssl___a_OBJECTS)\n-libgsoapssl_a_AR = $(AR) $(ARFLAGS)\n-libgsoapssl_a_LIBADD =\n-am_libgsoapssl_a_OBJECTS = libgsoapssl_a-stdsoap2_ssl.$(OBJEXT) \\\n-\tlibgsoapssl_a-dom.$(OBJEXT)\n-libgsoapssl_a_OBJECTS = $(am_libgsoapssl_a_OBJECTS)\n-DEFAULT_INCLUDES = -I. -I$(top_builddir)@am__isrc@\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \\\n-\t$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)\n-CCLD = $(CC)\n-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@\n-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \\\n-\t$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)\n-CXXLD = $(CXX)\n-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \\\n-\t-o $@\n-SOURCES = $(libgsoap___a_SOURCES) $(libgsoap_a_SOURCES) \\\n-\t$(libgsoapck___a_SOURCES) $(libgsoapck_a_SOURCES) \\\n-\t$(libgsoapssl___a_SOURCES) $(l'..b'AKE) $(AM_MAKEFLAGS) install-recursive\n-install-exec: install-exec-recursive\n-install-data: install-data-recursive\n-uninstall: uninstall-recursive\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-recursive\n-install-strip:\n-\t$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t `test -z \'$(STRIP)\' || \\\n-\t echo "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'"` install\n-mostlyclean-generic:\n-\n-clean-generic:\n-\t-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-\t-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)\n-clean: clean-recursive\n-\n-clean-am: clean-generic clean-libLIBRARIES mostlyclean-am\n-\n-distclean: distclean-recursive\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-recursive\n-\n-dvi-am:\n-\n-html: html-recursive\n-\n-info: info-recursive\n-\n-info-am:\n-\n-install-data-am: install-includeHEADERS install-nobase_pkgdataDATA\n-\t@$(NORMAL_INSTALL)\n-\t$(MAKE) $(AM_MAKEFLAGS) install-data-hook\n-\n-install-dvi: install-dvi-recursive\n-\n-install-exec-am: install-libLIBRARIES\n-\n-install-html: install-html-recursive\n-\n-install-info: install-info-recursive\n-\n-install-man:\n-\n-install-pdf: install-pdf-recursive\n-\n-install-ps: install-ps-recursive\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-recursive\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-recursive\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic\n-\n-pdf: pdf-recursive\n-\n-pdf-am:\n-\n-ps: ps-recursive\n-\n-ps-am:\n-\n-uninstall-am: uninstall-includeHEADERS uninstall-libLIBRARIES \\\n-\tuninstall-nobase_pkgdataDATA\n-\n-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \\\n-\tinstall-data-am install-strip\n-\n-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \\\n-\tall all-am check check-am clean clean-generic \\\n-\tclean-libLIBRARIES ctags ctags-recursive distclean \\\n-\tdistclean-compile distclean-generic distclean-tags distdir dvi \\\n-\tdvi-am html html-am info info-am install install-am \\\n-\tinstall-data install-data-am install-data-hook install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-includeHEADERS install-info \\\n-\tinstall-info-am install-libLIBRARIES install-man \\\n-\tinstall-nobase_pkgdataDATA install-pdf install-pdf-am \\\n-\tinstall-ps install-ps-am install-strip installcheck \\\n-\tinstallcheck-am installdirs installdirs-am maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \\\n-\tuninstall uninstall-am uninstall-includeHEADERS \\\n-\tuninstall-libLIBRARIES uninstall-nobase_pkgdataDATA\n-\n-\n-stdsoap2_ck.c: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ck.c\n-\n-stdsoap2_cpp.cpp: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_cpp.cpp\n-\n-stdsoap2_ck_cpp.cpp: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ck_cpp.cpp\n-\n-stdsoap2_ssl.c: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ssl.c\n-\n-stdsoap2_ssl_cpp.cpp: stdsoap2.cpp\n-\t$(LN_S) -f $(srcdir)/stdsoap2.cpp stdsoap2_ssl_cpp.cpp\n-dom_cpp.cpp: dom.cpp\n-\t$(LN_S) -f $(srcdir)/dom.cpp dom_cpp.cpp\n-\n-install-data-hook:\n-\t$(LN_S) -f $(top_builddir)/gsoap/src/soapcpp2 $(top_builddir)/gsoap/soapcpp2 || echo "ok, link already exists".\n-\t$(LN_S) -f $(top_builddir)/gsoap/wsdl/wsdl2h $(top_builddir)/gsoap/wsdl2h || echo "ok, link already exists".\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/README.txt
--- a/GEMBASSY-1.0.3/gsoap/bin/README.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-This directory contains pre-built soapcpp2 and wsdl2h executables:
-
-macosx MAC OS X universal binaries
-win32 Windows 386 compatible
-linux386 Linux i386 compatible
-
-For other platforms: see installation instructions in the root directory.

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/linux386/soapcpp2

Binary file GEMBASSY-1.0.3/gsoap/bin/linux386/soapcpp2 has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/linux386/wsdl2h

Binary file GEMBASSY-1.0.3/gsoap/bin/linux386/wsdl2h has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/macosx/soapcpp2

Binary file GEMBASSY-1.0.3/gsoap/bin/macosx/soapcpp2 has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/macosx/wsdl2h

Binary file GEMBASSY-1.0.3/gsoap/bin/macosx/wsdl2h has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/win32/soapcpp2.exe

Binary file GEMBASSY-1.0.3/gsoap/bin/win32/soapcpp2.exe has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/bin/win32/wsdl2h.exe

Binary file GEMBASSY-1.0.3/gsoap/bin/win32/wsdl2h.exe has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/README.txt
--- a/GEMBASSY-1.0.3/gsoap/custom/README.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,69 +0,0 @@
-
-OVERVIEW
-
-This directory contains custom serializers for common data types.
-
-CONTENTS
-
-Custom serializers replace the soapcpp2-generated serialization routines.
-See the notes in the source files on specific usage.
-
-The following serializers are available:
-
-long_double.* Serializes long double (extended double) type
-struct_tm.* Serializes <time.h> struct tm
-struct_timeval.* Serializes struct timeval (precision in usec)
-duration.* Serializes LONG64 values as xsd:duration
-
-USAGE
-
-To use a custom serializer add an import statement to your gSOAP header file:
-
-#import "struct_tm.h"
-
-This replaces time_t for xsd__dateTime by struct tm. You can use xsd__dateTime
-as XML elements and attributes:
-
-struct ns__example
-{ @xsd__dateTime start; // attribute
- xsd__dateTime end; // element
-};
-
-Then compile with soapcpp2 and cc and link struct_tm.c
-
-HOW TO MODIFY TYPEMAP.DAT TO AUTOMATE THE MAPPING TO A CUSTOM TYPE WITH WSDL2H
-
-The mapping is specified in typemap.dat as follows:
-
-xsd__dateTime = #import "custom/struct_tm.h"
-
-which maps xsd:dateTime to struct tm when wsdl2h is applied to a WSDL.
-
-xsd__decimal = #import "custom/long_double.h" | long double
-
-this maps xsd:decimal to long double (the column after | specifies usage).
-
-IMPLEMENTING YOUR OWN CUSTOM SERIALIZERS
-
-To build your own custom serializers: a custom serializer is typically declared
-in the imported file as follows
-
-extern typedef Type X;
-
-To implement custom serializers you should implement the following routines:
-
-void soap_default_X(struct soap*, X*);
- sets default values for X
-void soap_serialize_X(struct soap*, const X*);
- analyzes X for id-ref serialization (maybe empty)
-int soap_out_X(struct soap*, const char *tag, int id, const X*, const char *type);
- emits X in XML as <tag xsi:type=type> (type is optional)
-X *soap_in_X(struct soap*, const char *tag, X*, const char *type);
- parses X from XML as <tag xsi:type=type>
-
-To support XML attribute serialization, you should also define:
-
-int soap_s2X(struct soap*, const char *value, X*);
- converts string to X and returns SOAP_OK
-const char *soap_X2s(struct soap*, X);
- converts X to string (or NULL when error)

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/duration.c
--- a/GEMBASSY-1.0.3/gsoap/custom/duration.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,208 +0,0 @@
-/*
- duration.c
-
- Custom serializer for xsd:duration stored in a LONG64 with ms precision
- - the LONG64 int can represent 106751991167 days forward and backward
- - LONG64 is long long int under Unix/Linux
- - millisecond resolution (1/1000 sec) means 1 second = 1000
- - when adding to a time_t value, conversion may be needed since time_t
-   may (or may) not have seconds resolution
- - durations longer than a month are always output in days, rather than
-   months to avoid days-per-month conversion
- - durations expressed in years and months are not well defined, since
-   there is no reference starting time; the decoder assumes 30 days per
-   month and conversion of P4M gives 120 days and therefore the duration
-   P4M and P120D are assumed identical, while they may yield different
-   result depending on the reference starting time
-
- Compile this file and link it with your code.
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2009, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2009, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-/* soapH.h generated by soapcpp2 from .h file containing #import "duration.h":*/
-#include "soapH.h"
-
-void soap_default_xsd__duration(struct soap *soap, LONG64 *a)
-{ (void)soap; /* appease -Wall -Werror */
-  *a = 0;
-}
-
-const char *soap_xsd__duration2s(struct soap *soap, LONG64 a)
-{ LONG64 d;
-  int k, h, m, s, f;
-  if (a < 0)
-  { strcpy(soap->tmpbuf, "-P");
-    k = 2;
-    a = -a;
-  }
-  else
-  { strcpy(soap->tmpbuf, "P");
-    k = 1;
-  }
-  f = a % 1000;
-  a /= 1000;
-  s = a % 60;
-  a /= 60;
-  m = a % 60;
-  a /= 60;
-  h = a % 24;
-  d = a / 24;
-  if (d)
-    sprintf(soap->tmpbuf + k, SOAP_LONG_FORMAT "D", d);
-  if (h || m || s || f)
-  { if (d)
-      k = strlen(soap->tmpbuf);
-    if (f)
-      sprintf(soap->tmpbuf + k, "T%dH%dM%d.%03dS", h, m, s, f);
-    else
-      sprintf(soap->tmpbuf + k, "T%dH%dM%dS", h, m, s);
-  }
-  else if (!d)
-    strcpy(soap->tmpbuf + k, "T0S");
-  return soap->tmpbuf;
-}
-
-int soap_out_xsd__duration(struct soap *soap, const char *tag, int id, const LONG64 *a, const char *type)
-{ if (soap_element_begin_out(soap, tag, soap_embedded_id(soap, id, a, SOAP_TYPE_xsd__duration), type)
-   || soap_string_out(soap, soap_xsd__duration2s(soap, *a), 0))
-    return soap->error;
-  return soap_element_end_out(soap, tag);
-}
-
-int soap_s2xsd__duration(struct soap *soap, const char *s, LONG64 *a)
-{ LONG64 sign = 1, Y = 0, M = 0, D = 0, H = 0, N = 0, S = 0;
-  float f = 0;
-  *a = 0;
-  if (s)
-  { if (*s == '-')
-    { sign = -1;
-      s++;
-    }
-    if (*s++ != 'P')
-      return soap->error = SOAP_TYPE;
-    /* date part */
-    while (s && *s)
-    { LONG64 n;
-      char k;
-      if (*s == 'T')
-      { s++;
- break;
-      }
-      if (sscanf(s, SOAP_LONG_FORMAT "%c", &n, &k) != 2)
- return soap->error = SOAP_TYPE;
-      s = strchr(s, k);
-      if (!s)
- return soap->error = SOAP_TYPE;
-      switch (k)
-      { case 'Y':
-   Y = n;
-   break;
- case 'M':
-   M = n;
-   break;
- case 'D':
-   D = n;
-   break;
- default:
-   return soap->error = SOAP_TYPE;
-      }
-      s++;
-    }
-    /* time part */
-    while (s && *s)
-    { LONG64 n;
-      char k;
-      if (sscanf(s, SOAP_LONG_FORMAT "%c", &n, &k) != 2)
- return soap->error = SOAP_TYPE;
-      s = strchr(s, k);
-      if (!s)
- return soap->error = SOAP_TYPE;
-      switch (k)
-      { case 'H':
-   H = n;
-   break;
- case 'M':
-   N = n;
-   break;
- case '.':
-   S = n;
-   if (sscanf(s, "%g", &f) != 1)
-     return soap->error = SOAP_TYPE;
-   s = NULL;
-   continue;
- case 'S':
-   S = n;
-   break;
- default:
-   return soap->error = SOAP_TYPE;
-      }
-      s++;
-    }
-    /* convert Y-M-D H:N:S.f to signed long long int */
-    *a = sign * ((((((((((((Y * 12) + M) * 30) + D) * 24) + H) * 60) + N) * 60) + S) * 1000) + (long)(1000.0 * f));
-  }
-  return soap->error;
-}
-
-LONG64 *soap_in_xsd__duration(struct soap *soap, const char *tag, LONG64 *a, const char *type)
-{ if (soap_element_begin_in(soap, tag, 0, NULL))
-    return NULL;
-  if (*soap->type
-   && soap_match_tag(soap, soap->type, type)
-   && soap_match_tag(soap, soap->type, ":duration"))
-  { soap->error = SOAP_TYPE;
-    soap_revert(soap);
-    return NULL;
-  }
-  a = (LONG64*)soap_id_enter(soap, soap->id, a, SOAP_TYPE_xsd__duration, sizeof(LONG64), 0, NULL, NULL, NULL);
-  if (*soap->href)
-    a = (LONG64*)soap_id_forward(soap, soap->href, a, 0, SOAP_TYPE_xsd__duration, 0, sizeof(LONG64), 0, NULL);
-  else if (a)
-  { if (soap_s2xsd__duration(soap, soap_value(soap), a))
-      return NULL;
-  }
-  if (soap->body && soap_element_end_in(soap, tag))
-    return NULL;
-  return a;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/duration.h
--- a/GEMBASSY-1.0.3/gsoap/custom/duration.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,72 +0,0 @@
-/*
- duration.h
-
- Custom serializer for xsd:duration stored in a LONG64 with ms precision
- - a LONG64 int can represent 106751991167 days forward and backward
- - LONG64 is long long int under Unix/Linux
- - millisecond resolution (1/1000 sec) means 1 second = 1000
- - when adding to a time_t value, conversion may be needed since time_t
-   may (or may) not have seconds resolution
- - durations longer than a month are always output in days, rather than
-   months to avoid days-per-month conversion inacurracies
- - durations expressed in years and months are not well defined, since
-   there is no reference starting time; the decoder assumes 30 days per
-   month and conversion of P4M gives 120 days and therefore the duration
-   P4M and P120D are assumed identical, while they should give different
-   results depending on the reference starting time
-
- #import this file into your gSOAP .h file
-
- To automate the wsdl2h-mapping of xsd:dateTime to struct tm, add this
- line to the typemap.dat file:
-
- xsd__duration = #import "custom/duration.h" | xsd__duration
-
- The typemap.dat file is used by wsdl2h to map types (wsdl2h option -t).
-
- Compile and link your code with custom/duration.c
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2009, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2009, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-extern typedef long long xsd__duration; /* duration in ms (1/1000 sec) */

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/long_double.c
--- a/GEMBASSY-1.0.3/gsoap/custom/long_double.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,135 +0,0 @@
-/*
- long_double.c
-
- Custom serializer for the long double (extended double) type as
- xsd:decimal.
-
- Compile this file and link it with your code.
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2007, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2007, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-/* soapH.h generated by soapcpp2: */
-#include "soapH.h"
-#include <float.h>
-
-int soap_s2decimal(struct soap *soap, const char *s, long double *p)
-{ if (s)
-  { if (!*s)
-      return soap->error = SOAP_TYPE;
-    if (!soap_tag_cmp(s, "INF"))
-      *p = (long double)DBL_PINFTY;
-    else if (!soap_tag_cmp(s, "+INF"))
-      *p = (long double)DBL_PINFTY;
-    else if (!soap_tag_cmp(s, "-INF"))
-      *p = (long double)DBL_NINFTY;
-    else if (!soap_tag_cmp(s, "NaN"))
-      *p = (long double)DBL_NAN;
-    else
-    {
-#if defined(HAVE_STRTOLD_L)
-      char *r;
-      *p = strtold_l(s, &r, NULL);
-      if (*r)
-#elif defined(HAVE_STRTOLD)
-      char *r;
-      *p = strtold(s, &r);
-      if (*r)
-#endif
-#if defined(HAVE_SSCANF_L)
-        if (sscanf_l(s, NULL, "%Lg", p) != 1)
-          soap->error = SOAP_TYPE;
-#elif defined(HAVE_SSCANF)
-        if (sscanf(s, "%Lg", p) != 1)
-          soap->error = SOAP_TYPE;
-#else
-        soap->error = SOAP_TYPE;
-#endif
-    }
-  }
-  return soap->error;
-}
-
-const char *soap_decimal2s(struct soap *soap, long double n)
-{ char *s;
-  if (soap_isnan(n))
-    return "NaN";
-  if (soap_ispinfd(n))
-    return "INF";
-  if (soap_isninfd(n))
-    return "-INF";
-  s = soap->tmpbuf;
-#if defined(HAVE_SPRINTF_L)
-  sprintf_l(s, NULL, "%.*Lg", LDBL_DIG, n);
-#else
-  sprintf(s, "%.*Lg", LDBL_DIG, n);
-  s = strchr(s, ',');   /* convert decimal comma to DP */
-  if (s)
-    *s = '.';
-#endif
-  return soap->tmpbuf;
-}
-
-int
-soap_outdecimal(struct soap *soap, const char *tag, int id, const long double *p, const char *type, int n)
-{ if (soap_element_begin_out(soap, tag, soap_embedded_id(soap, id, p, n), type)
-   || soap_string_out(soap, soap_decimal2s(soap, *p), 0))
-    return soap->error;
-  return soap_element_end_out(soap, tag);
-}
-
-long double *
-soap_indecimal(struct soap *soap, const char *tag, long double *p, const char *type, int t)
-{ if (soap_element_begin_in(soap, tag, 0, type))
-    return NULL;
-  p = (long double*)soap_id_enter(soap, soap->id, p, t, sizeof(long double), 0, NULL, NULL, NULL);
-  if (*soap->href)
-    p = (long double*)soap_id_forward(soap, soap->href, p, 0, t, 0, sizeof(long double), 0, NULL);
-  else if (p)
-  { if (soap_s2decimal(soap, soap_value(soap), p))
-      return NULL;
-  }
-  if (soap->body && soap_element_end_in(soap, tag))
-    return NULL;
-  return p;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/long_double.h
--- a/GEMBASSY-1.0.3/gsoap/custom/long_double.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,59 +0,0 @@
-/*
- long_double.h
-
- Custom serializer for the long double (extended double) type as
- xsd:decimal.
-
- #import this file into your gSOAP .h file.
-
- Add this line:
- xsd__decimal = #import "custom/long_double.h" | long double
- to typemap.dat to automate the mapping with wsdl2h.
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2008, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2008, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-extern int soap_s2decimal(struct soap *soap, const char *s, long double *p);
-extern const char *soap_decimal2s(struct soap *soap, long double n);
-extern int soap_outdecimal(struct soap*, const char*, int, const long double*, const char*, int);
-extern long double *soap_indecimal(struct soap*, const char*, long double*, const char*, int);

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/struct_timeval.c
--- a/GEMBASSY-1.0.3/gsoap/custom/struct_timeval.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,179 +0,0 @@
-/*
- struct_timeval.c
-
- Custom serializer for struct timeval
-
- Compile this file and link it with your code.
-
- Changes:
- Feb 8, 2008: fixed local time to internal GMT conversion
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2008, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2008, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-/* soapH.h generated by soapcpp2 from .h file containing #import "struct_timeval.h": */
-#include "soapH.h"
-
-void soap_default_xsd__dateTime(struct soap *soap, struct timeval *a)
-{ memset(a, 0, sizeof(struct timeval));
-}
-
-void soap_serialize_xsd__dateTime(struct soap *soap, struct timeval const *a)
-{ }
-
-const char *soap_xsd__dateTime2s(struct soap *soap, const struct timeval a)
-{ char *s = soap->tmpbuf;
-  size_t n;
-  soap_dateTime2s(soap, a.tv_sec); /* assuming result is in tmpbuf! */
-  n = strlen(s);
-  if (s[n-1] == 'Z')
-    n--;
-  sprintf(s + n, ".%.6dZ", a.tv_usec);
-  return s;
-}
-
-int soap_out_xsd__dateTime(struct soap *soap, const char *tag, int id, const struct timeval *a, const char *type)
-{ if (soap_element_begin_out(soap, tag, soap_embedded_id(soap, id, a, SOAP_TYPE_xsd__dateTime), type)
-   || soap_string_out(soap, soap_xsd__dateTime2s(soap, *a), 0))
-    return soap->error;
-  return soap_element_end_out(soap, tag);
-}
-
-int soap_s2xsd__dateTime(struct soap *soap, const char *s, struct timeval *a)
-{ memset((void*)a, 0, sizeof(struct timeval));
-  if (s)
-  { char rest[32];
-    const char *t;
-    struct tm tm;
-    memset((void*)&tm, 0, sizeof(struct tm));
-    rest[sizeof(rest)-1] = '\0';
-    if (strchr(s, '-'))
-      t = "%d-%d-%dT%d:%d:%d%31s";
-    else if (strchr(s, ':'))
-      t = "%4d%2d%2dT%d:%d:%d%31s";
-    else /* parse non-XSD-standard alternative ISO 8601 format */
-      t = "%4d%2d%2dT%2d%2d%2d%31s";
-    if (sscanf(s, t, &tm.tm_year, &tm.tm_mon, &tm.tm_mday, &tm.tm_hour, &tm.tm_min, &tm.tm_sec, rest) < 6)
-      return soap->error = SOAP_TYPE;
-    tm.tm_wday = -1;
-    tm.tm_yday = -1;
-    if (tm.tm_year == 1)
-      tm.tm_year = 70;
-    else
-      tm.tm_year -= 1900;
-    tm.tm_mon--;
-    tm.tm_isdst = 0;
-    if (*rest)
-    { if (*rest == '.')
-      { double f = 0;
-        for (s = rest + 1; *s; s++)
-          if (*s < '0' || *s > '9')
-            break;
- sscanf(rest, "%lg", &f);
-        a->tv_usec = (int)(f*1000000.0);
-      }
-      else
-      { s = rest;
-        a->tv_usec = 0;
-      }
-    }
-    if (*s)
-    { if (*s == '+' || *s == '-')
-      { int h = 0, m = 0;
-        if (s[3] == ':')
-        { /* +hh:mm */
-   sscanf(s, "%d:%d", &h, &m);
-          if (h < 0)
-            m = -m;
-        }
-        else /* +hhmm */
-        { m = (int)atol(s);
-          h = m / 100;
-          m = m % 100;
-        }
-        tm.tm_hour -= h;
-        tm.tm_min -= m;
- /* put hour and min in range */
-        tm.tm_hour += tm.tm_min / 60;
-        tm.tm_min %= 60;
-        if (tm.tm_min < 0)
-        { tm.tm_min += 60;
-   tm.tm_hour--;
-        }
-        tm.tm_mday += tm.tm_hour / 24;
-        tm.tm_hour %= 24;
-        if (tm.tm_hour < 0)
-        { tm.tm_hour += 24;
-          tm.tm_mday--;
-        }
- /* note: day of the month may be out of range, timegm() handles it */
-      }
-      a->tv_sec = soap_timegm(&tm);
-    }
-    else
-      a->tv_sec = mktime(&tm);
-  }
-  return soap->error;
-}
-
-struct timeval *soap_in_xsd__dateTime(struct soap *soap, const char *tag, struct timeval *a, const char *type)
-{ if (soap_element_begin_in(soap, tag, 0, NULL))
-    return NULL;
-  if (*soap->type
-   && soap_match_tag(soap, soap->type, type)
-   && soap_match_tag(soap, soap->type, ":dateTime"))
-  { soap->error = SOAP_TYPE;
-    soap_revert(soap);
-    return NULL;
-  }
-  a = (struct timeval*)soap_id_enter(soap, soap->id, a, SOAP_TYPE_xsd__dateTime, sizeof(struct timeval), 0, NULL, NULL, NULL);
-  if (*soap->href)
-    a = (struct timeval*)soap_id_forward(soap, soap->href, a, 0, SOAP_TYPE_xsd__dateTime, 0, sizeof(struct timeval), 0, NULL);
-  else if (a)
-  { if (soap_s2xsd__dateTime(soap, soap_value(soap), a))
-      return NULL;
-  }
-  if (soap->body && soap_element_end_in(soap, tag))
-    return NULL;
-  return a;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/struct_timeval.h
--- a/GEMBASSY-1.0.3/gsoap/custom/struct_timeval.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,66 +0,0 @@
-/*
- struct_timeval.h
-
- Custom serializer for struct timeval
-
- #import this file into your gSOAP .h file to enable struct timeval
- serialization and use the serializable xsd__dateTime type.
-
- To automate the wsdl2h-mapping of xsd:dateTime to struct timeval, add
- this line to the typemap.dat file:
-
- xsd__dateTime = #import "custom/struct_timeval.h" | xsd__dateTime
-
- The typemap.dat file is used by wsdl2h to map types (wsdl2h option -t).
-
- Link your code with struct_timeval.c
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2007, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2007, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-#include <sys/time.h>
-
-extern typedef volatile struct timeval
-{ extern long tv_sec; // transient member: don't serialize
- extern long tv_usec; // transient member: don't serialize
-} xsd__dateTime;

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/struct_tm.c
--- a/GEMBASSY-1.0.3/gsoap/custom/struct_tm.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,180 +0,0 @@
-/*
- struct_tm.c
-
- Custom serializer for <time.h> struct tm
-
- Compile this file and link it with your code.
-
- Changes:
- Feb 8, 2008: fixed local time to internal GMT conversion
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2008, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2008, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-/* soapH.h generated by soapcpp2 from .h file containing #import "struct_tm.h": */
-#include "soapH.h"
-
-void soap_default_xsd__dateTime(struct soap *soap, struct tm *a)
-{ memset(a, 0, sizeof(struct tm));
-}
-
-void soap_serialize_xsd__dateTime(struct soap *soap, struct tm const *a)
-{ }
-
-const char *soap_xsd__dateTime2s(struct soap *soap, const struct tm a)
-{ strftime(soap->tmpbuf, sizeof(soap->tmpbuf), "%Y-%m-%dT%H:%M:%SZ", &a);
-  return soap->tmpbuf;
-}
-
-int soap_out_xsd__dateTime(struct soap *soap, const char *tag, int id, const struct tm *a, const char *type)
-{ if (soap_element_begin_out(soap, tag, soap_embedded_id(soap, id, a, SOAP_TYPE_xsd__dateTime), type)
-   || soap_string_out(soap, soap_xsd__dateTime2s(soap, *a), 0))
-    return soap->error;
-  return soap_element_end_out(soap, tag);
-}
-
-int soap_s2xsd__dateTime(struct soap *soap, const char *s, struct tm *a)
-{ memset((void*)a, 0, sizeof(struct tm));
-  if (s)
-  { char zone[32];
-    const char *t;
-    if (strchr(s, '-'))
-      t = "%d-%d-%dT%d:%d:%d%31s";
-    else if (strchr(s, ':'))
-      t = "%4d%2d%2dT%d:%d:%d%31s";
-    else /* parse non-XSD-standard alternative ISO 8601 format */
-      t = "%4d%2d%2dT%2d%2d%2d%31s";
-    if (sscanf(s, t, &a->tm_year, &a->tm_mon, &a->tm_mday, &a->tm_hour, &a->tm_min, &a->tm_sec, zone) < 6)
-      return soap->error = SOAP_TYPE;
-    a->tm_wday = -1;
-    a->tm_yday = -1;
-    if (a->tm_year == 1)
-      a->tm_year = 70;
-    else
-      a->tm_year -= 1900;
-    a->tm_mon--;
-    if (*zone == '.')
-    { for (s = zone + 1; *s; s++)
-        if (*s < '0' || *s > '9')
-          break;
-    }
-    else
-      s = zone;
-    if (*s)
-    { if (*s == '+' || *s == '-')
-      { int h = 0, m = 0;
-        if (s[3] == ':')
-        { /* +hh:mm */
-   sscanf(s, "%d:%d", &h, &m);
-          if (h < 0)
-            m = -m;
-        }
-        else /* +hhmm */
-        { m = (int)atol(s);
-          h = m / 100;
-          m = m % 100;
-        }
-        a->tm_hour -= h;
-        a->tm_min -= m;
-      }
-    }
-    else /* if no time zone then convert to internal GMT without considering DST */
-    { int minuteswest;
-#if defined(HAVE_GETTIMEOFDAY)
-      struct timeval tv;
-      struct timezone tz;
-      gettimeofday(&tv, &tz);
-      minuteswest = tz.tz_minuteswest;
-#elif defined(HAVE_FTIME)
-      struct timeb tb;
-      memset((void*)&tb, 0, sizeof(tb));
-#ifdef __BORLAND__
-      ::ftime(&tb);
-#else
-      ftime(&tb);
-#endif
-      minuteswest = tb.timezone;
-#else
-      /* local timezone unknown */
-      minuteswest = 0;
-#endif
-      a->tm_min += minuteswest;
-    }
-    /* put hour and min in range */
-    a->tm_hour += a->tm_min / 60;
-    a->tm_min %= 60;
-    if (a->tm_min < 0)
-    { a->tm_min += 60;
-      a->tm_hour--;
-    }
-    a->tm_mday += a->tm_hour / 24;
-    a->tm_hour %= 24;
-    if (a->tm_hour < 0)
-    { a->tm_hour += 24;
-      a->tm_mday--;
-    }
-  }
-  return soap->error;
-}
-
-struct tm *soap_in_xsd__dateTime(struct soap *soap, const char *tag, struct tm *a, const char *type)
-{ if (soap_element_begin_in(soap, tag, 0, NULL))
-    return NULL;
-  if (*soap->type
-   && soap_match_tag(soap, soap->type, type)
-   && soap_match_tag(soap, soap->type, ":dateTime"))
-  { soap->error = SOAP_TYPE;
-    soap_revert(soap);
-    return NULL;
-  }
-  a = (struct tm*)soap_id_enter(soap, soap->id, a, SOAP_TYPE_xsd__dateTime, sizeof(struct tm), 0, NULL, NULL, NULL);
-  if (*soap->href)
-    a = (struct tm*)soap_id_forward(soap, soap->href, a, 0, SOAP_TYPE_xsd__dateTime, 0, sizeof(struct tm), 0, NULL);
-  else if (a)
-  { if (soap_s2xsd__dateTime(soap, soap_value(soap), a))
-      return NULL;
-  }
-  if (soap->body && soap_element_end_in(soap, tag))
-    return NULL;
-  return a;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/custom/struct_tm.h
--- a/GEMBASSY-1.0.3/gsoap/custom/struct_tm.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,75 +0,0 @@
-/*
- struct_tm.h
-
- Custom serializer for <time.h> struct tm
-
- #import this file into your gSOAP .h file to enable struct tm
- serialization and use the serializable xsd__dateTime type.
-
- To automate the wsdl2h-mapping of xsd:dateTime to struct tm, add this
- line to the typemap.dat file:
-
- xsd__dateTime = #import "custom/struct_tm.h" | xsd__dateTime
-
- The typemap.dat file is used by wsdl2h to map types (wsdl2h option -t).
-
- Link your code with custom/struct_tm.c
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2007, Robert van Engelen, Genivia Inc., All Rights Reserved.
-This part of the software is released under ONE of the following licenses:
-GPL, the gSOAP public license, OR Genivia's license for commercial use.
---------------------------------------------------------------------------------
-gSOAP public license.
-
-The contents of this file are subject to the gSOAP Public License Version 1.3
-(the "License"); you may not use this file except in compliance with the
-License. You may obtain a copy of the License at
-http://www.cs.fsu.edu/~engelen/soaplicense.html
-Software distributed under the License is distributed on an "AS IS" basis,
-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
-for the specific language governing rights and limitations under the License.
-
-The Initial Developer of the Original Code is Robert A. van Engelen.
-Copyright (C) 2000-2007, Robert van Engelen, Genivia, Inc., All Rights Reserved.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-#include <time.h>
-
-/** externally declared, replicated here as a copy (gSOAP volatile) */
-extern typedef volatile struct tm
-{ int tm_sec; //< seconds (0 - 60)
- int tm_min; //< minutes (0 - 59)
- int tm_hour; //< hours (0 - 23)
- int tm_mday; //< day of month (1 - 31)
- int tm_mon; //< month of year (0 - 11)
- int tm_year; //< year - 1900
- int tm_wday; //< day of week (Sunday = 0)
- int tm_yday; //< day of year (0 - 365)
- int tm_isdst; //< is summer time in effect?
- char* tm_zone; //< abbreviation of timezone (not used)
-} xsd__dateTime;

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/dom.c
--- a/GEMBASSY-1.0.3/gsoap/dom.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1142 +0,0 @@\n-/*\n-\tdom.c[pp]\n-\n-\tgSOAP DOM implementation v3\n-\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2012, Robert van Engelen, Genivia, Inc. All Rights Reserved.\n-This part of the software is released under ONE of the following licenses:\n-GPL, or the gSOAP public license, or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-gSOAP public license.\n-\n-The contents of this file are subject to the gSOAP Public License Version 1.3\n-(the "License"); you may not use this file except in compliance with the\n-License. You may obtain a copy of the License at\n-http://www.cs.fsu.edu/~engelen/soaplicense.html\n-Software distributed under the License is distributed on an "AS IS" basis,\n-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License\n-for the specific language governing rights and limitations under the License.\n-\n-The Initial Developer of the Original Code is Robert A. van Engelen.\n-Copyright (C) 2000-2012 Robert A. van Engelen, Genivia inc. All Rights Reserved.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#include "stdsoap2.h"\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serialize_xsd__anyType(struct soap*, struct soap_dom_element const*);\n-SOAP_FMAC3 void SOAP_FMAC4 soap_traverse_xsd__anyType(struct soap*, struct soap_dom_element*, const char*, soap_walker, soap_walker);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_default_xsd__anyType(struct soap*, struct soap_dom_element *);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_xsd__anyType(struct soap*, const struct soap_dom_element *, const char*, const char*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_out_xsd__anyType(struct soap*, const char*, int, const struct soap_dom_element *, const char*);\n-SOAP_FMAC3 struct soap_dom_element * SOAP_FMAC4 soap_get_xsd__anyType(struct soap*, struct soap_dom_element *, const char*, const char*);\n-SOAP_FMAC1 struct soap_dom_element * SOAP_FMAC2 soap_in_xsd__anyType(struct soap*, const char*, struct soap_dom_element *, const char*);\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serialize_xsd__anyAttribute(struct soap*, struct soap_dom_attribute const*);\n-SOAP_FMAC3 void SOAP_FMAC4 soap_traverse_xsd__anyAttribute(struct soap*, struct soap_dom_attribute*, const char*, soap_walker, soap_walker);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_default_xsd__anyAttribute(struct soap*, struct soap_dom_attribute *);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_xsd__anyAttribute(struct soap*, const struct soap_dom_attribute *, const char*, const char*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_out_xsd__anyAttribute(struct soap*, const char*, int, const struct soap_dom_attribute *, const char*);\n-SOAP_FMAC3 struct soap_dom_attribute * SOAP_FMAC4 soap_get_xsd__anyAttribute(struct soap*, struct soap_dom_attribute *, const char*, const char*);\n-SOAP_FMAC1 struct soap_dom_attribu'..b'is->elt;\n-}\n-\n-/******************************************************************************/\n-\n-soap_dom_element_iterator &soap_dom_element_iterator::operator++()\n-{ while (elt)\n- { elt = soap_dom_next_element(elt);\n- if (!elt)\n- break;\n- if (name && elt->name)\n- { if (!soap_tag_cmp(elt->name, name))\n- { if (nstr && elt->nstr)\n- { if (!soap_tag_cmp(elt->nstr, nstr))\n-\t break;\n- }\n- else\n- break;\n- }\n- }\n- else if (type)\n- { if (elt->type == type)\n- break;\n- }\n- else\n- break;\n- }\n- return *this;\n-}\n-\n-/******************************************************************************\\\n- *\n- *\tsoap_dom_attribute_iterator class\n- *\n-\\******************************************************************************/\n-\n-soap_dom_attribute_iterator::soap_dom_attribute_iterator()\n-{ att = NULL;\n- nstr = NULL;\n- name = NULL;\n-}\n-\n-/******************************************************************************/\n-\n-soap_dom_attribute_iterator::soap_dom_attribute_iterator(struct soap_dom_attribute *att)\n-{ this->att = att;\n- nstr = NULL;\n- name = NULL;\n-}\n-\n-/******************************************************************************/\n-\n-soap_dom_attribute_iterator::~soap_dom_attribute_iterator()\n-{ }\n-\n-/******************************************************************************/\n-\n-bool soap_dom_attribute_iterator::operator==(const soap_dom_attribute_iterator &iter) const\n-{ return this->att == iter.att;\n-}\n-\n-/******************************************************************************/\n-\n-bool soap_dom_attribute_iterator::operator!=(const soap_dom_attribute_iterator &iter) const\n-{ return this->att != iter.att;\n-}\n-\n-/******************************************************************************/\n-\n-struct soap_dom_attribute &soap_dom_attribute_iterator::operator*() const\n-{ return *this->att;\n-}\n-\n-/******************************************************************************/\n-\n-soap_dom_attribute_iterator &soap_dom_attribute_iterator::operator++()\n-{ while (att)\n- { att = soap_dom_next_attribute(att);\n- if (!att)\n- break;\n- if (name && att->name)\n- { if (!soap_tag_cmp(att->name, name))\n- { if (nstr && att->nstr)\n- { if (!soap_tag_cmp(att->nstr, nstr))\n-\t break;\n- }\n- else\n- break;\n- }\n- }\n- else\n- break;\n- }\n- return *this;\n-}\n-\n-/******************************************************************************\\\n- *\n- *\tI/O\n- *\n-\\******************************************************************************/\n-\n-#ifndef UNDER_CE\n-\n-std::ostream &operator<<(std::ostream &o, const struct soap_dom_element &e)\n-{ if (!e.soap)\n- { struct soap soap;\n- soap_init2(&soap, SOAP_IO_DEFAULT, SOAP_XML_GRAPH);\n- soap_serialize_xsd__anyType(&soap, &e);\n- soap_begin_send(&soap);\n- soap.ns = 2; /* do not dump namespace table */\n- soap_out_xsd__anyType(&soap, NULL, 0, &e, NULL);\n- soap_end_send(&soap);\n- soap_end(&soap);\n- soap_done(&soap);\n- }\n- else\n- { std::ostream *os = e.soap->os;\n- e.soap->os = &o;\n- soap_mode omode = e.soap->omode;\n- soap_set_omode(e.soap, SOAP_XML_GRAPH);\n- soap_serialize_xsd__anyType(e.soap, &e);\n- soap_begin_send(e.soap);\n- e.soap->ns = 2; /* do not dump namespace table */\n- soap_out_xsd__anyType(e.soap, NULL, 0, &e, NULL);\n- soap_end_send(e.soap);\n- e.soap->os = os;\n- e.soap->omode = omode;\n- }\n- return o;\n-}\n-\n-/******************************************************************************/\n-\n-std::istream &operator>>(std::istream &i, struct soap_dom_element &e)\n-{ if (!e.soap)\n- e.soap = soap_new();\n- std::istream *is = e.soap->is;\n- e.soap->is = &i;\n- if (soap_begin_recv(e.soap)\n- || !soap_in_xsd__anyType(e.soap, NULL, &e, NULL)\n- || soap_end_recv(e.soap))\n- { /* handle error? Note: e.soap->error is set and app should check */\n- }\n- e.soap->is = is;\n- return i;\n-}\n-\n-#endif\n-\n-#endif\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/dom.cpp
--- a/GEMBASSY-1.0.3/gsoap/dom.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/README.txt
--- a/GEMBASSY-1.0.3/gsoap/extras/README.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
-
-The 'extras' directory contains useful additions.
-
-All contributions are covered by the gSOAP public license, unless specifically
-stated otherwise in the source. The following authors provided the
-contributions included in this directory:
-
-ckdb.h ckdb.c Simple Cookie database manager (store/load)
-ckdbtest.h ckdbtest.c Test code for Simple Cookie database manager
-fault.cpp Print SOAP Fault messages to C++ streams
-logging.cpp Log send, receive, and trace messages on streams
-soapdefs.h To enable logging
-
-fault.cpp contributed by A. Kelly
-logging.cpp contributed by M. Helmick

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/ckdb.c
--- a/GEMBASSY-1.0.3/gsoap/extras/ckdb.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,89 +0,0 @@
-/*
- ckdb.c
-
- HTTP cookie database manager.
-
- The contents of this file are subject to the gSOAP Public License
- Version 1.0 (the "License"); you may not use this file except in
- compliance with the License. You may obtain a copy of the License at
- http://www.cs.fsu.edu/~engelen/soaplicense.html Software distributed
- under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY
- OF ANY KIND, either express or implied. See the License for the
- specific language governing rights and limitations under the License.
-
- The Initial Developer of the Original Code is Robert A. van Engelen.
- Copyright (C) 2000-2002 Robert A. van Engelen. All Rights Reserved.
-
-1. Compile ckdb.h:
-   soapcpp2 -cpckdb ckdb.h
-2. Compile ckdb.c:
-   gcc -DWITH_COOKIES -DWITH_NOGLOBAL -c ckdb.c
-3. Compile and link with main program, e.g. ckdbtest.c:
-   soapcpp2 -c ckdbtest.h
-   gcc -DWITH_COOKIES ckdbtest.c ckdb.o stdsoap2.c soapC.c soapClient.c
-
-*/
-
-#include <sys/stat.h>
-#include "stdsoap2.h"
-#define WITH_NOGLOBAL
-#undef SOAP_FMAC3
-#define SOAP_FMAC3 static
-#include "ckdbC.c"
-
-int soap_save_cookies(struct soap *soap, const char *pathname)
-{ int socket = soap->socket;
-  int sendfd = soap->sendfd;
-  soap_begin(soap);
-  soap->socket = -1; /* make sure plain I/O is used */
-  soap->sendfd = open(pathname, O_CREAT|O_TRUNC|O_WRONLY, S_IREAD|S_IWRITE);
-  if (soap->sendfd >= 0)
-  { soap_serialize_cookie(soap, (struct cookie*)soap->cookies);
-    soap_begin_send(soap);
-    soap_put_cookie(soap, (struct cookie*)soap->cookies, "jar", NULL);
-    soap_end_send(soap);
-    close(soap->sendfd);
-    soap->socket = socket;
-    soap->sendfd = sendfd;
-    return SOAP_OK;
-  }
-  soap->socket = socket;
-  soap->sendfd = sendfd;
-  return SOAP_EOF;
-}
-
-int soap_load_cookies(struct soap *soap, const char *pathname)
-{ int socket = soap->socket;
-  int recvfd = soap->recvfd;
-  soap_begin(soap);
-  soap->socket = -1; /* make sure plain I/O is used */
-  soap->recvfd = open(pathname, O_RDONLY);
-  if (soap->recvfd >= 0)
-  { if (soap_begin_recv(soap))
-    { close(soap->recvfd);
-      soap->socket = socket;
-      soap->recvfd = recvfd;
-      return soap->error;
-    }
-    soap->cookies = (struct soap_cookie*)soap_get_cookie(soap, NULL, "jar", NULL);
-    if (!soap->cookies && soap->error)
-    { close(soap->recvfd);
-      soap->socket = socket;
-      soap->recvfd = recvfd;
-      return soap->error;
-    }
-    if (soap_end_recv(soap))
-    { close(soap->recvfd);
-      soap->socket = socket;
-      soap->recvfd = recvfd;
-      return soap->error;
-    }
-    close(soap->recvfd);
-    soap->socket = socket;
-    soap->recvfd = recvfd;
-    return SOAP_OK;
-  }
-  soap->socket = socket;
-  soap->recvfd = recvfd;
-  return SOAP_EOF;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/ckdb.h
--- a/GEMBASSY-1.0.3/gsoap/extras/ckdb.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,34 +0,0 @@
-/*
- ckdb.h
-
- HTTP cookie database manager. See ckdb.c for more details.
-
- The contents of this file are subject to the gSOAP Public License
- Version 1.0 (the "License"); you may not use this file except in
- compliance with the License. You may obtain a copy of the License at
- http://www.cs.fsu.edu/~engelen/soaplicense.html Software distributed
- under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY
- OF ANY KIND, either express or implied. See the License for the
- specific language governing rights and limitations under the License.
-
- The Initial Developer of the Original Code is Robert A. van Engelen.
- Copyright (C) 2000-2002 Robert A. van Engelen. All Rights Reserved.
-
-*/
-
-/* struct cookie must be a mirror image of struct soap_cookie in stdsoap2.h */
-struct cookie
-{ struct cookie *next;
-  char *name;
-  char *value;
-  char *domain;
-  char *path;
-  long expire;
-  unsigned int version;
-  short secure;
-  [
-  short session; /* transient: do not (de)serialize */
-  short env; /* transient: do not (de)serialize */
-  short modified; /* transient: do not (de)serialize */
-  ]
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/ckdbtest.c
--- a/GEMBASSY-1.0.3/gsoap/extras/ckdbtest.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,53 +0,0 @@
-/*
- ckdbtest.c
-
- Test client for HTTP cookie database manager.
-
- Copyright (C) 2000-2002 Robert A. van Engelen. All Rights Reserved.
-
-1. Compile ckdb.h:
-   soapcpp2 -cnpckdb ckdb.h
-2. Compile ckdb.c:
-   gcc -DWITH_COOKIES -c ckdb.c
-3. Compile and link ckdbtest.c:
-   soapcpp2 -c ckdbtest.h
-   gcc -DWITH_COOKIES ckdbtest.c ckdb.o stdsoap2.c soapC.c soapClient.c
-4. Execute
-   Cookies will be stored in 'jar.xml'
-
-*/
-
-#include "soapH.h"
-#include "ckdbtest.nsmap"
-
-char ckserver[] = "http://www.cs.fsu.edu/~engelen/ck.cgi";
-
-int main()
-{ struct soap soap;
-  char *r;
-  soap_init(&soap);
-  if (soap_call_ck__demo(&soap, ckserver, NULL, &r))
-  { soap_print_fault(&soap, stderr);
-    soap_print_fault_location(&soap, stderr);
-    exit(-1);
-  }
-  printf("The server responded with: %s\n", r);
-  if (soap_save_cookies(&soap, "jar.xml"))
-    fprintf(stderr, "Cannot store cookies\n");
-  soap_free_cookies(&soap);
-  if (soap_load_cookies(&soap, "jar.xml"))
-    fprintf(stderr, "Cannot restore cookies\n");
-  else
-    printf("Got cookies (%s=%s)\n", soap.cookies->name, soap.cookies->value);
-  if (soap_call_ck__demo(&soap, ckserver, NULL, &r))
-  { soap_print_fault(&soap, stderr);
-    soap_print_fault_location(&soap, stderr);
-    exit(-1);
-  }
-  printf("The server responded with: %s\n", r);
-  if (soap_save_cookies(&soap, "jar.xml"))
-    fprintf(stderr, "Cannot store cookies\n");
-  soap_end(&soap); /* This will delete the deserialized cookies too! */
-  soap.cookies = NULL; /* so make sure this is NULL */
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/ckdbtest.h
--- a/GEMBASSY-1.0.3/gsoap/extras/ckdbtest.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-//gsoap ck service name: ckdbtest
-//gsoap ck service location: http://www.cs.fsu.edu/~engelen
-//gsoap ck service namespace: http://www.cs.fsu.edu/~engelen/ck.wsdl
-//gsoap ck service encoding: encoded
-//gsoap ck schema namespace: urn:ck
-int ck__demo(char **r);

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/fault.cpp
--- a/GEMBASSY-1.0.3/gsoap/extras/fault.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,50 +0,0 @@
-/*
- Contributed by Allan Kelly, June 17, 2002
- Provides C++ alternatives for
- soap_print_fault and soap_print_fault_location functions
-
- Note: soap_stream_fault in stdsoap2.cpp provides similar functionality
-*/
-
-/******************************************************************************/
-
-SOAP_FMAC1
-void
-SOAP_FMAC2
-soap_print_fault(struct soap *soap, std::ostream& msg)
-{ if (soap->error)
-  { if (!*soap_faultcode(soap))
-      soap_set_fault(soap);
-    if (!*soap_faultstring(soap))
-      *soap_faultstring(soap) = "";
-    msg << "SOAP FAULT: "
-        << *soap_faultcode(soap) << std::endl
-        << "\"" << *soap_faultstring(soap) << "\"" << std::endl;
-    if (*soap_faultdetail(soap))
-      msg << "Detail: " << *soap_faultdetail(soap) << std::endl;
-  }
-}
-
-/******************************************************************************/
-
-SOAP_FMAC1
-void
-SOAP_FMAC2
-soap_print_fault_location(struct soap *soap, std::ostream& msg)
-{ int c;
-  if (soap->error && soap->buflen > 0)
-  { if (soap->bufidx == 0)
-      soap->bufidx = 1;
-    c = soap->buf[soap->bufidx-1];
-    soap->buf[soap->bufidx-1] = '\0';
-    if (soap->bufidx < soap->buflen)
-      msg << soap->buf << static_cast<char> (c) << std::endl
-          << "** HERE **" << std::endl << soap->buf+soap->bufidx
-          << std::endl;
-    else
-      msg << soap->buf << static_cast<char> (c) << std::endl
-          << "** HERE **" << std::endl;
-  }
-}
-
-/******************************************************************************/

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/logging.cpp
--- a/GEMBASSY-1.0.3/gsoap/extras/logging.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,64 +0,0 @@
-// logging.cpp
-//
-// Place this file in the same direcory as stdsoap2.h
-// Requires soapdefs.h (compile stdsoap2.cpp with -DWITH_SOAPDEFS_H
-// and -DDEBUG_CALLBACKS)
-//
-// Runtime/Customer logging by Mike Helmick
-// Copyright (c) 2002 - Mike Helmick. Convergys IMG. All Rights Reserved.
-// This contributed code is covered under the MPL 1.1 license
-
-#include "stdsoap2.h" // includes "soapdefs.h" when compiled with -DWITH_SOAPDEFS_H
-
-void soap_recv_callback(struct soap*, const char*, size_t len);
-void soap_sent_callback(struct soap*, const char*, size_t len);
-void soap_test_callback(struct soap*, const char*, size_t len);
-
-void
-soap_dispatch_callback(struct soap *soap, int idx, const char *msg, size_t len)
-{ if (!soap->user)
- { // you can set stuff up here, streams etc.
- // soap->user is used to pass user-defined data
- // soap->user is never set nor cleared by gSOAP
- soap->user = (void*)&cout;
- // don't forget to clean up the streams in the main code
- // (before discarding the soap runtime environment)
- }
- switch (idx)
- { case SOAP_INDEX_RECV:
- soap_recv_callback(soap, msg, len);
- break;
- case SOAP_INDEX_SENT:
- soap_sent_callback(soap, msg, len);
- break;
- case SOAP_INDEX_TEST:
- soap_test_callback(soap, msg, len);
- break;
- }
-}
-
-// Note: 'msg' is not 0-terminated!
-void
-soap_recv_callback(struct soap *soap, const char *msg, size_t len)
-{ ostream& os = *(ostream*)soap->user;
-  os << endl
- << "Received:" << endl
- << "----------------------------------------" << endl;
-  os.write(msg, len);
-  os << "----------------------------------------" << endl;
-}
-
-void
-soap_sent_callback(struct soap *soap, const char *msg, size_t len)
-{ ostream& os = *(ostream*)soap->user;
-  os << endl
- << "Sent:" << endl
- << "----------------------------------------" << endl;
-  os.write(msg, len);
-  os << "----------------------------------------" << endl;
-}
-
-void
-soap_test_callback(struct soap *soap, const char *msg, size_t len)
-{ (*(ostream*)soap->user << "Trace: ").write(msg, len);
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/extras/soapdefs.h
--- a/GEMBASSY-1.0.3/gsoap/extras/soapdefs.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,28 +0,0 @@
-// soapdefs.h
-// Place this file in the same directory as stdsoap2.h
-// This file will be included in stdsoap2.h when compiling with
-// -DWITH_SOAPDEFS_H (see stdsoap2.h line 16)
-// See extras/logging.cpp for customer logging
-//
-// Runtime/Customer logging by Mike Helmick
-// Copyright (c) 2002 - Mike Helmick. Convergys IMG. All Rights Reserved.
-// This contributed code si covered under the MPL 1.1 license
-
-#ifndef SOAPDEFS_H
-#define SOAPDEFS_H
-
-#ifdef DEBUG_CALLBACKS
-#ifndef DEBUG
-#define DEBUG
-#endif
-#define SOAP_MESSAGE sprintf
-#define DBGLOG(DBGFILE, CMD) \
-{ char fdebug[SOAP_BUFLEN+1];\
- CMD;\
- soap_dispatch_callback(soap, SOAP_INDEX_##DBGFILE, fdebug, strlen(fdebug));\
-}
-#define DBGMSG(DBGFILE, MSG, LEN) soap_dispatch_callback(soap, SOAP_INDEX_##DBGFILE, MSG, LEN);
-void soap_dispatch_callback(struct soap*, int, const char*, size_t);
-#endif
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-error2.Po
--- a/GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-error2.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-init2.Po
--- a/GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-init2.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-soapcpp2.Po
--- a/GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-soapcpp2.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-soapcpp2_lex.Po
--- a/GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-soapcpp2_lex.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-soapcpp2_yacc.Po
--- a/GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-soapcpp2_yacc.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-symbol2.Po
--- a/GEMBASSY-1.0.3/gsoap/src/.deps/soapcpp2-symbol2.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/Makefile
--- a/GEMBASSY-1.0.3/gsoap/src/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,569 +0,0 @@\n-# Makefile.in generated by automake 1.10 from Makefile.am.\n-# gsoap/src/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,\n-# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-####### This is the input file for automake, which will generate Makefile.in ##########\n-\n-\n-pkgdatadir = $(datadir)/gsoap\n-pkglibdir = $(libdir)/gsoap\n-pkgincludedir = $(includedir)/gsoap\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = i386-apple-darwin13.1.0\n-host_triplet = i386-apple-darwin13.1.0\n-bin_PROGRAMS = soapcpp2$(EXEEXT)\n-subdir = gsoap/src\n-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \\\n-\tsoapcpp2_lex.c soapcpp2_yacc.c soapcpp2_yacc.h\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs\n-CONFIG_HEADER = $(top_builddir)/config.h\n-CONFIG_CLEAN_FILES =\n-am__installdirs = "$(DESTDIR)$(bindir)"\n-binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)\n-PROGRAMS = $(bin_PROGRAMS)\n-am_soapcpp2_OBJECTS = soapcpp2-soapcpp2_yacc.$(OBJEXT) \\\n-\tsoapcpp2-soapcpp2_lex.$(OBJEXT) soapcpp2-symbol2.$(OBJEXT) \\\n-\tsoapcpp2-error2.$(OBJEXT) soapcpp2-init2.$(OBJEXT) \\\n-\tsoapcpp2-soapcpp2.$(OBJEXT)\n-soapcpp2_OBJECTS = $(am_soapcpp2_OBJECTS)\n-am__DEPENDENCIES_1 =\n-soapcpp2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)\n-soapcpp2_LINK = $(CCLD) $(soapcpp2_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \\\n-\t$(LDFLAGS) -o $@\n-DEFAULT_INCLUDES = -I. -I$(top_builddir)\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \\\n-\t$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)\n-CCLD = $(CC)\n-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@\n-LEXCOMPILE = $(LEX) $(LFLAGS) $(AM_LFLAGS)\n-YLWRAP = $(top_srcdir)/ylwrap\n-YACCCOMPILE = $(YACC) $(YFLAGS) $(AM_YFLAGS)\n-SOURCES = $(soapcpp2_SOURCES)\n-DIST_SOURCES = $(soapcpp2_SOURCES)\n-ETAGS = etags\n-CTAGS = ctags\n-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)\n-ACLOCAL = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run aclocal-1.10\n-AMTAR = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run tar\n-AUTOCONF = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run autoconf\n-AUTOHEADER = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run autoheader\n-AUTOMAKE = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run automake-1.10\n-AWK = awk\n-BISON_DEFINE = -DWITH_BISON\n-CC = gcc\n-CCDEPMODE = depmode=gcc3\n-CFLAGS = -Wno-deprecated-declarations\n-CPP = gcc -E\n-CPPFLAGS = \n-CXX = g++\n-CXXDEPMODE = depmode=gcc3\n-CXXFLAGS = -Wno-deprecated-declarations\n-CYGPATH_W = echo\n-DEFS = -DHAVE_CONFIG_H\n-DEPDIR = .deps\n-ECHO_C = \\c\n-ECHO_N = \n-ECHO_T = \n-EGREP = /usr/bin/grep -E\n-ENABLE_SAMPLES = \n-EXEEXT = \n-GREP = /usr/bin/grep\n-INSTALL = /usr/bin/install -c\n-INSTALL_DATA = ${INSTALL} -m 644\n-INSTALL_PROGRAM = ${INSTALL}\n-INSTALL_SCRIPT = ${INSTALL}\n-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s\n-LDFLAGS = \n-LEX = flex\n-LEXLIB = -ll\n-LEX_DEFINE = -DWITH_FLEX\n-LEX_FLAGS = -l\n-LEX_OUTPUT_ROOT = lex'..b'=`$(am__cd) $(top_builddir) && pwd` \\\n-\t && cd $(top_srcdir) \\\n-\t && gtags -i $(GTAGS_ARGS) $$here\n-\n-distclean-tags:\n-\t-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags\n-\n-distdir: $(DISTFILES)\n-\t@srcdirstrip=`echo "$(srcdir)" | sed \'s/[].[^$$\\\\*]/\\\\\\\\&/g\'`; \\\n-\ttopsrcdirstrip=`echo "$(top_srcdir)" | sed \'s/[].[^$$\\\\*]/\\\\\\\\&/g\'`; \\\n-\tlist=\'$(DISTFILES)\'; \\\n-\t dist_files=`for file in $$list; do echo $$file; done | \\\n-\t sed -e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \\\n-\t fi; \\\n-\t cp -pR $$d/$$file $(distdir)$$dir || exit 1; \\\n-\t else \\\n-\t test -f $(distdir)/$$file \\\n-\t || cp -p $$d/$$file $(distdir)/$$file \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(PROGRAMS)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(bindir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\t$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t `test -z \'$(STRIP)\' || \\\n-\t echo "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'"` install\n-mostlyclean-generic:\n-\n-clean-generic:\n-\t-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-\t-rm -f soapcpp2_lex.c\n-\t-rm -f soapcpp2_yacc.c\n-\t-rm -f soapcpp2_yacc.h\n-clean: clean-am\n-\n-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-am\n-\n-install-exec-am: install-binPROGRAMS\n-\n-install-html: install-html-am\n-\n-install-info: install-info-am\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-ps: install-ps-am\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-binPROGRAMS\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \\\n-\tclean-generic ctags distclean distclean-compile \\\n-\tdistclean-generic distclean-tags distdir dvi dvi-am html \\\n-\thtml-am info info-am install install-am install-binPROGRAMS \\\n-\tinstall-data install-data-am install-dvi install-dvi-am \\\n-\tinstall-exec install-exec-am install-html install-html-am \\\n-\tinstall-info install-info-am install-man install-pdf \\\n-\tinstall-pdf-am install-ps install-ps-am install-strip \\\n-\tinstallcheck installcheck-am installdirs maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic pdf pdf-am ps ps-am tags uninstall \\\n-\tuninstall-am uninstall-binPROGRAMS\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/Makefile.am
--- a/GEMBASSY-1.0.3/gsoap/src/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-####### This is the input file for automake, which will generate Makefile.in ##########
-
-
-## not a GNU package. You can remove this line, if
-## you have all needed files, that a GNU package needs
-AUTOMAKE_OPTIONS = foreign 1.4
-
-
-#LIBS=
-AM_YFLAGS=-d -v
-AM_LFLAGS=$(LEX_FLAGS)
-
-bin_PROGRAMS=soapcpp2
-
-soapcpp2_CFLAGS=$(BISON_DEFINE) $(LEX_DEFINE) $(C_DEBUG_FLAGS) $(SOAPCPP2_IMPORTPATH) -D$(platform)
-soapcpp2_LDADD=$(YACC_LIB) $(LEXLIB)
-soapcpp2_SOURCES= soapcpp2_yacc.y soapcpp2_lex.l symbol2.c error2.c init2.c soapcpp2.c
-
-CLEANFILES= *~ soapcpp2_lex.c soapcpp2_yacc.c soapcpp2_yacc.h y.output soapcpp2_yacc.output
-
-
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/Makefile.in
--- a/GEMBASSY-1.0.3/gsoap/src/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,569 +0,0 @@\n-# Makefile.in generated by automake 1.10 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,\n-# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-####### This is the input file for automake, which will generate Makefile.in ##########\n-\n-VPATH = @srcdir@\n-pkgdatadir = $(datadir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkgincludedir = $(includedir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-bin_PROGRAMS = soapcpp2$(EXEEXT)\n-subdir = gsoap/src\n-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \\\n-\tsoapcpp2_lex.c soapcpp2_yacc.c soapcpp2_yacc.h\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs\n-CONFIG_HEADER = $(top_builddir)/config.h\n-CONFIG_CLEAN_FILES =\n-am__installdirs = "$(DESTDIR)$(bindir)"\n-binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)\n-PROGRAMS = $(bin_PROGRAMS)\n-am_soapcpp2_OBJECTS = soapcpp2-soapcpp2_yacc.$(OBJEXT) \\\n-\tsoapcpp2-soapcpp2_lex.$(OBJEXT) soapcpp2-symbol2.$(OBJEXT) \\\n-\tsoapcpp2-error2.$(OBJEXT) soapcpp2-init2.$(OBJEXT) \\\n-\tsoapcpp2-soapcpp2.$(OBJEXT)\n-soapcpp2_OBJECTS = $(am_soapcpp2_OBJECTS)\n-am__DEPENDENCIES_1 =\n-soapcpp2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)\n-soapcpp2_LINK = $(CCLD) $(soapcpp2_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \\\n-\t$(LDFLAGS) -o $@\n-DEFAULT_INCLUDES = -I. -I$(top_builddir)@am__isrc@\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \\\n-\t$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)\n-CCLD = $(CC)\n-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@\n-LEXCOMPILE = $(LEX) $(LFLAGS) $(AM_LFLAGS)\n-YLWRAP = $(top_srcdir)/ylwrap\n-YACCCOMPILE = $(YACC) $(YFLAGS) $(AM_YFLAGS)\n-SOURCES = $(soapcpp2_SOURCES)\n-DIST_SOURCES = $(soapcpp2_SOURCES)\n-ETAGS = etags\n-CTAGS = ctags\n-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)\n-ACLOCAL = @ACLOCAL@\n-AMTAR = @AMTAR@\n-AUTOCONF = @AUTOCONF@\n-AUTOHEADER = @AUTOHEADER@\n-AUTOMAKE = @AUTOMAKE@\n-AWK = @AWK@\n-BISON_DEFINE = @BISON_DEFINE@\n-CC = @CC@\n-CCDEPMODE = @CCDEPMODE@\n-CFLAGS = @CFLAGS@\n-CPP = @CPP@\n-CPPFLAGS = @CPPFLAGS@\n-CXX = @CXX@\n-CXXDEPMODE = @CXXDEPMODE@\n-CXXFLAGS = @CXXFLAGS@\n-CYGPATH_W = @CYGPATH_W@\n-DEFS = @DEFS@\n-DEPDIR = @DEPDIR@\n-ECHO_C = @ECHO_C@\n-ECHO_N = @ECHO_N@\n-ECHO_T = @ECHO_T@\n-EGREP = @EGREP@\n-ENABLE_SAMPLES = @ENABLE_SAMPLES@\n-EXEEXT = @EXEEXT@\n-GREP = @GREP@\n-INSTALL = @INSTALL@\n-INSTALL_DATA = @INSTALL_DATA@\n-INSTALL_PROGRAM = @INSTALL_PROGRAM@\n-INSTALL_SCRIPT = @INSTALL_SCRIPT@\n-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@\n-LDFLAGS = @LDFLAGS@\n-LEX = @LEX@\n-LEXLIB = @LEXLIB@\n-LEX_DEFINE = @LEX_DEFINE@\n-LEX_FLAGS = @LEX_FLAGS@\n-LEX_OUTPUT_ROOT = @LEX_OUTPUT_ROOT@\n-LIBOBJS = @LIBOBJS@\n-LIBS = @LIBS@\n-LN_S = @LN_S@\n-LTLIBOBJS = @LTLIBOBJS@\n-MAKEINFO = @MAKEINFO@\n-MKDIR_P = @MKDIR_P@\n-OBJEXT = @OBJEXT@\n-PACKAGE = @PACKAGE@\n-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@\n-PACKAGE_NAME = @PACKAGE_NAME@\n-PACKAGE_STRING = @PACKAGE_S'..b'=`$(am__cd) $(top_builddir) && pwd` \\\n-\t && cd $(top_srcdir) \\\n-\t && gtags -i $(GTAGS_ARGS) $$here\n-\n-distclean-tags:\n-\t-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags\n-\n-distdir: $(DISTFILES)\n-\t@srcdirstrip=`echo "$(srcdir)" | sed \'s/[].[^$$\\\\*]/\\\\\\\\&/g\'`; \\\n-\ttopsrcdirstrip=`echo "$(top_srcdir)" | sed \'s/[].[^$$\\\\*]/\\\\\\\\&/g\'`; \\\n-\tlist=\'$(DISTFILES)\'; \\\n-\t dist_files=`for file in $$list; do echo $$file; done | \\\n-\t sed -e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \\\n-\t fi; \\\n-\t cp -pR $$d/$$file $(distdir)$$dir || exit 1; \\\n-\t else \\\n-\t test -f $(distdir)/$$file \\\n-\t || cp -p $$d/$$file $(distdir)/$$file \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(PROGRAMS)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(bindir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\t$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t `test -z \'$(STRIP)\' || \\\n-\t echo "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'"` install\n-mostlyclean-generic:\n-\n-clean-generic:\n-\t-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-\t-rm -f soapcpp2_lex.c\n-\t-rm -f soapcpp2_yacc.c\n-\t-rm -f soapcpp2_yacc.h\n-clean: clean-am\n-\n-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-am\n-\n-install-exec-am: install-binPROGRAMS\n-\n-install-html: install-html-am\n-\n-install-info: install-info-am\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-ps: install-ps-am\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-binPROGRAMS\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \\\n-\tclean-generic ctags distclean distclean-compile \\\n-\tdistclean-generic distclean-tags distdir dvi dvi-am html \\\n-\thtml-am info info-am install install-am install-binPROGRAMS \\\n-\tinstall-data install-data-am install-dvi install-dvi-am \\\n-\tinstall-exec install-exec-am install-html install-html-am \\\n-\tinstall-info install-info-am install-man install-pdf \\\n-\tinstall-pdf-am install-ps install-ps-am install-strip \\\n-\tinstallcheck installcheck-am installdirs maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic pdf pdf-am ps ps-am tags uninstall \\\n-\tuninstall-am uninstall-binPROGRAMS\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/MakefileManual
--- a/GEMBASSY-1.0.3/gsoap/src/MakefileManual Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,47 +0,0 @@
-#       gSOAP soapcpp2 Makefile by Robert van Engelen, Genivia Inc.
-# Use this to build the soapcpp2 tool when autoconf/automake are not
-# available.
-#
-# Dependences:
-# Flex (or Lex)
-# Bison
-#
-# Mac OS X universal binary:
-# CC=gcc -arch i386 -arch ppc
-CC=gcc
-#       use LEX=flex -l or LEX=lex
-LEX=flex -l
-#       use YACC=bison or YACC=yacc -d -v -s soapcpp2_yacc
-YACC=bison
-# For static linkage with Flex use:
-LIBS=/usr/lib/libfl.a
-# For static linkage with Lex use:
-# LIBS=/usr/lib/libl.a
-COFLAGS=-O1
-#       For static linking use:
-# COFLAGS=-O1 -static
-#       For debugging use:
-# COFLAGS=-g
-CWFLAGS=-Wall
-#
-CIFLAGS=
-#       use -DWITH_BISON or -DWITH_YACC
-#       use -DWITH_FLEX or -DWITH_LEX
-CMFLAGS=-DWITH_BISON -DWITH_FLEX
-#
-CFLAGS= $(CWFLAGS) $(COFLAGS) $(CIFLAGS) $(CMFLAGS)
-#
-soapcpp2: soapcpp2.h soapcpp2_yacc.tab.o symbol2.o error2.o lex.yy.o init2.o soapcpp2.o
- $(CC) $(CFLAGS) symbol2.o error2.o soapcpp2_yacc.tab.o lex.yy.o init2.o soapcpp2.o $(LIBS) -o $@
- cp -f soapcpp2 ../bin
-soapcpp2_yacc.tab.c: soapcpp2_yacc.y soapcpp2.h error2.h
- $(YACC) -d -v soapcpp2_yacc.y
-lex.yy.c: soapcpp2_yacc.tab.h soapcpp2_yacc.tab.c soapcpp2_lex.l
- $(LEX) soapcpp2_lex.l
-.c.o: soapcpp2.h soapcpp2_yacc.tab.h error2.h
- $(CC) $(CFLAGS) -c $<
-.PHONY: clean distclean
-clean:
- rm -f *.o
-distclean:
- rm -f soapcpp2 *.o lex.yy.* soapcpp2_yacc.tab.h soapcpp2_yacc.tab.c y.tab.* *.output

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/README.txt
--- a/GEMBASSY-1.0.3/gsoap/src/README.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,116 +0,0 @@
-The gSOAP 'soapcpp2' source-to-source code compiler
-
-INSTRUCTIONS
-
-The gSOAP soapcpp2 tool translates annotated C/C++ header files with interface
-defitions for services and clients to service and client implementation code.
-It also maps the C/C++ types to XML types, with the ability to generate XML
-schema and WSDL documents.
-
-When starting from WSDL and/or XML schemas, first use the gSOAP 'wsdl2h' tool
-to translate these into C/C++ header file with interface definitions. Then use
-'soapcpp2' to translate these into implementation code.
-
-See also the README.txt in the 'wsdl' directory and documentation on the use of
-'wsdl2h' with 'soapcpp2'.
-
-CONTENTS
-
-This part of the distribution contains the following files:
-
-README.txt This file
-MakefileManual Extra makefile when autoconf/automake fail to produce one
-soapcpp2.h Main header file
-soapcpp2.c Main application
-symbol2.c Symbol table handling and code generation module
-error2.h Header file for error2.c
-error2.c Error handling routines
-init2.c Compiler symbol table initialization
-soapcpp2_lex.l Flex/Lex tokens
-soapcpp2_yacc.y Yacc/Bison grammar
-
-INSTALLATION
-
-Use './configure' and 'make' in the root directory, as explained in the
-installation instructions.
-
-To build 'soapcpp2' when autoconf/automake fail, use:
-
- make -f MakefileManual
-
-The above command assumes you have Bison and Flex installed. For Yacc, please
-edit MakefileManual and change as follows:
-
-YACC=yacc -d -v -s soapcpp2_yacc
-CMFLAGS=-DWITH_YACC -DWITH_FLEX
-
-QNX INSTALLATION
-
-On QNX the bison.simple file is located in $QNX_HOST/usr/share/bison.simple
-Update your .profile to include:
-
-export BISON_SIMPLE=$QNX_HOST/usr/share/bison/bison.simple
-export BISON_HAIRY=$QNX_HOST/usr/share/bison/bison.hairy
-
-WIN32 INSTALLATION
-
-You need to install Flex and Bison to build soapcpp2.
-
-An MSN article explains how to do this with MS VS2005:
-
-http://msdn.microsoft.com/en-us/library/aa730877(VS.80).aspx#vccustombr_topic3
-
-The older Bison v1.6 can crash on Win32 systems if YYINITDEPTH is too small:
-Compile with /DYYINITDEPTH=5000
-
-COMMAND LINE OPTIONS
-
--1      generate SOAP 1.1 bindings
--2      generate SOAP 1.2 bindings
--0      remove SOAP bindings, use REST
--C generate client-side code only
--S generate server-side code only
--T generate server auto-test code
--L don't generate soapClientLib/soapServerLib
--a use SOAPAction with WS-Addressing to invoke server-side operations
--A require SOAPAction to invoke server-side operations
--b serialize byte arrays char[N] as string
--c      generate C source code
--dpath  use path to save files
--e generate SOAP RPC encoding style bindings
--fN file split of N XML serializer implementations per file (N>=10)
--h display help info
--Ipath  use path(s) for #import (paths separated with ':', or ';' for windows)
--i      generate C++ service proxies and objects inherited from soap struct
--j      generate C++ service proxies and objects that share a soap struct
--k      generate data structure walkers (experimental)
--l      generate linkable modules (experimental)
--m      generate Matlab(tm) code for MEX compiler
--n      use service name to rename service functions and namespace table
--pname  save files with new prefix name instead of 'soap'
--Qname  use name as the C++ namespace for decls, including custom serializers
--qname  use name as the C++ namespace of all declarations
--s      generate deserialization code with strict XML validation checks
--t      generate code for fully xsi:type typed SOAP/XML messaging
--u uncomment comments in WSDL/schema output by suppressing XML comments
--v display version info
--w don't generate WSDL and schema files
--x don't generate sample XML message files
--y include C/C++ type access information in sample XML messages
--z1 generate deprecated old-style C++ service proxies and objects
-infile header file to parse (or stdin)
-
-DOCUMENTATION
-
-See soapdoc2.pdf for documentation.
-
-LICENSE
-
-The gSOAP 'soapcpp2' tool and (generated) source code are released under GPL or
-a commercial license. The commercial license is available from Genivia.
-Please visit http://genivia.com/Products/gsoap/contract.html
-
-COPYRIGHT NOTICE
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2011, Robert van Engelen, Genivia, Inc. All Rights Reserved.

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/error2.c
--- a/GEMBASSY-1.0.3/gsoap/src/error2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,152 +0,0 @@
-/*
- error2.c
-
- Error handling.
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This part of the software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-#include "soapcpp2.h"
-
-#ifdef HAVE_CONFIG_H
-#include "soapcpp2_yacc.h"
-#else
-#include "soapcpp2_yacc.tab.h"
-#endif
-
-#define MAXERR 10
-
-extern char yytext[]; /* lexeme found by the lexical analyzer */
-
-static int lexerrno = 0;
-static int synerrno = 0;
-static int semerrno = 0;
-static int semwarno = 0;
-
-char errbuf[1024]; /* to hold error messages */
-
-/*
-yyerror - called by parser from an error production with nonterminal `error'
-*/
-void yyerror(char *s)
-{ fprintf(stderr, "%s(%d): %s\n", filename, yylineno, s);
-}
-
-/*
-lexerror - called by lexical analyzer upon failure to recognize a token
-*/
-void lexerror(const char *s)
-{ fprintf(stderr, "%s(%d): %s: %s\n", filename, yylineno, s, yytext);
- if (lexerrno++ >= MAXERR)
- execerror("too many syntactic errors, bailing out");
-}
-
-/*
-synerror - called by a semantic action in the yacc grammar
-*/
-void synerror(const char *s)
-{ fprintf(stderr, "%s(%d): Syntax error: %s\n", filename, yylineno-1, s);
- if (synerrno++ >= MAXERR)
- execerror("too many syntactic errors, bailing out");
-}
-
-/*
-semerror - report semantic error from static checking
-*/
-void semerror(const char *s)
-{ fprintf(stderr, "\n%s(%d): **ERROR**: %s\n\n", filename, yylineno, s);
- if (semerrno++ >= MAXERR)
- execerror("too many semantic errors, bailing out");
-}
-
-/*
-semwarn - report semantic warning from static checking
-*/
-void semwarn(const char *s)
-{ fprintf(stderr, "\n%s(%d): *WARNING*: %s\n\n", filename, yylineno, s);
- semwarno++;
-}
-
-/*
-compliancewarn - report compliance warning
-*/
-void compliancewarn(const char *s)
-{ fprintf(stderr, "Compliance warning: %s\n", s);
-}
-
-/*
-typerror - report type error (a semantic error)
-*/
-void typerror(const char *s)
-{ fprintf(stderr, "%s(%d): Type error: %s\n", filename, yylineno, s);
- if (semerrno++ >= MAXERR)
- execerror("too many semantic errors, bailing out");
-}
-
-/*
-execerror - print error message and terminate execution
-*/
-void execerror(const char *s)
-{ fprintf(stderr, "Critical error: %s\n", s);
- exit(1);
-}
-
-/*
-progerror - called when check(expr) failed, i.e. upon programming error
-*/
-void progerror(const char *s, const char *f, int l)
-{ fprintf(stderr, "Program failure: %s in file %s line %d\n", s, f, l);
- exit(1);
-}
-
-/*
-errstat - show error statistics
-*/
-int errstat(void)
-{ if (!lexerrno && !synerrno && !semerrno)
- { fprintf(stderr, "\nCompilation successful ");
- if (semwarno)
- fprintf(stderr, "(%d warning%s)\n\n", semwarno, semwarno>1?"s":"");
- else
- fprintf(stderr, "\n\n");
- return 0;
- }
- fprintf(stderr, "\nThere were errors:\n");
- if (lexerrno)
- fprintf(stderr, "%d lexical error%s\n", lexerrno, lexerrno>1?"s":"");
- if (synerrno)
- fprintf(stderr, "%d syntax error%s\n", synerrno, synerrno>1?"s":"");
- if (semerrno)
- fprintf(stderr, "%d semantic error%s\n", semerrno, semerrno>1?"s":"");
- if (semwarno)
- fprintf(stderr, "%d warning%s\n", semwarno, semwarno>1?"s":"");
- fprintf(stderr, "\n");
- return -1;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/error2.h
--- a/GEMBASSY-1.0.3/gsoap/src/error2.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,52 +0,0 @@
-/*
- error2.h
-
- Error handling.
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This part of the software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-extern char errbuf[];
-
-#ifdef WIN32_WITHOUT_SOLARIS_FLEX
-extern void soapcpp2error(char*);
-#else
-extern void yyerror(char*);
-#endif
-
-extern void lexerror(const char*);
-extern void synerror(const char *);
-extern void semerror(const char *);
-extern void semwarn(const char *);
-extern void compliancewarn(const char *);
-extern void typerror(const char*);
-extern void execerror(const char*);
-extern void progerror(const char*, const char*, int);
-extern int errstat(void);

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/init2.c
--- a/GEMBASSY-1.0.3/gsoap/src/init2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,206 +0,0 @@
-/*
- init2.c
-
- Symbol table initialization.
-
-gSOAP XML Web services tools
-Copyright (C) 2000-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This part of the software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
-
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-#include "soapcpp2.h"
-
-#ifdef HAVE_CONFIG_H
-#include "soapcpp2_yacc.h"
-#else
-#include "soapcpp2_yacc.tab.h"
-#endif
-
-typedef struct Keyword
-{ char *s; /* name */
-  Token t; /* token */
-} Keyword;
-
-static Keyword keywords[] =
-{ { "asm", NONE },
- { "auto", AUTO },
- { "bool", BOOL },
- { "break", BREAK },
- { "case", CASE },
- { "catch", NONE },
- { "char", CHAR },
- { "class", CLASS },
- { "const", CONST },
- { "const_cast", NONE },
- { "continue", CONTINUE },
- { "default", DEFAULT },
- { "delete", NONE },
- { "do", DO },
- { "double", DOUBLE },
- { "dynamic_cast", NONE },
- { "else", ELSE },
- { "enum", ENUM },
- { "errno", NONE },
- { "explicit", EXPLICIT },
- { "export", NONE },
- { "extern", EXTERN },
- { "false", CFALSE },
- { "float", FLOAT },
- { "for", FOR },
- { "friend", FRIEND },
- { "goto", GOTO },
- { "if", IF },
- { "inline", INLINE },
- { "int", INT },
- { "int8_t", CHAR },
- { "int16_t", SHORT },
- { "int32_t", INT },
- { "int64_t", LLONG },
- { "long", LONG },
- { "LONG64", LLONG },
- { "mutable", NONE },
- { "namespace", NAMESPACE },
- { "new", NONE },
- { "NULL", null },
- { "operator", OPERATOR },
- { "private", PRIVATE },
- { "protected", PROTECTED },
- { "public", PUBLIC },
- { "register", REGISTER },
- { "reinterpret_cast", NONE },
- { "restrict", NONE },
- { "return", RETURN },
- { "short", SHORT },
- { "signed", SIGNED },
- { "size_t", SIZE },
- { "sizeof", SIZEOF },
- { "static", STATIC },
- { "static_cast", NONE },
- { "struct", STRUCT },
- { "switch", SWITCH },
- { "template", TEMPLATE },
- { "this", NONE },
- { "throw", NONE },
- { "time_t", TIME },
- { "true", CTRUE },
- { "typedef", TYPEDEF },
- { "typeid", NONE },
- { "typename", TYPENAME },
- { "uint8_t", UCHAR },
- { "uint16_t", USHORT },
- { "uint32_t", UINT },
- { "uint64_t", ULLONG },
- { "ULONG64", ULLONG },
- { "union", UNION },
- { "unsigned", UNSIGNED },
- { "using", USING },
- { "virtual", VIRTUAL },
- { "void", VOID },
- { "volatile", VOLATILE },
- { "wchar_t", WCHAR },
- { "while", WHILE },
-
- { "operator!", NONE },
- { "operator~", NONE },
- { "operator=", NONE },
- { "operator+=", NONE },
- { "operator-=", NONE },
- { "operator*=", NONE },
- { "operator/=", NONE },
- { "operator%=", NONE },
- { "operator&=", NONE },
- { "operator^=", NONE },
- { "operator|=", NONE },
- { "operator<<=", NONE },
- { "operator>>=", NONE },
- { "operator||", NONE },
- { "operator&&", NONE },
- { "operator|", NONE },
- { "operator^", NONE },
- { "operator&", NONE },
- { "operator==", NONE },
- { "operator!=", NONE },
- { "operator<", NONE },
- { "operator<=", NONE },
- { "operator>", NONE },
- { "operator>=", NONE },
- { "operator<<", NONE },
- { "operator>>", NONE },
- { "operator+", NONE },
- { "operator-", NONE },
- { "operator*", NONE },
- { "operator/", NONE },
- { "operator%", NONE },
- { "operator++", NONE },
- { "operator--", NONE },
- { "operator->", NONE },
- { "operator[]", NONE },
- { "operator()", NONE },
-
- { "mustUnderstand", MUSTUNDERSTAND },
-
- { "soap", ID },
- { "SOAP_ENV__Header", ID },
- { "dummy", ID },
- { "soap_header", ID },
-
- { "SOAP_ENV__Fault", ID },
- { "SOAP_ENV__Code", ID },
- { "SOAP_ENV__Subcode", ID },
- { "SOAP_ENV__Reason", ID },
- { "SOAP_ENV__Text", ID },
- { "SOAP_ENV__Detail", ID },
- { "SOAP_ENV__Value", ID },
- { "SOAP_ENV__Node", ID },
- { "SOAP_ENV__Role", ID },
- { "faultcode", ID },
- { "faultstring", ID },
- { "faultactor", ID },
- { "detail", ID },
- { "__type", ID },
- { "fault", ID },
- { "__any", ID },
-
- { "_QName", ID },
- { "_XML", ID },
- { "std::string", TYPE },
- { "std::wstring", TYPE },
-
- { "/*?*/", NONE },
-
- { 0, 0 }
-};
-
-/*
-init - initialize symbol table with predefined keywords
-*/
-void init(void)
-{ struct Keyword *k;
-  for (k = keywords; k->s; k++)
-    install(k->s, k->t);
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/soapcpp2.c
--- a/GEMBASSY-1.0.3/gsoap/src/soapcpp2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,329 +0,0 @@\n-/*\n-\tsoapcpp2.c\n-\n-\tMain compiler and code generator batch program.\n-\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This part of the software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#include "soapcpp2.h"\n-\n-#ifndef SOAPCPP2_IMPORT_PATH\n-#define SOAPCPP2_IMPORT_PATH (NULL)\n-#endif\n-\n-extern void init(void);\n-extern int yyparse(void);\n-extern FILE *yyin;\n-\n-extern char *ns_cname(char*, char*);\n-\n-FILE *fmsg;\t\t/* fd to flush compiler messages */\n-\n-int vflag = 0;\t\t/* SOAP version, -1=no SOAP, 0=not set, 1=1.1, 2=1.2 */\n-int wflag = 0;\t\t/* when set, don\'t generate WSDL and schema files */\n-int Cflag = 0;\t\t/* when set, generate only files for clients */\n-int cflag = 0;\t\t/* when set, generate files with .c extension */\n-int aflag = 0;\t\t/* when set, use value of SOAP Action to dispatch method at server side */\n-int Aflag = 0;\t\t/* when set, require SOAP Action to dispatch method at server side */\n-int bflag = 0;\t\t/* when set, serialize byte arrays char[N] as string */\n-int eflag = 0;\t\t/* when set, use SOAP RPC encoding by default */\n-unsigned long fflag = 0;/* multi-file split for each bundle of -fN defs */\n-int iflag = 0;\t\t/* when set, generate new style proxy/object classes inherited from soap struct */\n-int jflag = 0;\t\t/* when set, generate new style proxy/object classes */\n-int kflag = 0;\t\t/* when set, generate data traversal/walker routines */\n-int mflag = 0;\t\t/* when set, generate code that requires array/binary classes to explicitly remove malloced array */\n-int nflag = 0;\t\t/* when set, names the namespaces global struct \'%NAME%_namespaces */\n-int lflag = 0;\t\t/* when set, create library */\n-int Lflag = 0;\t\t/* when set, don\'t generate soapClientLib/soapServerLib */\n-int Qflag = 0;\t\t/* when set, use C++ namespaces for custom serializers */\n-int sflag = 0;\t\t/* when set, generate strict validation checks */\n-int Sflag = 0;\t\t/* when set, generate only files for servers */\n-int Tflag = 0;\t\t/* when set, generates server auto-test code */\n-int tflag = 0;\t\t/* when set, generates typed messsages (with xsi:type attributes) */\n-int uflag = 0;\t\t/* when set, uncomment WSDL and schema output */\n-int xflag = 0;\t\t/* when set, don\'t generate sample XML message files */\n-int yflag = 0;\t\t/* when set, add C/C++ info in sample XML messages */\n-int zflag = 0;\t\t/* when set, use backward compatibility option */\n-\n-int stop_flag = 0;\n-\n-char dirpath[1024];\t/* directory path for generated source files */\n-char *prefix = "soap";\t/* file name prefix for generated source files */\n-char filename[1024];\t/* current file name */\n-char *importpath = SOAPCPP2_IMPORT_PATH; /* default file import path */\n-\n-/*\n-IMPORT'..b'n\\\n--s generate deserialization code with strict XML validation checks\\n\\\n--t generate code for fully xsi:type typed SOAP/XML messaging\\n\\\n--u\tuncomment comments in WSDL/schema output by suppressing XML comments\\n\\\n--v\tdisplay version info\\n\\\n--w\tdon\'t generate WSDL and schema files\\n\\\n--x\tdon\'t generate sample XML message files\\n\\\n--y\tinclude C/C++ type access information in sample XML messages\\n\\\n--z1\tgenerate deprecated old-style C++ service proxies and objects\\n\\\n-infile\theader file to parse (or stdin)\\n\\\n-\\n");\n-\t\t\t\t\t\texit(0);\n-\t\t\t\t\tcase \'I\':\n-\t\t\t\t\t\ta++;\n-\t\t\t\t\t\tg = 0;\n-\t\t\t\t\t\ts = NULL;\n-\t\t\t\t\t\tif (*a)\n-\t\t\t\t\t\t\ts = a;\n-\t\t\t\t\t\telse if (i < argc && argv[++i])\n-\t\t\t\t\t\t\ts = argv[i];\n-\t\t\t\t\t\telse\n-\t\t\t\t\t\t\texecerror("Option -I requires an import path");\n-\t\t\t\t\t\tif (importpath && s)\n-\t\t\t\t\t\t{\tchar *t\t= emalloc(strlen(importpath) + strlen(s) + 2);\n-\t\t\t\t\t\t\tstrcpy(t, importpath);\n-\t\t\t\t\t\t\tstrcat(t, SOAP_PATHSEP);\n-\t\t\t\t\t\t\tstrcat(t, s);\n-\t\t\t\t\t\t\timportpath = t;\n-\t\t\t\t\t\t}\n-\t\t\t\t\t\telse\n-\t\t\t\t\t\t\timportpath = s;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'i\':\n-\t\t\t\t\t\tiflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'j\':\n-\t\t\t\t\t\tjflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'k\':\n-\t\t\t\t\t\tkflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'m\':\n-\t\t\t\t\t\tmflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'n\':\n-\t\t\t\t\t\tnflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'l\':\n-\t\t\t\t\t\tlflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'L\':\n-\t\t\t\t\t\tLflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'s\':\n-\t\t\t\t\t\tsflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'S\':\n-\t\t\t\t\t\tSflag = 1;\n-\t\t\t\t\t\tif (Cflag)\n- \t\t\t\t\t fprintf(stderr, "soapcpp2: using both options -C and -S omits client/server code\\n");\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'T\':\n-\t\t\t\t\t\tTflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'t\':\n-\t\t\t\t\t\ttflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'u\':\n-\t\t\t\t\t\tuflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'w\':\n-\t\t\t\t\t\twflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'x\':\n-\t\t\t\t\t\txflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'y\':\n-\t\t\t\t\t\tyflag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'p\':\n-\t\t\t\t\t\ta++;\n-\t\t\t\t\t\tg = 0;\n-\t\t\t\t\t\tif (*a)\n-\t\t\t\t\t\t\tprefix = ns_cname(a, NULL);\n-\t\t\t\t\t\telse if (i < argc && argv[++i])\n-\t\t\t\t\t\t\tprefix = ns_cname(argv[i], NULL);\n-\t\t\t\t\t\telse\n-\t\t\t\t\t\t\texecerror("Option -p requires an output file name prefix");\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'Q\':\n-\t\t\t\t\t\tQflag = 1;\n-\t\t\t\t\t\t/* fall through */\n-\t\t\t\t\tcase \'q\':\n-\t\t\t\t\t\ta++;\n-\t\t\t\t\t\tg = 0;\n-\t\t\t\t\t\tif (*a)\n-\t\t\t\t\t\t\tnamespaceid = ns_cname(a, NULL);\n-\t\t\t\t\t\telse if (i < argc && argv[++i])\n-\t\t\t\t\t\t\tnamespaceid = ns_cname(argv[i], NULL);\n-\t\t\t\t\t\telse\n-\t\t\t\t\t\t\texecerror("Option -q requires a namespace name");\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'0\':\n-\t\t\t\t\t\tvflag = -1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'1\':\n-\t\t\t\t\t\tvflag = 1;\n-\t\t\t\t\t\tenvURI = "http://schemas.xmlsoap.org/soap/envelope/";\n-\t\t\t\t\t\tencURI = "http://schemas.xmlsoap.org/soap/encoding/";\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'2\':\n-\t\t\t\t\t\tvflag = 2;\n-\t\t\t\t\t\tenvURI = "http://www.w3.org/2003/05/soap-envelope";\n-\t\t\t\t\t\tencURI = "http://www.w3.org/2003/05/soap-encoding";\n-\t\t\t\t\t\trpcURI = "http://www.w3.org/2003/05/soap-rpc";\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'v\':\n-\t\t\t\t\t\tstop_flag = 1;\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase \'z\':\n-\t\t\t\t\t\ta++;\n-\t\t\t\t\t\tg = 0;\n-\t\t\t\t\t\tif (*a)\n-\t\t\t\t\t\t\tzflag = *a - \'0\';\n-\t\t\t\t\t\telse if (i < argc && argv[++i])\n-\t\t\t\t\t\t\tzflag = *argv[i] - \'0\';\n-\t\t\t\t\t\telse\n-\t\t\t\t\t\t\texecerror("Option -z requires a digit");\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tdefault:\n- \t\t\t\t\tfprintf(stderr, "soapcpp2: Unknown option %s\\n", a);\n- \t\t\t\t\texit(1);\n-\t\t\t\t}\n-\t\t}\n-\t\telse if (!(yyin = fopen(argv[i], "r")))\n-\t\t{\tsprintf(errbuf, "Cannot open file \\"%s\\" for reading", argv[i]);\n-\t\t\texecerror(errbuf);\n-\t\t}\n-\t\telse\n-\t\t\tstrcpy(filename, argv[i]);\n-\t}\n-\tfprintf(fmsg, "\\n** The gSOAP code generator for C and C++, soapcpp2 release "VERSION"\\n** Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc.\\n** All Rights Reserved. This product is provided \\"as is\\", without any warranty.\\n** The soapcpp2 tool is released under one of the following licenses:\\n** GPL or the commercial license by Genivia Inc.\\n\\n");\n-\tif (stop_flag)\n-\t exit(0);\n-\tinit();\n-\tif (yyparse())\n-\t\tsynerror("skipping the remaining part of the input");\n-\treturn errstat();\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/soapcpp2.h
--- a/GEMBASSY-1.0.3/gsoap/src/soapcpp2.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,414 +0,0 @@\n-/*\n-\tsoapcpp2.h\n-\n-\tCommon declarations.\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This part of the software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#include <stdio.h>\n-#include <stdlib.h>\n-#include <errno.h>\n-#include <string.h>\n-#include <ctype.h>\n-#include <time.h>\n-#include "error2.h"\n-\n-#ifndef VERSION\n-# define VERSION "2.8.17r" /* Current version */\n-# define GSOAP_VERSION 20817\n-#endif\n-\n-#ifdef WIN32\n-# pragma warning(disable : 4996)\n-# ifndef WITH_BISON\n-# define WITH_BISON\n-# endif\n-#endif\n-\n-/* #define DEBUG */ /* uncomment to debug */\n-\n-#ifdef DEBUG\n-# define\tcheck(expr, msg) (void)((expr) ? 0 : (progerror(msg, __FILE__, __LINE__), 0))\n-# define DBGLOG(DBGCMD) { DBGCMD; }\n-#else\n-# define check(expr, msg) (void)(expr)\n-# define DBGLOG(DBGCMD)\n-#endif\n-\n-#ifdef WIN32\n-# ifdef WITH_BISON\n-# ifdef WIN32_WITHOUT_SOLARIS_FLEX\n-# define yyparse soapcpp2parse\n-# define yylex soapcpp2lex\n-# define yyerror soapcpp2error\n-# define yylval soapcpp2lval\n-# define yychar soapcpp2char\n-# define yydebug soapcpp2debug\n-# define yynerrs soapcpp2nerrs\n-# define yylineno soapcpp2lineno\n-# define yytext soapcpp2text\n-# define yyin soapcpp2in\n-# define yywrap soapcpp2wrap\n-# endif\n-# endif\n-#endif\n-\n-#ifdef WIN32\n-# define SOAP_PATHCAT "\\\\"\n-# define SOAP_PATHSEP ";"\n-# define LONG64 __int64\n-#else\n-# define SOAP_PATHCAT "/"\n-# define SOAP_PATHSEP ":"\n-# define LONG64 long long\n-#endif\n-\n-#if defined(WIN32)\n-# define SOAP_LONG_FORMAT "%I64d"\n-# define SOAP_ULONG_FORMAT "%I64u"\n-# define SOAP_XLONG_FORMAT "%I64x"\n-#elif defined(TRU64)\n-# define SOAP_LONG_FORMAT "%ld"\n-# define SOAP_ULONG_FORMAT "%lu"\n-# define SOAP_XLONG_FORMAT "%lx"\n-#endif\n-\n-#ifndef SOAP_LONG_FORMAT\n-# define SOAP_LONG_FORMAT "%lld"\t/* printf format for 64 bit ints */\n-#endif\n-#ifndef SOAP_ULONG_FORMAT\n-# define SOAP_ULONG_FORMAT "%llu"\t/* printf format for unsigned 64 bit ints */\n-#endif\n-#ifndef SOAP_XLONG_FORMAT\n-# define SOAP_XLONG_FORMAT "%llx"\t/* printf format for unsigned 64 bit hex ints */\n-#endif\n-\n-extern int yylineno;\n-\n-typedef\tenum Bool {False, True} Bool;\n-\n-typedef\tint Token;\n-\n-typedef\tenum Type\n-{\tTnone,\n-\tTvoid,\t\t/* primitive types */\n-\tTchar,\n-\tTwchar,\n-\tTshort,\n-\tTint,\n-\tTlong,\n-\tTllong,\n-\tTfloat,\n-\tTdouble,\n-\tTldouble,\n-\tTuchar,\n-\tTushort,\n-\tTuint,\n-\tTulong,\n-\tTullong,\n-\tTtime,\n-\tTenum,\n-\tTclass,\t\t/* compound types */\n-\tTstruct,\n-\tTunion,\n-\tTpointer,\n-\tTreference,\n-\tTarray,\n-\tTtemplate,\n-\tTfun\n-} Type;\n-\n-#define\tTYPES (Tfun+1)\t/* number of type (operators) enumerated above */\n-\n-typedef'..b'response; /* funcs only: points to response struct */\n-\tint\twidth;\n-\tint\ttransient;\n-\tconst char *imported;\n-\tstruct\tTnode *next;\n- Bool\tgenerated;\n- Bool\tclassed;\t/* class qualified */\n- Bool\twsdl;\n-\tint\tnum;\n-\tchar\t*pattern;\n-\tLONG64\tminLength;\n-\tLONG64\tmaxLength;\n-} Tnode;\n-\n-typedef\tunion Value {\n-\tLONG64\ti;\n-\tdouble\tr;\n-\tconst char *s;\n-} Value;\n-\n-typedef\tstruct IDinfo {\n-\tTnode\t*typ;\n-\tStorage\tsto;\n-\tBool\thasval;\t\t/* if true, identifier is constant */\n-\tValue\tval;\t\t/* ... with this value */\n-\tint\toffset;\n-\tLONG64\tminOccurs;\n-\tLONG64\tmaxOccurs;\n-} IDinfo;\n-\n-typedef\tstruct Entry {\n-\tSymbol\t*sym;\n-\tchar\t*tag;\n-\tIDinfo\tinfo;\n-\tLevel\tlevel;\n-\tint\tlineno;\n-\tstruct\tEntry *next;\n-} Entry;\n-\n-typedef\tstruct Table {\n-\tSymbol\t*sym;\n-\tLevel\tlevel;\n-\tEntry\t*list;\n-\tstruct\tTable *prev;\n-} Table;\n-\n-typedef struct FNinfo {\n-\tTnode\t*ret;\n-\tTable\t*args;\n-} FNinfo;\n-\n-typedef\tstruct Node {\n-\tTnode\t*typ;\n-\tStorage\tsto;\n-\tBool\thasval;\t\t/* if true, this node has a constant value */\n-\tValue\tval;\t\t/* ... this is the value */\n-\tLONG64\tminOccurs;\n-\tLONG64\tmaxOccurs;\n-\tchar\t*pattern;\n-\tLONG64\tminLength;\n-\tLONG64\tmaxLength;\n-} Node;\n-\n-#define ACTION\t\t 0x0000\n-#define REQUEST_ACTION\t 0x0001\n-#define RESPONSE_ACTION\t 0x0002\n-#define FAULT_ACTION\t 0x0004\n-#define HDRIN\t\t 0x0010\t\n-#define HDROUT\t\t 0x0020\n-#define MIMEIN\t\t 0x0040\n-#define MIMEOUT\t\t 0x0080\n-#define COMMENT\t\t 0x0100\n-#define ENCODING\t 0x0200\n-#define RESPONSE_ENCODING 0x0400\n-#define STYLE 0x0800\n-#define FAULT 0x1000\n-#define PROTOCOL 0x2000\n-\n-typedef struct Data\n-{\tstruct Data *next;\n-\tchar *name;\n-\tchar *text;\n-} Data;\n-\n-typedef struct Method\n-{\tstruct Method *next;\n-\tchar *name;\n-\tshort mess; /* see #defines above */\n-\tchar *part;\n-} Method;\n-\n-typedef struct Service\n-{\tstruct Service *next;\n-\tchar *ns;\n-\tchar *name;\n-\tchar *porttype;\n-\tchar *portname;\n-\tchar *binding;\n-\tchar *definitions;\n-\tchar *transport;\n-\tchar *URL;\n-\tchar *executable;\n-\tchar *import;\n-\tchar *URI;\n-\tchar *URI2;\n-\tchar *WSDL;\n-\tchar *style;\n-\tchar *encoding;\n-\tchar *protocol;\n-\tint xsi_type;\n-\tchar *elementForm;\n-\tchar *attributeForm;\n-\tchar *documentation;\n-\tstruct Method *list;\n-\tstruct Data *data;\n-} Service;\n-\n-typedef struct Pragma\n-{\tstruct Pragma *next;\n-\tchar *pragma;\n-} Pragma;\n-\n-extern Entry *enter(Table*, Symbol*), *entry(Table*, Symbol*), *reenter(Table*, Symbol*), *enumentry(Symbol*);\n-\n-extern int merge(Table*, Table*);\n-\n-extern Table *mktable(Table*);\n-\n-extern Tnode *mkmethod(Tnode*, Table*);\n-\n-extern char *emalloc(size_t);\n-\n-extern Tnode *mktype(Type, void*, int);\n-extern Tnode *mksymtype(Tnode*, Symbol*);\n-extern Tnode *mktemplate(Tnode*, Symbol*);\n-\n-extern int is_transient(Tnode*);\n-extern int is_response(Tnode*);\n-\n-extern Table *typetable, *enumtable, *classtable, *booltable, *templatetable;\n-\n-extern void compile(Table*);\n-extern void freetable(Table*);\n-extern Entry *unlinklast(Table*); \n-\n-extern FILE *fmsg;\n-\n-extern int aflag;\n-extern int Aflag;\n-extern int bflag;\n-extern int vflag;\n-extern int wflag;\n-extern int cflag;\n-extern int Cflag;\n-extern int eflag;\n-extern unsigned long fflag;\n-extern int iflag;\n-extern int jflag;\n-extern int kflag;\n-extern int mflag;\n-extern int nflag;\n-extern int nflag;\n-extern int lflag;\n-extern int Lflag;\n-extern int Qflag;\n-extern int sflag;\n-extern int Sflag;\n-extern int Tflag;\n-extern int tflag;\n-extern int uflag;\n-extern int xflag;\n-extern int yflag;\n-extern int zflag;\n-extern char dirpath[1024];\n-extern char filename[1024];\n-extern char *prefix;\n-extern char *importpath;\n-extern int custom_header;\n-extern int custom_fault;\n-extern Pragma *pragmas;\n-extern Service *services;\n-extern char *namespaceid;\n-extern int transient;\n-extern int imports;\n-extern char *imported;\n-extern int typeNO;\n-\n-extern char *envURI;\n-extern char *encURI;\n-extern char *rpcURI;\n-extern char *xsiURI;\n-extern char *xsdURI;\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/soapcpp2_lex.l
--- a/GEMBASSY-1.0.3/gsoap/src/soapcpp2_lex.l Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1064 +0,0 @@\n-/*\n-\tsoapcpp2_lex.l\n-\n-\tFlex/Lex tokenizer.\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This part of the software is released under ONE of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-%{\n-#include "soapcpp2.h"\n-\n-#ifdef HAVE_CONFIG_H\n-#include "soapcpp2_yacc.h"\n-#else\n-#include "soapcpp2_yacc.tab.h"\n-#endif\n-\n-#ifdef WITH_BISON\n-YYSTYPE yylval;\n-#undef YY_INPUT\n-#define YY_INPUT(buf, result, max_size) \\\n-\t{ \\\n-\tint c = getc(yyin); \\\n-\tresult = (c == EOF) ? YY_NULL : (buf[0] = c, 1); \\\n-\t}\n-#endif\n-\n-#ifndef WITH_LEX\n-#define MAX_IMPORT_DEPTH 16\n-static struct importlist { struct importlist *next; char name[1]; } *importlist = NULL;\n-static char fnstk[MAX_IMPORT_DEPTH][1024];\n-static int lnstk[MAX_IMPORT_DEPTH];\n-static char *imstk[MAX_IMPORT_DEPTH];\n-static YY_BUFFER_STATE instk[MAX_IMPORT_DEPTH];\n-#endif\n-int imports = 0;\n-char *imported = NULL;\n-static void check_id(const char*);\n-static Token install_id(void);\n-static Token install_tag(void);\n-static Token install_int(void);\n-static Token install_hex(void);\n-static Token install_num(void);\n-static Token install_chr(void);\n-static Token install_str(void);\n-static Token install_pragma(void);\n-static void directive(void), option(void);\n-static Token error_chr(void);\n-static Token error_str(void);\n-static int convchar(int*);\n-static int hexchar(int*);\n-static int octchar(int*);\n-static void module(const char *name, const char *fullname);\n-static void import(const char *file);\n-static int magic(const char *name);\n-%}\n-ws\t\t[ \\t\\v\\r\\f\\n\\x1A\\xA0]\n-digit\t\t[0-9]\n-alpha\t\t[a-zA-Z_]\n-id\t\t({alpha}|:{alpha})({alpha}|{digit}|::|:{alpha})*\n-tag\t\t`[^`\\t\\v\\r\\f\\n>]+`\n-int\t\t{digit}+\n-hex\t\t0[xX][0-9a-fA-F]+\n-num\t\t{int}(\\.{int}([Ee][+-]?{int})?|(\\.{int})?[Ee][+-]?{int})\n-chr\t\t\'(\\\\\'|[^\'\\n])*\'\n-str\t\tL?\\"(\\\\\\"|\\\\\\n|[^"])*\\"\n-module\t\t#module{ws}+.*\\n\n-import\t\t#import{ws}+.*\\n\n-%x MLCOMMENT\n-%%\n-{ws}\t\t\t{ /* skip white space */ }\n-"/*"\t\t\t{ BEGIN(MLCOMMENT); }\n-<MLCOMMENT>.|\\n\t\t{ }\n-<MLCOMMENT>"*/"\t\t{ BEGIN(INITIAL); }\n-<MLCOMMENT><<EOF>>\t{ execerror("Unclosed multiline comment at the end of file"); }\n-"//"\\/*"gsoapopt".*\\n\t{ option(); }\n-"//"\\/*"gsoap".*\\n\t{ directive(); }\n-"//".*\\n\t\t{ /* skip single line comment */ }\n-"+="\t\t\t{ return PA; }\n-"-="\t\t\t{ return NA; }\n-"*="\t\t\t{ return TA; }\n-"/="\t\t\t{ return DA; }\n-"%="\t\t\t{ return MA; }\n-"&="\t\t\t{ return AA; }\n-"^="\t\t\t{ return XA; }\n-"|="\t\t\t{ return OA; }\n-"<<="\t\t\t{ return LA; }\n-">>="\t\t\t{ return RA; }\n-"||"\t\t\t{ return OR; }\n-"&&"\t\t\t{ return AN; }\n-"=="\t\t\t{ return EQ; }\n-"!="\t\t\t{ return NE; }\n-"<="\t\t\t{ return LE; }\n-">="\t\t\t{ return GE; }\n-"<<"\t\t\t{ return L'..b'\treturn \'\\f\';\n-\t\tcase \'n\':\treturn \'\\n\';\n-\t\tcase \'r\':\treturn \'\\r\';\n-\t\tcase \'t\':\treturn \'\\t\';\n-\t\tcase \'v\':\treturn \'\\v\';\n-\t\tcase \'x\':\treturn hexchar(p);\n-\t\tcase \'0\':\n-\t\tcase \'1\':\n-\t\tcase \'2\':\n-\t\tcase \'3\':\n-\t\tcase \'4\':\n-\t\tcase \'5\':\n-\t\tcase \'6\':\n-\t\tcase \'7\':\t(*p)--;\n-\t\t\t\treturn octchar(p);\n-\t\tdefault:\treturn yytext[*p-1];\n-\t}\n-}\n-\n-static int\n-hexchar(int *p)\n-{\tint i, d, c = 0;\n-\tfor (i = 0; isxdigit(d = yytext[*p]) && i < 2; i++)\n-\t{\tc = (c << 4) + (d <= \'9\' ? d - \'0\' : toupper(d) - \'7\');\n-\t\t(*p)++;\n-\t}\n-\treturn c;\n-}\n-\n-static int\n-octchar(int *p)\n-{\tint i, d, c = 0;\n-\tfor (i = 0; (d = yytext[*p]) >= \'0\' && d <= \'7\' && i < 3; i++)\n-\t{\tc = (c << 3) + d - \'0\';\n-\t\t(*p)++;\n-\t}\n-\treturn c;\n-}\n-\n-static void module(const char *name, const char *fullname)\n-{ if (!fullname)\n- fullname = name;\n- if (imports)\n- { Pragma **pp;\n- char *s = emalloc(strlen(fullname)+15);\n- sprintf(s, "#include \\"%sH.h\\"", fullname);\n- for (pp = &pragmas; *pp; pp = &(*pp)->next)\n- if (!strcmp((*pp)->pragma, s))\n- break;\n- if (!*pp)\n- { *pp = (Pragma*)emalloc(sizeof(Pragma));\n- (*pp)->pragma = s;\n- (*pp)->next = NULL;\n- }\n- imported = (char*)emalloc(strlen(fullname)+1);\n- strcpy(imported, fullname);\n- fprintf(stderr, "Importing module \'%s\'\\n\\n", fullname);\n- }\n- else\n- { lflag = 1;\n- typeNO = magic(name);\n- prefix = (char*)emalloc(strlen(fullname)+1);\n- strcpy(prefix, fullname);\n- fprintf(stderr, "Compiling module \'%s\' (magic number = %d)\\n\\n", fullname, typeNO);\n- }\n-}\n-\n-static int magic(const char *name)\n-{ size_t i;\n- int n;\n- if (strlen(name) > 4)\n- semerror("#module name length must not exceed four characters");\n- n = 0;\n- for (i = 0; i < strlen(name); i++)\n- if (name[i] >= \'a\' && name[i] <= \'z\')\n- n = 26*n + name[i] - \'a\';\n- else if (name[i] >= \'A\' && name[i] <= \'Z\')\n- n = 26*n + name[i] - \'A\';\n- else\n- semerror("#module name must be alphabetic and the length must not exceed four characters.\\nUse \'#module name longname\' for longer names.");\n- return 4699*n + 153424;\n-}\n-\n-#ifdef WITH_LEX\n-static void import(const char *file)\n-{ execerror("Cannot #import: soapcpp2 not compiled with flex (replace lex with flex)");\n-}\n-#else\n-static void import(const char *file)\n-{ char buf[1024];\n- struct importlist *p;\n- for (p = importlist; p; p = p->next)\n- if (!strcmp(p->name, file))\n- return;\n- if (imports >= MAX_IMPORT_DEPTH)\n- execerror("Imports nested too deep");\n- instk[imports] = YY_CURRENT_BUFFER;\n- strcpy(fnstk[imports], filename);\n- lnstk[imports] = yylineno;\n- imstk[imports] = imported;\n- yylineno = 1;\n- /* imported = NULL; this is useful to change the semantics of #import to NOT consider non-module imports to be part of the current module */\n- imports++;\n- if (!(yyin = fopen(file, "r")))\n- { if (importpath)\n- { char *s, *t;\n- s = importpath;\n- do\n- { size_t n;\n- t = strstr(s, SOAP_PATHSEP);\n- if (t)\n- { if (t - s >= sizeof(buf))\n-\t t = s + sizeof(buf) - 1;\n-\t strncpy(buf, s, t - s);\n-\t buf[t - s] = \'\\0\';\n-\t s = t + sizeof(SOAP_PATHSEP) - 1;\n-\t}\n-\telse\n- { strcpy(buf, s);\n- s = NULL;\n-\t}\n- n = strlen(buf) - 1;\n-#ifdef __VMS\n- if (buf[n] != \']\' && buf[n] != \':\')\n- strcat(buf, ":");\n-#else\n- if (buf[n] != SOAP_PATHCAT[0])\n-\t strcat(buf, SOAP_PATHCAT);\n-#endif\n- strcat(buf, file);\n- yyin = fopen(buf, "r");\n- }\n- while (s && !yyin);\n- }\n- if (!yyin)\n- { sprintf(errbuf, "#import: Cannot open file \\"%s\\" for reading.\\nHint: use option -I<path> (for example -Igsoap/import"SOAP_PATHSEP"gsoap/custom:.)", file);\n- execerror(errbuf);\n- }\n- }\n- p = (struct importlist*)malloc(sizeof(struct importlist) + strlen(file)); /* has already + 1 byte size */\n- strcpy(p->name, file);\n- p->next = importlist;\n- importlist = p;\n- strcpy(filename, file);\n- yy_switch_to_buffer(yy_create_buffer(yyin, YY_BUF_SIZE));\n-}\n-#endif\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/soapcpp2_yacc.y
--- a/GEMBASSY-1.0.3/gsoap/src/soapcpp2_yacc.y Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1927 +0,0 @@\n-/*\n-\tsoapcpp2_yacc.y\n-\n-\tYacc/Bison grammar.\n-\n-\tBuild notes:\n-\n-\t1. Bison 1.6 is known to crash on Win32 systems if YYINITDEPTH is too\n-\tsmall Compile with -DYYINITDEPTH=5000\n-\n-\t2. This grammar has one shift/reduce conflict related to the use of a\n-\tclass declaration with a base class (e.g. class Y : public X) and the\n-\tuse of a maxOccurs (class Y :10). Internally the conflict is resolved\n-\tin favor of a shift by Bison/Yacc, which leads to the correct parsing\n-\tbehavior. Therefore, the warning can be ignored. If this leads to an\n-\terror, then please enable the following directive (around line 121):\n-\n-%expect 1 // Bison: ignore one shift/reduce conflict\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This part of the software is released under ONE of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-%{\n-\n-#include "soapcpp2.h"\n-\n-#ifdef WIN32\n-#ifndef __STDC__\n-#define __STDC__\n-#endif\n-#define YYINCLUDED_STDLIB_H\n-#ifdef WIN32_WITHOUT_SOLARIS_FLEX\n-extern int soapcpp2lex(void);\n-#else\n-extern int yylex(void);\n-#endif\n-#else\n-extern int yylex(void);\n-#endif\n-\n-extern int is_XML(Tnode*);\n-\n-#define MAXNEST 16\t/* max. nesting depth of scopes */\n-\n-struct Scope\n-{\tTable\t*table;\n-\tEntry\t*entry;\n-\tNode\tnode;\n-\tLONG64\tval;\n-\tint\toffset;\n-\tBool\tgrow;\t/* true if offset grows with declarations */\n-\tBool\tmask;\t/* true if enum is mask */\n-}\tstack[MAXNEST],\t/* stack of tables and offsets */\n-\t*sp;\t\t/* current scope stack pointer */\n-\n-Table\t*classtable = (Table*)0,\n-\t*enumtable = (Table*)0,\n-\t*typetable = (Table*)0,\n-\t*booltable = (Table*)0,\n-\t*templatetable = (Table*)0;\n-\n-char\t*namespaceid = NULL;\n-int\ttransient = 0;\n-int\tpermission = 0;\n-int\tcustom_header = 1;\n-int\tcustom_fault = 1;\n-Pragma\t*pragmas = NULL;\n-Tnode\t*qname = NULL;\n-Tnode\t*xml = NULL;\n-\n-/* function prototypes for support routine section */\n-static Entry\t*undefined(Symbol*);\n-static Tnode\t*mgtype(Tnode*, Tnode*);\n-static Node\top(const char*, Node, Node), iop(const char*, Node, Node), relop(const char*, Node, Node);\n-static void\tmkscope(Table*, int), enterscope(Table*, int), exitscope(void);\n-static int\tinteger(Tnode*), real(Tnode*), numeric(Tnode*);\n-static void\tadd_soap(void), add_XML(void), add_qname(void), add_header(Table*), add_fault(Table*), add_response(Entry*, Entry*), add_result(Tnode*);\n-extern char\t*c_storage(Storage), *c_type(Tnode*), *c_ident(Tnode*);\n-extern int\tis_primitive_or_string(Tnode*), is_stdstr(Tnode*), is_binary(Tnode*), is_external(Tnode*), is_mutable(Tnode*), has_attachment(Tnode*);\n-\n-/* Temporaries used in semantic rules */\n-int\ti;\n-char\t*s, *s1, *'..b'p3->info.typ = mkpointer(mkvoid());\n- p3->info.minOccurs = 0;\n- custom_fault = 0;\n- }\n- s4 = lookup("SOAP_ENV__Reason");\n- p4 = entry(classtable, s4);\n- if (!p4 || !p4->info.typ->ref)\n- { t = mktable((Table*)0);\n- if (!p4)\n- { p4 = enter(classtable, s4);\n- p4->info.typ = mkstruct(t, 4);\n- p4->info.typ->id = s4;\n- }\n- else\n- p4->info.typ->ref = t;\n- p3 = enter(t, lookup("SOAP_ENV__Text"));\n- p3->info.typ = mkstring();\n- p3->info.minOccurs = 0;\n- }\n- s3 = lookup("SOAP_ENV__Fault");\n- p3 = entry(classtable, s3);\n- if (!p3 || !p3->info.typ->ref)\n- { t = mktable(NULL);\n- if (!p3)\n- { p3 = enter(classtable, s3);\n- p3->info.typ = mkstruct(t, 9*4);\n- p3->info.typ->id = s3;\n- }\n- else\n- p3->info.typ->ref = t;\n- p3 = enter(t, lookup("faultcode"));\n- p3->info.typ = qname;\n- p3->info.minOccurs = 0;\n- p3 = enter(t, lookup("faultstring"));\n- p3->info.typ = mkstring();\n- p3->info.minOccurs = 0;\n- p3 = enter(t, lookup("faultactor"));\n- p3->info.typ = mkstring();\n- p3->info.minOccurs = 0;\n- p3 = enter(t, lookup("detail"));\n- p3->info.typ = mkpointer(p2->info.typ);\n- p3->info.minOccurs = 0;\n- p3 = enter(t, s1);\n- p3->info.typ = mkpointer(p1->info.typ);\n- p3->info.minOccurs = 0;\n- p3 = enter(t, s4);\n- p3->info.typ = mkpointer(p4->info.typ);\n- p3->info.minOccurs = 0;\n- p3 = enter(t, lookup("SOAP_ENV__Node"));\n- p3->info.typ = mkstring();\n- p3->info.minOccurs = 0;\n- p3 = enter(t, lookup("SOAP_ENV__Role"));\n- p3->info.typ = mkstring();\n- p3->info.minOccurs = 0;\n- p3 = enter(t, lookup("SOAP_ENV__Detail"));\n- p3->info.typ = mkpointer(p2->info.typ);\n- p3->info.minOccurs = 0;\n- }\n-}\n-\n-static void\n-add_soap(void)\n-{ Symbol *s = lookup("soap");\n- p = enter(classtable, s);\n- p->info.typ = mkstruct(NULL, 0);\n- p->info.typ->transient = -2;\n- p->info.typ->id = s;\n-}\n-\n-static void\n-add_XML(void)\n-{ Symbol *s = lookup("_XML");\n- s->token = TYPE;\n- p = enter(typetable, s);\n- xml = p->info.typ = mksymtype(mkstring(), s);\n- p->info.sto = Stypedef;\n-}\n-\n-static void\n-add_qname(void)\n-{ Symbol *s = lookup("_QName");\n- s->token = TYPE;\n- p = enter(typetable, s);\n- qname = p->info.typ = mksymtype(mkstring(), s);\n- p->info.sto = Stypedef;\n-}\n-\n-static void\n-add_header(Table *gt)\n-{ Table *t;\n- Entry *p;\n- Symbol *s = lookup("SOAP_ENV__Header");\n- imported = NULL;\n- p = entry(classtable, s);\n- if (!p || !p->info.typ->ref)\n- { t = mktable((Table*)0);\n- if (!p)\n- p = enter(classtable, s);\n- p->info.typ = mkstruct(t, 0);\n- p->info.typ->id = s;\n- custom_header = 0;\n- }\n-}\n-\n-static void\n-add_response(Entry *fun, Entry *ret)\n-{ Table *t;\n- Entry *p, *q;\n- Symbol *s;\n- size_t i = 0, j, n = strlen(fun->sym->name);\n- char *r = (char*)emalloc(n+100);\n- strcpy(r, fun->sym->name);\n- strcat(r, "Response");\n- do\n- { for (j = 0; j < i; j++)\n- r[n+j+8] = \'_\';\n- r[n+i+8] = \'\\0\';\n- if (!(s = lookup(r)))\n- s = install(r, ID);\n- i++;\n- } while (entry(classtable, s));\n- free(r);\n- t = mktable((Table*)0);\n- q = enter(t, ret->sym);\n- q->info = ret->info;\n- if (q->info.typ->type == Treference)\n- q->info.typ = (Tnode*)q->info.typ->ref;\n- p = enter(classtable, s);\n- p->info.typ = mkstruct(t, 4);\n- p->info.typ->id = s;\n- fun->info.typ->response = p;\n-}\n-\n-static void\n-add_result(Tnode *typ)\n-{ Entry *p;\n- if (!typ->ref || !((Tnode*)typ->ref)->ref)\n- { semwarn("response struct/class must be declared before used in function prototype");\n- return;\n- }\n- for (p = ((Table*)((Tnode*)typ->ref)->ref)->list; p; p = p->next)\n- if (p->info.sto & Sreturn)\n- return;\n- for (p = ((Table*)((Tnode*)typ->ref)->ref)->list; p; p = p->next)\n- { if (p->info.typ->type != Tfun && !(p->info.sto & Sattribute) && !is_transient(p->info.typ) && !(p->info.sto & (Sprivate|Sprotected)))\n- p->info.sto = (Storage)((int)p->info.sto | (int)Sreturn);\n- return;\n- }\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/src/symbol2.c
--- a/GEMBASSY-1.0.3/gsoap/src/symbol2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,12970 +0,0 @@\n-/*\n-\tsymbol2.c\n-\n-\tSymbol table handling, type analysis, and code generation.\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This part of the software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#include "soapcpp2.h"\n-\n-#ifdef HAVE_CONFIG_H\n-#include "soapcpp2_yacc.h"\n-#else\n-#include "soapcpp2_yacc.tab.h"\n-#endif\n-\n-char *envURI = "http://schemas.xmlsoap.org/soap/envelope/";\n-char *encURI = "http://schemas.xmlsoap.org/soap/encoding/";\n-char *rpcURI = "http://www.w3.org/2003/05/soap-rpc";\n-char *xsiURI = "http://www.w3.org/2001/XMLSchema-instance";\n-char *xsdURI = "http://www.w3.org/2001/XMLSchema";\n-char *tmpURI = "http://tempuri.org";\n-\n-static\tSymbol *symlist = (Symbol*) 0;\t/* pointer to linked list of symbols */\n-static\tSymbol *nslist = (Symbol*) 0;\t/* pointer to linked list of namespace prefix symbols */\n-\n-static Tnode *Tptr[TYPES];\n-\n-Service *services = NULL;\n-\n-FILE *fout, *fhead, *fclient, *fserver, *fheader, *flib, *fmatlab, *fmheader;\n-\n-int partnum = 0;\n-\n-int typeNO = 1;\t/* unique no. assigned to all types */\n-\n-static int is_anytype_flag = 0; /* anytype is used */\n-static int has_nsmap = 0;\n-\n-int tagcmp(const char *s, const char *t);\n-int tagncmp(const char *s, const char *t, size_t n);\n-\n-long minlen(Tnode *typ);\n-long maxlen(Tnode *typ);\n-\n-int is_soap12(const char*);\n-int has_detail_string(void);\n-int has_Detail_string(void);\n-\n-void needs_lang(Entry *e);\n-\n-int is_mutable(Tnode *typ);\n-int is_header_or_fault(Tnode *typ);\n-int is_body(Tnode *typ);\n-int is_volatile(Tnode* typ);\n-int is_untyped(Tnode* typ);\n-int is_primclass(Tnode* typ);\n-int is_imported(Tnode* typ);\n-int is_template(Tnode* typ);\n-int is_mask(Tnode* typ);\n-int is_attachment(Tnode* typ);\n-int has_attachment(Tnode* typ);\n-int is_void(Tnode* typ);\n-int has_external(Tnode *typ);\n-int has_volatile(Tnode *typ);\n-\n-int is_invisible(const char *name);\n-int is_invisible_empty(Tnode *p);\n-\n-int is_eq_nons(const char *s, const char *t);\n-int is_eq(const char *s, const char *t);\n-\n-int is_item(Entry *p);\n-int is_self(Entry *p);\n-\n-const char *cstring(const char*);\n-const char *xstring(const char*);\n-\n-/*\n-install - add new symbol\n-*/\n-Symbol *\n-install(const char *name, Token token)\n-{ Symbol *p;\n- p = (Symbol*)emalloc(sizeof(Symbol));\n- p->name = emalloc(strlen(name)+1);\n- strcpy(p->name, name);\n- p->token = token;\n- p->next = symlist;\n- symlist = p;\n- return p;\n-}\n-\n-/*\n-lookup - search for an identifier\'s name. If found, return pointer to symbol table entry. Return pointer 0 if not found.\n-*/\n-Symbol *\n-lookup(const ch'..b'- fprintf(fout,"\\n\\t\\t\\t\\tif (!soap_in_%s(soap, NULL, p, \\"%s\\"))", c_ident((Tnode*)p->info.typ->ref), xsi_type((Tnode*)p->info.typ->ref));\n- fprintf(fout,"\\n\\t\\t\\t\\t{\\tif (soap->error != SOAP_NO_TAG)\\n\\t\\t\\t\\t\\t\\treturn NULL;");\n- fprintf(fout,"\\n\\t\\t\\t\\t\\tsoap->error = SOAP_OK;");\n- fprintf(fout,"\\n\\t\\t\\t\\t\\tbreak;");\n- fprintf(fout,"\\n\\t\\t\\t\\t}");\n- fprintf(fout,"\\n\\t\\t\\t}");\n- fprintf(fout,"\\n\\t\\t\\tsoap_pop_block(soap, NULL);");\n- if (p->info.minOccurs > 0)\n- fprintf(fout,"\\n\\t\\t\\tif (%sa->__size < " SOAP_LONG_FORMAT ")\\n\\t\\t\\t{\\tsoap->error = SOAP_OCCURS;\\n\\t\\t\\t\\treturn NULL;\\n\\t\\t\\t}", strict_check(), p->info.minOccurs);\n- if (p->info.maxOccurs > 1)\n- fprintf(fout,"\\n\\t\\t\\tif (%sa->__size > " SOAP_LONG_FORMAT ")\\n\\t\\t\\t{\\tsoap->error = SOAP_OCCURS;\\n\\t\\t\\t\\treturn NULL;\\n\\t\\t\\t}", strict_check(), p->info.maxOccurs);\n- if (((Tnode*)p->info.typ->ref)->type == Tclass\n- || has_class((Tnode*)p->info.typ->ref)\n- || (((Tnode*)p->info.typ->ref)->type == Tstruct && !cflag))\n- fprintf(fout,"\\n\\t\\t\\tif (soap->blist->size)\\n\\t\\t\\t\\ta->%s = soap_new_%s(soap, soap->blist->size/sizeof(%s));\\n\\t\\t\\telse\\n\\t\\t\\t\\ta->%s = NULL;", ident(p->sym->name), c_ident((Tnode*)p->info.typ->ref), c_type((Tnode*)p->info.typ->ref), ident(p->sym->name));\n- else\n- fprintf(fout,"\\n\\t\\t\\ta->%s = (%s)soap_malloc(soap, soap->blist->size);", ident(p->sym->name), c_type(p->info.typ));\n- fprintf(fout,"\\n\\t\\t\\tsoap_save_block(soap, NULL, (char*)a->%s, 1);", ident(p->sym->name));\n- fprintf(fout,"\\n\\t\\t}");\n- fprintf(fout,"\\n\\t\\tif (soap_element_end_in(soap, tag))\\n\\t\\t\\treturn NULL;");\n- }\n- if (has_getter(typ))\n- fprintf(fout,"\\n\\t\\tif (a->get(soap))\\n\\t\\t\\treturn NULL;");\n- fprintf(fout,"\\n\\t}\\n\\telse\\n\\t{\\t");\n- if (is_attachment(typ))\n- fprintf(fout,"\\n#ifndef WITH_LEANER\\n\\t\\tif (*soap->href != \'#\')\\n\\t\\t{\\tif (soap_dime_forward(soap, &a->__ptr, &a->__size, &a->id, &a->type, &a->options))\\n\\t\\t\\t\\treturn NULL;\\n\\t\\t}\\n\\t\\telse\\n#endif\\n\\t\\t\\t");\n- if (typ->type == Tclass)\n- fprintf(fout,"a = (%s)soap_id_forward(soap, soap->href, (void*)a, 0, %s, 0, sizeof(%s), 0, soap_copy_%s);", c_type_id(typ, "*"), soap_type(typ), c_type(typ), c_ident(typ));\n- else\n- fprintf(fout,"a = (%s)soap_id_forward(soap, soap->href, (void*)a, 0, %s, 0, sizeof(%s), 0, NULL);", c_type_id(typ, "*"), soap_type(typ), c_type(typ));\n- fprintf(fout,"\\n\\t\\tif (soap->body && soap_element_end_in(soap, tag))\\n\\t\\t\\treturn NULL;");\n- fprintf(fout,"\\n\\t}");\n- fprintf(fout,"\\n\\treturn a;\\n}");\n-}\n-\n-const char *\n-cstring(const char *s)\n-{ size_t n;\n- char *t;\n- const char *r;\n- for (n = 0, r = s; *r; n++, r++)\n- if (*r == \'"\' || *r == \'\\\\\')\n- n++;\n- else if (*r < 32)\n- n += 3;\n- r = t = (char*)emalloc(n + 1);\n- for (; *s; s++)\n- { if (*s == \'"\' || *s == \'\\\\\')\n- { *t++ = \'\\\\\';\n- *t++ = *s;\n- }\n- else if (*s < 32)\n- { sprintf(t, "\\\\%03o", (unsigned int)(unsigned char)*s);\n- t += 4;\n- }\n- else\n- *t++ = *s;\n- }\n- *t = \'\\0\';\n- return r;\n-}\n-\n-const char *\n-xstring(const char *s)\n-{ size_t n;\n- char *t;\n- const char *r;\n- for (n = 0, r = s; *r; n++, r++)\n- { if (*r < 32 || *r >= 127)\n- n += 4;\n- else if (*r == \'<\' || *r == \'>\')\n- n += 3;\n- else if (*r == \'&\')\n- n += 4;\n- else if (*r == \'"\')\n- n += 5;\n- else if (*r == \'\\\\\')\n- n += 1;\n- }\n- r = t = (char*)emalloc(n + 1);\n- for (; *s; s++)\n- { if (*s < 32 || *s >= 127)\n- { sprintf(t, "&#%.2x;", (unsigned char)*s);\n- t += 5;\n- }\n- else if (*s == \'<\')\n- { strcpy(t, "<");\n- t += 4;\n- }\n- else if (*s == \'>\')\n- { strcpy(t, ">");\n- t += 4;\n- }\n- else if (*s == \'&\')\n- { strcpy(t, "&");\n- t += 5;\n- }\n- else if (*s == \'"\')\n- { strcpy(t, """);\n- t += 6;\n- }\n- else if (*s == \'\\\\\')\n- { strcpy(t, "\\\\\\\\");\n- t += 2;\n- }\n- else\n- *t++ = *s;\n- }\n- *t = \'\\0\';\n- return r;\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/stdsoap2.c
--- a/GEMBASSY-1.0.3/gsoap/stdsoap2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,16999 +0,0 @@\n-/*\n-\tstdsoap2.c[pp] 2.8.17r\n-\n-\tgSOAP runtime engine\n-\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc., All Rights Reserved.\n-This part of the software is released under ONE of the following licenses:\n-GPL, or the gSOAP public license, or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-Contributors:\n-\n-Wind River Systems Inc., for the following additions under gSOAP public license:\n- - vxWorks compatible options\n---------------------------------------------------------------------------------\n-gSOAP public license.\n-\n-The contents of this file are subject to the gSOAP Public License Version 1.3\n-(the "License"); you may not use this file except in compliance with the\n-License. You may obtain a copy of the License at\n-http://www.cs.fsu.edu/~engelen/soaplicense.html\n-Software distributed under the License is distributed on an "AS IS" basis,\n-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License\n-for the specific language governing rights and limitations under the License.\n-\n-The Initial Developer of the Original Code is Robert A. van Engelen.\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc., All Rights Reserved.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#define GSOAP_LIB_VERSION 20817\n-\n-#ifdef AS400\n-# pragma convert(819)\t/* EBCDIC to ASCII */\n-#endif\n-\n-#include "stdsoap2.h"\n-#if defined(VXWORKS) && defined(WM_SECURE_KEY_STORAGE)\n-#include <ipcom_key_db.h>\n-#endif\n-#if GSOAP_VERSION != GSOAP_LIB_VERSION\n-# error "GSOAP VERSION MISMATCH IN LIBRARY: PLEASE REINSTALL PACKAGE"\n-#endif\n-\n-#ifdef __BORLANDC__\n-# pragma warn -8060\n-#else\n-# ifdef WIN32\n-# ifdef UNDER_CE\n-# pragma comment(lib, "ws2.lib")\t/* WinCE */\n-# else\n-# pragma comment(lib, "ws2_32.lib")\n-# endif\n-# pragma warning(disable : 4996) /* disable deprecation warnings */\n-# endif\n-#endif\n-\n-#ifdef __cplusplus\n-SOAP_SOURCE_STAMP("@(#) stdsoap2.cpp ver 2.8.17r 2013-12-18 00:00:00 GMT")\n-extern "C" {\n-#else\n-SOAP_SOURCE_STAMP("@(#) stdsoap2.c ver 2.8.17r 2013-12-18 00:00:00 GMT")\n-#endif\n-\n-/* 8bit character representing unknown/nonrepresentable character data (e.g. not supported by current locale with multibyte support enabled) */\n-#ifndef SOAP_UNKNOWN_CHAR\n-#define SOAP_UNKNOWN_CHAR (127)\n-#endif\n-\n-/* EOF=-1 */\n-#define SOAP_LT (soap_wchar)(-2) /* XML-specific \'<\' */\n-#define SOAP_TT (soap_wchar)(-3) /* XML-specific \'</\' */\n-#define SOAP_GT (soap_wchar)(-4) /* XML-specific \'>\' */\n-#define SOAP_QT (soap_wchar)(-5) /* XML-specific \'"\' */\n-#define SOAP_AP (soap_wchar)(-6) /* XML-specific \'\'\' */\n-\n-#define soap_blank(c)\t\t((c)+1 > 0 && (c) <= 32)\n-#define soap_notblank(c)\t((c) > 32)\n-\n-#if defined(WIN32) && !defined(UNDER_CE)\n-#d'..b'ault: %s [%s]\\n\\"%s\\"\\nDetail: %s\\n", soap->version ? "SOAP 1." : "Error ", soap->version ? (int)soap->version : soap->error, *c, v ? v : "no subcode", s ? s : "[no reason]", d ? d : "[no detail]");\n- else if (len > 40)\n- sprintf(buf, "%s%d fault: %s\\n", soap->version ? "SOAP 1." : "Error ", soap->version ? (int)soap->version : soap->error, *c);\n- else\n- buf[0] = \'\\0\';\n-#endif\n- }\n- return buf;\n-}\n-#endif\n-#endif\n-\n-/******************************************************************************/\n-#ifndef PALM_1\n-#ifndef WITH_NOSTDLIB\n-SOAP_FMAC1\n-void\n-SOAP_FMAC2\n-soap_print_fault_location(struct soap *soap, FILE *fd)\n-{\n-#ifndef WITH_LEAN\n- int i, j, c1, c2;\n- if (soap->error && soap->error != SOAP_STOP && soap->bufidx <= soap->buflen && soap->buflen > 0 && soap->buflen <= SOAP_BUFLEN)\n- { i = (int)soap->bufidx - 1;\n- if (i <= 0)\n- i = 0;\n- c1 = soap->buf[i];\n- soap->buf[i] = \'\\0\';\n- if ((int)soap->buflen >= i + 1024)\n- j = i + 1023;\n- else\n- j = (int)soap->buflen - 1;\n- c2 = soap->buf[j];\n- soap->buf[j] = \'\\0\';\n- fprintf(fd, "%s%c\\n\\n", soap->buf, c1);\n- if (soap->bufidx < soap->buflen)\n- fprintf(fd, "%s\\n", soap->buf + soap->bufidx);\n- soap->buf[i] = (char)c1;\n- soap->buf[j] = (char)c2;\n- }\n-#endif\n-}\n-#endif\n-#endif\n-\n-/******************************************************************************/\n-#ifndef PALM_1\n-SOAP_FMAC1\n-int\n-SOAP_FMAC2\n-soap_register_plugin_arg(struct soap *soap, int (*fcreate)(struct soap*, struct soap_plugin*, void*), void *arg)\n-{ register struct soap_plugin *p;\n- register int r;\n- if (!(p = (struct soap_plugin*)SOAP_MALLOC(soap, sizeof(struct soap_plugin))))\n- return soap->error = SOAP_EOM;\n- p->id = NULL;\n- p->data = NULL;\n- p->fcopy = NULL;\n- p->fdelete = NULL;\n- r = fcreate(soap, p, arg);\n- if (!r && p->fdelete)\n- { p->next = soap->plugins;\n- soap->plugins = p;\n- DBGLOG(TEST, SOAP_MESSAGE(fdebug, "Registered \'%s\' plugin\\n", p->id));\n- return SOAP_OK;\n- }\n- DBGLOG(TEST, SOAP_MESSAGE(fdebug, "Could not register plugin \'%s\': plugin returned error %d (or fdelete callback not set)\\n", p->id ? p->id : "?", r));\n- SOAP_FREE(soap, p);\n- return r;\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifndef PALM_1\n-static void *\n-fplugin(struct soap *soap, const char *id)\n-{ register struct soap_plugin *p;\n- for (p = soap->plugins; p; p = p->next)\n- if (p->id == id || !strcmp(p->id, id))\n- return p->data;\n- return NULL;\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifndef PALM_2\n-SOAP_FMAC1\n-void *\n-SOAP_FMAC2\n-soap_lookup_plugin(struct soap *soap, const char *id)\n-{ return soap->fplugin(soap, id);\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifdef __cplusplus\n-}\n-#endif\n-\n-/******************************************************************************\\\n- *\n- *\tC++ soap struct methods\n- *\n-\\******************************************************************************/\n-\n-#ifdef __cplusplus\n-soap::soap()\n-{ soap_init(this);\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifdef __cplusplus\n-soap::soap(soap_mode m)\n-{ soap_init1(this, m);\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifdef __cplusplus\n-soap::soap(soap_mode im, soap_mode om)\n-{ soap_init2(this, im, om);\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifdef __cplusplus\n-soap::soap(const struct soap& soap)\n-{ soap_copy_context(this, &soap);\n-}\n-#endif\n-\n-/******************************************************************************/\n-#ifdef __cplusplus\n-soap::~soap()\n-{ soap_destroy(this);\n- soap_end(this);\n- soap_done(this);\n-}\n-#endif\n-\n-/******************************************************************************/\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/stdsoap2.cpp
--- a/GEMBASSY-1.0.3/gsoap/stdsoap2.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/stdsoap2.h
--- a/GEMBASSY-1.0.3/gsoap/stdsoap2.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2780 +0,0 @@\n-/*\n-\tstdsoap2.h 2.8.17r\n-\n-\tgSOAP runtime engine\n-\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc., All Rights Reserved.\n-This part of the software is released under ONE of the following licenses:\n-GPL, or the gSOAP public license, or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-Contributors:\n-\n-Wind River Systems, Inc., for the following additions\n- - vxWorks compatible\n---------------------------------------------------------------------------------\n-gSOAP public license.\n-\n-The contents of this file are subject to the gSOAP Public License Version 1.3\n-(the "License"); you may not use this file except in compliance with the\n-License. You may obtain a copy of the License at\n-http://www.cs.fsu.edu/~engelen/soaplicense.html\n-Software distributed under the License is distributed on an "AS IS" basis,\n-WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License\n-for the specific language governing rights and limitations under the License.\n-\n-The Initial Developer of the Original Code is Robert A. van Engelen.\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc., All Rights Reserved.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#define GSOAP_VERSION 20817\n-\n-#ifdef WITH_SOAPDEFS_H\n-# include "soapdefs.h"\t\t/* include user-defined stuff */\n-#endif\n-\n-#ifndef _THREAD_SAFE\n-# define _THREAD_SAFE\n-#endif\n-\n-#ifndef OPENSERVER\n-# ifndef _REENTRANT\n-# define _REENTRANT\n-# endif\n-#endif\n-\n-#ifndef SOAP_FMAC1\t/* stdsoap2.h declaration macro */\n-# define SOAP_FMAC1\n-#endif\n-\n-#ifndef SOAP_FMAC2\t/* stdsoap2.h declaration macro */\n-# define SOAP_FMAC2\n-#endif\n-\n-#ifndef SOAP_FMAC3\t/* (de)serializer declaration macro */\n-# define SOAP_FMAC3\n-#endif\n-\n-#ifndef SOAP_FMAC3S\t/* string converter for (de)serializer declaration macro */\n-# define SOAP_FMAC3S SOAP_FMAC3\n-#endif\n-\n-#ifndef SOAP_FMAC4\t/* (de)serializer declaration macro */\n-# define SOAP_FMAC4\n-#endif\n-\n-#ifndef SOAP_FMAC4S\t/* string converter for (de)serializer declaration macro */\n-# define SOAP_FMAC4S SOAP_FMAC4\n-#endif\n-\n-#ifndef SOAP_FMAC5\t/* stub/skeleton declaration macro */\n-# define SOAP_FMAC5\n-#endif\n-\n-#ifndef SOAP_FMAC6\t/* stub/skeleton declaration macro */\n-# define SOAP_FMAC6\n-#endif\n-\n-#ifndef SOAP_CMAC\t/* class declaration macro */\n-# define SOAP_CMAC\n-#endif\n-\n-#ifndef SOAP_NMAC\t/* namespace table declaration macro */\n-# define SOAP_NMAC\n-#endif\n-\n-#ifndef SOAP_SOURCE_STAMP\n-# define SOAP_SOURCE_STAMP(str)\n-#endif\n-\n-/* gSOAP 2.7.4 and higher: fast look-aside buffering is stable */\n-#ifndef WITH_FAST\n-# define WITH_FAST\n-#endif\n-\n-#ifndef STDSOAP_H\n-#define STDSOAP_H\n-\n-#if defined(__vxworks) || defined(__VXWORKS__)\n-# ifndef VXWORKS\n-# define VXWO'..b'ct soap*, size_t);\n-SOAP_FMAC1 size_t SOAP_FMAC2 soap_tell(struct soap*);\n-SOAP_FMAC1 char* SOAP_FMAC2 soap_dime_option(struct soap*, unsigned short, const char*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_getdimehdr(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_getdime(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_putdimehdr(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_putdime(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_getmimehdr(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_getmime(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_putmimehdr(struct soap*, struct soap_multipart*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_putmime(struct soap*);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_set_dime(struct soap*);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_set_mime(struct soap*, const char *boundary, const char *start);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_clr_dime(struct soap*);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_clr_mime(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_set_dime_attachment(struct soap*, char *ptr, size_t size, const char *type, const char *id, unsigned short optype, const char *option);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_set_mime_attachment(struct soap*, char *ptr, size_t size, enum soap_mime_encoding encoding, const char *type, const char *id, const char *location, const char *description);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_post_check_mime_attachments(struct soap *soap);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_check_mime_attachments(struct soap *soap);\n-SOAP_FMAC1 struct soap_multipart* SOAP_FMAC2 soap_get_mime_attachment(struct soap *soap, void *handle);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_match_cid(struct soap*, const char*, const char*);\n-#endif\n-\n-SOAP_FMAC1 int SOAP_FMAC2 soap_register_plugin_arg(struct soap*, int (*fcreate)(struct soap*, struct soap_plugin*, void*), void*);\n-SOAP_FMAC1 void* SOAP_FMAC2 soap_lookup_plugin(struct soap*, const char*);\n-\n-SOAP_FMAC1 const char* SOAP_FMAC2 soap_attr_value(struct soap *soap, const char *name, int flag);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_set_attr(struct soap *soap, const char *name, const char *value, int flag);\n-SOAP_FMAC1 void SOAP_FMAC2 soap_clr_attr(struct soap *soap);\n-\n-SOAP_FMAC1 const char* SOAP_FMAC2 soap_url(struct soap *soap, const char*, const char*);\n-SOAP_FMAC1 size_t SOAP_FMAC2 soap_encode_url(const char*, char*, size_t);\n-SOAP_FMAC1 const char* SOAP_FMAC2 soap_encode_url_string(struct soap*, const char*);\n-#ifdef WITH_COOKIES\n-SOAP_FMAC1 void SOAP_FMAC2 soap_getcookies(struct soap *soap, const char *val);\n-SOAP_FMAC1 extern struct soap_cookie* SOAP_FMAC2 soap_set_cookie(struct soap*, const char*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern struct soap_cookie* SOAP_FMAC2 soap_cookie(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern char* SOAP_FMAC2 soap_cookie_value(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern char* SOAP_FMAC2 soap_env_cookie_value(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern time_t SOAP_FMAC2 soap_cookie_expire(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern int SOAP_FMAC2 soap_set_cookie_expire(struct soap*, const char*, long, const char*, const char*);\n-SOAP_FMAC1 extern int SOAP_FMAC2 soap_set_cookie_session(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern int SOAP_FMAC2 soap_clr_cookie_session(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern void SOAP_FMAC2 soap_clr_cookie(struct soap*, const char*, const char*, const char*);\n-SOAP_FMAC1 extern int SOAP_FMAC2 soap_getenv_cookies(struct soap*);\n-SOAP_FMAC1 extern struct soap_cookie* SOAP_FMAC2 soap_copy_cookies(struct soap*, const struct soap*);\n-SOAP_FMAC1 extern void SOAP_FMAC2 soap_free_cookies(struct soap*);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_putsetcookies(struct soap *soap);\n-SOAP_FMAC1 int SOAP_FMAC2 soap_putcookies(struct soap *soap, const char *domain, const char *path, int secure);\n-#endif\n-\n-#ifdef __cplusplus\n-} /* extern "C" */\n-#endif\n-\n-#endif /* STDSOAP_H */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/typemap.dat
--- a/GEMBASSY-1.0.3/gsoap/typemap.dat Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,393 +0,0 @@\n-#\ttypemap.dat\n-#\n-#\tUse this file to define namespace prefix and type bindings for\n-#\tthe generated header files by the \'wsdl2h\' tool. typemap.dat is the\n-#\tdefault file processed by \'wsdl2h\' to customize its output. You can use\n-#\twsdl2h option -t to specify an alternate file.\n-#\n-#\tXML namespace prefix bindings can be provided to override the default\n-#\tchoice of the ns1, ns2, ... prefixes generated by wsdl2h. It is highly\n-#\trecommended to provide namespace prefixes for your project\'s XML\n-#\tnamespaces. In this way, changes to the WSDL (or newer releases of\n-#\twsdl2h) will have a minimal impact on coding.\n-#\tBindings for namespace prefixes are of the form:\n-#\t\tprefix = "URI"\n-#\n-#\tType bindings can be provided to bind XML schema types to C/C++\n-#\ttypes for your project.\n-#\tType bindings are of the form:\n-#\t\tprefix__type = declaration | use | ptr-use\n-#\twhere \'prefix__type\' is the C/C++-translation of the schema type,\n-#\t\'declaration\' introduces the type in the header file, the optional\n-#\t\'use\' specifies how the type is used directly, and the optional\n-#\t\'ptr-use\' specifies how the type is used as a pointer type.\n-#\tFor example:\n-#\t\txsd__string = | char* | char*\n-#\tor using wide strings:\n-#\t\txsd__string = | wchar_t* | wchar_t*\n-#\tor using C++ strings, which need a pointer (added by default):\n-#\t\txsd__string = | std::string\n-#\tor using C++ wstrings:\n-#\t\txsd__string = | std::wstring\n-#\tAfter enabling this line, all XSD strings will be mapped to char* or\n-#\tstd::wstring, respectively to support Unicode. Note that the\n-#\t\'declaration\' part is empty in this case.\n-#\n-#\tWhen a type binding requires only the usage to be changed, the\n-#\tdeclaration part can be replaced by elipsis ..., as in:\n-#\t\tprefix__type = ... | use | ptr-use\n-#\tThis ensure that the wsdl2h-generated type definition is preserved,\n-#\twhile the use and ptr-use are remapped.\n-#\tFor example, this is useful to map schema polymorphic types to C types,\n-#\twhere we need to be able to both handle a base type and its extensions\n-#\tas per schema extensibility. Say base type ns:base allows derived\n-#\textensions and we need to map this to C types as follows:\n-#\t\tns__base = ... | int __type_base; void*\n-#\twhere __type_base and void* are used to (de)serialize any data type,\n-#\tincluding base and its derived types.\n-#\n-#\tAdditional data and function members can be provided to extend a\n-#\tgenerated struct or class.\n-#\tClass and struct extensions are of the form:\n-#\t\tprefix__type = $ member-declaration\n-#\tFor example, to add a constructor and destructor to class myns__record:\n-#\t\tmyns__record = $ myns__record();\n-#\t\tmyns__record = $ ~myns__record();\n-#\t\n-#\tType remappings can be given to map a type to another type:\n-#\t\tprefix__type1 == prefix__type2\n-#\twhich replaces \'prefix__type1\' by \'prefix__type2\' in the wsdl2h output.\n-#\tFor example:\n-#\t\tSOAP_ENC__boolean == xsd__boolean\n-#\n-#\tAny other material to be included in the generated header file can be\n-#\tprovided by enclosing the text within brackets [ and ]. Brackets MUST\n-#\tappear at the start of a new line.\n-#\tFor example, to include a note:\n-#[\n-#// TODO: Don\'t forget to bind the namespace prefixes!\n-#]\n-#\tThis comment appears as the first line in the generated header file.\n-#\n-#-------------------------------------------------------------------------------\n-#gSOAP XML Web services tools\n-#Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-#This software is released under one of the following two licenses:\n-#GPL or Genivia\'s license for commercial use.\n-#-------------------------------------------------------------------------------\n-#GPL license.\n-#\n-#This program is free software; you can redistribute it and/or modify it under\n-#the terms of the GNU General Public License as published by the Free Software\n-#Foundation; either version 2 of the License, or (at your option) any later\n-#version.\n-#\n-#This program is distributed in the hope that it will be useful, but WITHOUT ANY'..b'pe\t\t= | wsdd__ProbeMatchType\n-wsdd10__ResolveType\t\t= | wsdd__ResolveType\n-wsdd10__ResolveMatchesType\t= | wsdd__ResolveMatchesType\n-wsdd10__ResolveMatchType\t= | wsdd__ResolveMatchType\n-wsdd10__ScopesType\t\t= | wsdd__ScopesType\n-wsdd10__SecurityType\t\t= | wsdd__SecurityType\n-wsdd10__SigType\t\t\t= | wsdd__SigType\n-wsdd10__AppSequenceType\t\t= | wsdd__AppSequenceType\n-\n-#\tWS-Policy\n-\n-wsp\t= <http://schemas.xmlsoap.org/ws/2004/09/policy>\n-\n-#\tWS-SecureConversation\n-\n-wsc\t= <http://schemas.xmlsoap.org/ws/2005/02/sc>\n-\n-#\tWS-Trust 1.0\n-\n-wst\t= <http://schemas.xmlsoap.org/ws/2005/02/trust>\n-\n-#\tWS-Security wsse 2004 v1.0 and 1.1 and old wsse 2002 schema\n-\n-wsse11\t= <http://docs.oasis-open.org/wss/oasis-wss-wssecurity-secext-1.1.xsd>\n-wsse\t= <http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-secext-1.0.xsd>\n-wsse2\t= <http://schemas.xmlsoap.org/ws/2002/12/secext>\n-\n-_wsse2__Security == _wsse__Security\n-wsse2__Security == wsse__Security\n-\n-#\twsu 2004\n-\n-wsu\t= <http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd>\n-\n-_wsu__Id\t\t= | char*\n-_wsu__Created\t\t= | time_t\n-_wsu__Expires\t\t= | time_t\n-\n-wsu__AttributedDateTime\t= | time_t\n-wsu__AttributedURI\t= | char*\n-\n-#\tBindings for ds and xenc for WS-Security protocols:\n-\n-ds\t= <http://www.w3.org/2000/09/xmldsig#>\n-xenc\t= <http://www.w3.org/2001/04/xmlenc#>\n-\n-#\txlink\n-\n-xlink\t= <http://www.w3.org/1999/xlink>\n-\n-_xlink__actuate\t\t= | char*\n-_xlink__arcrole\t\t= | char*\n-_xlink__from\t\t= | char*\n-_xlink__href\t\t= | char*\n-_xlink__label\t\t= | char*\n-_xlink__role\t\t= | char*\n-_xlink__show\t\t= | char*\n-_xlink__to\t\t= | char*\n-_xlink__title\t\t= | char*\n-_xlink__type\t\t= | char*\n-\n-#\twsrp routing protocol (deprecated)\n-\n-wsrp\t= <http://schemas.xmlsoap.org/rp/>\n-\n-#\tONVIF recommended prefixes as per 8/20/12\n-#\thttp://www.onvif.org/onvif/ver10/device/wsdl/devicemgmt.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/event/wsdl/event.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/display.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/deviceio.wsdl\n-#\thttp://www.onvif.org/onvif/ver20/imaging/wsdl/imaging.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/media/wsdl/media.wsdl\n-#\thttp://www.onvif.org/onvif/ver20/ptz/wsdl/ptz.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/receiver.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/recording.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/search.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/network/wsdl/remotediscovery.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/replay.wsdl\n-#\thttp://www.onvif.org/onvif/ver20/analytics/wsdl/analytics.wsdl\n-#\thttp://www.onvif.org/onvif/ver10/analyticsdevice.wsdl\t\n-#\thttp://www.onvif.org/onvif/ver10/schema/onvif.xsd\n-\n-tds\t= "http://www.onvif.org/ver10/device/wsdl"\n-tev\t= "http://www.onvif.org/ver10/events/wsdl"\n-tls\t= "http://www.onvif.org/ver10/display/wsdl"\n-tmd\t= "http://www.onvif.org/ver10/deviceIO/wsdl"\n-timg\t= "http://www.onvif.org/ver20/imaging/wsdl"\n-trt\t= "http://www.onvif.org/ver10/media/wsdl"\n-tptz\t= "http://www.onvif.org/ver20/ptz/wsdl"\n-trv\t= "http://www.onvif.org/ver10/receiver/wsdl"\n-trc\t= "http://www.onvif.org/ver10/recording/wsdl"\n-tse\t= "http://www.onvif.org/ver10/search/wsdl"\n-trp\t= "http://www.onvif.org/ver10/replay/wsdl"\n-tan\t= "http://www.onvif.org/ver20/analytics/wsdl"\n-tad\t= "http://www.onvif.org/ver10/analyticsdevice/wsdl"\n-tdn\t= "http://www.onvif.org/ver10/network/wsdl"\n-tt\t= "http://www.onvif.org/ver10/schema"\n-\n-#\tOASIS recommended prefixes\n-\n-wsnt\t= "http://docs.oasis-open.org/wsn/b-2"\n-wsntw\t= "http://docs.oasis-open.org/wsn/bw-2"\n-wsrfbf\t= "http://docs.oasis-open.org/wsrf/bf-2"\n-wsrfr\t= "http://docs.oasis-open.org/wsrf/r-2"\n-wsrfrw = "http://docs.oasis-open.org/wsrf/rw-2"\n-wstop\t= "http://docs.oasis-open.org/wsn/t-1"\n-\n-#\tPrefix bindings for WhiteMesa interoperability testing round 2:\n-\n-i\t= "http://soapinterop.org/"\n-s\t= "http://soapinterop.org/xsd"\n-\n-#\tPrefix binding for Amazon Web Services:\n-\n-aws\t= "urn:PI/DevCentral/SoapService"\n-\n-#\tPrefix binding for Mappoint Web services:\n-\n-mpt\t= "http://s.mappoint.net/mappoint-30/"\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-mime.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-mime.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-schema.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-schema.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-service.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-service.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-soap.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-soap.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-types.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-types.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsdl.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsdl.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsdl2h.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsdl2h.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsdlC.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsdlC.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsp.Po
--- a/GEMBASSY-1.0.3/gsoap/wsdl/.deps/wsdl2h-wsp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/Makefile
--- a/GEMBASSY-1.0.3/gsoap/wsdl/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,616 +0,0 @@\n-# Makefile.in generated by automake 1.10 from Makefile.am.\n-# gsoap/wsdl/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,\n-# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-####### This is the input file for automake, which will generate Makefile.in ##########\n-\n-\n-pkgdatadir = $(datadir)/gsoap\n-pkglibdir = $(libdir)/gsoap\n-pkgincludedir = $(includedir)/gsoap\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = i386-apple-darwin13.1.0\n-host_triplet = i386-apple-darwin13.1.0\n-bin_PROGRAMS = wsdl2h$(EXEEXT)\n-subdir = gsoap/wsdl\n-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs\n-CONFIG_HEADER = $(top_builddir)/config.h\n-CONFIG_CLEAN_FILES =\n-am__installdirs = "$(DESTDIR)$(bindir)"\n-binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)\n-PROGRAMS = $(bin_PROGRAMS)\n-am__objects_1 = wsdl2h-wsdlC.$(OBJEXT)\n-am_wsdl2h_OBJECTS = wsdl2h-wsdl2h.$(OBJEXT) wsdl2h-wsdl.$(OBJEXT) \\\n-\twsdl2h-schema.$(OBJEXT) wsdl2h-types.$(OBJEXT) \\\n-\twsdl2h-service.$(OBJEXT) wsdl2h-soap.$(OBJEXT) \\\n-\twsdl2h-mime.$(OBJEXT) wsdl2h-wsp.$(OBJEXT) $(am__objects_1)\n-wsdl2h_OBJECTS = $(am_wsdl2h_OBJECTS)\n-am__DEPENDENCIES_1 =\n-wsdl2h_DEPENDENCIES = $(SOAP_CPP_LIB) $(am__DEPENDENCIES_1)\n-wsdl2h_LINK = $(CXXLD) $(wsdl2h_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \\\n-\t$(LDFLAGS) -o $@\n-DEFAULT_INCLUDES = -I. -I$(top_builddir)\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \\\n-\t$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)\n-CXXLD = $(CXX)\n-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \\\n-\t-o $@\n-SOURCES = $(wsdl2h_SOURCES)\n-DIST_SOURCES = $(wsdl2h_SOURCES)\n-ETAGS = etags\n-CTAGS = ctags\n-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)\n-ACLOCAL = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run aclocal-1.10\n-AMTAR = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run tar\n-AUTOCONF = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run autoconf\n-AUTOHEADER = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run autoheader\n-AUTOMAKE = ${SHELL} /Users/kotone/dev/build/gsoap-2.8/missing --run automake-1.10\n-AWK = awk\n-BISON_DEFINE = -DWITH_BISON\n-CC = gcc\n-CCDEPMODE = depmode=gcc3\n-CFLAGS = -Wno-deprecated-declarations\n-CPP = gcc -E\n-CPPFLAGS = \n-CXX = g++\n-CXXDEPMODE = depmode=gcc3\n-CXXFLAGS = -Wno-deprecated-declarations\n-CYGPATH_W = echo\n-DEFS = -DHAVE_CONFIG_H\n-DEPDIR = .deps\n-ECHO_C = \\c\n-ECHO_N = \n-ECHO_T = \n-EGREP = /usr/bin/grep -E\n-ENABLE_SAMPLES = \n-EXEEXT = \n-GREP = /usr/bin/grep\n-INSTALL = /usr/bin/install -c\n-INSTALL_DATA = ${INSTALL} -m 644\n-INSTALL_PROGRAM = ${INSTALL}\n-INSTALL_SCRIPT = ${INSTALL}\n-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s\n-LDFLAGS = \n-LEX = flex\n-LEXLIB = -ll\n-LEX_DEFINE = -DWITH_FLEX\n-LEX_FLAGS = -l\n-LEX_OUTPUT_ROOT = lex.yy\n-LIBOBJS = ${LIBOBJDIR}mktime$U.o\n-LIBS = \n-LN_S = ln -s\n-LTLIBOBJS = ${LIBOBJDIR}mktime$U.l'..b'"$(top_srcdir)" | sed \'s/[].[^$$\\\\*]/\\\\\\\\&/g\'`; \\\n-\tlist=\'$(DISTFILES)\'; \\\n-\t dist_files=`for file in $$list; do echo $$file; done | \\\n-\t sed -e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \\\n-\t fi; \\\n-\t cp -pR $$d/$$file $(distdir)$$dir || exit 1; \\\n-\t else \\\n-\t test -f $(distdir)/$$file \\\n-\t || cp -p $$d/$$file $(distdir)/$$file \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: $(BUILT_SOURCES)\n-\t$(MAKE) $(AM_MAKEFLAGS) check-am\n-all-am: Makefile $(PROGRAMS)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(bindir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: $(BUILT_SOURCES)\n-\t$(MAKE) $(AM_MAKEFLAGS) install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\t$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t `test -z \'$(STRIP)\' || \\\n-\t echo "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'"` install\n-mostlyclean-generic:\n-\n-clean-generic:\n-\t-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-\t-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)\n-clean: clean-am\n-\n-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-am\n-\n-install-exec-am: install-binPROGRAMS\n-\n-install-html: install-html-am\n-\n-install-info: install-info-am\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-ps: install-ps-am\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-binPROGRAMS\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \\\n-\tclean-generic ctags distclean distclean-compile \\\n-\tdistclean-generic distclean-tags distdir dvi dvi-am html \\\n-\thtml-am info info-am install install-am install-binPROGRAMS \\\n-\tinstall-data install-data-am install-dvi install-dvi-am \\\n-\tinstall-exec install-exec-am install-html install-html-am \\\n-\tinstall-info install-info-am install-man install-pdf \\\n-\tinstall-pdf-am install-ps install-ps-am install-strip \\\n-\tinstallcheck installcheck-am installdirs maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic pdf pdf-am ps ps-am tags uninstall \\\n-\tuninstall-am uninstall-binPROGRAMS\n-\n-# WSDL2H_EXTRA_FLAGS=-DWITH_OPENSSL -DWITH_GZIP # defined in configure.in\n-# WSDL2H_EXTRA_LIBS=-lssl -lcrypto -lz # defined in configure.in\n-\n-$(SOAP_CPP_SRC) : $(SOAPHEADER)\n-\t$(SOAP) $(SOAP_FLAGS) $(SOAPHEADER)\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/Makefile.am
--- a/GEMBASSY-1.0.3/gsoap/wsdl/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,34 +0,0 @@
-####### This is the input file for automake, which will generate Makefile.in ##########
-
-
-## not a GNU package. You can remove this line, if
-## you have all needed files, that a GNU package needs
-AUTOMAKE_OPTIONS = foreign 1.4
-
-# INCLUDES=-I$(top_srcdir)/gsoap
-# AM_LDFLAGS=$(INCLUDES) -I$(srcdir) -L$(srcdir)
-AM_LDFLAGS=-L$(srcdir) -I$(top_srcdir)/gsoap -I$(top_srcdir)/gsoap/plugin
-AM_CPPFLAGS=-I$(top_srcdir)/gsoap -I$(top_srcdir)/gsoap/plugin
-SOAP=$(top_builddir)/gsoap/src/soapcpp2
-SOAP_CPP_LIB=$(top_builddir)/gsoap/$(WSDL2H_SOAP_CPP_LIB)
-SOAP_CPP_SRC=wsdlC.cpp
-SOAPHEADER=$(srcdir)/wsdl.h
-SOAP_FLAGS=-SC -pwsdl -I$(srcdir) -I$(top_srcdir)/gsoap/import
-BUILT_SOURCES=$(SOAP_CPP_SRC)
-# WSDL2H_EXTRA_FLAGS=-DWITH_OPENSSL -DWITH_GZIP # defined in configure.in
-# WSDL2H_EXTRA_LIBS=-lssl -lcrypto -lz # defined in configure.in
-
-$(SOAP_CPP_SRC) : $(SOAPHEADER)
- $(SOAP) $(SOAP_FLAGS) $(SOAPHEADER)
-
-#LIBS=
-
-bin_PROGRAMS=wsdl2h
-
-wsdl2h_CFLAGS=$(C_DEBUG_FLAGS) $(WSDL2H_EXTRA_FLAGS)
-wsdl2h_CXXFLAGS=$(C_DEBUG_FLAGS) $(WSDL2H_EXTRA_FLAGS)
-wsdl2h_CPPFLAGS=$(AM_CPPFLAGS) $(SOAPCPP2_NONAMESPACES) -D$(platform)
-wsdl2h_SOURCES=wsdl2h.cpp wsdl.cpp schema.cpp types.cpp service.cpp soap.cpp mime.cpp wsp.cpp $(SOAP_CPP_SRC)
-wsdl2h_LDADD=$(SOAP_CPP_LIB) $(WSDL2H_EXTRA_LIBS)
-
-CLEANFILES= *~ *C.cpp *H.h *Stub.h *.nsmap

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/Makefile.in
--- a/GEMBASSY-1.0.3/gsoap/wsdl/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,616 +0,0 @@\n-# Makefile.in generated by automake 1.10 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,\n-# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-####### This is the input file for automake, which will generate Makefile.in ##########\n-\n-VPATH = @srcdir@\n-pkgdatadir = $(datadir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkgincludedir = $(includedir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-bin_PROGRAMS = wsdl2h$(EXEEXT)\n-subdir = gsoap/wsdl\n-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/configure.in\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs\n-CONFIG_HEADER = $(top_builddir)/config.h\n-CONFIG_CLEAN_FILES =\n-am__installdirs = "$(DESTDIR)$(bindir)"\n-binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)\n-PROGRAMS = $(bin_PROGRAMS)\n-am__objects_1 = wsdl2h-wsdlC.$(OBJEXT)\n-am_wsdl2h_OBJECTS = wsdl2h-wsdl2h.$(OBJEXT) wsdl2h-wsdl.$(OBJEXT) \\\n-\twsdl2h-schema.$(OBJEXT) wsdl2h-types.$(OBJEXT) \\\n-\twsdl2h-service.$(OBJEXT) wsdl2h-soap.$(OBJEXT) \\\n-\twsdl2h-mime.$(OBJEXT) wsdl2h-wsp.$(OBJEXT) $(am__objects_1)\n-wsdl2h_OBJECTS = $(am_wsdl2h_OBJECTS)\n-am__DEPENDENCIES_1 =\n-wsdl2h_DEPENDENCIES = $(SOAP_CPP_LIB) $(am__DEPENDENCIES_1)\n-wsdl2h_LINK = $(CXXLD) $(wsdl2h_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \\\n-\t$(LDFLAGS) -o $@\n-DEFAULT_INCLUDES = -I. -I$(top_builddir)@am__isrc@\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \\\n-\t$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)\n-CXXLD = $(CXX)\n-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \\\n-\t-o $@\n-SOURCES = $(wsdl2h_SOURCES)\n-DIST_SOURCES = $(wsdl2h_SOURCES)\n-ETAGS = etags\n-CTAGS = ctags\n-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)\n-ACLOCAL = @ACLOCAL@\n-AMTAR = @AMTAR@\n-AUTOCONF = @AUTOCONF@\n-AUTOHEADER = @AUTOHEADER@\n-AUTOMAKE = @AUTOMAKE@\n-AWK = @AWK@\n-BISON_DEFINE = @BISON_DEFINE@\n-CC = @CC@\n-CCDEPMODE = @CCDEPMODE@\n-CFLAGS = @CFLAGS@\n-CPP = @CPP@\n-CPPFLAGS = @CPPFLAGS@\n-CXX = @CXX@\n-CXXDEPMODE = @CXXDEPMODE@\n-CXXFLAGS = @CXXFLAGS@\n-CYGPATH_W = @CYGPATH_W@\n-DEFS = @DEFS@\n-DEPDIR = @DEPDIR@\n-ECHO_C = @ECHO_C@\n-ECHO_N = @ECHO_N@\n-ECHO_T = @ECHO_T@\n-EGREP = @EGREP@\n-ENABLE_SAMPLES = @ENABLE_SAMPLES@\n-EXEEXT = @EXEEXT@\n-GREP = @GREP@\n-INSTALL = @INSTALL@\n-INSTALL_DATA = @INSTALL_DATA@\n-INSTALL_PROGRAM = @INSTALL_PROGRAM@\n-INSTALL_SCRIPT = @INSTALL_SCRIPT@\n-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@\n-LDFLAGS = @LDFLAGS@\n-LEX = @LEX@\n-LEXLIB = @LEXLIB@\n-LEX_DEFINE = @LEX_DEFINE@\n-LEX_FLAGS = @LEX_FLAGS@\n-LEX_OUTPUT_ROOT = @LEX_OUTPUT_ROOT@\n-LIBOBJS = @LIBOBJS@\n-LIBS = @LIBS@\n-LN_S = @LN_S@\n-LTLIBOBJS = @LTLIBOBJS@\n-MAKEINFO = @MAKEINFO@\n-MKDIR_P = @MKDIR_P@\n-OBJEXT = @OBJEXT@\n-PACKAGE = @PACKAGE@\n-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@\n-PACKAGE_NAME = @PACKAGE_NAME@\n-PACKAGE_STRING = @PACKAGE_STRING@\n-PACKAGE_TARNAME = @PACKAGE_TARNAME@\n-PACKAGE_VERSION = @PACKAGE_VERSION@\n-PATH_SEPARATOR = '..b'"$(top_srcdir)" | sed \'s/[].[^$$\\\\*]/\\\\\\\\&/g\'`; \\\n-\tlist=\'$(DISTFILES)\'; \\\n-\t dist_files=`for file in $$list; do echo $$file; done | \\\n-\t sed -e "s|^$$srcdirstrip/||;t" \\\n-\t -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \\\n-\t fi; \\\n-\t cp -pR $$d/$$file $(distdir)$$dir || exit 1; \\\n-\t else \\\n-\t test -f $(distdir)/$$file \\\n-\t || cp -p $$d/$$file $(distdir)/$$file \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: $(BUILT_SOURCES)\n-\t$(MAKE) $(AM_MAKEFLAGS) check-am\n-all-am: Makefile $(PROGRAMS)\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(bindir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: $(BUILT_SOURCES)\n-\t$(MAKE) $(AM_MAKEFLAGS) install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\t$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t `test -z \'$(STRIP)\' || \\\n-\t echo "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'"` install\n-mostlyclean-generic:\n-\n-clean-generic:\n-\t-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-\t-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)\n-clean: clean-am\n-\n-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-am\n-\n-install-exec-am: install-binPROGRAMS\n-\n-install-html: install-html-am\n-\n-install-info: install-info-am\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-ps: install-ps-am\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-binPROGRAMS\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \\\n-\tclean-generic ctags distclean distclean-compile \\\n-\tdistclean-generic distclean-tags distdir dvi dvi-am html \\\n-\thtml-am info info-am install install-am install-binPROGRAMS \\\n-\tinstall-data install-data-am install-dvi install-dvi-am \\\n-\tinstall-exec install-exec-am install-html install-html-am \\\n-\tinstall-info install-info-am install-man install-pdf \\\n-\tinstall-pdf-am install-ps install-ps-am install-strip \\\n-\tinstallcheck installcheck-am installdirs maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic pdf pdf-am ps ps-am tags uninstall \\\n-\tuninstall-am uninstall-binPROGRAMS\n-\n-# WSDL2H_EXTRA_FLAGS=-DWITH_OPENSSL -DWITH_GZIP # defined in configure.in\n-# WSDL2H_EXTRA_LIBS=-lssl -lcrypto -lz # defined in configure.in\n-\n-$(SOAP_CPP_SRC) : $(SOAPHEADER)\n-\t$(SOAP) $(SOAP_FLAGS) $(SOAPHEADER)\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/MakefileManual
--- a/GEMBASSY-1.0.3/gsoap/wsdl/MakefileManual Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,63 +0,0 @@
-#       gSOAP wsdl2h Makefile by Robert van Engelen, Genivia Inc.
-#       Use this to build the soapcpp2 tool when autoconf/automake are not
-#       available.
-#
-# Dependences:
-#       Build soapcpp2 first (should be in ../bin/soapcpp2)
-#
-# Use 'make secure' to build SSL-capable wsdlh2 tool (requires OpenSSL)
-#
-# Mac OS X universal binary:
-# CPP=g++ -arch i386 -arch ppc
-CPP=g++
-#
-GSOAP=../bin/soapcpp2
-SOAPH=../stdsoap2.h
-SOAPC=../stdsoap2.c
-SOAPCPP=../stdsoap2.cpp
-#
-LIBS=-lm
-#
-COFLAGS=-O1
-# For static linking use:
-# COFLAGS=-O1 -static
-# For debugging use:
-# COFLAGS=-DDEBUG -g
-# COFLAGS=-g
-CWFLAGS=-Wall
-#
-CIFLAGS=-I.. -I../plugin
-#
-CMFLAGS=
-#
-CFLAGS= $(CWFLAGS) $(COFLAGS) $(CIFLAGS) $(CMFLAGS)
-#
-wsdl2h: wsdlC.o wsdl.o schema.o soap.o mime.o wsp.o types.o service.o wsdl2h.cpp $(SOAPCPP)
- $(CPP) $(CFLAGS) -o wsdl2h wsdl2h.cpp wsdlC.o wsdl.o schema.o soap.o mime.o wsp.o types.o service.o $(SOAPCPP) $(LIBS)
- cp -f wsdl2h ../bin
-wsdlC.o: wsdlC.cpp
- $(CPP) -c $(CFLAGS) wsdlC.cpp
-wsdlC.cpp: schema.h soap.h mime.h dime.h http.h wsdl.h includes.h imports.h wsp.h sp.h wsam.h wsrmp.h wsu.h wst.h
- $(GSOAP) -I../import -SC -pwsdl wsdl.h
-types.o: types.h types.cpp
- $(CPP) -c $(CFLAGS) types.cpp
-service.o: types.h service.h service.cpp
- $(CPP) -c $(CFLAGS) service.cpp
-wsdl.o: wsdl.h wsdl.cpp includes.h imports.h
- $(CPP) -c $(CFLAGS) wsdl.cpp
-schema.o: schema.h schema.cpp includes.h imports.h
- $(CPP) -c $(CFLAGS) schema.cpp
-soap.o: soap.h soap.cpp includes.h imports.h
- $(CPP) -c $(CFLAGS) soap.cpp
-mime.o: mime.h mime.cpp includes.h imports.h
- $(CPP) -c $(CFLAGS) mime.cpp
-wsp.o: wsp.h wsp.cpp includes.h imports.h
- $(CPP) -c $(CFLAGS) wsp.cpp
-secure:
- rm -f *.o
- make CMFLAGS=-DWITH_OPENSSL LIBS="../plugin/httpda.c ../plugin/md5evp.c -lcrypto -lssl -lm" wsdl2h
-.PHONY: clean distclean
-clean:
- rm -f *.o wsdlH.h wsdlStub.h wsdlC.cpp wsdlClient.cpp wsdlServer.cpp wsdlClientLib.cpp wsdlServerLib.cpp
-distclean:
- rm -f *.o *.wsdl. *.xsd *.xml *.nsmap wsdl2h wsdlH.h wsdlStub.h wsdlC.cpp wsdlClient.cpp wsdlServer.cpp wsdlClientLib.cpp wsdlServerLib.cpp

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/README.txt
--- a/GEMBASSY-1.0.3/gsoap/wsdl/README.txt Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,215 +0,0 @@\n-The gSOAP WSDL parser \'wsdl2h\'\r\n-\r\n-INSTRUCTIONS\r\n-\r\n-The gSOAP WSDL parser converts one or more WSDLs into a gSOAP header file for\r\n-processing with the gSOAP soapcpp2 compiler to generate client stubs/proxies\r\n-and server skeletons/objects to access services or build new services.\r\n-\r\n-For example:\r\n-\r\n-$ wsdl2h -o XMethodsQuery.h http://www.xmethods.net/wsdl/query.wsdl\r\n-\r\n-Note: if an error occurs when running wsdl2h, please try again later. The\r\n-XMethods site is very popular and suffers under load. It may also be the case\r\n-that XMethods removed certain services. In that case, try another on-line WSDL.\r\n-\r\n-This generates the XMethodsQuery.h header file with Web service operations\r\n-and C++ data types. This header file is intended to be processed with soapcpp2\r\n-to generate the stub and/or skeleton code.\r\n-\r\n-You need to have stlvector.h present in the current directory (stlvector.h is\r\n-in the package) to support STL vectors. To build without STL, use option -s:\r\n-\r\n-$ wsdl2h -s -o XMethodsQuery.h http://www.xmethods.net/wsdl/query.wsdl\r\n-\r\n-Or to build a pure C application, use option -c:\r\n-\r\n-$ wsdl2h -c -o XMethodsQuery.h http://www.xmethods.net/wsdl/query.wsdl\r\n-\r\n-Other useful options to control the output are -e and -y (see below).\r\n-\r\n-The above commands are to be followed by the soapcpp2 compilation phase:\r\n-\r\n-$ soapcpp2 -C XMethodsQuery.h\r\n-\r\n-Where option -C indicates client-side only files (soapcpp2 generates both\r\n-client and server stubs and skeletons by default).\r\n-\r\n-The generated XMethodsQuery.h includes the definitions of data types and\r\n-service operations of the XMethods Query Web service. To develop a C++ client\r\n-application, you can use the generated \'soapXMethodsQuerySoapProxy\' class and\r\n-\'XMethodsQuerySoap.nsmap\' XML namespace table to access the Web service. Both\r\n-need to be \'#include\'d in your source. Then compile and link the soapC.cpp,\r\n-soapClient.cpp, and stdsoap2.cpp sources to complete the build. More\r\n-information on this process can be found in the gSOAP documentation.\r\n-\r\n-When parsing a WSDL, the output file name is the WSDL input file name with\r\n-extension \'.h\' instead of \'.wsdl\'. When an input file is absent or a WSDL file\r\n-from a Web location is accessed, the header output will be produced on the\r\n-standard output. Input may also consist of schema files, which is useful when\r\n-you to need to generate code for serializing schema instances.\r\n-\r\n-USING A TYPEMAP FILE TO CONTROL THE INPUT AND OUTPUT\r\n-\r\n-The typemap.dat is the default file processed by \'wsdl2h\' to customize the\r\n-generated header file output. The default typemap.dat file is located in the\r\n-\'WS\' directory. Use wsdl2h option -t to specify an alternate file.\r\n-\r\n-The typemap.dat file can be used to define namespace prefix and type bindings\r\n-for the generated header files by the \'wsdl2h\' tool. XML namespace prefix\r\n-bindings can be provided to override the default choice of the ns1, ns2, ...\r\n-prefixes generated by \'wsdl2h\'. It is highly recommended to provide namespace\r\n-prefixes for your project\'s XML namespaces. In this way, changes to the WSDL\r\n-(or newer releases of wsdl2h) will have a minimal impact on coding.\r\n-\r\n-Bindings for namespace prefixes in typemap.dat are of the form:\r\n-\tprefix = "URI"\r\n-\r\n-For example, to bind the \'google\' prefix to the Google API\'s namespace:\r\n-\tgoogle = "urn:GoogleSearch"\r\n-\r\n-Type bindings can by provided to bind XML schema types to C/C++ types for your\r\n-project.\r\n-\r\n-Type bindings are of the form:\r\n-\tprefix__type = declaration | use | ptr-use\r\n-where \'declaration\' introduces the type in the header file, \'use\' specifies how\r\n-the type is used directly, \'ptr-use\' specifies how the type is used as a\r\n-pointer type.\r\n-\r\n-For example:\r\n-\txsd__string = | char* | char*\r\n-After enabling this line, all XSD strings will be mapped to char* and since\r\n-char* is already a pointer type, the \'ptr-use\' part is the same as \'use\' part.\r\n-Note that the \'declaration\' part is emp'..b"combined.\r\n-\r\n-OUTPUT FORMAT\r\n-\r\n-The output file is a gSOAP-formatted header file. The header file syntax is\r\n-augmented with annotations reflecting WSDL and schema-specific bindings and\r\n-validation constraints.\r\n-\r\n-We suggest the use of Doxygen (www.doxygen.org) to produce documented for the\r\n-generated header file. However, we STRONGLY recommend user to inspect the\r\n-generated header file first for warnings and other annotations (which do not\r\n-appear in Doxygen's output) indicating potential problems.\r\n-\r\n-Note that Doxygen's license model does not infinge on your ownership of the\r\n-generated gSOAP source code output when you purchased a commercial license.\r\n-\r\n-COMMAND LINE OPTIONS\r\n-\r\n--a generate indexed struct names for local elements with anonymous types\r\n--b\tbi-directional operations to serve one-way response messages (duplex)\r\n--c generate C source code\r\n--d use DOM to populate xs:any and xsd:anyType elements\r\n--e don't qualify enum names\r\n--f generate flat C++ class hierarchy\r\n--g generate global top-level element declarations\r\n--h display help info\r\n--Ipath use path to find files\r\n--i don't import (advanced option)\r\n--j\tdon't generate SOAP_ENV__Header and SOAP_ENV__Detail definitions\r\n--k\tdon't generate SOAP_ENV__Header mustUnderstand qualifiers\r\n--l include license information in output\r\n--m use xsd.h module to import primitive types\r\n--Nname use name for service prefixes to produce a service for each binding\r\n--nname use name as the base namespace prefix instead of 'ns'\r\n--ofile output to file\r\n--P don't create polymorphic types with C++ inheritance from xsd__anyType\r\n--p create polymorphic types with C++ inheritance from base xsd__anyType\r\n--qname use name for the C++ namespace for all service declarations\r\n--rhost[:port[:uid:pwd]]\r\n- connect via proxy host, port, and proxy credentials\r\n--r:uid:pwd\r\n- connect with authentication credentials (digest auth requires SSL)\r\n--R generate REST operations for REST bindings in the WSDL\r\n--s don't generate STL code (no std::string and no std::vector)\r\n--tfile use type map file instead of the default file typemap.dat\r\n--u don't generate unions\r\n--v verbose output\r\n--W suppress warnings\r\n--w always wrap response parameters in a response struct (<=1.1.4 behavior)\r\n--x don't generate _XML any/anyAttribute extensibility elements\r\n--y generate typedef synonyms for structs and enums\r\n--z1 compatibility with 2.7.6e: generate pointer-based arrays\r\n--z2 compatibility with 2.7.15: qualify element/attribute referenced members\r\n--z3 compatibility with 2.7.16 to 2.8.7: qualify element/attribute references\r\n--z4 compatibility up to 2.8.11: don't generate union structs in std::vector\r\n--z5 compatibility up to 2.8.15\r\n--_ don't generate _USCORE (replace with UNICODE _x005f)\r\n-infile.wsdl infile.xsd http://www... list of input sources (if none use stdin)\r\n-\r\n-DOCUMENTATION\r\n-\r\n-See soapdoc2.pdf for documentation.\r\n-\r\n-INSTALLATION\r\n-\r\n-Use './configure' and 'make' in the root directory, as explained in the \r\n-installation instructions.\r\n-\r\n-To build 'wsdl2h' when autoconf/automake fail, use:\r\n-\r\n-\tmake -f MakefileManual\r\n-\r\n-ENABLING HTTPS SSL/TLS CONNECTIVITY AND HTTP DIGEST AUTHENTICATION\r\n-\r\n-To build 'wsdl2h' with secure features, use:\r\n-\r\n-\tmake -f MakefileManual secure\r\n-\r\n-If you don't have OpenSSL installed, you cannot build an SSL-secure version of\r\n-wsdl2h. In that case we recommend downloading the WSDL and schema files for\r\n-processing with the non-SSL-enabled wsdl2h tool.\r\n-\r\n-LICENSE\r\n-\r\n-The gSOAP WSDL parser 'wsdl2h' and source code are released under GPL or\r\n-a commercial license. The commercial license is available from Genivia.\r\n-Please visit http://genivia.com/Products/gsoap/contract.html\r\n-\r\n-COPYRIGHT NOTICE\r\n-\r\n-gSOAP XML Web services tools\r\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia, Inc. All Rights Reserved.\r\n"

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/dime.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/dime.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,44 +0,0 @@
-/*
- dime.h
-
- WSDL/DIME binding schema
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-//gsoap dime schema documentation: WSDL/DIME binding schema
-//gsoap dime schema namespace: http://schemas.xmlsoap.org/ws/2002/04/dime/wsdl/
-
-#import "imports.h"
-
-class dime__message
-{ public:
- @xsd__anyURI layout;
-// @xsd__boolean wsdl__required;
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/gwsdl.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/gwsdl.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,73 +0,0 @@
-/*
- gwsdl.h
-
- OGSI GWSDL binding schema interface
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia, Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-//gsoap gwsdl schema documentation: OGSI GWSDL binding schema
-//gsoap gwsdl schema namespace: http://www.gridforum.org/namespaces/2003/03/gridWSDLExtensions
-//gsoap sd schema namespace: http://www.gridforum.org/namespaces/2003/03/serviceData
-
-#import "schema.h"
-
-class wsdl__operation;
-
-enum sd__mutability { static_, constant, extendable, mutable_ };
-
-class sd__serviceData
-{ public:
- @xsd__NMTOKEN name;
- @xsd__QName type;
- @xsd__boolean nillable = false;
- @xsd__string minOccurs; // xsd:nonNegativeInteger
- @xsd__string maxOccurs; // xsd:nonNegativeInteger|unbounded
- @enum sd__mutability mutability = extendable;
- @xsd__boolean modifiable = false;
- /* has any content */
- public:
-};
-
-class sd__staticServiceDataValues
-{ public:
- int __type; /* any content, probably should use DOM */
- void* _any;
-};
-
-class gwsdl__portType
-{ public:
- @xsd__NMTOKEN name;
- @xsd__QName extends; // a list of QNames
- xsd__string documentation; // <wsdl:documentation>?
- std::vector<wsdl__operation*> operation; // <wsdl:operation>*
- std::vector<sd__serviceData> sd__serviceData_;
- sd__staticServiceDataValues *sd__staticServiceDataValues_;
- public:
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/http.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/http.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,62 +0,0 @@
-/*
- http.h
-
- WSDL/HTTP binding schema interface
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-//gsoap http schema documentation: WSDL 1.1 HTTP binding schema
-//gsoap http schema namespace: http://schemas.xmlsoap.org/wsdl/http/
-
-//gsoap whttp schema documentation: WSDL 2.0 HTTP binding schema
-//gsoap whttp schema namespace: http://www.w3.org/ns/wsdl/http
-
-#import "imports.h"
-
-class http__address
-{ public:
- @xsd__anyURI location;
-};
-
-class http__binding
-{ public:
- @xsd__NMTOKEN verb;
-};
-
-class http__operation
-{ public:
- @xsd__anyURI location;
-};
-
-class whttp__header
-{ public:
- @xsd__string name;
- @xsd__QName type;
- @xsd__boolean required = false;
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/imports.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/imports.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,51 +0,0 @@
-/*
- imports.h
-
- Common XSD types and externs for gSOAP header file import
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-#import "stlvector.h"
-
-typedef char *xsd__anyURI,
- *xsd__ID,
- *xsd__NCName,
- *xsd__NMTOKEN,
- *xsd__NMTOKENS,
- *xsd__QName,
- *xsd__string;
-typedef bool xsd__boolean;
-
-extern class ostream;
-extern class istream;
-
-#include "includes.h"
-
-extern class SetOfString;

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/includes.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/includes.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,162 +0,0 @@
-/*
- includes.h
-
- Common project definitions
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-#ifndef INCLUDES_H
-#define INCLUDES_H
-
-#include "stdsoap2.h"
-
-#ifdef WITH_OPENSSL
-#include "httpda.h"
-#endif
-
-#define WSDL2H_VERSION "2.8.17r"
-
-#ifdef WIN32
-# pragma warning(disable : 4996)
-#endif
-
-#include <utility>
-#include <iterator>
-#include <vector>
-#include <set>
-#include <map>
-
-using namespace std;
-
-struct ltstr
-{ bool operator()(const char *s1, const char *s2) const
-  { return strcmp(s1, s2) < 0;
-  }
-};
-
-struct eqstr
-{ const char *s;
-  eqstr(const char *s) : s(s) { }
-  bool operator()(const char *t) const
-  { return strcmp(s, t) == 0;
-  }
-};
-
-typedef set<const char*, ltstr> SetOfString;
-
-typedef pair<const char*, const char*> Pair;
-
-struct ltpair
-{ bool operator()(Pair s1, Pair s2) const
-  { int cmp = strcmp(s1.first, s2.first);
-    if (cmp == 0)
-      cmp = strcmp(s1.second, s2.second);
-    return cmp < 0;
-  }
-};
-
-typedef map<const char*, const char*, ltstr> MapOfStringToString;
-
-typedef map<Pair, const char*, ltpair> MapOfPairToString;
-
-typedef map<const char*, size_t, ltstr> MapOfStringToNum;
-
-typedef vector<const char*> VectorOfString;
-
-extern int _flag,
-           aflag,
-           bflag,
-    cflag,
-    dflag,
-    eflag,
-    fflag,
-    gflag,
-    iflag,
-    jflag,
-    kflag,
-    mflag,
-    pflag,
-    Pflag,
-    Rflag,
-    sflag,
-    uflag,
-    vflag,
-    wflag,
-    Wflag,
-    xflag,
-    yflag,
-    zflag;
-
-extern FILE *stream;
-
-extern SetOfString exturis;
-
-#define MAXINFILES (1000)
-
-extern int infiles;
-extern char *infile[MAXINFILES], *outfile, *proxy_host, *proxy_userid, *proxy_passwd, *auth_userid, *auth_passwd;
-extern const char *mapfile, *import_path, *cwd_path, *cppnamespace;
-
-extern int proxy_port;
-
-extern const char *service_prefix;
-extern const char *schema_prefix;
-
-extern const char elementformat[];
-extern const char pointerformat[];
-extern const char attributeformat[];
-extern const char vectorformat_open[];
-extern const char vectorformat[];
-extern const char pointervectorformat[];
-extern const char arrayformat[];
-extern const char arraysizeformat[];
-extern const char arrayoffsetformat[];
-extern const char sizeformat[];
-extern const char choiceformat[];
-extern const char schemaformat[];
-extern const char serviceformat[];
-extern const char paraformat[];
-extern const char anonformat[];
-extern const char copyrightnotice[];
-extern const char licensenotice[];
-
-extern void *emalloc(size_t size);
-extern char *estrdup(const char *s);
-extern char *estrdupf(const char *s);
-
-extern void text(const char*);
-
-class Types;
-class Message;
-class Operation;
-class Service;
-class Definitions;
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/mime.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/mime.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,66 +0,0 @@
-/*
- mime.cpp
-
- WSDL/MIME binding schema
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-#include "wsdlH.h" // cannot include "schemaH.h"
-#include "includes.h"
-
-extern const char *qname_token(const char*, const char*);
-
-////////////////////////////////////////////////////////////////////////////////
-//
-// mime:multipartRelated
-//
-////////////////////////////////////////////////////////////////////////////////
-
-int mime__multipartRelated::traverse(wsdl__definitions& definitions)
-{ if (vflag)
-    cerr << "Analyzing mime multpartRelated " << endl;
-  for (vector<mime__part>::iterator pt = part.begin(); pt != part.end(); ++pt)
-    (*pt).traverse(definitions);
-  return SOAP_OK;
-}
-
-////////////////////////////////////////////////////////////////////////////////
-//
-// mime:part
-//
-////////////////////////////////////////////////////////////////////////////////
-
-int mime__part::traverse(wsdl__definitions& definitions)
-{ if (vflag)
-    cerr << "Analyzing mime part " << endl;
-  for (vector<soap__header>::iterator hd = soap__header_.begin(); hd != soap__header_.end(); ++hd)
-    (*hd).traverse(definitions);
-  return SOAP_OK;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/mime.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/mime.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,69 +0,0 @@
-/*
- mime.h
-
- mime and xmime binding schema
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-//gsoap mime schema documentation: WSDL/MIME binding schema
-//gsoap mime schema namespace: http://schemas.xmlsoap.org/wsdl/mime/
-
-//gsoap xmime schema documentation: xmime binding schema
-//gsoap xmime schema namespace: http://www.w3.org/2005/05/xmlmime
-
-#import "imports.h"
-#import "soap.h"
-
-class mime__content
-{ public:
- @xsd__NMTOKEN part;
- @xsd__string type;
-};
-
-class mime__part
-{ public:
- soap__body *soap__body_;
- std::vector<soap__header> soap__header_;
- std::vector<mime__content> content;
-  public:
-   int traverse(wsdl__definitions&);
-};
-
-class mime__multipartRelated
-{ public:
- std::vector<mime__part> part;
-  public:
-   int traverse(wsdl__definitions&);
-};
-
-class mime__mimeXml
-{ public:
- @xsd__NMTOKEN part;
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/schema.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/schema.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1699 +0,0 @@\n-/*\n-\tschema.cpp\n-\n-\tXSD binding schema implementation\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-*/\n-\n-#include "wsdlH.h"\t\t// cannot include "schemaH.h"\n-#include "includes.h"\n-\n-extern struct Namespace namespaces[];\n-\n-extern "C" {\n-extern int warn_ignore(struct soap*, const char*);\n-}\n-\n-extern const char *qname_token(const char*, const char*);\n-extern int is_builtin_qname(const char*);\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tschema\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-xs__schema::xs__schema()\n-{ soap = soap_new1(SOAP_XML_TREE | SOAP_C_UTFSTRING);\n-#ifdef HTTPDA_H\n- soap_register_plugin(soap, http_da);\n-#endif\n-#ifdef WITH_OPENSSL\n- soap_ssl_client_context(soap, SOAP_SSL_NO_AUTHENTICATION, NULL, NULL, NULL, NULL, NULL);\n-#endif\n- soap_set_namespaces(soap, namespaces);\n- soap_default(soap);\n- soap->fignore = warn_ignore;\n- soap->encodingStyle = NULL;\n- soap->proxy_host = proxy_host;\n- soap->proxy_port = proxy_port;\n- soap->proxy_userid = proxy_userid;\n- soap->proxy_passwd = proxy_passwd;\n- targetNamespace = NULL;\n- version = NULL;\n- updated = false;\n- location = NULL;\n- redirs = 0;\n-}\n-\n-xs__schema::xs__schema(struct soap *copy)\n-{ soap = soap_copy(copy);\n- soap->socket = SOAP_INVALID_SOCKET;\n- soap->recvfd = 0;\n- soap->sendfd = 1;\n- soap_default(soap);\n- soap->fignore = warn_ignore;\n- soap->encodingStyle = NULL;\n- targetNamespace = NULL;\n- version = NULL;\n- updated = false;\n- location = NULL;\n- redirs = 0;\n-}\n-\n-xs__schema::xs__schema(struct soap *copy, const char *cwd, const char *loc)\n-{ soap = soap_copy(copy);\n- soap->socket = SOAP_INVALID_SOCKET;\n- soap->recvfd = 0;\n- soap->sendfd = 1;\n- /* no longer required, since we keep the host name:\n- strcpy(soap->host, copy->host);\n- */\n- soap_default(soap);\n- soap->fignore = warn_ignore;\n- soap->encodingStyle = NULL;\n- targetNamespace = NULL;\n- version = NULL;\n- updated = false;\n- location = NULL;\n- redirs = 0;\n- read(cwd, loc);\n-}\n-\n-xs__schema::~xs__schema()\n-{ }\n-\n-int xs__schema::get(struct soap *soap)\n-{ return preprocess();\n-}\n-\n-int xs__schema::preprocess()\n-{ // process xs:include recursively\n- // NOTE: includes are context sensitive (take context info), so keep including\n- for (vector<xs__include>::iterator in = include.begin(); in != include.end(); ++in)\n- { (*in).preprocess(*this); // read schema and recurse over <include>\n- if ((*in).schemaPtr())\n- insert(*(*in).schemaPtr());\n- }\n- for (vector<xs__redefine>::iterator re = redefine.begin(); re != redefine.end('..b's__schema *xs__attributeGroup::schemaPtr() const\n-{ return schemaRef;\n-}\n-\n-xs__attributeGroup *xs__attributeGroup::attributeGroupPtr() const\n-{ return attributeGroupRef;\n-}\n-\n-int xs__any::traverse(xs__schema &schema)\n-{ if (vflag)\n- cerr << " Analyzing schema any" << endl;\n- for (vector<xs__element>::iterator i = element.begin(); i != element.end(); ++i)\n- (*i).traverse(schema);\n- return SOAP_OK;\n-}\n-\n-xs__group::xs__group()\n-{ schemaRef = NULL;\n- groupRef = NULL;\n-}\n-\n-int xs__group::traverse(xs__schema &schema)\n-{ if (vflag)\n- cerr << " Analyzing schema group" << endl;\n- schemaRef = &schema;\n- if (all)\n- all->traverse(schema);\n- else if (choice)\n- choice->traverse(schema);\n- else if (sequence)\n- sequence->traverse(schema);\n- groupRef = NULL;\n- if (ref)\n- { const char *token = qname_token(ref, schema.targetNamespace);\n- if (token)\n- { for (vector<xs__group>::iterator i = schema.group.begin(); i != schema.group.end(); ++i)\n- if (!strcmp((*i).name, token))\n- { groupRef = &(*i);\n- if (vflag)\n- cerr << " Found group \'" << (name?name:"") << "\' ref \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n- }\n- if (!groupRef)\n- { for (vector<xs__import>::const_iterator i = schema.import.begin(); i != schema.import.end(); ++i)\n- { xs__schema *s = (*i).schemaPtr();\n- if (s)\n- { token = qname_token(ref, s->targetNamespace);\n- if (token)\n- { for (vector<xs__group>::iterator j = s->group.begin(); j != s->group.end(); ++j)\n- { if (!strcmp((*j).name, token))\n- { groupRef = &(*j);\n- if (vflag)\n- cerr << " Found group \'" << (name?name:"") << "\' ref \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n-\t }\n-\t if (groupRef)\n- break;\n- }\n- }\n- }\n- }\n- if (!groupRef)\n- if (!Wflag)\n- cerr << "Warning: could not find group \'" << (name?name:"") << "\' ref \'" << (ref?ref:"") << "\' in schema \'" << (schema.targetNamespace?schema.targetNamespace:"") << "\'" << endl;\n- }\n- return SOAP_OK;\n-}\n-\n-void xs__group::schemaPtr(xs__schema *schema)\n-{ schemaRef = schema;\n-}\n-\n-xs__schema* xs__group::schemaPtr() const\n-{ return schemaRef;\n-}\n-\n-void xs__group::groupPtr(xs__group *group)\n-{ groupRef = group;\n-}\n-\n-xs__group* xs__group::groupPtr() const\n-{ return groupRef;\n-}\n-\n-int xs__enumeration::traverse(xs__schema &schema)\n-{ if (vflag)\n- cerr << " Analyzing schema enumeration \'" << (value?value:"") << "\'" << endl;\n- return SOAP_OK;\n-}\n-\n-int xs__pattern::traverse(xs__schema &schema)\n-{ if (vflag)\n- cerr << " Analyzing schema pattern" << endl;\n- return SOAP_OK;\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tI/O\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-ostream &operator<<(ostream &o, const xs__schema &e)\n-{ if (!e.soap)\n- { struct soap soap;\n- soap_init2(&soap, SOAP_IO_DEFAULT, SOAP_XML_TREE | SOAP_C_UTFSTRING);\n- soap_set_namespaces(&soap, namespaces);\n- e.soap_serialize(&soap);\n- soap_begin_send(&soap);\n- e.soap_out(&soap, "xs:schema", 0, NULL);\n- soap_end_send(&soap);\n- soap_end(&soap);\n- soap_done(&soap);\n- }\n- else\n- { ostream *os = e.soap->os;\n- e.soap->os = &o;\n- e.soap_serialize(e.soap);\n- soap_begin_send(e.soap);\n- e.soap_out(e.soap, "xs:schema", 0, NULL);\n- soap_end_send(e.soap);\n- e.soap->os = os;\n- }\n- return o;\n-}\n-\n-istream &operator>>(istream &i, xs__schema &e)\n-{ if (!e.soap)\n- { e.soap = soap_new();\n- soap_set_namespaces(e.soap, namespaces);\n- }\n- istream *is = e.soap->is;\n- e.soap->is = &i;\n- if (soap_begin_recv(e.soap)\n- || !e.soap_in(e.soap, "xs:schema", NULL)\n- || soap_end_recv(e.soap))\n- { // handle error? Note: e.soap->error is set and app should check\n- }\n- e.soap->is = is;\n- return i;\n-}\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/schema.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/schema.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,498 +0,0 @@\n-/*\n-\tschema.h\n-\n-\tXSD binding schema interface\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-*/\n-\n-//gsoap xs schema documentation:\tXSD binding schema\n-//gsoap xs schema namespace:\t\thttp://www.w3.org/2001/XMLSchema\n-//gsoap xs schema elementForm:\t\tqualified\n-//gsoap xs schema attributeForm:\tunqualified\n-\n-/* For the wsdl:arrayType attribute to support old style SOAP arrays: */\n-//gsoap wsdl schema namespace:\t\thttp://schemas.xmlsoap.org/wsdl/\n-\n-#import "imports.h"\n-\n-class xs__schema;\t\t\t// forward declaration\n-class xs__simpleType;\t\t\t// forward declaration\n-class xs__complexType;\t\t\t// forward declaration\n-class xs__extension;\t\t\t// forward declaration\n-class xs__restriction;\t\t\t// forward declaration\n-class xs__seqchoice;\t\t\t// forward declaration\n-class xs__group;\t\t\t// forward declaration\n-class xs__list;\t\t\t\t// forward declaration\n-class xs__union;\t\t\t// forward declaration\n-\n-class xs__annotation\n-{ public:\n-\tchar\t\t\t\t*documentation;\n-};\n-\n-enum xs__formChoice { unqualified, qualified };\n-\n-class xs__element\n-{ public:\n-\t// @xsd__ID\t\t\tid;\n-\t@xsd__NCName\t\t\tname;\n-\t@xsd__QName\t\t\tref;\n-\t@xsd__QName\t\t\ttype;\n-\t@xsd__string\t\t\tdefault_;\n-\t@xsd__QName\t\t\tdefault__;\t\t// also get QName value if element type is QName\n-\t@xsd__string\t\t\tfixed;\n-\t@xsd__QName\t\t\tfixed_;\t\t\t// also get QName value if element type is QName\n-\t@enum xs__formChoice\t\t*form;\n-\t@xsd__boolean\t\t\tnillable\t\t= false;\n-\t@xsd__boolean\t\t\tabstract\t\t= false;\n-\t@xsd__QName\t\t\tsubstitutionGroup;\n-\t@xsd__string\t\t\tminOccurs;\t\t// xsd:nonNegativeInteger\n-\t@xsd__string\t\t\tmaxOccurs;\t\t// xsd:nonNegativeInteger|unbounded\n-\t@xsd__string\t\t\txmime__expectedContentTypes;\n-\txs__annotation\t\t\t*annotation;\n-\txs__simpleType\t\t\t*simpleType;\t\t// choice\n-\txs__complexType\t\t\t*complexType;\t\t// choice\n-\txsd__string\t\t\tunique;\t\t\t// dummy, not used\n- private:\n-\txs__schema\t\t\t*schemaRef;\t\t// schema to which this belongs\n- \txs__element\t\t\t*elementRef;\t\t// traverse() finds ref\n- \txs__simpleType\t\t\t*simpleTypeRef;\t\t// traverse() finds type or = simpleType above\n- \txs__complexType\t\t\t*complexTypeRef;\t// traverse() finds type or = complexType above\n-\tstd::vector<xs__element*>\tsubstitutions;\t\t// traverse() finds substitutionGroup elements for this abstract element\n- public:\n-\t\t\t\t\txs__element();\n- \tint\t\t\t\ttraverse(xs__schema&);\n-\tvoid\t\t\t\tschemaPtr(xs__schema*);\n-\tvoid\t\t\t\telementPtr(xs__element*);\n-\tvoid\t\t\t\tsimpleTypePtr(xs__simpleType*);\n-\tvoid\t\t\t\tcomplexTypePtr(xs__complexType*);\n-\txs__schema\t\t\t*schemaPtr() const;\n-\txs__element\t\t\t*elementPtr() const;\n-\txs__simpleType\t\t\t*simpleTypePtr() const;\n-\txs__complexType\t\t\t*complexTypePtr() const;\n-\tconst std::vector<xs__element*'..b');\n- \tint\t\t\t\ttraverse(xs__schema&);\n-\tvoid\t\t\t\titemTypePtr(xs__simpleType*);\n-\txs__simpleType\t\t\t*itemTypePtr() const;\n-};\n-\n-class xs__union\n-{ public:\n-\t@xsd__NMTOKENS\t\t\tmemberTypes;\t// check if NMTOKENS is ok???\n-\tstd::vector<xs__simpleType>\tsimpleType;\n- public:\n- \tint\t\t\t\ttraverse(xs__schema&);\n-};\n-\n-class xs__complexContent\n-{ public:\n-\t@xsd__boolean\t\t\tmixed\t\t\t= false;\n-\txs__extension\t\t\t*extension;\n- \txs__restriction\t\t\t*restriction;\n- public:\n- \tint\t\t\t\ttraverse(xs__schema&);\n-};\n-\n-class xs__complexType\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\t@xsd__boolean\t\t\tabstract\t\t= false;\n-\t@xsd__boolean\t\t\tmixed\t\t\t= false;\n-\txs__annotation\t\t\t*annotation;\n-\txs__simpleContent\t\t*simpleContent;\n-\txs__complexContent\t\t*complexContent;\n-\txs__all\t\t\t\t*all;\n-\txs__seqchoice\t\t\t*choice;\n-\txs__seqchoice\t\t\t*sequence;\n-\txs__any\t\t\t\t*any;\n-\tstd::vector<xs__attribute>\tattribute;\n-\tstd::vector<xs__attributeGroup>\tattributeGroup;\n-\txs__anyAttribute\t\t*anyAttribute;\n- private:\n-\txs__schema\t\t\t*schemaRef;\n- \tint\t\t\t\tlevel;\n- public:\n-\t\t\t\t\txs__complexType();\n- \tint\t\t\t\ttraverse(xs__schema&);\n-\tvoid\t\t\t\tschemaPtr(xs__schema*);\n-\txs__schema\t\t\t*schemaPtr() const;\n-\tint\t\t\t\tbaseLevel();\n-};\n-\n-class xs__import\n-{ public:\n-\t@xsd__anyURI\t\t\tnamespace_;\n-\t@xsd__anyURI\t\t\tschemaLocation;\n- private:\n- \txs__schema\t\t\t*schemaRef;\t\t// set by WSDL parser or via schemaLocation\n- public:\n-\t\t\t\t\txs__import();\n- \tint\t\t\t\ttraverse(xs__schema&);\n-\tvoid\t\t\t\tschemaPtr(xs__schema*);\n-\txs__schema\t\t\t*schemaPtr() const;\n-};\n-\n-class xs__include\n-{ public:\n-\t@xsd__anyURI\t\t\tschemaLocation;\n- private:\n- \txs__schema\t\t\t*schemaRef;\n- public:\n-\t\t\t\t\txs__include();\n- \tint\t\t\t\tpreprocess(xs__schema&);\n- \tint\t\t\t\ttraverse(xs__schema&);\n-\tvoid\t\t\t\tschemaPtr(xs__schema*);\n-\txs__schema\t\t\t*schemaPtr() const;\n-};\n-\t\n-class xs__redefine\n-{ public:\n-\t@xsd__anyURI\t\t\tschemaLocation;\n-\tstd::vector<xs__group>\t\tgroup;\n-\tstd::vector<xs__attributeGroup>\tattributeGroup;\n-\tstd::vector<xs__simpleType>\tsimpleType;\n-\tstd::vector<xs__complexType>\tcomplexType;\n- private:\n- \txs__schema\t\t\t*schemaRef;\n- public:\n-\t\t\t\t\txs__redefine();\n- \tint\t\t\t\tpreprocess(xs__schema&);\n- \tint\t\t\t\ttraverse(xs__schema&);\n-\tvoid\t\t\t\tschemaPtr(xs__schema*);\n-\txs__schema\t\t\t*schemaPtr() const;\n-};\n-\t\n-class xs__schema\n-{ public:\n-\t@xsd__anyURI\t\t\ttargetNamespace\t\t= "";\n-\t@xsd__string\t\t\tversion;\n-\t@enum xs__formChoice\t\tattributeFormDefault\t= unqualified;\n-\t@enum xs__formChoice\t\telementFormDefault\t= unqualified;\n-\txs__annotation\t\t\t*annotation;\n-\tstd::vector<xs__include>\tinclude;\n-\tstd::vector<xs__redefine>\tredefine;\n-\tstd::vector<xs__import>\t\timport;\n-\tstd::vector<xs__attribute>\tattribute;\n-\tstd::vector<xs__element>\telement;\n-\tstd::vector<xs__group>\t\tgroup;\n-\tstd::vector<xs__attributeGroup>\tattributeGroup;\n-\tstd::vector<xs__simpleType>\tsimpleType;\n-\tstd::vector<xs__complexType>\tcomplexType;\n- \tstruct soap\t\t\t*soap;\n- private:\n-\tbool\t\t\t\tupdated;\n-\tchar*\t\t\t\tlocation;\n-\tint\t\t\t\tredirs;\n-\tSetOfString\t\t\tbuiltinTypeSet;\n-\tSetOfString\t\t\tbuiltinElementSet;\n-\tSetOfString\t\t\tbuiltinAttributeSet;\n- public:\n-\t\t\t\t\txs__schema();\n-\t\t\t\t\txs__schema(struct soap*);\n-\t\t\t\t\txs__schema(struct soap*, const char*, const char*);\n-\tvirtual\t\t\t\t~xs__schema();\n-\tint\t\t\t\tget(struct soap*);\t// gSOAP getter is triggered after parsing\n-\tint\t\t\t\tpreprocess();\n-\tint\t\t\t\tinsert(xs__schema&);\n-\tint\t\t\t\ttraverse();\n-\tint\t\t\t\tread(const char*, const char*);\n-\tvoid\t\t\t\tsourceLocation(const char*);\n-\tconst char*\t\t\tsourceLocation();\n-\tint\t\t\t\terror();\n-\tvoid\t\t\t\tprint_fault();\n-\tvoid\t\t\t\tbuiltinType(const char*);\n-\tvoid\t\t\t\tbuiltinElement(const char*);\n-\tvoid\t\t\t\tbuiltinAttribute(const char*);\n-\tconst SetOfString&\t\tbuiltinTypes() const;\n-\tconst SetOfString&\t\tbuiltinElements() const;\n-\tconst SetOfString&\t\tbuiltinAttributes() const;\n-\tbool\t\t\t\tempty() const;\n-\tfriend ostream&\t\t\toperator<<(ostream&, const xs__schema&);\n-\tfriend istream&\t\t\toperator>>(istream&, xs__schema&);\n-};\n-\n-extern ostream &operator<<(ostream &o, const xs__schema &e);\n-extern istream &operator>>(istream &i, xs__schema &e);\n-\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/service.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/service.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3039 +0,0 @@\n-/*\n-\tservice.cpp\n-\n-\tGenerate gSOAP service structures from WSDL.\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This part of the software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-TODO:\tconsider adding support for non-SOAP HTTP operations\n- add headerfault output definitions\n-\n-*/\n-\n-#include "types.h"\n-#include "service.h"\n-\n-#include <algorithm>\n-\n-#define URI_CHAR(c) (((c) > 32 && (c) != \'"\' && (c) != \'<\' && (c) != \'>\' && (c) != \'\\\\\' && (c) != \'^\' && (c) != \'`\' && (c) <= \'z\') || (c) == \'~\')\n-\n-static const char *urienc(struct soap*, const char*);\n-static bool imported(const char *tag);\n-static void comment(const char *start, const char *middle, const char *end, const char *text);\n-static void page(const char *page, const char *title, const char *text);\n-static void section(const char *section, const char *title, const char *text);\n-static void banner(const char*);\n-static void banner(const char*, const char*);\n-static void ident();\n-static void gen_policy(Service&, const vector<const wsp__Policy*>&, const char*, Types&);\n-static void gen_policy_enablers(const Service&);\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tDefinitions methods\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-Definitions::Definitions()\n-{ }\n-\n-void Definitions::collect(const wsdl__definitions &definitions)\n-{ // Collect information: analyze WSDL definitions and imported definitions\n- analyze(definitions);\n- for (vector<wsdl__import>::const_iterator import = definitions.import.begin(); import != definitions.import.end(); ++import)\n- if ((*import).definitionsPtr())\n- analyze(*(*import).definitionsPtr());\n-}\n-\n-void Definitions::analyze(const wsdl__definitions &definitions)\n-{ // Analyze WSDL and build Service information\n- int binding_count = 0;\n- // Determine number of relevant SOAP service bindings (service prefix option only)\n- for (vector<wsdl__binding>::const_iterator i = definitions.binding.begin(); i != definitions.binding.end(); ++i)\n- { for (vector<wsdl__ext_operation>::const_iterator j = (*i).operation.begin(); j != (*i).operation.end(); ++j)\n- { if ((*j).operationPtr())\n- { binding_count++;\n- break;\n- }\n- }\n- }\n- if (binding_count == 0 && definitions.name && (!definitions.portType.empty() || !definitions.interface_.empty()))\n- fprintf(stderr, "\\nWarning: WSDL \\"%s\\" has no bindings to implement operations\\n", definitions.name);\n- else if (binding_count > 1 && !service_prefix)\n- { // This puts all operations under a single binding\n- fprintf(stderr, "\\nWarning: %d service bindings found, but collected as one s'..b' break;\n- default:\n- if (*s >= 32)\n- fputc(*s, stream);\n- }\n- }\n- if (k)\n- fputc(\'\\n\', stream);\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tWS-Policy\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-static void gen_policy(Service& service, const vector<const wsp__Policy*>& policy, const char *text, Types& types)\n-{ if (!policy.empty())\n- { fprintf(stream, "\\n - WS-Policy applicable to the %s:\\n", text);\n- for (vector<const wsp__Policy*>::const_iterator p = policy.begin(); p != policy.end(); ++p)\n- if (*p)\n- (*p)->generate(service, types, 0);\n- }\n-}\n-\n-static void gen_policy_enablers(const Service& service)\n-{ fprintf(stream, "\\n/**\\n");\n- page(service.name, " Binding", service.name);\n- section(service.name, "_policy_enablers Policy Enablers of Binding ", service.name);\n- fprintf(stream, "\\nBased on policies, this service imports");\n- for (VectorOfString::const_iterator i = service.imports.begin(); i != service.imports.end(); ++i)\n- fprintf(stream, " %s", *i); \n- fprintf(stream, "\\n\\n - WS-Policy reminders and enablers:\\n");\n- fprintf(stream, " - WS-Addressing 1.0 (2005/08, accepts 2004/08):\\n\\t@code\\n\\t#import \\"wsa5.h\\" // to be added to this header file for the soapcpp2 build step\\n\\t@endcode\\n\\t@code\\n\\t#include \\"plugin/wsaapi.h\\"\\n\\tsoap_register_plugin(soap, soap_wsa); // register the wsa plugin in your code\\n\\t// See the user guide gsoap/doc/wsa/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, " - WS-Addressing (2004/08):\\n\\t@code\\n\\t#import \\"wsa.h\\" // to be added to this header file for the soapcpp2 build step\\n\\t@endcode\\n\\t@code\\n\\t#include \\"plugin/wsaapi.h\\"\\n\\tsoap_register_plugin(soap, soap_wsa); // register the wsa plugin in your code\\n\\t// See the user guide gsoap/doc/wsa/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, " - WS-ReliableMessaging 1.0:\\n\\t@code\\n\\t#import \\"wsrm5.h\\" // to be added to this header file for the soapcpp2 build step\\n\\t@endcode\\n\\t@code\\n\\t#include \\"plugin/wsrmapi.h\\"\\n\\tsoap_register_plugin(soap, soap_wsa); // register the wsa plugin in your code\\n\\tsoap_register_plugin(soap, soap_wsrm); // register the wsrm plugin in your code\\n\\t// See the user guide gsoap/doc/wsrm/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, " - WS-ReliableMessaging 1.1:\\n\\t@code\\n\\t#import \\"wsrm.h\\" // to be added to this header file for the soapcpp2 build step\\n\\t@endcode\\n\\t@code\\n\\t#include \\"plugin/wsrmapi.h\\"\\n\\tsoap_register_plugin(soap, soap_wsa); // register the wsa plugin in your code\\n\\tsoap_register_plugin(soap, soap_wsrm); // register the wsrm plugin in your code\\n\\t// See the user guide gsoap/doc/wsrm/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, " - WS-Security (SOAP Message Security) 1.0 (accepts 1.1):\\n\\t@code\\n\\t#import \\"wsse.h\\" // to be added to this header file for the soapcpp2 build step\\n\\t@endcode\\n\\t@code\\n\\t#include \\"plugin/wsseapi.h\\"\\n\\tsoap_register_plugin(soap, soap_wsse); // register the wsse plugin in your code\\n\\t// See the user guide gsoap/doc/wsse/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, " - WS-Security (SOAP Message Security) 1.1 (accepts 1.0):\\n\\t@code\\n\\t#import \\"wsse11.h\\" // to be added to this header file for the soapcpp2 build step\\n\\t@endcode\\n\\t@code\\n\\t#include \\"plugin/wsseapi.h\\"\\n\\tsoap_register_plugin(soap, soap_wsse); // register the wsse plugin in your code\\n\\t// See the user guide gsoap/doc/wsse/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, " - HTTP Digest Authentication:\\n\\t@code\\n\\t#include \\"plugin/httpda.h\\"\\n\\tsoap_register_plugin(soap, soap_http_da); // register the HTTP DA plugin in your code\\n\\t// See the user guide gsoap/doc/httpda/html/index.html\\n\\t@endcode\\n");\n- fprintf(stream, "*/\\n\\n");\n- for (VectorOfString::const_iterator i = service.imports.begin(); i != service.imports.end(); ++i)\n- fprintf(stream, "#import \\"%s\\"\\n", *i); \n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/service.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/service.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,130 +0,0 @@
-/*
- service.h
-
- Service structures
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-#ifndef SERVICE_H
-#define SERVICE_H
-
-#include "includes.h"
-#include "wsdlH.h"
-
-class Message
-{ public:
-    const char *name;
-    const char *URI;
-    soap__styleChoice style;
-    soap__useChoice use;
-    const char *encodingStyle;
-    const char *action;
-    wsdl__message *message;
-    xs__element *element;
-    const char *body_parts;
-    wsdl__part *part;
-    bool mustUnderstand;
-    vector<soap__header> header;
-    vector<wsoap__header> wheader;
-    mime__multipartRelated *multipartRelated; // MIME
-    mime__content *content; // REST/MIME
-    const char *layout; // DIME
-    const char *documentation;
-    const char *ext_documentation;
-    vector<const wsp__Policy*> policy;
-    void generate(Types&, const char *sep, bool anonymous, bool remark, bool response, bool optional);
-};
-
-typedef map<const char*, Message*, ltstr> MapOfStringToMessage;
-
-class Operation
-{ public:
-    const char *prefix;
-    const char *URI;
-    const char *name;
-    const char *mep; // WSDL 2.0
-    const char *protocol;
-    soap__styleChoice style;
-    const char *parameterOrder;
-    const char *action;
-    const char *input_name;
-    const char *output_name;
-    Message *input; // name, use, and parts
-    Message *output; // name, use, and parts
-    vector<Message*> infault;
-    vector<Message*> outfault;
-    const char *documentation;
-    const char *operation_documentation;
-    vector<const wsp__Policy*> policy;
-    void generate(Types&, Service&);
-};
-
-class Service
-{ public:
-    const char *prefix; // a gSOAP service has a unique namespace
-    const char *URI;
-    const char *name; // binding name
-    const char *type; // portType
-    const char *transport; // binding transport
-    SetOfString location; // WSDL may specify multiple locations via <Port> -> <Binding>
-    vector<Operation*> operation;
-    MapOfStringToMessage header;
-    MapOfStringToMessage headerfault;
-    MapOfStringToMessage fault;
-    MapOfStringToString service_documentation;
-    MapOfStringToString port_documentation;
-    MapOfStringToString binding_documentation;
-    vector<const wsp__Policy*> policy;
-    VectorOfString imports;
-    Service();
-    void generate(Types&);
-    void add_import(const char*);
-    void del_import(const char*);
-};
-
-typedef map<const char*, Service*, ltstr> MapOfStringToService;
-
-class Definitions
-{ public:
-    Types types; // to process schema type information
-    MapOfStringToService services; // service information gathered
-    bool soap12;
-    Definitions();
-    void collect(const wsdl__definitions&);
-    void compile(const wsdl__definitions&);
-  private:
-    void analyze(const wsdl__definitions&);
-    void analyze_headers(const wsdl__definitions&, Service*, wsdl__ext_ioput*, wsdl__ext_ioput*);
-    void analyze_faults(const wsdl__definitions&, Service*, Operation*, vector<wsdl__ext_operation>::const_iterator&);
-    Message *analyze_fault(const wsdl__definitions&, Service*, const wsdl__ext_fault&);
-    void generate();
-};
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/soap.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/soap.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,231 +0,0 @@\n-/*\n-\tsoap.cpp\n-\n-\tWSDL/SOAP binding schema\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-*/\n-\n-#include "wsdlH.h"\t\t// cannot include "schemaH.h"\n-#include "includes.h"\n-\n-extern const char *qname_token(const char*, const char*);\n-extern int is_builtin_qname(const char*);\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tsoap:header\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-int soap__header::traverse(wsdl__definitions& definitions)\n-{ if (vflag)\n- cerr << " Analyzing soap header in wsdl namespace \'" << (definitions.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- messageRef = NULL;\n- partRef = NULL;\n- const char *token = qname_token(message, definitions.targetNamespace);\n- if (token)\n- { for (vector<wsdl__message>::iterator message = definitions.message.begin(); message != definitions.message.end(); ++message)\n- { if ((*message).name && !strcmp((*message).name, token))\n- { messageRef = &(*message);\n- if (vflag)\n-\t cerr << " Found soap header part \'" << (part?part:"") << "\' message \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n- }\n- }\n- if (!messageRef)\n- { for (vector<wsdl__import>::iterator import = definitions.import.begin(); import != definitions.import.end(); ++import)\n- { wsdl__definitions *importdefinitions = (*import).definitionsPtr();\n- if (importdefinitions)\n- { token = qname_token(message, importdefinitions->targetNamespace);\n- if (token)\n- { for (vector<wsdl__message>::iterator message = importdefinitions->message.begin(); message != importdefinitions->message.end(); ++message)\n- { if ((*message).name && !strcmp((*message).name, token))\n- { messageRef = &(*message);\n- if (vflag)\n-\t cerr << " Found soap header part \'" << (part?part:"") << "\' message \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n- }\n-\t}\n- }\n- }\n- }\n- if (messageRef)\n- { if (part)\n- { for (vector<wsdl__part>::iterator pt = messageRef->part.begin(); pt != messageRef->part.end(); ++pt)\n- if ((*pt).name && !strcmp((*pt).name, part))\n-\t{ partRef = &(*pt);\n-\t break;\n- }\n- }\n- if (!partRef)\n- cerr << "Warning: soap header has no matching part in message \'" << (message?message:"") << "\' in wsdl definitions \'" << definitions.name << "\' namespace \'" << (definitions.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- }\n- else\n- cerr << "Warning: could not find soap header part \'" << (part?'..b'sage.end(); ++message)\n- { if ((*message).name && !strcmp((*message).name, token))\n- { messageRef = &(*message);\n- if (vflag)\n-\t cerr << " Found soap headerfault part \'" << (part?part:"") << "\' message \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n- }\n- }\n- else\n- { for (vector<wsdl__import>::iterator import = definitions.import.begin(); import != definitions.import.end(); ++import)\n- { wsdl__definitions *importdefinitions = (*import).definitionsPtr();\n- if (importdefinitions)\n- { token = qname_token(message, importdefinitions->targetNamespace);\n- if (token)\n- { for (vector<wsdl__message>::iterator message = importdefinitions->message.begin(); message != importdefinitions->message.end(); ++message)\n- { if ((*message).name && !strcmp((*message).name, token))\n- { messageRef = &(*message);\n- if (vflag)\n-\t cerr << " Found soap headerfault part \'" << (part?part:"") << "\' message \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n- }\n-\t}\n- }\n- }\n- }\n- if (messageRef)\n- { if (part)\n- { for (vector<wsdl__part>::iterator pt = messageRef->part.begin(); pt != messageRef->part.end(); ++pt)\n- if ((*pt).name && !strcmp((*pt).name, part))\n-\t{ partRef = &(*pt);\n-\t break;\n- }\n- }\n- if (!partRef)\n- cerr << "Warning: soap headerfault has no matching part in message \'" << (message?message:"") << "\' in wsdl definitions \'" << definitions.name << "\' namespace \'" << (definitions.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- }\n- else\n- cerr << "Warning: could not find soap headerfault part \'" << (part?part:"") << "\' message \'" << (message?message:"") << "\' in wSDL definitions \'" << definitions.name << "\' namespace \'" << (definitions.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- return SOAP_OK;\n-}\n-\n-void soap__headerfault::messagePtr(wsdl__message *message)\n-{ messageRef = message;\n-}\n-\n-wsdl__message *soap__headerfault::messagePtr() const\n-{ return messageRef;\n-}\n-\n-void soap__headerfault::partPtr(wsdl__part *part)\n-{ partRef = part;\n-}\n-\n-wsdl__part *soap__headerfault::partPtr() const\n-{ return partRef;\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\twsoap:header\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-int wsoap__header::traverse(wsdl__definitions& definitions)\n-{ if (vflag)\n- cerr << " Analyzing soap header in wsdl namespace \'" << (definitions.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- elementRef = NULL;\n- // WSDL 2.0\n- if (element)\n- { if (definitions.types)\n- { for (vector<xs__schema*>::iterator schema = definitions.types->xs__schema_.begin(); schema != definitions.types->xs__schema_.end(); ++schema)\n- { const char *token = qname_token(element, (*schema)->targetNamespace);\n- if (token)\n- { for (vector<xs__element>::iterator element = (*schema)->element.begin(); element != (*schema)->element.end(); ++element)\n- { if ((*element).name && !strcmp((*element).name, token))\n- { elementRef = &(*element);\n- if (vflag)\n- cerr << " Found soap header element \'" << (token?token:"") << "\'" << endl;\n- break;\n- }\n- }\n- }\n- }\n- }\n- if (!elementRef)\n- { if (is_builtin_qname(element))\n- definitions.builtinElement(element);\n- else\n- if (!Wflag)\n- cerr << "Warning: no soap header element \'" << element << "\' in wsdl definitions \'" << (definitions.name?definitions.name:"") << "\' namespace \'" << (definitions.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- }\n- }\n- return SOAP_OK;\n-}\n-\n-void wsoap__header::elementPtr(xs__element *element)\n-{ elementRef = element;\n-}\n-\n-xs__element *wsoap__header::elementPtr() const\n-{ return elementRef;\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/soap.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/soap.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,140 +0,0 @@
-/*
- soap.h
-
- WSDL/SOAP binding schema
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-//gsoap soap schema documentation: WSDL 1.1 SOAP binding schema
-//gsoap soap schema namespace: http://schemas.xmlsoap.org/wsdl/soap/
-
-//gsoap wsoap schema documentation: WSDL 2.0 SOAP binding schema
-//gsoap wsoap schema namespace: http://www.w3.org/ns/wsdl/soap
-
-#import "imports.h"
-
-class wsdl__definitions; // forward declaration
-class wsdl__message; // forward declaration
-class wsdl__part; // forward declaration
-
-enum soap__styleChoice { rpc, document };
-
-class soap__binding
-{ public:
- @xsd__anyURI transport;
- @enum soap__styleChoice *style;
-};
-
-class soap__operation
-{ public:
- @xsd__anyURI soapAction;
- @xsd__boolean soapActionRequired = true;
- @enum soap__styleChoice *style;
-};
-
-enum soap__useChoice { literal, encoded };
-
-class soap__body
-{ public:
- @xsd__anyURI encodingStyle;
- @xsd__NMTOKENS parts;
- @enum soap__useChoice use;
- @xsd__anyURI namespace_;
-};
-
-class soap__fault
-{ public:
- @xsd__NMTOKEN name;
- @xsd__anyURI encodingStyle;
- @enum soap__useChoice use;
- @xsd__anyURI namespace_;
-};
-
-class soap__headerfault
-{ public:
- @xsd__QName message;
- @xsd__NMTOKEN part;
- @enum soap__useChoice use;
- @xsd__anyURI encodingStyle;
- @xsd__anyURI namespace_;
-  private:
-   wsdl__message *messageRef;
-   wsdl__part *partRef;
-  public:
-   int traverse(wsdl__definitions&);
- void messagePtr(wsdl__message*);
- void partPtr(wsdl__part*);
- wsdl__message *messagePtr() const;
- wsdl__part *partPtr() const;
-};
-
-class soap__header
-{ public:
- @xsd__QName message;
- @xsd__NMTOKEN part;
- @enum soap__useChoice use;
- @xsd__anyURI encodingStyle;
- @xsd__anyURI namespace_;
- std::vector<soap__headerfault> headerfault; // <soap:headerfault>*
-  private:
-   wsdl__message *messageRef;
-   wsdl__part *partRef;
-  public:
-   int traverse(wsdl__definitions&);
- void messagePtr(wsdl__message*);
- void partPtr(wsdl__part*);
- wsdl__message *messagePtr() const;
- wsdl__part *partPtr() const;
-};
-
-class soap__address
-{ public:
- @xsd__anyURI location;
-};
-
-class wsoap__module
-{ public:
- @xsd__anyURI ref;
- @xsd__boolean required = false;
-};
-
-class wsoap__header
-{ public:
- @xsd__QName element;
- @xsd__boolean mustUnderstand_ = false;
- @xsd__boolean required = false;
-  private:
-   xs__element *elementRef;
-  public:
-   int traverse(wsdl__definitions&);
- void elementPtr(xs__element*);
- xs__element *elementPtr() const;
-};
-
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/sp.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/sp.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,70 +0,0 @@
-/*
- sp.h
-
- WS-SecurityPolicy 1.2 binding schemas
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2010, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-//gsoap sp schema documentation: WS-SecurityPolicy binding
-//gsoap sp schema namespace: http://docs.oasis-open.org/ws-sx/ws-securitypolicy/200702
-// 1.1 //gsoap sp schema namespace: http://schemas.xmlsoap.org/ws/2005/07/securitypolicy
-//gsoap sp schema elementForm: qualified
-//gsoap sp schema attributeForm: unqualified
-
-#import "imports.h"
-#import "wsam.h"
-#import "wst.h"
-
-class sp__Header
-{ public:
- @xsd__NCName Name;
- @xsd__anyURI Namespace;
-};
-
-class sp__Parts
-{ public:
- xsd__string Body;
- std::vector<sp__Header> Header;
- xsd__string Attachments;
-};
-
-class sp__Elements
-{ public:
- @xsd__anyURI XPathVersion;
- std::vector<xsd__string> XPath;
-};
-
-class sp__Token : public wsp__Assertion
-{ public:
- @xsd__anyURI IncludeToken;
- wsa__EndpointReferenceType *Issuer;
- xsd__anyURI IssuerName;
- wst__Claims *wst__Claims_;
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/typemap.dat
--- a/GEMBASSY-1.0.3/gsoap/wsdl/typemap.dat Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/types.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/types.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,3289 +0,0 @@\n-/*\n-\ttypes.cpp\n-\n-\tGenerate gSOAP types from XML schemas (e.g. embedded in WSDL).\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2001-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-*/\n-\n-#include "types.h"\n-\n-static char *getline(char *s, size_t n, FILE *fd);\n-static const char *nonblank(const char *s);\n-static const char *fill(char *t, int n, const char *s, int e);\n-static const char *utf8(char *t, const char *s);\n-static const char *cstring(const char *s);\n-static const char *xstring(const char *s);\n-static bool is_integer(const char *s);\n-static LONG64 to_integer(const char *s);\n-static void documentation(const char *text);\n-static void operations(const char *t);\n-\n-static int comment_nest = 0; /* keep track of block comments to avoid nesting */\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tKeywords and reserved words\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-static const char *keywords[] =\n-{ "and",\n- "asm",\n- "auto",\n- "bool",\n- "break",\n- "case",\n- "catch",\n- "char",\n- "class",\n- "const",\n- "const_cast",\n- "continue",\n- "default",\n- "delete",\n- "do",\n- "double",\n- "dynamic_cast",\n- "else",\t\n- "enum",\n- "errno",\n- "explicit",\n- "export",\n- "extern",\n- "false",\n- "FILE",\n- "float",\n- "for",\n- "friend",\n- "goto",\n- "if",\n- "inline",\n- "int",\n- "interface",\n- "long",\n- "LONG64",\n- "max",\n- "min",\n- "mustUnderstand",\n- "mutable",\n- "namespace",\n- "new",\n- "not",\n- "NULL",\n- "operator",\n- "or",\n- "private",\n- "protected",\n- "public",\n- "_QName",\n- "register",\n- "reinterpret_cast",\n- "restrict",\n- "return",\n- "short",\n- "signed",\n- "size_t",\n- "sizeof",\n- "soap",\n- "static",\n- "static_cast",\n- "struct",\n- "switch",\n- "template",\n- "this",\n- "throw",\n- "time_t",\n- "true",\n- "typedef",\n- "typeid",\n- "typeof",\n- "typename",\n- "ULONG64",\n- "union",\n- "unsigned",\n- "using",\n- "virtual",\n- "void",\n- "volatile",\n- "wchar_t",\n- "while",\n- "XML",\n- "_XML",\n- "xor",\n-};\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tTypes methods\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-Types::Types()\n-{ init();\n-}\n-\n-int Types::read(const char *file)\n-{ FILE *fd;\n- char buf[1024], xsd[1024], def[1024], use[1024], ptr[1024], uri[1024];\n- const char *s;\n- short copy = 0;\n- strcpy(buf, file);\n- fd = fopen(buf, "r");\n- if (!fd && import_path)\n- { strcpy(buf, import_path);\n- strcat(buf, "/");\n- strcat(buf, file);\n- fd = fopen(buf, "r");\n- }\n- if (!fd)\n- { fprintf(stderr, "Canno'..b' else\n- { c4 = (unsigned char)*++s & 0x3F;\n- if (c < 0xFC)\n- c = ((c & 0x03) << 24) | (c1 << 18) | (c2 << 12) | (c3 << 6) | c4;\n- else\n- c = ((c & 0x01) << 30) | (c1 << 24) | (c2 << 18) | (c3 << 12) | (c4 << 6) | (*++s & 0x3F);\n- }\n- }\n- }\n- }\n- }\n- sprintf(t, "_x%.4x", c);\n- return s;\n-}\n-\n-static const char *cstring(const char *s)\n-{ size_t n;\n- char *t;\n- const char *r;\n- for (n = 0, r = s; *r; n++, r++)\n- if (*r == \'"\' || *r == \'\\\\\')\n- n++;\n- else if (*r < 32)\n- n += 3;\n- r = t = (char*)emalloc(n + 1);\n- for (; *s; s++)\n- { if (*s == \'"\' || *s == \'\\\\\')\n- { *t++ = \'\\\\\';\n- *t++ = *s;\n- }\n- else if (*s < 32)\n- { sprintf(t, "\\\\%03o", (unsigned int)(unsigned char)*s);\n- t += 4;\n- }\n- else\n- *t++ = *s;\n- }\n- *t = \'\\0\';\n- return r;\n-}\n-\n-static const char *xstring(const char *s)\n-{ size_t n;\n- char *t;\n- const char *r;\n- for (n = 0, r = s; *r; n++, r++)\n- { if (*r < 32 || *r >= 127)\n- n += 4;\n- else if (*r == \'<\' || *r == \'>\')\n- n += 3;\n- else if (*r == \'&\')\n- n += 4;\n- else if (*r == \'"\')\n- n += 5;\n- else if (*r == \'\\\\\')\n- n += 1;\n- }\n- r = t = (char*)emalloc(n + 1);\n- for (; *s; s++)\n- { if (*s < 32 || *s >= 127)\n- { sprintf(t, "&#%.2x;", (unsigned char)*s);\n- t += 5;\n- }\n- else if (*s == \'<\')\n- { strcpy(t, "<");\n- t += 4;\n- }\n- else if (*s == \'>\')\n- { strcpy(t, ">");\n- t += 4;\n- }\n- else if (*s == \'&\')\n- { strcpy(t, "&");\n- t += 5;\n- }\n- else if (*s == \'"\')\n- { strcpy(t, """);\n- t += 6;\n- }\n- else if (*s == \'\\\\\')\n- { strcpy(t, "\\\\\\\\");\n- t += 2;\n- }\n- else\n- *t++ = *s;\n- }\n- *t = \'\\0\';\n- return r;\n-}\n-\n-static LONG64 to_integer(const char *s)\n-{ LONG64 n;\n-#ifdef HAVE_STRTOLL\n- char *r;\n- n = soap_strtoll(s, &r, 10);\n-#else\n-# ifdef HAVE_SSCANF\n- sscanf(s, SOAP_LONG_FORMAT, &n);\n-# endif\n-#endif\n- return n;\n-}\n-\n-static bool is_integer(const char *s)\n-{ if ((*s == \'-\' || *s == \'+\') && s[1])\n- s++;\n- if (!*s || strlen(s) > 20)\n- return false;\n- while (*s && isdigit(*s))\n- s++;\n- return *s == \'\\0\';\n-}\n-\n-static void documentation(const char *text)\n-{ const char *s = text;\n- bool flag = true;\n- if (!s)\n- return;\n- while (*s)\n- { switch (*s)\n- { case \'\\n\':\n- case \'\\t\':\n- case \' \':\n- flag = true;\n- break;\n- default:\n- if (*s > 32)\n- { if (flag)\n- { fputc(\' \', stream);\n- flag = false;\n- }\n- fputc(*s, stream);\n- }\n- }\n- s++;\n- }\n- fputc(\'\\n\', stream);\n-}\n-\n-static void operations(const char *t)\n-{ if (!cflag)\n- fprintf(stream, "/// class %s operations:\\n/// - soap_new_%s(soap*) allocate\\n/// - soap_new_%s(soap*, int num) allocate array\\n/// - soap_new_req_%s(soap*, ...) allocate, set required members\\n/// - soap_new_set_%s(soap*, ...) allocate, set all public members\\n/// - int soap_read_%s(soap*, %s*) deserialize from a stream\\n/// - int soap_write_%s(soap, %s*) serialize to a stream\\n", t, t, t, t, t, t, t, t, t);\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tAllocation\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-void *emalloc(size_t size)\n-{ void *p = malloc(size);\n- if (!p)\n- { fprintf(stderr, "\\nError: Malloc failed\\n");\n- exit(1);\n- }\n- return p;\n-}\n-\n-char *estrdup(const char *s)\n-{ char *t = (char*)emalloc(strlen(s) + 1);\n- strcpy(t, s);\n- return t;\n-}\n-\n-char *estrdupf(const char *s)\n-{ char *t = (char*)emalloc(strlen(s) + 1);\n- char *p;\n- for (p = t; *s; s++)\n- { if (s[0] == \'/\' && s[1] == \'*\')\n- { for (s += 2; s[0] && s[1]; s++)\n- { if (s[0] == \'*\' && s[1] == \'/\')\n- { s++;\n- break;\n- }\n- }\n- continue;\n- }\n- *p++ = *s;\n- }\n- *p = \'\\0\';\n- return t;\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/types.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/types.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,116 +0,0 @@
-/*
- types.h
-
- WSDL parser and converter to gSOAP header file format
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-#ifndef TYPES_H
-#define TYPES_H
-
-#include "includes.h"
-#include "wsdlH.h"
-
-enum Type { NONE, CLASS, ENUM, STRUCT, TYPEDEF };
-
-enum Lookup { NOLOOKUP, LOOKUP };
-
-class Types
-{ public:
-    SetOfString knames; // keywords, reserved words, class names, and typedefs
-    MapOfStringToString modtypemap;
-    MapOfStringToString deftypemap;
-    MapOfStringToString usetypemap;
-    MapOfStringToString ptrtypemap;
-    MapOfStringToString eqvtypemap;
-    MapOfPairToString qnames; // (URI,name) -> name
-    MapOfStringToString uris; // URI -> prefix
-    MapOfStringToNum syms; // prefix -> count (ns1, ns2, ...)
-    SetOfString rnames; // reserved symbolic names to avoid clashes
-    SetOfString onames; // service operator names
-    MapOfPairToString enames; // enum symbolic names
-    VectorOfString scope; // de-anonymizer stack
-    int snum; // struct name index, TODO: consider map of URI to count per URI
-    int unum; // union name index, TODO: consider map of URI to count per URI
-    int gnum; // enum name index, TODO: consider map of URI to count per URI
-    bool with_union;
-    bool fake_union;
-    Types();
-    void init();
-    int read(const char *file);
-  private:
-    const char *fname(const char *prefix, const char *URI, const char *qname, SetOfString *reserved, enum Lookup lookup, bool isqname);
-  public:
-    const char *aname(const char *prefix, const char *URI, const char *qname);
-    const char *cname(const char *prefix, const char *URI, const char *qname);
-    const char *tname(const char *prefix, const char *URI, const char *qname);
-    const char *tnameptr(bool, const char *prefix, const char *URI, const char *qname);
-    const char *pname(bool flag, const char *prefix, const char *URI, const char *qname);
-    const char *oname(const char *prefix, const char *URI, const char *qname);
-    const char *ename(const char *type, const char *value, bool isqname);
-    const char *sname(const char *URI, const char *name);
-    const char *gname(const char *URI, const char *name);
-    const char *uname(const char *URI);
-    const char *nsprefix(const char *prefix, const char *URI);
-    const char *prefix(const char *name);
-    const char *uri(const char *name);
-    const char *deftname(enum Type type, const char *pointer, bool is_pointer, const char *prefix, const char *URI, const char *qname);
-    bool is_defined(const char *prefix, const char *URI, const char *qname);
-    bool is_nillable(const xs__element& element);
-    bool is_basetypeforunion(const char *prefix, const char *URI, const char *type);
-    bool is_basetype(const char *prefix, const char *URI, const char *type);
-    void dump(FILE*);
-    void define(const char *URI, const char *name, const xs__complexType&);
-    void gen(const char *URI, const vector<xs__attribute>&);
-    void gen(const char *URI, const vector<xs__attributeGroup>&);
-    void gen(const char *URI, const vector<xs__all>&);
-    void gen(const char *URI, const vector<xs__element>&, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const vector<xs__group>&);
-    void gen(const char *URI, const vector<xs__any>&);
-    void gen(const char *URI, const vector<xs__contents>&);
-    void gen(const char *URI, const char *name, const xs__simpleType&, bool anonymous);
-    void gen(const char *URI, const char *name, const xs__complexType&, bool anonymous);
-    void gen(const char *URI, const xs__attribute&);
-    void gen(const char *URI, const xs__all&, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const xs__seqchoice&, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const char *name, const xs__seqchoice&, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const xs__element&, bool substok, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const xs__group&, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const xs__any&, const char *minOccurs, const char *maxOccurs);
-    void gen(const char *URI, const xs__anyAttribute&);
-    void gen_inh(const char *URI, const xs__complexType *complexType, bool anonymous);
-    void gen_soap_array(const char *name, const char *t, const char *item, const char *type);
-    void gen_substitutions(const char *URI, const xs__element &element);
-    void document(const xs__annotation*);
-    void modify(const char *name);
-    const char *format(const char *text);
-};
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsam.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsam.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,54 +0,0 @@
-/*
- wsam.h
-
- WS-Addressing and WS-Addressing Metadata
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2010, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-//gsoap wsa schema documentation: WS-Addressing
-//gsoap wsa schema namespace: http://www.w3.org/2005/08/addressing
-//gsoap wsa schema elementForm: qualified
-//gsoap wsa schema attributeForm: unqualified
-
-//gsoap wsam schema documentation: WS-Addressing Metadata
-//gsoap wsam schema namespace: http://www.w3.org/2007/05/addressing/metadata
-//gsoap wsam schema elementForm: qualified
-//gsoap wsam schema attributeForm: unqualified
-
-//gsoap wsaw schema documentation: WS-Addressing WSDL
-//gsoap wsaw schema namespace: http://www.w3.org/2006/05/addressing/wsdl
-//gsoap wsaw schema elementForm: qualified
-//gsoap wsaw schema attributeForm: unqualified
-
-class wsa__EndpointReferenceType
-{ public:
- xsd__anyURI Address;
- _XML __any;
-};
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsdl.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsdl.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1536 +0,0 @@\n-/*\n-\twsdl.cpp\n-\n-\tWSDL 1.1 and WSDL 2.0 binding schema implementation\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2012, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-*/\n-\n-#include "wsdlH.h"\n-#include "includes.h"\n-\n-extern struct Namespace namespaces[];\n-\n-const char *qname_token(const char *QName, const char *URI)\n-{ if (QName && QName[0] == \'"\' && QName[1] == \'"\' && QName[2] == \':\')\n- return QName + 3;\n- if (QName && URI && *QName == \'"\') // QNames are stored in the format "URI":name, unless the URI is in the nsmap\n- { size_t n = strlen(URI);\n- if (!strncmp(QName + 1, URI, n) && QName[n + 1] == \'"\')\n- return QName + n + 3;\n- }\n- return NULL;\n-}\n-\n-int is_builtin_qname(const char *QName)\n-{ if (iflag)\n- return 1;\n- if (QName)\n- { if (*QName == \'#\') // reserved QNames\n- return 0;\n- if (*QName != \'"\')\n- return 1;\t// if the QName does not start with a ", it must be in the nsmap\n- const char *s = strchr(QName + 1, \'"\');\n- if (s)\n- { size_t n = s - QName - 1;\n- for (SetOfString::const_iterator i = exturis.begin(); i != exturis.end(); ++i)\n- if (strlen(*i) == n && !strncmp(QName + 1, *i, n))\n- return 1; // QName is in exturis\n- }\n- }\n- return 0;\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\twsdl\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-extern "C" {\n-int warn_ignore(struct soap*, const char*);\n-int show_ignore(struct soap*, const char*);\n-}\n-\n-wsdl__definitions::wsdl__definitions()\n-{ soap = soap_new1(SOAP_XML_TREE | SOAP_C_UTFSTRING);\n-#ifdef HTTPDA_H\n- soap_register_plugin(soap, http_da);\n-#endif\n-#ifdef WITH_OPENSSL\n- soap_ssl_client_context(soap, SOAP_SSL_NO_AUTHENTICATION, NULL, NULL, NULL, NULL, NULL);\n-#endif\n- soap_set_namespaces(soap, namespaces);\n- soap_default(soap);\n- if (vflag)\n- soap->fignore = show_ignore;\n- else\n- soap->fignore = warn_ignore;\n- soap->encodingStyle = NULL;\n- soap->proxy_host = proxy_host;\n- soap->proxy_port = proxy_port;\n- soap->proxy_userid = proxy_userid;\n- soap->proxy_passwd = proxy_passwd;\n- name = NULL;\n- targetNamespace = soap_strdup(soap, "");\n- documentation = NULL;\n- types = NULL;\n- updated = false;\n- location = NULL;\n- redirs = 0;\n-}\n-\n-wsdl__definitions::wsdl__definitions(struct soap *copy, const char *cwd, const char *loc)\n-{ soap = soap_copy(copy);\n- soap->socket = SOAP_INVALID_SOCKET;\n- soap->recvfd = 0;\n- soap->sendfd = 1;\n- strcpy(soap->host, copy->host);\n- soap_default(soap);\n- soap->fignore = warn_ignore;\n- soap->encodingStyle = NULL;\n- updated = false;\n- location = NULL;\n- redirs = 0;'..b's.targetNamespace?definitions.targetNamespace:"") << "\'" << endl;\n- // process import first\n- for (vector<wsdl__import>::iterator im = definitionsRef->import.begin(); im != definitionsRef->import.end(); ++im)\n- (*im).traverse(definitions);\n- // then process the types\n- if (definitionsRef->types)\n- definitionsRef->types->traverse(definitions);\n- // process messages before portTypes\n- for (vector<wsdl__message>::iterator mg = definitionsRef->message.begin(); mg != definitionsRef->message.end(); ++mg)\n- (*mg).traverse(definitions);\n- // process portTypes before bindings\n- for (vector<wsdl__portType>::iterator pt = definitionsRef->portType.begin(); pt != definitionsRef->portType.end(); ++pt)\n- (*pt).traverse(definitions);\n- // process bindings\n- for (vector<wsdl__binding>::iterator bg = definitionsRef->binding.begin(); bg != definitionsRef->binding.end(); ++bg)\n- (*bg).traverse(definitions);\n- // process services\n- for (vector<wsdl__service>::iterator sv = definitionsRef->service.begin(); sv != definitionsRef->service.end(); ++sv)\n- (*sv).traverse(definitions);\n- if (vflag)\n- cerr << " End of imported wsdl namespace \'" << (namespace_?namespace_:"") << "\'" << endl;\n- }\n- return SOAP_OK;\n-}\n-\n-void wsdl__import::definitionsPtr(wsdl__definitions *definitions)\n-{ definitionsRef = definitions;\n- if (!definitionsRef && vflag)\n- cerr << "Warning: wsdl__import definitions set to NULL" << endl;\n-}\n-\n-wsdl__definitions *wsdl__import::definitionsPtr() const\n-{ return definitionsRef;\n-}\n-\n-wsdl__import::wsdl__import()\n-{ definitionsRef = NULL;\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tstreams\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-ostream &operator<<(ostream &o, const wsdl__definitions &e)\n-{ if (!e.soap)\n- { struct soap soap;\n- soap_init2(&soap, SOAP_IO_DEFAULT, SOAP_XML_TREE | SOAP_C_UTFSTRING);\n- soap_set_namespaces(&soap, namespaces);\n- e.soap_serialize(&soap);\n- soap_begin_send(&soap);\n- e.soap_out(&soap, "wsdl:definitions", 0, NULL);\n- soap_end_send(&soap);\n- soap_destroy(&soap);\n- soap_end(&soap);\n- soap_done(&soap);\n- }\n- else\n- { ostream *os = e.soap->os;\n- e.soap->os = &o;\n- e.soap_serialize(e.soap);\n- soap_begin_send(e.soap);\n- e.soap_out(e.soap, "wsdl:definitions", 0, NULL);\n- soap_end_send(e.soap);\n- e.soap->os = os;\n- }\n- return o;\n-}\n-\n-istream &operator>>(istream &i, wsdl__definitions &e)\n-{ if (!e.soap)\n- { e.soap = soap_new1(SOAP_XML_TREE | SOAP_C_UTFSTRING);\n- soap_set_namespaces(e.soap, namespaces);\n- }\n- istream *is = e.soap->is;\n- e.soap->is = &i;\n- if (soap_begin_recv(e.soap)\n- || !e.soap_in(e.soap, "wsdl:", NULL)\n- || soap_end_recv(e.soap))\n- { // handle error? Note: e.soap->error is set and app should check\n- }\n- e.soap->is = is;\n- return i;\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tMiscellaneous\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-extern "C" {\n-\n-int warn_ignore(struct soap *soap, const char *tag)\n-{ // We don\'t warn if the omitted element was an annotation or a documentation in an unexpected place\n- if (soap->mustUnderstand)\n- fprintf(stderr, "Error: element \'%s\' at level %d must be understood\\n", tag, soap->level);\n- if (!Wflag\n- && soap_match_tag(soap, tag, "xs:annotation")\n- && soap_match_tag(soap, tag, "xs:documentation")\n- && soap_match_tag(soap, tag, "xs:appinfo"))\n- fprintf(stderr, "Warning: unexpected element \'%s\' at level %d is skipped (safe to ignore)\\n", tag, soap->level);\n- if (soap->body && !soap_string_in(soap, 0, -1, -1))\n- return soap->error;\n- return SOAP_OK;\n-}\n-\n-int show_ignore(struct soap *soap, const char *tag)\n-{ warn_ignore(soap, tag);\n- soap_print_fault_location(soap, stderr);\n- return SOAP_OK;\n-}\n-\n-} // end extern "C"\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsdl.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsdl.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,382 +0,0 @@\n-/*\n-\twsdl.h\n-\n-\tWSDL 1.1 and WSDL 2.0 schemas\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-//gsoapopt w\n-\n-//gsoap wsdl schema documentation:\tWSDL 1.1/2.0 binding schema\n-//gsoap wsdl schema namespace:\t\thttp://schemas.xmlsoap.org/wsdl/\n-//gsoap wsdl schema namespace2:\t\thttp://www.w3.org/ns/wsdl\n-//gsoap wsdl schema elementForm:\tqualified\n-//gsoap wsdl schema attributeForm:\tunqualified\n-\n-#import "imports.h"\n-#import "schema.h"\n-#import "soap.h"\n-#import "mime.h"\n-#import "dime.h"\n-#import "http.h"\n-#import "gwsdl.h"\n-#import "wsam.h"\n-#import "wsp.h"\n-\n-class wsdl__definitions;\t\t// forward declaration\n-\n-class wsdl__import\n-{ public:\n-\t@xsd__anyURI\t\t\tnamespace_;\n-\t@xsd__anyURI\t\t\tlocation;\n- private:\n- \twsdl__definitions\t\t*definitionsRef;\n- public:\n-\t\t\t\t\twsdl__import();\n-\tint\t\t\t\tpreprocess(wsdl__definitions&);\n- \tint\t\t\t\ttraverse(wsdl__definitions&);\n-\tvoid\t\t\t\tdefinitionsPtr(wsdl__definitions*);\n-\twsdl__definitions\t\t*definitionsPtr() const;\n-};\n-\n-class wsdl__types : public xs__schema\t\t\t\t// WSDL 2.0 <types> inlined schema\n-{ public:\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n-\tstd::vector<xs__schema*>\txs__schema_; \t\t// <xs:schema>*\n- public:\n-\tint\t\t\t\tpreprocess(wsdl__definitions&);\n-\tint\t\t\t\ttraverse(wsdl__definitions&);\n-};\n-\n-class wsdl__part\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\t@xsd__QName\t\t\telement;\n-\t@xsd__QName\t\t\ttype;\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n- private:\n- \txs__element\t\t\t*elementRef;\t\t// traverse() finds element\n- \txs__simpleType\t\t\t*simpleTypeRef;\t\t// traverse() finds simpleType\n- \txs__complexType\t\t\t*complexTypeRef;\t// traverse() finds complexType\n- public:\n-\t\t\t\t\twsdl__part();\n- \tint\t\t\t\ttraverse(wsdl__definitions&);\n-\tvoid\t\t\t\telementPtr(xs__element*);\n-\tvoid\t\t\t\tsimpleTypePtr(xs__simpleType*);\n-\tvoid\t\t\t\tcomplexTypePtr(xs__complexType*);\n-\txs__element\t\t\t*elementPtr() const;\n-\txs__simpleType\t\t\t*simpleTypePtr() const;\n-\txs__complexType\t\t\t*complexTypePtr() const;\n-};\n-\n-class wsdl__message\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n-\tstd::vector<wsp__Policy>\twsp__Policy_;\t\t// <wsp:Policy>*\n-\tstd::vector<wsp__PolicyReference> wsp__PolicyReference_;// <wsp:PolicyReference>*\n-\tstd::vector<wsdl__part>\t\tpart;\t\t\t// <wsdl:part>*\n- public:\n- \tint\t\t\t\ttraverse(wsdl__definitions&);\n-};\n-\n-class wsdl__ioput\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\t@xsd__QName\t\t\tmessage;\n-\t@xsd__NMTOKEN\t\t\tmessageLabel;\t\t// WSDL 2.0\n-\t@xsd__QName\t\t\telement;\t\t// WSDL 2.0\n-\t@xsd__anyURI\t\t\twsa__Action;\n-\t@xsd__anyURI\t\t\twsam__Action;\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n-\twsp__Policy\t\t\t'..b'_;\t// <http:binding>?\n-\tstd::vector<wsoap__module>\twsoap__module_;\t\t// <wsoap:module>* WSDL 2.0\n-\tstd::vector<wsdl__ext_fault>\tfault;\t\t\t// <wsdl:fault>* WSDL 2.0\n-\tstd::vector<wsdl__ext_operation> operation;\t\t// <wsdl:operation>*\n- private:\n-\twsdl__portType\t\t\t*portTypeRef;\t\t// traverse() finds portType/interface\n- public:\n-\t\t\t\t\twsdl__binding();\n-\tint\t\t\t\ttraverse(wsdl__definitions&);\n-\tvoid\t\t\t\tportTypePtr(wsdl__portType*);\n-\twsdl__portType\t\t\t*portTypePtr() const;\n-};\n-\n-class wsdl__port\t\t\t// ... and WSDL 2.0 endpoint\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\t@xsd__QName\t\t\tbinding;\n-\t@xsd__anyURI\t\t\taddress;\t\t// WSDL 2.0\n-\t@xsd__NMTOKEN\t\t\twhttp__authenticationScheme; // WSDL 2.0\n-\t@xsd__NMTOKEN\t\t\twhttp__authenticationRealm; // WSDL 2.0\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n-\twsp__Policy\t\t\t*wsp__Policy_;\t\t// <wsp:Policy>?\n-\twsp__PolicyReference\t\t*wsp__PolicyReference_;\t// <wsp:PolicyReference>?\n-\twsa__EndpointReferenceType\t*wsa__EndpointReference;// <wsa:EndpointReference>?\n-\tsoap__address\t\t\t*soap__address_;\t// <soap:address>?\n-\thttp__address\t\t\t*http__address_;\t// <http:address>?\n- private:\n-\twsdl__binding\t\t\t*bindingRef;\t\t// traverse() finds binding\n- public:\n- \t\t\t\t\twsdl__port();\n-\tint\t\t\t\ttraverse(wsdl__definitions&);\n-\tvoid\t\t\t\tbindingPtr(wsdl__binding*);\n-\twsdl__binding\t\t\t*bindingPtr() const;\n-};\n-\n-class wsdl__service\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\t@xsd__QName\t\t\tinterface_;\t\t// WSDL 2.0\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n-\tstd::vector<wsp__Policy>\twsp__Policy_;\t\t// <wsp:Policy>*\n-\tstd::vector<wsp__PolicyReference> wsp__PolicyReference_;// <wsp:PolicyReference>*\n-\tstd::vector<wsdl__port>\t\tport;\t\t\t// <wsdl:port>* WSDL 1.1\n-\tstd::vector<wsdl__port>\t\tendpoint;\t\t// <wsdl:port>* WSDL 2.0\n- public:\n-\tint\t\t\t\ttraverse(wsdl__definitions&);\n-};\n-\n-class wsdl__definitions\n-{ public:\n-\t@xsd__NMTOKEN\t\t\tname;\n-\t@xsd__anyURI\t\t\ttargetNamespace\t\t= "";\n-\t@xsd__NMTOKEN\t\t\tversion;\n-\tstd::vector<wsdl__import>\timport;\t\t\t// <wsdl:import>*\n-\txsd__string\t\t\tdocumentation;\t\t// <wsdl:documentation>?\n-\txsd__string\t\t\twsp__UsingPolicy;\t// <wsp:UsingPolcy>?\n-\tstd::vector<wsp__Policy>\twsp__Policy_;\t\t// <wsp:Policy>*\n-\twsdl__types\t\t\t*types;\t\t\t// <wsdl:types>?\n-\tstd::vector<wsdl__message>\tmessage;\t\t// <wsdl:message>*\n-\tstd::vector<wsdl__portType>\tportType;\t\t// <wsdl:portType>* WSDL 1.1\n-\tstd::vector<wsdl__portType>\tinterface_;\t\t// <wsdl:interface>* WSDL 2.0\n-\tstd::vector<wsdl__binding>\tbinding;\t\t// <wsdl:binding>*\n-\tstd::vector<wsdl__service>\tservice;\t\t// <wsdl:service>*\n-\tstd::vector<gwsdl__portType>\tgwsdl__portType_;\t// <gwsdl:portType>* For the moment, we will hardcode this which makes it easier to access. WSDL 1.1 does not allow this to be extended anyway\n-\tstruct soap\t\t\t*soap;\n- private:\n-\tbool\t\t\t\tsoap12;\n-\tbool\t\t\t\tupdated;\n-\tchar*\t\t\t\tlocation;\n-\tint\t\t\t\tredirs;\n-\tSetOfString\t\t\tbuiltinTypeSet;\n-\tSetOfString\t\t\tbuiltinElementSet;\n-\tSetOfString\t\t\tbuiltinAttributeSet;\n- public:\n-\t\t\t\t\twsdl__definitions();\n-\t\t\t\t\twsdl__definitions(struct soap*, const char*, const char*);\n-\tvirtual\t\t\t\t~wsdl__definitions();\n-\tint\t\t\t\tget(struct soap*);\t// gSOAP getter is triggered after parsing\n-\tint\t\t\t\tpreprocess();\n-\tint\t\t\t\ttraverse();\n-\tint\t\t\t\tread(int, char**);\n-\tint\t\t\t\tread(const char *cwd, const char*);\n-\tconst char*\t\t\tsourceLocation();\n-\tint\t\t\t\terror();\n-\tvoid\t\t\t\tprint_fault();\n-\tvoid\t\t\t\tbuiltinType(const char*);\n-\tvoid\t\t\t\tbuiltinTypes(const SetOfString&);\n-\tvoid\t\t\t\tbuiltinElement(const char*);\n-\tvoid\t\t\t\tbuiltinElements(const SetOfString&);\n-\tvoid\t\t\t\tbuiltinAttribute(const char*);\n-\tvoid\t\t\t\tbuiltinAttributes(const SetOfString&);\n-\tconst SetOfString&\t\tbuiltinTypes() const;\n-\tconst SetOfString&\t\tbuiltinElements() const;\n-\tconst SetOfString&\t\tbuiltinAttributes() const;\n-\tfriend ostream&\t\t\toperator<<(ostream&, const wsdl__definitions&);\n-\tfriend istream&\t\t\toperator>>(istream&, wsdl__definitions&);\n-};\n-\n-extern ostream &operator<<(ostream &o, const wsdl__definitions &e);\n-extern istream &operator>>(istream &i, wsdl__definitions &e);\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsdl2h.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsdl2h.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,527 +0,0 @@\n-/*\n-\twsdl2h.cpp\n-\n-\tWSDL parser, translator, and generator (of the gSOAP header file format)\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2013, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-Build:\n-\tsoapcpp2 -ipwsdl wsdl.h\n-\tg++ -o wsdl2h wsdl2h.cpp types.cpp service.cpp wsdl.cpp schema.cpp wsdlC.cpp stdsoap2.cpp\n-\t\n-TODO:\n-\tResolve relative versus absolute import paths for reading imported WSDL/schema (use URL local addresses)\n-\tDo not generate abstract complexTypes, but include defs in derived types\n-\tHandle simpleType derivation from base64\n-\n-*/\n-\n-#include "includes.h"\n-#include "types.h"\n-#include "service.h"\n-\n-#ifndef WSDL2H_IMPORT_PATH\n-#define WSDL2H_IMPORT_PATH (NULL)\n-#endif\n-\n-#ifndef WSDL_TYPEMAP_FILE\n-#define WSDL_TYPEMAP_FILE "typemap.dat"\n-#endif\n-\n-static void init();\n-static void options(int argc, char **argv);\n-\n-int _flag = 0,\n- aflag = 0,\n- bflag = 0,\n- cflag = 0,\n- dflag = 0,\n- eflag = 0,\n- fflag = 0,\n- gflag = 0,\n- iflag = 0,\n- jflag = 0,\n- kflag = 0,\n- mflag = 0,\n- pflag = 0,\n- Pflag = 0,\n- Rflag = 0,\n- sflag = 0,\n- uflag = 0,\n- vflag = 0,\n- wflag = 0,\n- Wflag = 0,\n- xflag = 0,\n- yflag = 0,\n- zflag = 0;\n-\n-int infiles = 0;\n-char *infile[MAXINFILES],\n- *outfile = NULL,\n- *proxy_host = NULL,\n- *proxy_userid = NULL,\n- *proxy_passwd = NULL,\n- *auth_userid = NULL,\n- *auth_passwd = NULL;\n-const char\n- *mapfile = WSDL_TYPEMAP_FILE,\n- *import_path = WSDL2H_IMPORT_PATH,\n- *cwd_path = NULL,\n- *cppnamespace = NULL;\n-\n-int proxy_port = 8080;\n-\n-FILE *stream = stdout;\n-\n-SetOfString exturis;\n-\n-extern struct Namespace namespaces[];\n-\n-const char *service_prefix = NULL;\n-const char *schema_prefix = "ns";\n-\n-const char elementformat[] = " %-35s %-30s";\n-const char pointerformat[] = " %-35s *%-30s";\n-const char attributeformat[] = " @%-35s %-30s";\n-const char vectorformat[] = " std::vector<%-23s> %-30s";\n-const char pointervectorformat[] = " std::vector<%-22s> *%-30s";\n-const char vectorformat_open[] = " std::vector<%s";\n-const char arrayformat[] = " %-35s *__ptr%-25s";\n-const char arraysizeformat[] = " %-35s __size%-24s";\n-const char arrayoffsetformat[] = "// %-35s __offset%-22s";\n-const char sizeformat[] = " $%-35s __size%-24s";\n-const char choiceformat[] = " $%-35s __union%-23s";\n-const char schemaformat[] = "//gsoap %-5s schema %s:\\t%s\\n";\n-const char serviceformat[] = "//gsoap %-4s service %s:\\t%s %s\\n";\n-const char paraformat[] '..b'ility elements\\n\\\n--y generate typedef synonyms for structs and enums\\n\\\n--z1 compatibility with 2.7.6e: generate pointer-based arrays\\n\\\n--z2 compatibility with 2.7.7 to 2.7.15: qualify element/attribute references\\n\\\n--z3 compatibility with 2.7.16 to 2.8.7: qualify element/attribute references\\n\\\n--z4 compatibility up to 2.8.11: don\'t generate union structs in std::vector\\n\\\n--z5 compatibility up to 2.8.15\\n\\\n--_ don\'t generate _USCORE (replace with UNICODE _x005f)\\n\\\n-infile.wsdl infile.xsd http://www... list of input sources (if none: use stdin)\\n\\\n-\\n");\n- exit(0);\n- default:\n- fprintf(stderr, "wsdl2h: Unknown option %s\\n", a);\n- exit(1);\n- }\n- }\n- }\n- else\n- { infile[infiles++] = argv[i];\n- if (infiles >= MAXINFILES)\n- { fprintf(stderr, "wsdl2h: too many files\\n");\n- exit(1);\n- }\n- }\n- }\n- if (infiles)\n- { if (!outfile)\n- { if (strncmp(infile[0], "http://", 7) && strncmp(infile[0], "https://", 8))\n- { const char *s = strrchr(infile[0], \'.\');\n- if (s && (!soap_tag_cmp(s, ".wsdl") || !soap_tag_cmp(s, ".gwsdl") || !soap_tag_cmp(s, ".xsd")))\n- { outfile = estrdup(infile[0]);\n- outfile[s - infile[0] + 1] = \'h\';\n- outfile[s - infile[0] + 2] = \'\\0\';\n- }\n- else\n- { outfile = (char*)emalloc(strlen(infile[0]) + 3);\n- strcpy(outfile, infile[0]);\n- strcat(outfile, ".h");\n- }\n- }\n- }\n- if (outfile)\n- { stream = fopen(outfile, "w");\n- if (!stream)\n- { fprintf(stderr, "Cannot write to %s\\n", outfile);\n- exit(1);\n- }\n- if (cppnamespace)\n- fprintf(stream, "namespace %s {\\n", cppnamespace);\n- fprintf(stderr, "Saving %s\\n\\n", outfile);\n- }\n- }\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\tNamespaces\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-struct Namespace namespaces[] =\n-{\n- {"SOAP-ENV", "http://schemas.xmlsoap.org/soap/envelope/", "http://www.w3.org/*/soap-envelope"},\n- {"SOAP-ENC", "http://schemas.xmlsoap.org/soap/encoding/", "http://www.w3.org/*/soap-encoding"},\n- {"xsi", "http://www.w3.org/2001/XMLSchema-instance"},\n- {"xsd", "-"}, // http://www.w3.org/2001/XMLSchema"}, // don\'t use this, it might conflict with xs\n- {"xml", "http://www.w3.org/XML/1998/namespace"},\n- {"xs", "http://www.w3.org/2001/XMLSchema", "http://www.w3.org/*/XMLSchema" },\n- {"http", "http://schemas.xmlsoap.org/wsdl/http/"},\n- {"soap", "http://schemas.xmlsoap.org/wsdl/soap/", "http://schemas.xmlsoap.org/wsdl/soap*/"},\n- {"mime", "http://schemas.xmlsoap.org/wsdl/mime/"},\n- {"xmime", "http://www.w3.org/2005/05/xmlmime"},\n- {"dime", "http://schemas.xmlsoap.org/ws/2002/04/dime/wsdl/", "http://schemas.xmlsoap.org/ws/*/dime/wsdl/"},\n- {"sp", "http://docs.oasis-open.org/ws-sx/ws-securitypolicy/200702", "http://schemas.xmlsoap.org/ws/2005/07/securitypolicy"},\n- {"wsdl", "http://schemas.xmlsoap.org/wsdl/", "http://www.w3.org/ns/wsdl"},\n- {"wsdli", "http://www.w3.org/ns/wsdl-instance"},\n- {"wsdlx", "http://www.w3.org/ns/wsdl-extensions"},\n- {"wsoap", "http://www.w3.org/ns/wsdl/soap"},\n- {"whttp", "http://www.w3.org/ns/wsdl/http"},\n- {"wrpc", "http://www.w3.org/ns/wsdl/rpc"},\n- {"wsa_", "http://www.w3.org/2005/08/addressing"},\n- {"wsaw", "http://www.w3.org/2006/05/addressing/wsdl"},\n- {"wsam", "http://www.w3.org/2007/05/addressing/metadata"},\n- {"wsrmp", "http://schemas.xmlsoap.org/ws/2005/02/rm/policy", "http://docs.oasis-open.org/ws-rx/wsrmp/*"},\n- {"wsp", "http://www.w3.org/ns/ws-policy", "http://schemas.xmlsoap.org/ws/2004/09/policy"},\n- {"wst", "http://docs.oasis-open.org/ws-sx/ws-trust/200512"},\n- {"wsu_", "http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd"},\n- {"gwsdl", "http://www.gridforum.org/namespaces/2003/03/gridWSDLExtensions"},\n- {NULL, NULL}\n-};\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsp.cpp
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsp.cpp Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,658 +0,0 @@\n-/*\n-\twsp.cpp\n-\n-\tWS-Policy 1.2 and 1.5 binding schema\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2001-2010, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-*/\n-\n-#include "wsdlH.h"\n-#include "includes.h"\n-#include "types.h"\n-#include "service.h"\n-\n-static wsp__Policy *search(const char *URI, wsdl__definitions& definitions);\n-static wsp__Policy *search(const char *URI, wsp__Policy *policy);\n-static wsp__Policy *search(const char *URI, wsp__Content *content);\n-static void gen_parts(const sp__Parts& parts, Types& types, const char *what, const char *name, int indent);\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\twsp:OperatorContentType\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-int wsp__Content::traverse(wsdl__definitions& definitions)\n-{ if (vflag)\n- cerr << " Analyzing wsp Policy" << endl;\n- if (Policy)\n- Policy->traverse(definitions);\n- if (PolicyReference)\n- PolicyReference->traverse(definitions);\n- for (vector<wsp__Content*>::iterator i = All.begin(); i != All.end(); ++i)\n- { if (*i)\n- (*i)->traverse(definitions);\n- }\n- for (vector<wsp__Content*>::iterator j = ExactlyOne.begin(); j != ExactlyOne.end(); ++j)\n- { if (*j)\n- (*j)->traverse(definitions);\n- }\n- return SOAP_OK;\n-}\n-\n-void wsp__Content::generate(Service& service, Types& types, int indent) const\n-{ static const char stabs[] = "\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t";\n- const char *tabs;\n- if (indent > 8)\n- indent = 8;\n- tabs = stabs + 9 - indent;\n- // Recursive policies and references\n- if (Policy)\n- Policy->generate(service, types, indent);\n- if (PolicyReference && PolicyReference->policyPtr())\n- PolicyReference->policyPtr()->generate(service, types, indent);\n- // WS-Policy All\n- if (!All.empty())\n- { fprintf(stream, "%s- All of the following:\\n", tabs);\n- for (vector<wsp__Content*>::const_iterator p = All.begin(); p != All.end(); ++p)\n- if (*p)\n- (*p)->generate(service, types, indent + 1);\n- }\n- // WS-Policy ExactlyOne\n- if (!ExactlyOne.empty())\n- { fprintf(stream, "%s- Exactly one of the following:\\n", tabs);\n- for (vector<wsp__Content*>::const_iterator p = ExactlyOne.begin(); p != ExactlyOne.end(); ++p)\n- if (*p)\n- (*p)->generate(service, types, indent + 1);\n- }\n- // WS-SecurityPolicy Parts (TODO: do we need vectors of these?)\n- for (vector<sp__Parts>::const_iterator sp = sp__SignedParts.begin(); sp != sp__SignedParts.end(); ++sp)\n- gen_parts(*sp, types, "sign", "[4.1.1] WS-Security Signed Parts", indent);\n- for (vector<sp__Parts>::const_iterator ep = sp__EncryptedParts.begin(); ep != sp__EncryptedParts.end();'..b' types, indent + 1);\n- service.add_import("wsrm.h");\n- }\n- if (wsrmp__DeliveryAssurance)\n- { fprintf(stream, "%s- WS-ReliableMessaging Delivery Assurance%s:\\n", tabs, wsrmp__DeliveryAssurance->Optional ? " (optional)" : wsrmp__DeliveryAssurance->Ignorable ? " (ignorable)" : "");\n- if (wsrmp__DeliveryAssurance->Policy)\n- wsrmp__DeliveryAssurance->Policy->generate(service, types, indent + 1);\n- service.add_import("wsrm.h");\n- }\n- if (wsrmp__AtLeastOnce)\n- fprintf(stream, "%s- At Least Once\\n", tabs);\n- if (wsrmp__AtMostOnce)\n- fprintf(stream, "%s- At Most Once\\n", tabs);\n- if (wsrmp__ExactlyOnce)\n- fprintf(stream, "%s- Exactly Once\\n", tabs);\n- if (wsrmp__InOrder)\n- fprintf(stream, "%s- In Order\\n", tabs);\n- // All else\n- for (vector<_XML>::const_iterator x = __any.begin(); x != __any.end(); ++x)\n- { if (*x && *(*x))\n- { fprintf(stream, "%s- Other policy requirements:\\n\\t@verbatim\\n", tabs);\n- text(*x);\n- fprintf(stream, "\\t@endverbatim\\n");\n- }\n- }\n-}\n-\n-static void gen_parts(const sp__Parts& parts, Types& types, const char *what, const char *name, int indent)\n-{ static const char stabs[] = "\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t";\n- const char *tabs;\n- if (indent > 8)\n- indent = 8;\n- tabs = stabs + 9 - indent;\n- fprintf(stream, "%s- %s requirements:\\n", tabs, name);\n- if (parts.Body)\n- fprintf(stream, "%s -# Body:\\n\\t@code\\n\\t#include \\"plugin/wsseapi.h\\"\\n\\tsoap_wsse_%s_body(soap, <algorithm>, <key>, <keylen>);\\n\\t@endcode\\n", tabs, what);\n- if (!parts.Header.empty())\n- { fprintf(stream, "%s -# Header elements:\\n\\t@code\\n\\t#include \\"plugin/wsseapi.h\\"\\n\\tsoap_wsse_set_wsu_id(soap, \\"", tabs);\n- for (vector<sp__Header>::const_iterator h = parts.Header.begin(); h != parts.Header.end(); ++h)\n- { if ((*h).Name)\n- fprintf(stream, "%s ", types.aname(NULL, (*h).Namespace, (*h).Name));\n- else if ((*h).Namespace)\n- fprintf(stream, "%s: ", types.nsprefix(NULL, (*h).Namespace));\n- }\n- fprintf(stream, "\\");\\n\\t@endcode\\n");\n- }\n- if (parts.Attachments)\n- fprintf(stream, "%s -# Attachments as defined in SwAProfile1.1\\n", tabs);\n-}\n-\n-////////////////////////////////////////////////////////////////////////////////\n-//\n-//\twsp:PolicyReference\n-//\n-////////////////////////////////////////////////////////////////////////////////\n-\n-int wsp__PolicyReference::traverse(wsdl__definitions& definitions)\n-{ policyRef = NULL;\n- if (!URI || !*URI)\n- { cerr << "PolicyReference has no URI" << endl;\n- return SOAP_OK;\n- }\n- if (*URI == \'#\')\n- { policyRef = search(URI + 1, definitions);\n- if (!policyRef)\n- { cerr << "PolicyReference URI=\\"" << URI << "\\" not found" << endl;\n- return SOAP_OK;\n- }\n- }\n- return SOAP_OK;\n-}\n-\n-void wsp__PolicyReference::policyPtr(wsp__Policy *Policy)\n-{ policyRef = Policy;\n-}\n-\n-wsp__Policy *wsp__PolicyReference::policyPtr() const\n-{ return policyRef;\n-}\n-\n-static wsp__Policy *search(const char *URI, wsdl__definitions& definitions)\n-{ for (vector<wsp__Policy>::iterator p = definitions.wsp__Policy_.begin(); p != definitions.wsp__Policy_.end(); ++p)\n- { wsp__Policy *policy = search(URI, &(*p));\n- if (policy)\n- return policy;\n- }\n- return NULL;\n-}\n-\n-static wsp__Policy *search(const char *URI, wsp__Policy *policy)\n-{ if (!policy)\n- return NULL;\n- if (policy->wsu__Id && !strcmp(URI, policy->wsu__Id))\n- return policy;\n- return search(URI, (wsp__Content*)policy);\n-}\n-\n-static wsp__Policy *search(const char *URI, wsp__Content *content)\n-{ wsp__Policy *policy;\n- policy = search(URI, content->Policy);\n- if (policy)\n- return policy;\n- for (vector<wsp__Content*>::iterator i = content->All.begin(); i != content->All.end(); ++i)\n- { policy = search(URI, *i);\n- if (policy)\n- return policy;\n- }\n- for (vector<wsp__Content*>::iterator j = content->ExactlyOne.begin(); j != content->ExactlyOne.end(); ++j)\n- { policy = search(URI, *j);\n- if (policy)\n- return policy;\n- }\n- return NULL;\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsp.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsp.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,269 +0,0 @@\n-/*\n-\twsp.h\n-\n-\tWS-Policy 1.2 and 1.5 binding schema\n-\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2001-2010, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-This software is released under one of the following licenses:\n-GPL or Genivia\'s license for commercial use.\n---------------------------------------------------------------------------------\n-GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n---------------------------------------------------------------------------------\n-A commercial use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-\n-*/\n-\n-//gsoap wsp schema documentation:\tWS-Policy binding\n-//gsoap wsp schema namespace:\t\thttp://www.w3.org/ns/ws-policy\n-// 1.2 //gsoap wsp schema namespace:\thttp://schemas.xmlsoap.org/ws/2004/09/policy\n-//gsoap wsp schema elementForm:\t\tqualified \n-//gsoap wsp schema attributeForm:\tunqualified \n-\n-#import "imports.h"\n-#import "wsu.h"\n-\n-class wsp__Policy;\n-class wsp__Content;\n-\n-extern class Service;\n-extern class Types;\n-\n-class wsp__PolicyReference\n-{ public:\n-\t@xsd__anyURI\t\t\tURI;\n-\t@xsd__string\t\t\tDigest;\n-\t@xsd__anyURI\t\t\tDigestAlgorithm;\n- private:\n-\twsp__Policy\t\t\t*policyRef;\n- public:\n-\tint\t\t\t\ttraverse(wsdl__definitions&);\n-\tvoid\t\t\t\tpolicyPtr(wsp__Policy*);\n-\twsp__Policy\t\t\t*policyPtr() const;\n-};\n-\n-class wsp__Assertion\n-{ public:\n-\t@bool\t\t\t\tOptional = false;\n-\t@bool\t\t\t\tIgnorable = false;\n-\twsp__Content\t\t\t*Policy;\n-};\n-\n-#import "sp.h"\n-#import "wsrmp.h"\n-#import "wsam.h"\n-\n-class wsp__Content\n-{ public:\n-\twsp__Policy\t\t\t*Policy;\n-\twsp__PolicyReference\t\t*PolicyReference;\n-\tstd::vector<wsp__Content*>\tAll;\n-\tstd::vector<wsp__Content*>\tExactlyOne;\n-\n-\tstd::vector<sp__Parts>\t\tsp__SignedParts;\n-\tstd::vector<sp__Parts>\t\tsp__EncryptedParts;\n-\tstd::vector<sp__Parts>\t\tsp__RequiredParts;\n-\n-\tsp__Elements\t\t\t*sp__SignedElements;\n-\tsp__Elements\t\t\t*sp__EncryptedElements;\n-\tsp__Elements\t\t\t*sp__ContentEncryptedElements;\n-\tsp__Elements\t\t\t*sp__RequiredElements;\n-\n-\tsp__Token\t\t\t*sp__UsernameToken;\n-\tsp__Token\t\t\t*sp__IssuedToken;\n-\tsp__Token\t\t\t*sp__X509Token;\n-\tsp__Token\t\t\t*sp__KerberosToken;\n-\tsp__Token\t\t\t*sp__SpnegoContextToken;\n-\tsp__Token\t\t\t*sp__SecurityContextToken;\n-\tsp__Token\t\t\t*sp__SecureConversationToken;\n-\tsp__Token\t\t\t*sp__SamlToken;\n-\tsp__Token\t\t\t*sp__RelToken;\n-\tsp__Token\t\t\t*sp__HttpsToken;\n-\tsp__Token\t\t\t*sp__KeyValueToken;\n-\n-\twsp__Assertion\t\t\t*sp__TransportBinding;\n-\twsp__Assertion\t\t\t*sp__TransportToken;\n-\twsp__Assertion\t\t\t*sp__AlgorithmSuite;\n-\twsp__Assertion\t\t\t*sp__Layout;\n-\twsp__Assertion\t\t\t*sp__SymmetricBinding;\n-\twsp__Assertion\t\t\t*sp__AsymmetricBinding;\n-\twsp__Assertion\t\t\t*sp__ProtectionToken;\n-\twsp__Assertion\t\t\t*sp__InitiatorToken;\n-\twsp__Assertion\t\t\t*sp__InitiatorSignatureToken;\n-\twsp__Assertion\t\t\t*sp__InitiatorEncryptionToken;\n-\twsp__Assertion\t\t\t*sp__RecipientToken;\n-\n-\twsp__Assertion\t\t\t*sp__SupportingTokens;\n-\twsp__Assertion\t\t\t*sp__SignedSupportingTokens;\n-\twsp__Assertion\t\t\t*sp__EndorsingSupportingTokens;\n-\twsp__Assertion\t\t\t*sp__SignedEndorsingSupportingTokens;\n-\twsp__Assertion\t\t\t*sp__SignedEncryptedSupportingTokens;\n-\twsp__Assertion\t\t\t*sp__Encrypted'..b'\twsrmp__ExactlyOnce;\n-\txsd__string\t\t\twsrmp__InOrder;\n-\n-\twsp__Assertion\t\t\t*sp__NoPassword;\n-\twsp__Assertion\t\t\t*sp__HashPassword;\n-\n-\twsp__Assertion\t\t\t*sp__IncludeTimestamp;\n-\twsp__Assertion\t\t\t*sp__EncryptBeforeSigning;\n-\twsp__Assertion\t\t\t*sp__EncryptSignature;\n-\twsp__Assertion\t\t\t*sp__ProtectTokens;\n-\twsp__Assertion\t\t\t*sp__OnlySignEntireHeadersAndBody;\n-\n-\txsd__string\t\t\tsp__RequireDerivedKeys;\n-\txsd__string\t\t\tsp__RequireImpliedDerivedKeys;\n-\txsd__string\t\t\tsp__RequireExplicitDerivedKeys;\n-\n-\txsd__string\t\t\tsp__WssUsernameToken10;\n-\txsd__string\t\t\tsp__WssUsernameToken11;\n-\n-\txsd__string\t\t\tsp__RequireExternalReference;\n-\txsd__string\t\t\tsp__RequireInternalReference;\n-\n-\txsd__string\t\t\tsp__RequireKeyIdentifierReference;\n-\txsd__string\t\t\tsp__RequireIssuerSerialReference;\n-\txsd__string\t\t\tsp__RequireEmbeddedTokenReference;\n-\txsd__string\t\t\tsp__RequireThumbprintReference;\n-\n-\txsd__string\t\t\tsp__WssX509V3Token10;\n-\txsd__string\t\t\tsp__WssX509Pkcs7Token10;\n-\txsd__string\t\t\tsp__WssX509PkiPathV1Token10;\n-\txsd__string\t\t\tsp__WssX509V1Token11;\n-\txsd__string\t\t\tsp__WssX509V3Token11;\n-\txsd__string\t\t\tsp__WssX509Pkcs7Token11;\n-\txsd__string\t\t\tsp__WssX509PkiPathV1Token11;\n-\n-\txsd__string\t\t\tsp__WssKerberosV5ApReqToken11;\n-\txsd__string\t\t\tsp__WssGssKerberosV5ApReqToken11;\n-\n-\txsd__string\t\t\tsp__WssRelV10Token10;\n-\txsd__string\t\t\tsp__WssRelV20Token10;\n-\txsd__string\t\t\tsp__WssRelV10Token11;\n-\txsd__string\t\t\tsp__WssRelV20Token11;\n-\n-\txsd__string\t\t\tsp__MustNotSendCancel;\n-\txsd__string\t\t\tsp__MustNotSendAmend;\n-\txsd__string\t\t\tsp__MustNotSendRenew;\n-\n-\txsd__string\t\t\tsp__MustSupportRefKeyIdentifier;\n-\txsd__string\t\t\tsp__MustSupportRefIssuerSerial;\n-\txsd__string\t\t\tsp__MustSupportRefExternalURI;\n-\txsd__string\t\t\tsp__MustSupportRefEmbeddedToken;\n-\txsd__string\t\t\tsp__MustSupportRefThumbprint;\n-\txsd__string\t\t\tsp__MustSupportRefEncryptedKey;\n-\txsd__string\t\t\tsp__RequireSignatureConfirmation;\n-\n-\txsd__string\t\t\tsp__MustSupportClientChallenge;\n-\txsd__string\t\t\tsp__MustSupportServerChallenge;\n-\txsd__string\t\t\tsp__RequireClientEntropy;\n-\txsd__string\t\t\tsp__RequireServerEntropy;\n-\txsd__string\t\t\tsp__MustSupportIssuedTokens;\n-\txsd__string\t\t\tsp__RequireRequestSecurityTokenCollection;\n-\txsd__string\t\t\tsp__RequireAppliesTo;\n-\n-\txsd__string\t\t\tsp__RequireExternalUriReference;\n-\txsd__string\t\t\tsp__SC13SecurityContextToken;\n-\n-\txsd__string\t\t\tsp__Strict;\n-\txsd__string\t\t\tsp__Lax;\n-\txsd__string\t\t\tsp__LaxTsFirst;\n-\txsd__string\t\t\tsp__LaxTsLast;\n-\n-\txsd__string\t\t\tsp__HttpBasicAuthentication;\n-\txsd__string\t\t\tsp__HttpDigestAuthentication;\n-\txsd__string\t\t\tsp__RequireClientCertificate;\n-\n-\txsd__string\t\t\tsp__Basic256;\n-\txsd__string\t\t\tsp__Basic192;\n-\txsd__string\t\t\tsp__Basic128;\n-\txsd__string\t\t\tsp__TripleDes;\n-\txsd__string\t\t\tsp__Basic256Rsa15;\n-\txsd__string\t\t\tsp__Basic192Rsa15;\n-\txsd__string\t\t\tsp__Basic128Rsa15;\n-\txsd__string\t\t\tsp__TripleDesRsa15;\n-\txsd__string\t\t\tsp__Basic256Sha256;\n-\txsd__string\t\t\tsp__Basic192Sha256;\n-\txsd__string\t\t\tsp__Basic128Sha256;\n-\txsd__string\t\t\tsp__TripleDesSha256;\n-\txsd__string\t\t\tsp__Basic256Sha256Rsa15;\n-\txsd__string\t\t\tsp__Basic192Sha256Rsa15;\n-\txsd__string\t\t\tsp__Basic128Sha256Rsa15;\n-\txsd__string\t\t\tsp__TripleDesSha256Rsa15;\n-\n-\txsd__string\t\t\tsp__InclusiveC14N;\n-\txsd__string\t\t\tsp__SOAPNormalization10;\n-\txsd__string\t\t\tsp__STRTransform10;\n-\n-\txsd__string\t\t\tsp__Path10;\n-\txsd__string\t\t\tsp__XPathFilter20;\n-\txsd__string\t\t\tsp__AbsXPath;\n-\n-\txsd__string\t\t\twsam__AnonymousResponses;\n-\txsd__string\t\t\twsam__NonAnonymousResponses;\n-\n-\tstd::vector<_XML>\t\t__any;\n- public:\n-\tint\t\t\t\ttraverse(wsdl__definitions&);\n-\tvoid\t\t\t\tgenerate(Service& service, Types& types, int indent) const;\n-};\n-\n-class wsp__Policy : public wsp__Content\n-{ public:\n-\t@xsd__anyURI\t\t\txml__base;\n-\t@xsd__string\t\t\twsu__Id;\n-\t@xsd__anyURI\t\t\tTargetNamespace;\n-};\n-\n-class wsp__Attachment\n-{ public:\n-\twsp__Policy\t\t\t*Policy;\n-\twsp__PolicyReference\t\t*PolicyReference;\n-};\n-\n-class wsp__AppliesTo\n-{ public:\n-\t_XML\t\t\t\t__any;\n-};\n-\n-class wsp__PolicyAttachment\n-{ public:\n-\twsp__AppliesTo\t\t\t*AppliesTo;\n-\tstd::vector<wsp__Attachment>\tAttachment;\n-};\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsrmp.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsrmp.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,55 +0,0 @@
-/*
- wsrmp.h
-
- WS-ReliableMessaging Policy
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2010, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-
-*/
-
-//gsoap wsrmp schema documentation: WS-ReliableMessaging Policy binding
-//gsoap wsrmp schema namespace: http://schemas.xmlsoap.org/ws/2005/02/rm/policy
-//gsoap wsrmp schema elementForm: qualified
-//gsoap wsrmp schema attributeForm: unqualified
-
-#import "imports.h"
-
-class wsrmp__Timeout
-{ public:
-  @char *Milliseconds;
-};
-
-class wsrmp__RMAssertion : public wsp__Assertion
-{ public:
-  wsrmp__Timeout *InactivityTimeout;
-  wsrmp__Timeout *BaseRetransmissionInterval;;
-  wsrmp__Timeout *AcknowledgementInterval;
-  char           *ExponentialBackoff;
-// TODO: WCF netrmp extension elements go here, as necessary
-};
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wst.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wst.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,43 +0,0 @@
-/*
- wst.h
-
- WS-Trust
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-//gsoap wst schema documentation: WS-Trust
-//gsoap wst schema namespace: http://docs.oasis-open.org/ws-sx/ws-trust/200512
-//gsoap wst schema elementForm: qualified
-//gsoap wst schema attributeForm: unqualified
-
-class wst__Claims
-{ public:
- @xsd__string Dialect;
- xsd__string __item;
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/gsoap/wsdl/wsu.h
--- a/GEMBASSY-1.0.3/gsoap/wsdl/wsu.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,37 +0,0 @@
-/*
- wsu.h
-
- WS-Utility (namespace only)
-
---------------------------------------------------------------------------------
-gSOAP XML Web services tools
-Copyright (C) 2001-2008, Robert van Engelen, Genivia Inc. All Rights Reserved.
-This software is released under one of the following licenses:
-GPL or Genivia's license for commercial use.
---------------------------------------------------------------------------------
-GPL license.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-Place, Suite 330, Boston, MA 02111-1307 USA
-
-Author contact information:
-engelen@genivia.com / engelen@acm.org
---------------------------------------------------------------------------------
-A commercial use license is available from Genivia, Inc., contact@genivia.com
---------------------------------------------------------------------------------
-*/
-
-//gsoap wsu schema documentation: WS-Utility
-//gsoap wsu schema namespace: http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd
-//gsoap wsu schema elementForm: qualified
-//gsoap wsu schema attributeForm: unqualified

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/.deps/gfile.Po
--- a/GEMBASSY-1.0.3/include/.deps/gfile.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/.deps/ghttp.Po
--- a/GEMBASSY-1.0.3/include/.deps/ghttp.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/.deps/gplot.Po
--- a/GEMBASSY-1.0.3/include/.deps/gplot.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/.deps/gpost.Po
--- a/GEMBASSY-1.0.3/include/.deps/gpost.Po Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-# dummy

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.B1.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.B1.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:B1>
-   <sequence></sequence>
-   <params>
-    <method></method>
-   </params>
-  </ns1:B1>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.B1.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.B1.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:B1Response>
-   <result></result>
-  </ns1:B1Response>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.B2.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.B2.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:B2>
-   <sequence></sequence>
-  </ns1:B2>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.B2.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.B2.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:B2Response>
-   <result></result>
-  </ns1:B2Response>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.DoubleHelix.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.DoubleHelix.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:DoubleHelix>
-   <sequence></sequence>
-   <params>
-    <speed>0.0</speed>
-   </params>
-  </ns1:DoubleHelix>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.DoubleHelix.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.DoubleHelix.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:DoubleHelixResponse>
-   <result></result>
-  </ns1:DoubleHelixResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.Ew.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.Ew.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:Ew>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <output></output>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:Ew>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.Ew.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.Ew.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:EwResponse>
-   <result></result>
-  </ns1:EwResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.P2.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.P2.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:P2>
-   <sequence></sequence>
-   <params>
-    <output></output>
-    <tag></tag>
-   </params>
-  </ns1:P2>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.P2.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.P2.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:P2Response>
-   <result></result>
-  </ns1:P2Response>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.S_value.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.S_value.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:S_value>
-   <sequence></sequence>
-   <params>
-    <sharp>0</sharp>
-   </params>
-  </ns1:S_value>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.S_value.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.S_value.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:S_valueResponse>
-   <result></result>
-  </ns1:S_valueResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.aaui.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.aaui.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:aaui>
-   <sequence></sequence>
-   <params>
-    <id></id>
-    <tag></tag>
-   </params>
-  </ns1:aaui>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.aaui.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.aaui.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:aauiResponse>
-   <result></result>
-  </ns1:aauiResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_counter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_counter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:amino_counter>
-   <sequence></sequence>
-   <params>
-    <CDSid></CDSid>
-    <output></output>
-   </params>
-  </ns1:amino_counter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_counter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_counter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:amino_counterResponse>
-   <result></result>
-  </ns1:amino_counterResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_info.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_info.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:amino_info>
-   <sequence></sequence>
-  </ns1:amino_info>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_info.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.amino_info.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:amino_infoResponse>
-   <result></result>
-  </ns1:amino_infoResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_counter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_counter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_counter>
-   <sequence></sequence>
-   <params>
-    <position></position>
-    <PatLen>0</PatLen>
-    <upstream>0</upstream>
-    <downstream>0</downstream>
-   </params>
-  </ns1:base_counter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_counter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_counter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_counterResponse>
-   <result></result>
-  </ns1:base_counterResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_entropy.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_entropy.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_entropy>
-   <sequence></sequence>
-   <params>
-    <upstream>0</upstream>
-    <position></position>
-    <downstream>0</downstream>
-    <output></output>
-    <PatLength>0</PatLength>
-   </params>
-  </ns1:base_entropy>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_entropy.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_entropy.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_entropyResponse>
-   <result></result>
-  </ns1:base_entropyResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_information_content.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_information_content.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_information_content>
-   <sequence></sequence>
-   <params>
-    <upstream>0</upstream>
-    <position></position>
-    <downstream>0</downstream>
-    <output></output>
-    <PatLength>0</PatLength>
-   </params>
-  </ns1:base_information_content>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_information_content.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_information_content.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_information_contentResponse>
-   <result></result>
-  </ns1:base_information_contentResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_relative_entropy.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_relative_entropy.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_relative_entropy>
-   <sequence></sequence>
-   <params>
-    <upstream>0</upstream>
-    <position></position>
-    <downstream>0</downstream>
-    <output></output>
-    <PatLength>0</PatLength>
-   </params>
-  </ns1:base_relative_entropy>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_relative_entropy.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_relative_entropy.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_relative_entropyResponse>
-   <result></result>
-  </ns1:base_relative_entropyResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_z_value.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_z_value.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_z_value>
-   <sequence></sequence>
-   <params>
-    <limit>0</limit>
-    <position></position>
-    <PatLen>0</PatLen>
-    <upstream>0</upstream>
-    <downstream>0</downstream>
-   </params>
-  </ns1:base_z_value>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.base_z_value.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.base_z_value.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:base_z_valueResponse>
-   <result></result>
-  </ns1:base_z_valueResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.bui.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.bui.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:bui>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <position></position>
-    <id></id>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:bui>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.bui.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.bui.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:buiResponse>
-   <result></result>
-  </ns1:buiResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cai.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cai.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cai>
-   <sequence></sequence>
-   <params>
-    <w_output></w_output>
-    <translate>0</translate>
-    <output></output>
-    <w_filename></w_filename>
-    <w_absent></w_absent>
-    <tag></tag>
-   </params>
-  </ns1:cai>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cai.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cai.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:caiResponse>
-   <result></result>
-  </ns1:caiResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.calc_pI.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.calc_pI.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:calc_pI>
-   <sequence></sequence>
-  </ns1:calc_pI>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.calc_pI.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.calc_pI.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:calc_pIResponse>
-   <result></result>
-  </ns1:calc_pIResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cbi.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cbi.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cbi>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <id></id>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:cbi>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cbi.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cbi.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cbiResponse>
-   <result></result>
-  </ns1:cbiResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cgr.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cgr.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cgr>
-   <sequence></sequence>
-   <params>
-    <width>0</width>
-    <level>0</level>
-   </params>
-  </ns1:cgr>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cgr.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cgr.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cgrResponse>
-   <result></result>
-  </ns1:cgrResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.circular_map.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.circular_map.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:circular_map>
-   <sequence></sequence>
-   <params>
-    <gmap>0</gmap>
-   </params>
-  </ns1:circular_map>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.circular_map.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.circular_map.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:circular_mapResponse>
-   <result></result>
-  </ns1:circular_mapResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_compiler.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_compiler.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_compiler>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <id></id>
-    <data></data>
-    <output></output>
-    <del_key></del_key>
-    <startcodon>0</startcodon>
-    <stopcodon>0</stopcodon>
-   </params>
-  </ns1:codon_compiler>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_compiler.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_compiler.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_compilerResponse>
-   <result></result>
-  </ns1:codon_compilerResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_counter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_counter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_counter>
-   <sequence></sequence>
-   <params>
-    <CDSid></CDSid>
-    <output></output>
-   </params>
-  </ns1:codon_counter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_counter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_counter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_counterResponse>
-   <result></result>
-  </ns1:codon_counterResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_mva.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_mva.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_mva>
-   <sequence></sequence>
-   <params>
-    <parameter>0</parameter>
-    <naxis>0</naxis>
-    <translate>0</translate>
-    <data>0</data>
-    <method></method>
-    <output></output>
-    <del_key></del_key>
-   </params>
-  </ns1:codon_mva>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_mva.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_mva.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_mvaResponse>
-   <result></result>
-  </ns1:codon_mvaResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_usage.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_usage.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_usage>
-   <sequence></sequence>
-   <params>
-    <version>0</version>
-    <CDSid></CDSid>
-    <output></output>
-   </params>
-  </ns1:codon_usage>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_usage.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.codon_usage.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:codon_usageResponse>
-   <result></result>
-  </ns1:codon_usageResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.complement.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.complement.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:complement>
-   <sequence></sequence>
-  </ns1:complement>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.complement.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.complement.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:complementResponse>
-   <result></result>
-  </ns1:complementResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.consensus_z.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.consensus_z.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:consensus_z>
-   <array_seq SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array_seq>
-   <params>
-    <high>0</high>
-    <low>0.0</low>
-    <output></output>
-   </params>
-  </ns1:consensus_z>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.consensus_z.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.consensus_z.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:consensus_zResponse>
-   <result></result>
-  </ns1:consensus_zResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cor.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cor.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cor>
-   <array1 SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array1>
-   <array2 SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array2>
-   <params>
-    <sorted>0</sorted>
-    <method></method>
-   </params>
-  </ns1:cor>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cor.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cor.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:corResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:corResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cumulative.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cumulative.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cumulative>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:cumulative>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.cumulative.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.cumulative.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:cumulativeResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:cumulativeResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_enc.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_enc.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:delta_enc>
-   <sequence></sequence>
-  </ns1:delta_enc>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_enc.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_enc.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:delta_encResponse>
-   <result></result>
-  </ns1:delta_encResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_gcskew.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_gcskew.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:delta_gcskew>
-   <sequence></sequence>
-   <params>
-    <method></method>
-    <at>0</at>
-    <purine>0</purine>
-    <keto>0</keto>
-   </params>
-  </ns1:delta_gcskew>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_gcskew.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.delta_gcskew.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:delta_gcskewResponse>
-   <result></result>
-  </ns1:delta_gcskewResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.dinuc.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.dinuc.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:dinuc>
-   <sequence></sequence>
-   <params>
-    <position></position>
-    <id></id>
-    <output></output>
-    <translate>0</translate>
-    <del_key></del_key>
-   </params>
-  </ns1:dinuc>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.dinuc.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.dinuc.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:dinucResponse>
-   <result></result>
-  </ns1:dinucResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.dist_in_cc.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.dist_in_cc.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:dist_in_cc>
-   <sequence></sequence>
-   <position1>0</position1>
-   <position2>0</position2>
-  </ns1:dist_in_cc>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.dist_in_cc.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.dist_in_cc.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:dist_in_ccResponse>
-   <result></result>
-  </ns1:dist_in_ccResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.dnawalk.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.dnawalk.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:dnawalk>
-   <sequence></sequence>
-   <params>
-    <gmap>0</gmap>
-   </params>
-  </ns1:dnawalk>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.dnawalk.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.dnawalk.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:dnawalkResponse>
-   <result></result>
-  </ns1:dnawalkResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.enc.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.enc.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:enc>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <id></id>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:enc>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.enc.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.enc.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:encResponse>
-   <result></result>
-  </ns1:encResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.entrez.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.entrez.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:entrez>
-   <database></database>
-   <query></query>
-  </ns1:entrez>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.entrez.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.entrez.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:entrezResponse>
-   <result></result>
-  </ns1:entrezResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.filter_cds_by_atg.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.filter_cds_by_atg.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:filter_cds_by_atg>
-   <sequence></sequence>
-   <params>
-    <upstream>0</upstream>
-    <codon></codon>
-    <downstream>0</downstream>
-   </params>
-  </ns1:filter_cds_by_atg>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.filter_cds_by_atg.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.filter_cds_by_atg.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:filter_cds_by_atgResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:filter_cds_by_atgResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dif.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dif.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_dif>
-   <sequence></sequence>
-   <params>
-    <type></type>
-   </params>
-  </ns1:find_dif>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dif.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dif.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_difResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:find_difResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dnaAbox.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dnaAbox.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_dnaAbox>
-   <sequence></sequence>
-   <params>
-    <output></output>
-   </params>
-  </ns1:find_dnaAbox>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dnaAbox.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_dnaAbox.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_dnaAboxResponse>
-   <result></result>
-  </ns1:find_dnaAboxResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_iteron.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_iteron.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_iteron>
-   <sequence></sequence>
-   <params>
-    <output></output>
-   </params>
-  </ns1:find_iteron>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_iteron.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_iteron.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_iteronResponse>
-   <result></result>
-  </ns1:find_iteronResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ori_ter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ori_ter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_ori_ter>
-   <sequence></sequence>
-   <params>
-    <window>0</window>
-    <purine>0</purine>
-    <filter>0</filter>
-    <keto>0</keto>
-   </params>
-  </ns1:find_ori_ter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ori_ter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ori_ter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_ori_terResponse>
-   <result></result>
-  </ns1:find_ori_terResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_pattern.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_pattern.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_pattern>
-   <sequence></sequence>
-   <pattern></pattern>
-   <params>
-    <output></output>
-   </params>
-  </ns1:find_pattern>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_pattern.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_pattern.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_patternResponse>
-   <result></result>
-  </ns1:find_patternResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_ter>
-   <sequence></sequence>
-   <params>
->
-   </params>
-  </ns1:find_ter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.find_ter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:find_terResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:find_terResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.fop.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.fop.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:fop>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <output></output>
-    <tag></tag>
-   </params>
-  </ns1:fop>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.fop.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.fop.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:fopResponse>
-   <result></result>
-  </ns1:fopResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.gcsi.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.gcsi.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:gcsi>
-   <sequence></sequence>
-   <params>
-    <p>0</p>
-    <window>0</window>
-    <version>0</version>
-    <purine>0</purine>
-    <at>0</at>
-    <keto>0</keto>
-   </params>
-  </ns1:gcsi>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.gcsi.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.gcsi.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:gcsiResponse>
-   <result></result>
-  </ns1:gcsiResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.gcskew.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.gcskew.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:gcskew>
-   <sequence></sequence>
-   <params>
-    <window>0</window>
-    <slide>0</slide>
-    <cumulative>0</cumulative>
-    <at>0</at>
-    <purine>0</purine>
-    <keto>0</keto>
-    <output></output>
-   </params>
-  </ns1:gcskew>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.gcskew.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.gcskew.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:gcskewResponse>
-   <result></result>
-  </ns1:gcskewResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.gcwin.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.gcwin.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:gcwin>
-   <sequence></sequence>
-   <params>
-    <window>0</window>
-    <at>0</at>
-    <purine>0</purine>
-    <application></application>
-    <output></output>
-    <keto>0</keto>
-   </params>
-  </ns1:gcwin>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.gcwin.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.gcwin.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:gcwinResponse>
-   <result></result>
-  </ns1:gcwinResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genes_from_ori.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genes_from_ori.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genes_from_ori>
-   <sequence></sequence>
-   <direction></direction>
-   <params>
-    <window>0</window>
-    <purine>0</purine>
-    <output></output>
-    <keto>0</keto>
-   </params>
-  </ns1:genes_from_ori>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genes_from_ori.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genes_from_ori.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genes_from_oriResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:genes_from_oriResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.geneskew.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.geneskew.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:geneskew>
-   <sequence></sequence>
-   <params>
-    <window>0</window>
-    <slide>0</slide>
-    <cumulative>0</cumulative>
-    <base></base>
-    <gc3>0</gc3>
-    <output></output>
-   </params>
-  </ns1:geneskew>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.geneskew.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.geneskew.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:geneskewResponse>
-   <result></result>
-  </ns1:geneskewResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genome_map>
-   <sequence></sequence>
-   <params>
-    <window>0</window>
-    <name>0</name>
-    <output></output>
-    <amp>0.0</amp>
-   </params>
-  </ns1:genome_map>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genome_mapResponse>
-   <result></result>
-  </ns1:genome_mapResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map3.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map3.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genome_map3>
-   <sequence></sequence>
-   <params>
-    <width>0</width>
-    <datafilename></datafilename>
-    <gmap>0</gmap>
-    <output></output>
-    <height>0</height>
-   </params>
-  </ns1:genome_map3>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map3.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genome_map3.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genome_map3Response>
-   <result></result>
-  </ns1:genome_map3Response>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genomicskew.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genomicskew.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genomicskew>
-   <sequence></sequence>
-   <params>
-    <divide>0</divide>
-    <at>0</at>
-    <output></output>
-   </params>
-  </ns1:genomicskew>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.genomicskew.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.genomicskew.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:genomicskewResponse>
-   <result></result>
-  </ns1:genomicskewResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.grapher.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.grapher.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://10.6.10.21/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:grapher>
-   <array0 SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array0>
-   <array1 SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array1>
-  </ns1:grapher>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.grapher.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.grapher.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://10.6.10.21/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
- <ns1:grapherResponse>
- </ns1:grapherResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.help.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.help.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:help>
-   <keywords></keywords>
-  </ns1:help>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.help.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.help.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:helpResponse>
-   <result></result>
-  </ns1:helpResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.hydropathy.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.hydropathy.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:hydropathy>
-   <sequence></sequence>
-  </ns1:hydropathy>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.hydropathy.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.hydropathy.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:hydropathyResponse>
-   <result>0.0</result>
-  </ns1:hydropathyResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.icdi.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.icdi.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:icdi>
-   <sequence></sequence>
-   <params>
-    <translate>0</translate>
-    <id></id>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:icdi>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.icdi.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.icdi.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:icdiResponse>
-   <result></result>
-  </ns1:icdiResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.kmer_table.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.kmer_table.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:kmer_table>
-   <sequence></sequence>
-   <params>
-    <k>0</k>
-   </params>
-  </ns1:kmer_table>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.kmer_table.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.kmer_table.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:kmer_tableResponse>
-   <result></result>
-  </ns1:kmer_tableResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.lda_bias.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.lda_bias.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:lda_bias>
-   <sequence></sequence>
-   <params>
-    <variable></variable>
-    <coefficients>0</coefficients>
-   </params>
-  </ns1:lda_bias>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.lda_bias.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.lda_bias.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:lda_biasResponse>
-   <result></result>
-  </ns1:lda_biasResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.leading_strand.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.leading_strand.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:leading_strand>
-   <sequence></sequence>
-  </ns1:leading_strand>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.leading_strand.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.leading_strand.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:leading_strandResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:leading_strandResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.least_squares_fit.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.least_squares_fit.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:least_squares_fit>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:least_squares_fit>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.least_squares_fit.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.least_squares_fit.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:least_squares_fitResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:least_squares_fitResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.longest_ORF.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.longest_ORF.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:longest_ORF>
-   <sequence></sequence>
-  </ns1:longest_ORF>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.longest_ORF.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.longest_ORF.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:longest_ORFResponse>
-   <result></result>
-  </ns1:longest_ORFResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.max.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.max.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:max>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:max>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.max.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.max.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:maxResponse>
-   <result></result>
-  </ns1:maxResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.maxdex.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.maxdex.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:maxdex>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:maxdex>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.maxdex.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.maxdex.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:maxdexResponse>
-   <result></result>
-  </ns1:maxdexResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.mean.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.mean.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:mean>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:mean>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.mean.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.mean.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:meanResponse>
-   <result></result>
-  </ns1:meanResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.median.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.median.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:median>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:median>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.median.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.median.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:medianResponse>
-   <result></result>
-  </ns1:medianResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.min.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.min.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:min>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:min>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.min.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.min.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:minResponse>
-   <result></result>
-  </ns1:minResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.mindex.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.mindex.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:mindex>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:mindex>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.mindex.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.mindex.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:mindexResponse>
-   <result></result>
-  </ns1:mindexResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.molecular_weight.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.molecular_weight.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:molecular_weight>
-   <sequence></sequence>
-   <params>
-    <strand></strand>
-   </params>
-  </ns1:molecular_weight>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.molecular_weight.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.molecular_weight.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:molecular_weightResponse>
-   <result></result>
-  </ns1:molecular_weightResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.nsmap
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.nsmap Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,11 +0,0 @@
-
-#include "soapH.h"
-SOAP_NMAC struct Namespace namespaces[] =
-{
- {"SOAP-ENV", "http://schemas.xmlsoap.org/soap/envelope/", "http://www.w3.org/*/soap-envelope", NULL},
- {"SOAP-ENC", "http://schemas.xmlsoap.org/soap/encoding/", "http://www.w3.org/*/soap-encoding", NULL},
- {"xsi", "http://www.w3.org/2001/XMLSchema-instance", "http://www.w3.org/*/XMLSchema-instance", NULL},
- {"xsd", "http://www.w3.org/2001/XMLSchema", "http://www.w3.org/*/XMLSchema", NULL},
- {"ns1", "http://soap.g-language.org/GLANG", NULL, NULL},
- {NULL, NULL, NULL, NULL}
-};

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.nucleotide_periodicity.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.nucleotide_periodicity.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:nucleotide_periodicity>
-   <sequence></sequence>
-   <params>
-    <window>0</window>
-    <nucleotide></nucleotide>
-    <output></output>
-   </params>
-  </ns1:nucleotide_periodicity>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.nucleotide_periodicity.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.nucleotide_periodicity.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:nucleotide_periodicityResponse>
-   <result></result>
-  </ns1:nucleotide_periodicityResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_counter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_counter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:oligomer_counter>
-   <sequence></sequence>
-   <oligomer></oligomer>
-   <params>
-    <window>0</window>
-   </params>
-  </ns1:oligomer_counter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_counter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_counter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:oligomer_counterResponse>
-   <result></result>
-  </ns1:oligomer_counterResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_search.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_search.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:oligomer_search>
-   <sequence></sequence>
-   <oligomer></oligomer>
-   <params>
-    <return></return>
-   </params>
-  </ns1:oligomer_search>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_search.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.oligomer_search.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:oligomer_searchResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:oligomer_searchResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.over_lapping_finder.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.over_lapping_finder.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:over_lapping_finder>
-   <sequence></sequence>
-   <params>
-    <output></output>
-   </params>
-  </ns1:over_lapping_finder>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.over_lapping_finder.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.over_lapping_finder.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:over_lapping_finderResponse>
-   <result></result>
-  </ns1:over_lapping_finderResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.palindrome.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.palindrome.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:palindrome>
-   <sequence></sequence>
-   <params>
-    <gtmatch>0</gtmatch>
-    <output></output>
-    <loop>0</loop>
-    <shortest>0</shortest>
-   </params>
-  </ns1:palindrome>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.palindrome.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.palindrome.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:palindromeResponse>
-   <result></result>
-  </ns1:palindromeResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.peptide_mass.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.peptide_mass.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:peptide_mass>
-   <sequence></sequence>
-  </ns1:peptide_mass>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.peptide_mass.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.peptide_mass.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:peptide_massResponse>
-   <result></result>
-  </ns1:peptide_massResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.phx.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.phx.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:phx>
-   <sequence></sequence>
-   <params>
-    <usage></usage>
-    <translate>0</translate>
-    <output></output>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:phx>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.phx.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.phx.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:phxResponse>
-   <result></result>
-  </ns1:phxResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.plasmid_map.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.plasmid_map.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:plasmid_map>
-   <sequence></sequence>
-   <params>
-    <ptt></ptt>
-    <cgi>0</cgi>
-    <output></output>
-   </params>
-  </ns1:plasmid_map>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.plasmid_map.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.plasmid_map.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:plasmid_mapResponse>
-   <result></result>
-  </ns1:plasmid_mapResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.pubmed.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.pubmed.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://10.6.10.21/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
- <ns1:pubmed>
- </ns1:pubmed>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.pubmed.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.pubmed.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://10.6.10.21/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
- <ns1:pubmedResponse>
- </ns1:pubmedResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.query_arm.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.query_arm.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:query_arm>
-   <sequence></sequence>
-   <position>0</position>
-  </ns1:query_arm>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.query_arm.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.query_arm.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:query_armResponse>
-   <result></result>
-  </ns1:query_armResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.query_strand.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.query_strand.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:query_strand>
-   <sequence></sequence>
-   <position>0</position>
-   <params>
-    <direction></direction>
-   </params>
-  </ns1:query_strand>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.query_strand.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.query_strand.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:query_strandResponse>
-   <result></result>
-  </ns1:query_strandResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.rep_ori_ter.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.rep_ori_ter.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:rep_ori_ter>
-   <sequence></sequence>
-   <params>
-    <oriloc>0</oriloc>
-    <gcskew>0</gcskew>
-    <dif-threshold>0</dif-threshold>
-    <dbonly>0</dbonly>
-   </params>
-  </ns1:rep_ori_ter>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.rep_ori_ter.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.rep_ori_ter.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:rep_ori_terResponse>
-   <result></result>
-  </ns1:rep_ori_terResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.scs.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.scs.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:scs>
-   <sequence></sequence>
-   <params>
-    <id></id>
-    <translate>0</translate>
-    <del_key></del_key>
-    <tag></tag>
-   </params>
-  </ns1:scs>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.scs.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.scs.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:scsResponse>
-   <result></result>
-  </ns1:scsResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.seq2png.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.seq2png.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:seq2png>
-   <sequence></sequence>
-   <params>
-    <width>0</width>
-    <window>0</window>
-    <output></output>
-   </params>
-  </ns1:seq2png>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.seq2png.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.seq2png.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:seq2pngResponse>
-   <result></result>
-  </ns1:seq2pngResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.seqinfo.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.seqinfo.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:seqinfo>
-   <sequence></sequence>
-  </ns1:seqinfo>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.seqinfo.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.seqinfo.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:seqinfoResponse>
-   <result></result>
-  </ns1:seqinfoResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.shuffleseq.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.shuffleseq.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:shuffleseq>
-   <sequence></sequence>
-   <params>
-    <k>0</k>
-   </params>
-  </ns1:shuffleseq>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.shuffleseq.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.shuffleseq.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:shuffleseqResponse>
-   <result></result>
-  </ns1:shuffleseqResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.signature.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.signature.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:signature>
-   <sequence></sequence>
-   <params>
-    <wordlength>0</wordlength>
-    <bothstrand>0</bothstrand>
-    <oe>0</oe>
-    <seq></seq>
-    <memo></memo>
-    <header>0</header>
-   </params>
-  </ns1:signature>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.signature.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.signature.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:signatureResponse>
-   <result></result>
-  </ns1:signatureResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.splitprintseq.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.splitprintseq.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:splitprintseq>
-   <sequence></sequence>
-  </ns1:splitprintseq>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.splitprintseq.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.splitprintseq.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:splitprintseqResponse>
-   <result></result>
-  </ns1:splitprintseqResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.standard_deviation.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.standard_deviation.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:standard_deviation>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:standard_deviation>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.standard_deviation.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.standard_deviation.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:standard_deviationResponse>
-   <result></result>
-  </ns1:standard_deviationResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.sum.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.sum.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:sum>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:sum>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.sum.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.sum.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:sumResponse>
-   <result></result>
-  </ns1:sumResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.to_fasta.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.to_fasta.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:to_fasta>
-   <sequence></sequence>
-   <params>
-    <length>0</length>
-    <name></name>
-    <output></output>
-   </params>
-  </ns1:to_fasta>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.to_fasta.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.to_fasta.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:to_fastaResponse>
-   <result></result>
-  </ns1:to_fastaResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.togoWS.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.togoWS.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:togoWS>
-   <query></query>
-   <params>
-    <search></search>
-    <db></db>
-    <format></format>
-    <field></field>
-   </params>
-  </ns1:togoWS>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.togoWS.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.togoWS.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:togoWSResponse>
-   <result></result>
-  </ns1:togoWSResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.translate.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.translate.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:translate>
-   <sequence></sequence>
-  </ns1:translate>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.translate.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.translate.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:translateResponse>
-   <result></result>
-  </ns1:translateResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.ttest.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.ttest.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:ttest>
-   <array1 SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array1>
-   <array2 SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array2>
-   <params>
-    <paired>0</paired>
-   </params>
-  </ns1:ttest>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.ttest.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.ttest.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:ttestResponse>
-   <result SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </result>
-  </ns1:ttestResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.variance.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.variance.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:variance>
-   <array SOAP-ENC:arrayType="xsd:string[1]">
-    <item></item>
-
-    <item></item>
-   </array>
-  </ns1:variance>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.variance.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.variance.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:varianceResponse>
-   <result></result>
-  </ns1:varianceResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.view_cds.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.view_cds.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:view_cds>
-   <sequence></sequence>
-   <params>
-    <length>0</length>
-    <gap>0</gap>
-    <output></output>
-   </params>
-  </ns1:view_cds>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.view_cds.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.view_cds.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:view_cdsResponse>
-   <result></result>
-  </ns1:view_cdsResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.w_value.req.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.w_value.req.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:w_value>
-   <sequence></sequence>
-   <params>
-    <include></include>
-    <output></output>
-    <exclude></exclude>
-    <tag></tag>
-   </params>
-  </ns1:w_value>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/GLANGSoapBinding.w_value.res.xml
--- a/GEMBASSY-1.0.3/include/GLANGSoapBinding.w_value.res.xml Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<SOAP-ENV:Envelope
- xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
- xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:ns1="http://soap.g-language.org/GLANG">
- <SOAP-ENV:Body SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
-  <ns1:w_valueResponse>
-   <result></result>
-  </ns1:w_valueResponse>
- </SOAP-ENV:Body>
-</SOAP-ENV:Envelope>

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/Makefile
--- a/GEMBASSY-1.0.3/include/Makefile Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,645 +0,0 @@\n-# Makefile.in generated by automake 1.13.1 from Makefile.am.\n-# include/Makefile. Generated from Makefile.in by configure.\n-\n-# Copyright (C) 1994-2012 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-\n-\n-\n-am__make_dryrun = \\\n- { \\\n- am__dry=no; \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- echo \'am--echo: ; @echo "AM" OK\' | $(MAKE) -f - 2>/dev/null \\\n- | grep \'^AM OK$$\' >/dev/null || am__dry=yes;; \\\n- *) \\\n- for am__flg in $$MAKEFLAGS; do \\\n- case $$am__flg in \\\n- *=*|--*) ;; \\\n- *n*) am__dry=yes; break;; \\\n- esac; \\\n- done;; \\\n- esac; \\\n- test $$am__dry = yes; \\\n- }\n-pkgdatadir = $(datadir)/GEMBASSY\n-pkgincludedir = $(includedir)/GEMBASSY\n-pkglibdir = $(libdir)/GEMBASSY\n-pkglibexecdir = $(libexecdir)/GEMBASSY\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = x86_64-apple-darwin12.3.0\n-host_triplet = x86_64-apple-darwin12.3.0\n-subdir = include\n-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \\\n-\t$(top_srcdir)/depcomp\n-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4\n-am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \\\n-\t$(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \\\n-\t$(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \\\n-\t$(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \\\n-\t$(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \\\n-\t$(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/m4/mysql.m4 \\\n-\t$(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \\\n-\t$(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.ac\n-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \\\n-\t$(ACLOCAL_M4)\n-mkinstalldirs = $(install_sh) -d\n-CONFIG_HEADER = $(top_builddir)/src/config.h\n-CONFIG_CLEAN_FILES =\n-CONFIG_CLEAN_VPATH_FILES =\n-LIBRARIES = $(noinst_LIBRARIES)\n-ARFLAGS = cru\n-AM_V_AR = $(am__v_AR_$(V))\n-am__v_AR_ = $(am__v_AR_$(AM_DEFAULT_VERBOSITY))\n-am__v_AR_0 = @echo " AR " $@;\n-am__v_AR_1 = \n-libgfile_a_AR = $(AR) $(ARFLAGS)\n-libgfile_a_LIBADD =\n-am_libgfile_a_OBJECTS = gfile.$(OBJEXT)\n-libgfile_a_OBJECTS = $(am_libgfile_a_OBJECTS)\n-libghttp_a_AR = $(AR) $(ARFLAGS)\n-libghttp_a_LIBADD =\n-am_libghttp_a_OBJECTS = ghttp.$(OBJEXT)\n-libghttp_a_OBJECTS = $(am_libghttp_a_OBJECTS)\n-libgplot_a_AR = $(AR) $(ARFLAGS)\n-libgplot_a_LIBADD =\n-am_libgplot_a_OBJECTS = gplot.$(OBJEXT)\n-libgplot_a_OBJECTS = $(am_libgplot_a_OBJECTS)\n-libgpost_a_AR = $(AR) $(ARFLAGS)\n-libgpost_a_LIBADD =\n-am_libgpost_a_OBJECTS = gpost.$(OBJEXT)\n-libgpost_a_OBJECTS = $(am_libgpost_a_OBJECTS)\n-AM_V_P = $(am__v_P_$(V))\n-am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))\n-am__v_P_0 = false\n-am__v_P_1 = :\n-AM_V_GEN = $(am__v_GEN_$(V))\n-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))\n-am__v_GEN_0 = @echo " GEN " $@;\n-am__v_GEN_1 = \n-AM_V_at = $(am__v_at_$(V))\n-am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))\n-am__v_at_0 = @\n-am__v_at_1 = \n-DEFAULT_INCLUDES = -I. -I$(top_builddir)/src\n-depcomp = $(SHELL) $(top_srcdir)/depcomp\n-am__depfiles_maybe = depfiles\n-am__mv = mv -f\n-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \\\n-\t$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)\n-AM_V_lt = $(am__v_lt_$(V))\n-am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))\n-am__v_lt_0 = --silent\n-am__v_lt_1 = \n-LTCOMPILE'..b'^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \\\n-\tcase $$dist_files in \\\n-\t */*) $(MKDIR_P) `echo "$$dist_files" | \\\n-\t\t\t sed \'/\\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,\' | \\\n-\t\t\t sort -u` ;; \\\n-\tesac; \\\n-\tfor file in $$dist_files; do \\\n-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(LIBRARIES)\n-installdirs:\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-generic clean-libtool clean-noinstLIBRARIES \\\n-\tmostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-tags\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am:\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic \\\n-\tmostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am:\n-\n-.MAKE: install-am install-strip\n-\n-.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \\\n-\tclean-libtool clean-noinstLIBRARIES cscopelist-am ctags \\\n-\tctags-am distclean distclean-compile distclean-generic \\\n-\tdistclean-libtool distclean-tags distdir dvi dvi-am html \\\n-\thtml-am info info-am install install-am install-data \\\n-\tinstall-data-am install-dvi install-dvi-am install-exec \\\n-\tinstall-exec-am install-html install-html-am install-info \\\n-\tinstall-info-am install-man install-pdf install-pdf-am \\\n-\tinstall-ps install-ps-am install-strip installcheck \\\n-\tinstallcheck-am installdirs maintainer-clean \\\n-\tmaintainer-clean-generic mostlyclean mostlyclean-compile \\\n-\tmostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \\\n-\ttags tags-am uninstall uninstall-am\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gae.h
--- a/GEMBASSY-1.0.3/include/gae.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b"@@ -1,6762 +0,0 @@\n-/* gae.h\n- Generated by wsdl2h 2.8.6 from http://soap.g-language.org/g-language.wsdl and typemap.dat\n- 2013-04-04 13:42:50 GMT\n-\n- DO NOT INCLUDE THIS FILE DIRECTLY INTO YOUR PROJECT BUILDS\n- USE THE soapcpp2-GENERATED SOURCE CODE FILES FOR YOUR PROJECT BUILDS\n-\n- gSOAP XML Web services tools.\n- Copyright (C) 2001-2010 Robert van Engelen, Genivia Inc. All Rights Reserved.\n- Part of this software is released under one of the following licenses:\n- GPL or Genivia's license for commercial use.\n-*/\n-\n-/** @page page_notes Usage Notes\n-\n-NOTE:\n-\n- - Run soapcpp2 on gae.h to generate the SOAP/XML processing logic.\n- Use soapcpp2 option -I to specify paths for #import\n- To build with STL, 'stlvector.h' is imported from 'import' dir in package.\n- Use soapcpp2 option -i to generate improved proxy and server classes.\n- - Use wsdl2h options -c and -s to generate pure C code or C++ code without STL.\n- - Use 'typemap.dat' to control namespace bindings and type mappings.\n- It is strongly recommended to customize the names of the namespace prefixes\n- generated by wsdl2h. To do so, modify the prefix bindings in the Namespaces\n- section below and add the modified lines to 'typemap.dat' to rerun wsdl2h.\n- - Use Doxygen (www.doxygen.org) on this file to generate documentation.\n- - Use wsdl2h options -nname and -Nname to globally rename the prefix 'ns'.\n- - Use wsdl2h option -d to enable DOM support for xsd:anyType.\n- - Use wsdl2h option -g to auto-generate readers and writers for root elements.\n- - Struct/class members serialized as XML attributes are annotated with a '@'.\n- - Struct/class members that have a special role are annotated with a '$'.\n-\n-WARNING:\n-\n- DO NOT INCLUDE THIS FILE DIRECTLY INTO YOUR PROJECT BUILDS.\n- USE THE SOURCE CODE FILES GENERATED BY soapcpp2 FOR YOUR PROJECT BUILDS:\n- THE soapStub.h FILE CONTAINS THIS CONTENT WITHOUT ANNOTATIONS.\n-\n-LICENSE:\n-\n-@verbatim\n---------------------------------------------------------------------------------\n-gSOAP XML Web services tools\n-Copyright (C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-\n-This software is released under one of the following two licenses:\n-1) GPL or 2) Genivia's license for commercial use.\n---------------------------------------------------------------------------------\n-1) GPL license.\n-\n-This program is free software; you can redistribute it and/or modify it under\n-the terms of the GNU General Public License as published by the Free Software\n-Foundation; either version 2 of the License, or (at your option) any later\n-version.\n-\n-This program is distributed in the hope that it will be useful, but WITHOUT ANY\n-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-PARTICULAR PURPOSE. See the GNU General Public License for more details.\n-\n-You should have received a copy of the GNU General Public License along with\n-this program; if not, write to the Free Software Foundation, Inc., 59 Temple\n-Place, Suite 330, Boston, MA 02111-1307 USA\n-\n-Author contact information:\n-engelen@genivia.com / engelen@acm.org\n-\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n---------------------------------------------------------------------------------\n-2) A commercial-use license is available from Genivia, Inc., contact@genivia.com\n---------------------------------------------------------------------------------\n-@endverbatim\n-\n-*/\n-\n-\n-//gsoapopt cw\n-\n-/******************************************************************************\\\n- * *\n- * Definitions *\n- * http://soap.g-language.org/GLANG *\n- * *\n-\\****************************************************"..b' *_result\t///< Response parameter\n-);\n-\n-/******************************************************************************\\\n- * *\n- * Service Operation *\n- * ns1__hydropathy *\n- * *\n-\\******************************************************************************/\n-\n-\n-/// Operation "ns1__hydropathy" of service binding "GLANGSoapBinding"\n-\n-/**\n-\n-Operation details:\n-\n-\n- - SOAP RPC encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"\n-\n- - SOAP action: "http://soap.g-language.org/GLANG#hydropathy"\n-\n- - Addressing action: "http://soap.g-language.org/GLANG/GLANG/hydropathyRequest"\n-\n- - Addressing response action: "http://soap.g-language.org/GLANG/GLANG/hydropathyResponse"\n-\n-C stub function (defined in soapClient.c[pp] generated by soapcpp2):\n-@code\n- int soap_call_ns1__hydropathy(\n- struct soap *soap,\n- NULL, // char *endpoint = NULL selects default endpoint for this operation\n- NULL, // char *action = NULL selects default action for this operation\n- // request parameters:\n- char* sequence,\n- // response parameters:\n- float *_result\n- );\n-@endcode\n-\n-C server function (called from the service dispatcher defined in soapServer.c[pp]):\n-@code\n- int ns1__hydropathy(\n- struct soap *soap,\n- // request parameters:\n- char* sequence,\n- // response parameters:\n- float *_result\n- );\n-@endcode\n-\n-*/\n-\n-//gsoap ns1 service method-style:\thydropathy rpc\n-//gsoap ns1 service method-encoding:\thydropathy http://schemas.xmlsoap.org/soap/encoding/\n-//gsoap ns1 service method-action:\thydropathy http://soap.g-language.org/GLANG#hydropathy\n-//gsoap ns1 service method-output-action:\thydropathy http://soap.g-language.org/GLANG/GLANG/hydropathyResponse\n-int ns1__hydropathy(\n- char* _sequence,\t///< Request parameter\n- float *_result\t///< Response parameter\n-);\n-\n-/******************************************************************************\\\n- * *\n- * XML Data Binding *\n- * *\n-\\******************************************************************************/\n-\n-\n-/**\n-\n-@page page_XMLDataBinding XML Data Binding\n-\n-SOAP/XML services use data bindings contractually bound by WSDL and auto-\n-generated by wsdl2h and soapcpp2 (see Service Bindings). Plain data bindings\n-are adopted from XML schemas as part of the WSDL types section or when running\n-wsdl2h on a set of schemas to produce non-SOAP-based XML data bindings.\n-\n-The following readers and writers are C/C++ data type (de)serializers auto-\n-generated by wsdl2h and soapcpp2. Run soapcpp2 on this file to generate the\n-(de)serialization code, which is stored in soapC.c[pp]. Include "soapH.h" in\n-your code to import these data type and function declarations. Only use the\n-soapcpp2-generated files in your project build. Do not include the wsdl2h-\n-generated .h file in your code.\n-\n-XML content can be retrieved from:\n- - a file descriptor, using soap->recvfd = fd\n- - a socket, using soap->socket = ...\n- - a C++ stream, using soap->is = ...\n- - a buffer, using the soap->frecv() callback\n-\n-XML content can be stored to:\n- - a file descriptor, using soap->sendfd = fd\n- - a socket, using soap->socket = ...\n- - a C++ stream, using soap->os = ...\n- - a buffer, using the soap->fsend() callback\n-\n-\n-@section ns1 Top-level root elements of schema "http://soap.g-language.org/GLANG"\n-\n-*/\n-\n-/* End of gae.h */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gfile.c
--- a/GEMBASSY-1.0.3/include/gfile.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,430 +0,0 @@\n-/******************************************************************************\n-** @source GEMBASSY file routines\n-**\n-** @version 1.0\n-** @modified December 27 2012 Hidetoshi Itaya Created this file\n-** @@\n-**\n-** This library is free software; you can redistribute it and/or\n-** modify it under the terms of the GNU Library General Public\n-** License as published by the Free Software Foundation; either\n-** version 2 of the License, or (at your option) any later version.\n-**\n-** This library is distributed in the hope that it will be useful,\n-** but WITHOUT ANY WARRANTY; without even the implied warranty of\n-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n-** Library General Public License for more details.\n-**\n-** You should have received a copy of the GNU Library General Public\n-** License along with this library; if not, write to the\n-** Free Software Foundation, Inc., 59 Temple Place - Suite 330,\n-** Boston, MA 02111-1307, USA.\n-******************************************************************************/\n-\n-#include "gfile.h"\n-\n-\n-\n-\n-/* @func gValID ***************************************************************\n-**\n-** Checks if an input string is a valid ID\n-**\n-** @param id [r] [AjPStr] ID to check\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-ajint gValID(AjPStr id){\n- AjPFilebuff buff = NULL;\n- AjPStr url = NULL;\n- AjPStr line = NULL;\n- AjPRegexp pval = NULL;\n-\n- url = ajStrNewC("http://web.sfc.keio.ac.jp/~t11080hi/valID/valID.cgi?id=");\n- url = ajStrNew();\n- ajFmtPrintS(&url, "http://rest.g-language.org/%S", id);\n-\n- //ajStrAppendS(&url, id);\n-\n- if(!gFilebuffURLS(url, &buff)) {\n- return ajFalse;\n- }\n-\n- return ajTrue;\n-\n- ajBuffreadLine(buff, &line);\n-\n- pval = ajRegCompC("^0");\n-\n- if(ajRegExec(pval, line))\n- return ajFalse;\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gStrAppendURLS *******************************************************\n-**\n-** Downloads file from a specified URL and writes to given output file\n-**\n-** @param [r] url [AjPStr] URL to download file from\n-** @param [r] string [AjPStr] String to write into\n-** @return [AjBool] \n-** @@\n-******************************************************************************/\n-\n-AjBool gStrAppendURLS(AjPStr url, AjPStr* string){\n- AjPFilebuff buff = NULL;\n- AjPStr file = NULL;\n- AjPStr line = NULL;\n-\n- if(!*string)\n- *string = ajStrNew();\n-\n- if(!gFilebuffURLS(url, &buff))\n- return ajFalse;\n-\n- while(ajBuffreadLine(buff, &line)){\n- ajStrAppendS(string, line);\n- }\n-\n- ajFilebuffDel(&buff);\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gStrAppendURLC *******************************************************\n-**\n-** Downloads file from a specified URL and writes to given output file\n-**\n-** @param [r] url [char*] URL to download file from\n-** @param [r] string [AjPStr] String to write into\n-** @return [AjBool] \n-** @@\n-******************************************************************************/\n-\n-AjBool gStrAppendURLC(char* url, AjPStr* string){\n- if(!gStrAppendURLS(ajStrNewC(url), string))\n- {\n- return ajFalse;\n- }\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gFileOutURLS *********************************************************\n-**\n-** Downloads file from a specified URL and writes to given output file\n-**\n-** @param [r] url [AjPStr] URL to download file from\n-** @param [r] outf [AjPFile] File object to write into\n-** @return [AjBool] \n-** @@\n-******************************************************************************/\n-\n-AjBool gFileOutURLS(AjPStr url, AjPFile* outf){\n- AjPFilebuff buff = NULL;\n- AjPStr file = NULL;\n- AjPStr line = NULL;\n-\n- if(!gFilebuffURLS(url, &buff))\n- return ajFalse;\n-\n- while(ajBuffreadLine(buff, &line)){\n- ajWriteline(*outf, line);\n- }\n-\n- ajFilebuffDel(&buff);\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gFileOutURLC ***************************'..b'*\n-** Creates a genbank format string with sequence and features\n-**\n-** @param [r] seq [AjPSeq] Sequence object to write\n-** @param [r] inseq [AjPStr] String to write to\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-AjBool gFormatGenbank(AjPSeq seq, AjPStr *inseq){\n- AjPSeqout seqout = NULL;\n- AjPFeattabOut featout = NULL;\n- AjPFeattable feat = NULL;\n- AjPStr seqline = NULL;\n- AjPStr featline = NULL;\n- AjPFile seqfile = NULL;\n- AjPFile featfile = NULL;\n- AjPStr filename = NULL;\n- AjBool hasfeats = ajTrue;\n-\n- gAssignUniqueName(&filename);\n- feat = ajSeqGetFeatCopy(seq);\n-\n- if(!feat) {\n- hasfeats = ajFalse;\n- }\n-\n- seqout = ajSeqoutNew();\n-\n- if(!ajSeqoutOpenFilename(seqout,filename))\n- embExitBad();\n-\n- ajSeqoutSetFormatS(seqout,ajStrNewC("genbank"));\n- ajSeqoutWriteSeq(seqout,seq);\n- ajSeqoutClose(seqout);\n- ajSeqoutDel(&seqout);\n-\n- seqfile = ajFileNewInNameS(filename);\n- ajSysFileUnlinkS(filename);\n-\n- if(hasfeats) {\n- featout = ajFeattabOutNew();\n-\n- if(!ajFeattabOutOpen(featout,filename))\n- return ajFalse;\n-\n- ajFeattableWriteGenbank(featout,feat);\n-\n- ajFeattableDel(&feat);\n- //ajFeattabOutDel(&featout);\n- ajFileClose(&(featout->Handle));\n-\n- featfile = ajFileNewInNameS(filename);\n- ajSysFileUnlinkS(filename);\n- }\n-\n- while(ajReadline(seqfile,&seqline)){\n- if(hasfeats && ajStrMatchC(seqline,"ORIGIN\\n")){\n- while(ajReadline(featfile,&featline)){\n- ajStrAppendS(inseq, featline);\n- }\n- }\n- ajStrAppendS(inseq, seqline);\n- }\n-\n- ajStrDel(&seqline);\n- ajStrDel(&featline);\n- ajStrDel(&filename);\n- ajFileClose(&seqfile);\n- ajFileClose(&featfile);\n-\n- return hasfeats;\n-}\n-\n-\n-\n-\n-/* @func gGetFileContent ******************************************************\n-**\n-** Reads file content and sets it to string pointer\n-**\n-** @param [r] content [AjPSeq] String to write to\n-** @param [r] filename [AjPSeq] Filename to open\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-AjBool gGetFileContent(AjPStr* content, AjPStr filename){\n- AjPFile file = NULL;\n- AjPStr line = NULL;\n-\n- if((file = ajFileNewInNameS(filename)) == NULL)\n- return ajFalse;\n-\n- while(ajReadline(file, &line))\n- ajStrAppendS(content, line);\n-\n- if(file)\n- ajFileClose(&file);\n-\n- ajSysFileUnlinkS(filename);\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gtaiFileOutURLS ******************************************************\n-**\n-** Downloads file from a specified URL and inputs in file buffer\n-**\n-** @param [r] url [AjPStr] URL to download file from\n-** @param [r] buff [AjPFilebuff] File buffer to set\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-AjBool gtaiFileOutURLS(AjPStr url, AjPFile* outf, AjBool tai){\n- if(tai)\n- {\n- CURL *curl;\n- CURLcode curl_res;\n-\n- Memory *mem = malloc(sizeof(Memory*));\n-\n- mem->size = 0;\n- mem->memory = NULL;\n-\n- curl_global_init(CURL_GLOBAL_ALL);\n-\n- curl = curl_easy_init();\n-\n- if(curl)\n- {\n- curl_easy_setopt(curl, CURLOPT_URL, ajCharNewS(url));\n- curl_easy_setopt(curl, CURLOPT_FOLLOWLOCATION, 1);\n- curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, curl_write);\n- curl_easy_setopt(curl, CURLOPT_WRITEDATA, mem);\n- }\n-\n- curl_res = curl_easy_perform(curl);\n-\n- if(CURLE_OK == curl_res)\n- {\n- char* redir;\n- curl_res = curl_easy_getinfo(curl, CURLINFO_EFFECTIVE_URL, &redir);\n-\n- if((CURLE_OK == curl_res) && redir) {\n- ajStrAssignC(&url, redir);\n- ajStrExchangeCC(&url, "cai.csv", "tai.csv");\n- }\n- }\n-\n- free(mem);\n- curl_easy_cleanup(curl);\n- curl_global_cleanup();\n- }\n-\n- return gFileOutURLS(url, outf);\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gfile.h
--- a/GEMBASSY-1.0.3/include/gfile.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,25 +0,0 @@
-#ifndef gfile_h
-#define gfile_h
-
-#include "emboss.h"
-#include "curl/curl.h"
-#include "curl/easy.h"
-
-#include "gpost.h"
-
-/*
-** Prototype definitions
-*/
-
-AjBool gValID(AjPStr id);
-AjBool gStrAppendURLS(AjPStr url, AjPStr* string);
-AjBool gStrAppendURLC(char* url, AjPStr* string);
-AjBool gFileOutURLS(AjPStr url, AjPFile* outf);
-AjBool gFileOutURLC(char* url, AjPFile* outf);
-AjBool gFilebuffURLS(AjPStr url, AjPFilebuff* buff);
-AjBool gFilebuffURLC(char* url, AjPFilebuff* buff);
-AjBool gFormatGenbank(AjPSeq seq, AjPStr *str);
-void gAssignUniqueName(AjPStr *string);
-AjPStr gCreateUniqueName();
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/ghttp.c
--- a/GEMBASSY-1.0.3/include/ghttp.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,378 +0,0 @@\n-/******************************************************************************\n-** @source GEMBASSY http routines\n-**\n-** @version 1.0\n-** @modified December 27 2012 Hidetoshi Itaya Created this file\n-** @@\n-**\n-** This library is free software; you can redistribute it and/or\n-** modify it under the terms of the GNU Library General Public\n-** License as published by the Free Software Foundation; either\n-** version 2 of the License, or (at your option) any later version.\n-**\n-** This library is distributed in the hope that it will be useful,\n-** but WITHOUT ANY WARRANTY; without even the implied warranty of\n-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n-** Library General Public License for more details.\n-**\n-** You should have received a copy of the GNU Library General Public\n-** License along with this library; if not, write to the\n-** Free Software Foundation, Inc., 59 Temple Place - Suite 330,\n-** Boston, MA 02111-1307, USA.\n-******************************************************************************/\n-\n-#include "ghttp.h"\n-\n-\n-\n-\n-/* @func gHttpConvertS ********************************************************\n-**\n-** Converts result image to specified format\n-**\n-** @param [r] url [AjPStr] URL to lookup\n-** @param [r] outf [AjPFile*] File to write to\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-AjBool gHttpConvertS(AjPStr url, AjPFile* outf, AjPStr informat, AjPStr outformat)\n-{\n- AjPRegexp regexp = NULL;\n- AjPStr jobid = NULL;\n- AjPStr convert = NULL;\n-\n- regexp = ajRegCompC("^.+jobid=");\n-\n- if(!ajRegExec(regexp, url))\n- {\n- return ajFalse;\n- }\n-\n- if(!ajRegPost(regexp, &jobid))\n- {\n- return ajFalse;\n- }\n-\n- convert = ajFmtStr("http://soap.g-language.org/WS/convert.cgi?"\n- "jobid=%S&informat=%S&outformat=%S",\n- jobid, informat, outformat);\n-\n- if(!gHttpGetBinS(convert, outf)) {\n- return ajFalse;\n- }\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gHttpConvertC ********************************************************\n-**\n-** Converts result image to specified format\n-**\n-** @param [r] url [AjPStr] URL to lookup\n-** @param [r] outf [AjPFile*] File to write to\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-AjBool gHttpConvertC(char* url, AjPFile* outf, AjPStr informat, AjPStr outformat)\n-{\n- return gHttpConvertS(ajStrNewC(url), outf, informat, outformat);\n-}\n-\n-\n-\n-\n-/* @func gHttpGetBinS *********************************************************\n-**\n-** Writes out remote binary file to AjPFile\n-**\n-** @param [r] url [AjPStr] URL to lookup\n-** @param [r] outf [AjPFile*] File to write to\n-** @return [AjBool]\n-** @@\n-******************************************************************************/\n-\n-AjBool gHttpGetBinS(AjPStr url, AjPFile* outf)\n-{\n- AjPFile file = NULL;\n- AjPStr line = NULL;\n- AjPStr host = NULL;\n- AjPStr path = NULL;\n- AjPStr get = NULL;\n- ajint port = 80;\n- ajuint http = 0;\n- FILE *fp;\n-\n- AjPRegexp crlf = NULL;\n-\n- char buf[8];\n-\n- AjOSysSocket sock;\n-\n- get = ajStrNew();\n-\n- ajHttpUrlDeconstruct(url, &port, &host, &path);\n-\n- while(file==NULL || gHttpRedirect(file, &host, &port, &path))\n- {\n- if(ajStrGetCharFirst(path) != \'/\')\n-\tajStrInsertK(&path, 0, \'/\');\n-\n- ajFmtPrintS(&get, "GET http://%S:%d%S HTTP/1.1\\r\\n", host, port, path);\n-\n- fp = ajHttpOpen(NULL, host, port, get, &sock);\n-\n- file = ajFileNewFromCfile(fp);\n-\n- if(!file)\n-\treturn ajFalse;\n- }\n-\n- ajStrDel(&get);\n-\n- crlf = ajRegCompC("^\\r?\\n$");\n-\n- while(ajReadline(file, &line))\n- {\n- if(ajRegExec(crlf, line))\n-\tbreak;\n- }\n-\n- while(ajReadbinBinary(file, 1, 1, buf))\n- {\n- ajWritebinBinary(*outf, 1, 1, buf);\n- }\n-\n- ajFileClose(outf);\n- ajFileClose(&file);\n-\n- return ajTrue;\n-}\n-\n-\n-\n-\n-/* @func gHttpGetBinC ************'..b'\n- post = ajStrNew();\n- body = ajStrNew();\n- cont = ajStrNew();\n-\n- file = ajFileNewInNameS(filename);\n-\n- while(ajReadline(file, &line))\n- {\n- ajStrAppendS(&cont, line);\n- }\n-\n- ajHttpUrlDeconstruct(url, &port, &host, &path);\n-\n- while(buff==NULL || ajHttpRedirect(buff, &host, &port, &path, &http))\n- {\n- if(ajStrGetCharFirst(path) != \'/\')\n-\tajStrInsertK(&path, 0, \'/\');\n-\n- ajFmtPrintS(\n- &body,\n- "--xYzZY\\015\\012"\n- "Content-Disposition: form-data; name=\\"file\\";"\n- " filename=\\"%S\\"\\015\\012"\n- "Content-Type: text/plain\\015\\012"\n- "%S\\015\\012"\n- "\\015\\012--xYzZY--\\015\\012",\n- filename, cont\n- );\n-\n- ajFmtPrintS(\n- &post,\n- "POST http://%S%S\\n"\n- "Content-Length: %d\\n"\n- "Content-Type: multipart/form-data; boundary=xYzZY\\n\\n"\n- "%S",\n- host, path,\n- ajStrGetLen(body), body\n- );\n-\n- ajFmtPrint("%S", post);\n-\n- fp = ajHttpOpen(NULL, host, port, post, &sock);\n-\n- buff = ajFilebuffNewFromCfile(fp);\n-\n- if(!buff)\n-\treturn NULL;\n- }\n-\n- ajStrDel(&post);\n-\n- timo.seconds = 180;\n- ajSysTimeoutSet(&timo);\n- ajFilebuffLoadAll(buff);\n- ajSysTimeoutUnset(&timo);\n-\n- return buff;\n-}\n-\n-\n-\n-\n-/* @func gHttpPostCS **********************************************************\n-**\n-** Retrives the C file pointer from a given URL\n-**\n-** @param [r] [char*] URL to lookup\n-** @return [FILE*]\n-** @@\n-******************************************************************************/\n-\n-AjPFilebuff gHttpPostFileCS(char* url, AjPStr filename)\n-{\n- AjPFilebuff buff = NULL;\n-\n- buff = gHttpPostFileSS(ajStrNewC(url), filename);\n-\n- if(!buff)\n- return NULL;\n-\n- return buff;\n-}\n-\n-\n-\n-\n-/* @func gHttpRedirect ********************************************************\n-**\n-** Reads the header of http response in given buffer buff,\n-** if it includes a redirection response updates the host, port and get\n-** parameters using the \'Location\' header\n-**\n-** @param [u] buff [FILE*] file pointer\n-** @param [w] host [AjPStr*] Host name\n-** @param [w] port [ajint*] Port\n-** @param [w] path [AjPStr*] part of URL after port number\n-** @return [AjBool] returns true if the header includes a redirection response\n-** @@\n-******************************************************************************/\n-\n-AjBool gHttpRedirect(AjPFile file, AjPStr* host, ajint* port, AjPStr* path)\n-{\n- AjPFilebuff buff = NULL;\n-\n- AjPRegexp httpexp = NULL;\n- AjPRegexp nullexp = NULL;\n- AjPRegexp redirexp = NULL;\n-\n- AjPStr codestr = NULL;\n- AjPStr newurl = NULL;\n- AjPStr newhost = NULL;\n- AjPStr currline = NULL;\n-\n- ajuint httpcode = 0;\n-\n- AjBool isheader = ajFalse;\n- AjBool ret = ajFalse;\n-\n- httpexp = ajRegCompC("^HTTP/\\\\S+\\\\s+(\\\\d+)");\n-\n- ajReadline(file, &currline);\n-\n- ajDebug("gHttpRedirect: First line: \'%S\'\\n", currline);\n-\n- if(ajRegExec(httpexp, currline))\n- {\n- isheader = ajTrue;\n- ajRegSubI(httpexp, 1, &codestr);\n- ajStrToUint(codestr, &httpcode);\n- ajDebug("Header: codestr \'%S\' code \'%u\'\\n", codestr, httpcode);\n- ajStrDel(&codestr);\n- }\n-\n- if(isheader)\n- {\n- if(httpcode == 301 || httpcode == 302 || httpcode==307)\n- {\n-\t redirexp = ajRegCompC("^Location: (\\\\S+)");\n-\t nullexp = ajRegCompC("^\\r?\\n?$");\n-\n-\t while( ajReadline(file, &currline) &&\n-\t\t !ajRegExec(nullexp, currline))\n- {\n-\t ajDebug("gHttpRedirect: header line: \'%S\'\\n", currline);\n-\n-\t if(ajRegExec(redirexp, currline))\n- {\n-\t\t ajRegSubI(redirexp, 1, &newurl);\n-\t\t ajHttpUrlDeconstruct(newurl, port, &newhost, path);\n-\n-\t\t if(ajStrGetLen(newhost))\n-\t\t ajStrAssignS(host, newhost);\n-\n-\t\t ajStrDel(&newurl);\n-\t\t ajStrDel(&newhost);\n-\t\t ret = ajTrue;\n-\t\t break;\n- }\n- }\n-\n-\t ajRegFree(&redirexp);\n-\t ajRegFree(&nullexp);\n- }\n- }\n-\n- ajRegFree(&httpexp);\n- ajStrDel(&currline);\n-\n- return ret;\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/ghttp.h
--- a/GEMBASSY-1.0.3/include/ghttp.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-#ifndef ghttp_h
-#define ghttp_h
-
-#include "emboss.h"
-
-/*
-** Prototype definitions
-*/
-
-AjBool gHttpConvertS(AjPStr url, AjPFile* outf, AjPStr informat, AjPStr outformat);
-AjBool gHttpConvertC(char* res, AjPFile* outf, AjPStr informat, AjPStr outformat);
-AjBool gHttpGetBinS(AjPStr url, AjPFile* outf);
-AjBool gHttpGetBinC(char* url, AjPFile* outf);
-AjPFilebuff gHttpPostFileSS(AjPStr url, AjPStr filename);
-AjPFilebuff gHttpPostFileCS(char* url, AjPStr filename);
-AjBool gHttpRedirect(AjPFile file, AjPStr* host, ajint* port, AjPStr* path);
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/glibs.h
--- a/GEMBASSY-1.0.3/include/glibs.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,11 +0,0 @@
-#ifndef GLIBS
-#define GLIBS
-#include "../include/gfile.h"
-#include "../include/gfile.c"
-#include "../include/ghttp.h"
-#include "../include/ghttp.c"
-#include "../include/gplot.h"
-#include "../include/gplot.c"
-#include "../include/gpost.h"
-#include "../include/gpost.c"
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gplot.c
--- a/GEMBASSY-1.0.3/include/gplot.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,314 +0,0 @@
-/******************************************************************************
-** @source GEMBASSY plot routines
-**
-** @version 1.0
-** @modified December 27 2012 Hidetoshi Itaya Created this file
-** @@
-**
-** This library is free software; you can redistribute it and/or
-** modify it under the terms of the GNU Library General Public
-** License as published by the Free Software Foundation; either
-** version 2 of the License, or (at your option) any later version.
-**
-** This library is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-** Library General Public License for more details.
-**
-** You should have received a copy of the GNU Library General Public
-** License along with this library; if not, write to the
-** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
-** Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-
-#include "gplot.h"
-
-
-
-
-/* @funclist gPlotFilebuff ****************************************************
-**
-** Retrieves data from file buffer and plots the data using gPlotData
-**
-******************************************************************************/
-
-AjBool gPlotFilebuff(AjPFilebuff buff, AjPGraph graphs, gPlotParams *gpp)
-{
-  AjPStr  line = NULL;
-  AjPPStr temp = NULL;
-  AjPPStr name = NULL;
-  ajint   i    = 0;
-  ajint   j    = 0;
-  ajint   col  = 0;
-  ajint   flag = 0;
-  float **data = NULL;
-
-  while(ajBuffreadLine(buff, &line))
-    {
-
-    /*
-    ** Allocate first time only
-    */
-
-    if(!col)
-      {
-      col = ajStrCalcCountC(line, ",") + 1;
-
-      if((temp = (AjPPStr)malloc(sizeof(AjPStr) * col)) == NULL)
- {
- return ajFalse;
-      }
-
-      if((name = (AjPPStr)malloc(sizeof(AjPStr) * col)) == NULL)
- {
-   AJFREE(temp);
-   return ajFalse;
- }
-
-      if((data = (float**)malloc(sizeof(float*) * col)) == NULL)
- {
-   AJFREE(temp);
-   AJFREE(name);
-   return ajFalse;
- }
-      for(i = 0; i < col; ++i)
- {
-   if((data[i] = (float*)malloc(sizeof(float))) == NULL){
-     {
-       AJFREE(temp);
-       AJFREE(name);
-       for(j = 0; j < i; ++j)
- {
-   AJFREE(data[j]);
- }
-       AJFREE(data);
-       return ajFalse;
-     }
-   }
- }
-      }
-
-    ajStrExchangeCC(&line, ",", "\n");
-    ajStrParseSplit(line, &temp);
-
-    for(i = 0; i < col; ++i)
-      {
-        if((data[i] = (float*)realloc(data[i], sizeof(float) * (j + 1))) == NULL)
-          {
-            AJFREE(temp);
-            AJFREE(name);
-            for(j = 0; j < i; ++j)
-              {
-                AJFREE(data[j]);
-              }
-            AJFREE(data);
-            return ajFalse;
-          }
-
-        ajStrRemoveLastNewline(&(temp[i]));
-        if(ajStrIsFloat(temp[i]))
-          {
-            ajStrToFloat(temp[i], &(data[i][j]));
-            ++flag;
-          }
-        else
-          {
-            name[i] = ajStrNewS(temp[i]);
-          }
-      }
-    j = flag ? j + 1 : j;
-    flag = 0;
-    }
-
-  (*gpp).data    = data;
-  (*gpp).setNum  = 0;
-  (*gpp).dataNum = j;
-  (*gpp).typeNum = col;
-  if(!(*gpp).names)
-    (*gpp).names = name;
-
-  if(j < 2)
-    gPlotFlip(gpp);
-
-  gPlotData(graphs, gpp);
-
-  for(i = 0; i < (*gpp).typeNum; ++i)
-    AJFREE((*gpp).data[i]);
-  AJFREE((*gpp).data);
-
-  data = NULL;
-
-  ajStrDel(&line);
-
-  return ajTrue;
-}
-
-
-
-
-/* @funclist gPlotData ********************************************************
-**
-** Function to plot from given data
-**
-******************************************************************************/
-
-AjBool gPlotData(AjPGraph graphs, gPlotParams *gpp)
-{
-  AjPGraphdata gd = NULL;
-
-  float min = 0.0;
-  float max = 0.0;
-  float dif = 0.0;
-  ajint i;
-  ajint j;
-
-  ajint   setNum  = (*gpp).setNum;
-  ajint   dataNum = (*gpp).dataNum;
-  ajint   typeNum = (*gpp).typeNum;
-  AjPStr  title   = (*gpp).title;
-  AjPStr  xlab    = (*gpp).xlab;
-  AjPStr  ylab    = (*gpp).ylab;
-  AjPPStr names   = (*gpp).names;
-  float **data    = (*gpp).data;
-
-  float x[dataNum];
-  float y[dataNum];
-  float begin = data[0][0];
-  float end   = data[0][dataNum-1];
-  float range = end - begin;
-
-  int c[] = {1,3,9,13};
-
-  for(i = 1; i < typeNum; ++i)
-    {
-    for(j = 0; j < dataNum; ++j)
-      {
-      min = (min < data[i][j]) ? min : data[i][j];
-      max = (max > data[i][j]) ? max : data[i][j];
-    }
-  }
-
-  dif = (min == max) ? 20 : max - min;
-  max += dif / 20;
-  min -= dif / 20;
-
-  for(i = 1; i < typeNum; ++i)
-    {
-    gd = ajGraphdataNewI(dataNum);
-
-    ajGraphdataSetColour(gd, c[i-1]);
-    ajGraphdataSetMinmax(gd, begin, end, min, max);
-    ajGraphdataSetTruescale(gd, begin, end, min, max);
-    ajGraphdataSetTypeC(gd, "Multi 2D Plot");
-
-    for(j = 0; j <  dataNum; ++j)
-      {
-      x[j] = data[0][j];
-      y[j] = data[i][j];
-    }
-
-    ajGraphdataAddXY(gd, x, y);
-    ajGraphDataAdd(graphs, gd);
-
-    if(typeNum > 2)
-      {
-      float len = 0.0;
-
-      for(j = 1; j < typeNum; ++j)
- len = (len < (float)ajStrGetLen(names[j])) ?
-   (float)ajStrGetLen(names[j]) : len;
-
-      ajGraphAddLine(graphs,
-      range * 7.4/8 + begin, dif * (8.6-i*0.3)/8 + min,
-      range * 7.8/8 + begin, dif * (8.6-i*0.3)/8 + min,
-      c[i-1]);
-      ajGraphAddTextScaleS(graphs,
-    range * (7.3/8 - len*1/144) + begin,
-    dif * (8.6-i*0.3)/8 + min,
-    0, 0.4,
-    names[i]);
-    }
-
-    gd = NULL;
-  }
-
-  ajGraphxySetXstartF(graphs, begin);
-  ajGraphxySetXendF(graphs, end);
-  ajGraphxySetYstartF(graphs, min - ((max - min) / 10));
-  ajGraphxySetYendF(graphs, max + ((max - min) / 10));
-
-  //ajGraphSetTitleS(graphs, title);
-  ajGraphSetXlabelS(graphs, xlab);
-  ajGraphSetYlabelS(graphs, ylab);
-  ajGraphxySetflagOverlay(graphs, ajTrue);
-
-  ajGraphxyDisplay(graphs, AJFALSE);
-  ajGraphicsClose();
-
-  return ajTrue;
-}
-
-
-
-
-/* @funclist gPlotFlip ********************************************************
-**
-** Function to flip x and y data
-**
-******************************************************************************/
-
-AjBool gPlotFlip(gPlotParams *gpp)
-{
-  ajint   setNum  = (*gpp).setNum;
-  ajint   dataNum = (*gpp).typeNum;
-  ajint   typeNum = (*gpp).dataNum;
-  float **data    = (*gpp).data;
-
-  float **newdata;
-  ajint i;
-  ajint j;
-
-  if((newdata = (float**)malloc(sizeof(float*) * typeNum)) == NULL)
-    return ajFalse;
-  else
-    for(i = 0; i < typeNum + 1; ++i)
-      if((newdata[i] = (float*)malloc(sizeof(float))) == NULL)
- {
-   AJFREE(newdata);
-   return ajFalse;
- }
-
-  for(i = 0; i < dataNum; ++i){
-    if((newdata[0] = (float*)realloc(newdata[0],
-      sizeof(float) * (i + 1))) == NULL)
-      {
- for(j = 0; j < i; ++j)
-     AJFREE(newdata[j]);
- AJFREE(newdata);
- return ajFalse;
-      }
-    if((newdata[1] = (float*)realloc(newdata[1],
-      sizeof(float) * (i + 1))) == NULL)
-      {
- for(j = 0; j < i; ++j)
-     AJFREE(newdata[j]);
- AJFREE(newdata);
- return ajFalse;
-      }
-    newdata[0][i] = i;
-    newdata[1][i] = data[i][0];
-  }
-
-  for(i = 0; i < dataNum; ++i)
-    {
-      AJFREE((*gpp).data[i]);
-    }
-  AJFREE((*gpp).data);
-
-  (*gpp).dataNum = dataNum;
-  (*gpp).typeNum = 2;
-  (*gpp).data    = newdata;
-
-  return ajTrue;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gplot.h
--- a/GEMBASSY-1.0.3/include/gplot.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,45 +0,0 @@
-#ifndef GPLOT_H
-#define GPLOT_H
-
-#include "emboss.h"
-
-/* @datastatic gPlotParams*****************************************************
-**
-** gPlot plotting parameters
-**
-** @attr data [float**] Data used to plot
-** @attr setNum [size_t] Number of data sets
-** @attr typeNum [size_t] Number of data types
-** @attr dataNum [size_t] Number of data in set
-** @attr height [ajint] Height of graph - To be supported
-** @attr width [ajint] Width of graph - To be supported
-** @attr title [AjPStr] Graph title
-** @attr xlab [AjPStr] Label for X axis
-** @attr ylab [AjPStr] Label for Y axis
-** @attr names [AjPPStr] name of each data type
-** @@
-******************************************************************************/
-
-typedef struct gPlotStruct
-{
-  float **data;
-  size_t  setNum;
-  size_t  typeNum;
-  size_t  dataNum;
-  /*ajint   width  Not supported yet! ;*/
-  /*ajint   height Not supported yet! ;*/
-  AjPStr  title;
-  AjPStr  xlab;
-  AjPStr  ylab;
-  AjPPStr names;
-} gPlotParams;
-
-/*
-** Prototype Definitions
-*/
-
-AjBool gPlotFilebuff(AjPFilebuff buff, AjPGraph graphs, gPlotParams *gpp);
-AjBool gPlotData(AjPGraph graphs, gPlotParams *gpp);
-AjBool gPlotFlip(gPlotParams *gpp);
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gpost.c
--- a/GEMBASSY-1.0.3/include/gpost.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,139 +0,0 @@
-/******************************************************************************
-** @source The last resort for POSTing
-**
-** @version 1.0
-** @modified December 27 2012 Hidetoshi Itaya Created this file
-** @@
-**
-** This library is free software; you can redistribute it and/or
-** modify it under the terms of the GNU Library General Public
-** License as published by the Free Software Foundation; either
-** version 2 of the License, or (at your option) any later version.
-**
-** This library is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-** Library General Public License for more details.
-**
-** You should have received a copy of the GNU Library General Public
-** License along with this library; if not, write to the
-** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
-** Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "gpost.h"
-
-
-
-
-/* @func gFilePostCC **********************************************************
-**
-** Posts the file to given url
-**
-** @param [r] [char*] URL to lookup
-** @return [AjPFile]
-** @@
-******************************************************************************/
-
-AjBool gFilePostCC(char* url, char* filename, AjPStr* string)
-{
-  CURL *curl;
-  CURLcode res;
-
-  struct curl_httppost *post = NULL;
-  struct curl_httppost *last = NULL;
-
-  Memory *mem = malloc(sizeof(Memory*));
-
-  mem->size = 0;
-  mem->memory = NULL;
-
-  curl = curl_easy_init();
-
-  if(curl)
-    {
-      curl_formadd(&post, &last,
-                   CURLFORM_COPYNAME, "file",
-                   CURLFORM_FILE, filename,
-                   CURLFORM_END);
-
-      curl_easy_setopt(curl, CURLOPT_URL, url);
-      curl_easy_setopt(curl, CURLOPT_HTTPPOST, post);
-      curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, curl_write);
-      curl_easy_setopt(curl, CURLOPT_WRITEDATA, mem);
-
-      res = curl_easy_perform(curl);
-
-      if(res)
-        {
-          return 0;
-        }
-
-      curl_formfree(post);
-    }
-  else
-    {
-      return 0;
-    }
-
-  curl_easy_cleanup(curl);
-
-  ajStrAssignC(string, mem->memory);
-
-  return 1;
-}
-
-size_t curl_write(void* ptr, size_t size, size_t nmemb, void* data)
-{
-  if(size * nmemb == 0)
-    return 0;
-
-  size_t realsize = size * nmemb;
-  Memory* mem = (Memory*)data;
-  mem->memory = (char*)realloc(mem->memory,mem->size + realsize + 1);
-  if(mem->memory){
-    memcpy(&(mem->memory[mem->size]),ptr,realsize);
-    mem->size += realsize;
-    mem->memory[mem->size] = 0;
-  }
-
-  return realsize;
-}
-
-
-
-/* @func gFilePostCS **********************************************************
-**
-** Posts the file to given url
-**
-** @param [r] [char*] URL to lookup
-** @return [AjPFile]
-** @@
-******************************************************************************/
-
-AjBool gFilePostCS(char* url, AjPStr filename, AjPStr* string)
-{
-  if(!gFilePostCC(url, ajCharNewS(filename), string))
-    return ajFalse;
-
-  return ajTrue;
-}
-
-
-
-/* @func gFilePostSS **********************************************************
-**
-** Posts the file to given url
-**
-** @param [r] [char*] URL to lookup
-** @return [AjPFile]
-** @@
-******************************************************************************/
-
-AjBool gFilePostSS(AjPStr url, AjPStr filename, AjPStr* string)
-{
-  if(!gFilePostCC(ajCharNewS(url), ajCharNewS(filename), string))
-    return ajFalse;
-
-  return ajTrue;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/gpost.h
--- a/GEMBASSY-1.0.3/include/gpost.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-#ifndef gpost_h
-#define gpost_h
-
-#include "emboss.h"
-#include "curl/curl.h"
-#include "curl/easy.h"
-
-typedef struct{
- char* memory;
- size_t size;
-} Memory;
-
-/*
-** Prototype definitions
-*/
-
-AjBool gFilePostCC(char* url, char* filename, AjPStr* string);
-AjBool gFilePostCS(char* url, AjPStr filename, AjPStr* string);
-AjBool gFilePostSS(AjPStr url, AjPStr filename, AjPStr* string);
-size_t curl_write(void *ptr, size_t size, size_t nmemb, void *stream);
-
-#endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapC.c
--- a/GEMBASSY-1.0.3/include/soapC.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,29909 +0,0 @@\n-/* soapC.c\n- Generated by gSOAP 2.8.6 from gae.h\n-\n-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-The generated code is released under one of the following licenses:\n-1) GPL or 2) Genivia\'s license for commercial use.\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n-*/\n-\n-#if defined(__BORLANDC__)\n-#pragma option push -w-8060\n-#pragma option push -w-8004\n-#endif\n-\n-#include "soapH.h"\n-\n-#ifdef __cplusplus\n-extern "C" {\n-#endif\n-\n-SOAP_SOURCE_STAMP("@(#) soapC.c ver 2.8.6 2013-04-04 13:42:58 GMT")\n-\n-\n-#ifndef WITH_NOGLOBAL\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap *soap)\n-{\n-\tif (soap->header)\n-\t\tsoap_serialize_SOAP_ENV__Header(soap, soap->header);\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap *soap)\n-{\n-\tif (soap->header)\n-\t{\tsoap->part = SOAP_IN_HEADER;\n-\t\tif (soap_out_SOAP_ENV__Header(soap, "SOAP-ENV:Header", 0, soap->header, NULL))\n-\t\t\treturn soap->error;\n-\t\tsoap->part = SOAP_END_HEADER;\n-\t}\n-\treturn SOAP_OK;\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap *soap)\n-{\n-\tsoap->part = SOAP_IN_HEADER;\n-\tsoap->header = soap_in_SOAP_ENV__Header(soap, "SOAP-ENV:Header", NULL, NULL);\n-\tsoap->part = SOAP_END_HEADER;\n-\treturn soap->header == NULL;\n-}\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_header(struct soap *soap)\n-{\n-\tif (!soap->header)\n-\t{\tif ((soap->header = (struct SOAP_ENV__Header*)soap_malloc(soap, sizeof(struct SOAP_ENV__Header))))\n-\t\t\tsoap_default_SOAP_ENV__Header(soap, soap->header);\n-\t}\n-}\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_fault(struct soap *soap)\n-{\n-\tif (!soap->fault)\n-\t{\tsoap->fault = (struct SOAP_ENV__Fault*)soap_malloc(soap, sizeof(struct SOAP_ENV__Fault));\n-\t\tif (!soap->fault)\n-\t\t\treturn;\n-\t\tsoap_default_SOAP_ENV__Fault(soap, soap->fault);\n-\t}\n-\tif (soap->version == 2 && !soap->fault->SOAP_ENV__Code)\n-\t{\tsoap->fault->SOAP_ENV__Code = (struct SOAP_ENV__Code*)soap_malloc(soap, sizeof(struct SOAP_ENV__Code));\n-\t\tsoap_default_SOAP_ENV__Code(soap, soap->fault->SOAP_ENV__Code);\n-\t}\n-\tif (soap->version == 2 && !soap->fault->SOAP_ENV__Reason)\n-\t{\tsoap->fault->SOAP_ENV__Reason = (struct SOAP_ENV__Reason*)soap_malloc(soap, sizeof(struct SOAP_ENV__Reason));\n-\t\tsoap_default_SOAP_ENV__Reason(soap, soap->fault->SOAP_ENV__Reason);\n-\t}\n-}\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap *soap)\n-{\n-\tif (soap->fault)\n-\t\tsoap_serialize_SOAP_ENV__Fault(soap, soap->fault);\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap *soap)\n-{\n-\tif (soap->fault)\n-\t\treturn soap_put_SOAP_ENV__Fault(soap, soap->fault, "SOAP-ENV:Fault", NULL);\n-\treturn SOAP_OK;\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap *soap)\n-{\n-\treturn (soap->fault = soap_get_SOAP_ENV__Fault(soap, NULL, "SOAP-ENV:Fault", NULL)) == NULL;\n-}\n-\n-SOAP_FMAC3 const char ** SOAP_FMAC4 soap_faultcode(struct soap *soap)\n-{\n-\tsoap_fault(soap);\n-\tif (soap->version == 2 && soap->fault->SOAP_ENV__Code)\n-\t\treturn (const char**)&soap->fault->SOAP_ENV__Code->SOAP_ENV__Value;\n-\treturn (const char**)&soap->fault->faultcode;\n-}\n-\n-SOAP_FMAC3 const char ** SOAP_FMAC4 soap_faultsubcode(struct soap *soap)\n-{\n-\tsoap_fault(soap);\n-\tif (soap->version == 2)\n-\t{\tif (!soap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode)\n-\t\t{\tsoap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode = (struct SOAP_ENV__Code*)soap_malloc(soap, sizeof(struct SOAP_ENV__Code));\n-\t\t\tsoap_default_SOAP_ENV__Code(soap, soap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode);\n-\t\t}\n-\t\treturn (const char**)&soap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode->SOAP_ENV__Value;\n-\t}\n-\treturn (const char**)&soap->fault->faultcode;\n-}\n-\n-SOAP_FMAC3 const char * SOAP_FMAC4 soap_check_faultsubcode(struct soap *soap)\n-{\n-\tsoap_fault(soap);\n-\tif (soap->version == 2)\n-\t{\tif (soap->fault->SOAP_ENV__Code && soap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode && soap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode)\n-\t\t\treturn soap->fault->SOAP_ENV__Code->SOAP_ENV__Subcode->SOAP_EN'..b' (!soap_reference(soap, *a, SOAP_TYPE_string))\n-\t\tsoap_serialize_string(soap, *a);\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_PointerTostring(struct soap *soap, const char *tag, int id, char **const*a, const char *type)\n-{\n-\tid = soap_element_id(soap, tag, id, *a, NULL, 0, type, SOAP_TYPE_string);\n-\tif (id < 0)\n-\t\treturn soap->error;\n-\treturn soap_out_string(soap, tag, id, *a, type);\n-}\n-\n-SOAP_FMAC3 char *** SOAP_FMAC4 soap_in_PointerTostring(struct soap *soap, const char *tag, char ***a, const char *type)\n-{\n-\tif (soap_element_begin_in(soap, tag, 1, NULL))\n-\t\treturn NULL;\n-\tif (!a)\n-\t\tif (!(a = (char ***)soap_malloc(soap, sizeof(char **))))\n-\t\t\treturn NULL;\n-\t*a = NULL;\n-\tif (!soap->null && *soap->href != \'#\')\n-\t{\tsoap_revert(soap);\n-\t\tif (!(*a = soap_in_string(soap, tag, *a, type)))\n-\t\t\treturn NULL;\n-\t}\n-\telse\n-\t{\ta = (char ***)soap_id_lookup(soap, soap->href, (void**)a, SOAP_TYPE_string, sizeof(char *), 1);\n-\t\tif (soap->body && soap_element_end_in(soap, tag))\n-\t\t\treturn NULL;\n-\t}\n-\treturn a;\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_PointerTostring(struct soap *soap, char **const*a, const char *tag, const char *type)\n-{\n-\tregister int id = soap_embed(soap, (void*)a, NULL, 0, tag, SOAP_TYPE_PointerTostring);\n-\tif (soap_out_PointerTostring(soap, tag?tag:"byte", id, a, type))\n-\t\treturn soap->error;\n-\treturn soap_putindependent(soap);\n-}\n-\n-SOAP_FMAC3 char *** SOAP_FMAC4 soap_get_PointerTostring(struct soap *soap, char ***p, const char *tag, const char *type)\n-{\n-\tif ((p = soap_in_PointerTostring(soap, tag, p, type)))\n-\t\tif (soap_getindependent(soap))\n-\t\t\treturn NULL;\n-\treturn p;\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out__QName(struct soap *soap, const char *tag, int id, char *const*a, const char *type)\n-{\n-\treturn soap_outstring(soap, tag, id, a, type, SOAP_TYPE__QName);\n-}\n-\n-SOAP_FMAC3 char * * SOAP_FMAC4 soap_in__QName(struct soap *soap, const char *tag, char **a, const char *type)\n-{\tchar **p;\n-\tp = soap_instring(soap, tag, a, type, SOAP_TYPE__QName, 2, 0, -1);\n-\treturn p;\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put__QName(struct soap *soap, char *const*a, const char *tag, const char *type)\n-{\n-\tregister int id = soap_embed(soap, (void*)a, NULL, 0, tag, SOAP_TYPE__QName);\n-\tif (soap_out__QName(soap, tag?tag:"byte", id, a, type))\n-\t\treturn soap->error;\n-\treturn soap_putindependent(soap);\n-}\n-\n-SOAP_FMAC3 char ** SOAP_FMAC4 soap_get__QName(struct soap *soap, char **p, const char *tag, const char *type)\n-{\n-\tif ((p = soap_in__QName(soap, tag, p, type)))\n-\t\tif (soap_getindependent(soap))\n-\t\t\treturn NULL;\n-\treturn p;\n-}\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_default_string(struct soap *soap, char **a)\n-{\n-\t(void)soap; /* appease -Wall -Werror */\n-#ifdef SOAP_DEFAULT_string\n-\t*a = SOAP_DEFAULT_string;\n-#else\n-\t*a = (char *)0;\n-#endif\n-}\n-\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serialize_string(struct soap *soap, char *const*a)\n-{\n-\tsoap_reference(soap, *a, SOAP_TYPE_string);\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_string(struct soap *soap, const char *tag, int id, char *const*a, const char *type)\n-{\n-\treturn soap_outstring(soap, tag, id, a, type, SOAP_TYPE_string);\n-}\n-\n-SOAP_FMAC3 char * * SOAP_FMAC4 soap_in_string(struct soap *soap, const char *tag, char **a, const char *type)\n-{\tchar **p;\n-\tp = soap_instring(soap, tag, a, type, SOAP_TYPE_string, 1, 0, -1);\n-\treturn p;\n-}\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_string(struct soap *soap, char *const*a, const char *tag, const char *type)\n-{\n-\tregister int id = soap_embed(soap, (void*)a, NULL, 0, tag, SOAP_TYPE_string);\n-\tif (soap_out_string(soap, tag?tag:"byte", id, a, type))\n-\t\treturn soap->error;\n-\treturn soap_putindependent(soap);\n-}\n-\n-SOAP_FMAC3 char ** SOAP_FMAC4 soap_get_string(struct soap *soap, char **p, const char *tag, const char *type)\n-{\n-\tif ((p = soap_in_string(soap, tag, p, type)))\n-\t\tif (soap_getindependent(soap))\n-\t\t\treturn NULL;\n-\treturn p;\n-}\n-\n-#ifdef __cplusplus\n-}\n-#endif\n-\n-#if defined(__BORLANDC__)\n-#pragma option pop\n-#pragma option pop\n-#endif\n-\n-/* End of soapC.c */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapClient.c
--- a/GEMBASSY-1.0.3/include/soapClient.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,5174 +0,0 @@\n-/* soapClient.c\n- Generated by gSOAP 2.8.6 from gae.h\n-\n-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-The generated code is released under one of the following licenses:\n-1) GPL or 2) Genivia\'s license for commercial use.\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n-*/\n-\n-#if defined(__BORLANDC__)\n-#pragma option push -w-8060\n-#pragma option push -w-8004\n-#endif\n-#include "soapH.h"\n-#ifdef __cplusplus\n-extern "C" {\n-#endif\n-\n-SOAP_SOURCE_STAMP("@(#) soapClient.c ver 2.8.6 2013-04-04 13:42:58 GMT")\n-\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__codon_USCOREmva(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__codon_USCOREmvaInputParams *_params, char **_result)\n-{\tstruct ns1__codon_USCOREmva soap_tmp_ns1__codon_USCOREmva;\n-\tstruct ns1__codon_USCOREmvaResponse *soap_tmp_ns1__codon_USCOREmvaResponse;\n-\tif (!soap_endpoint)\n-\t\tsoap_endpoint = "http://soap.g-language.org/WS/g-language.cgi";\n-\tif (!soap_action)\n-\t\tsoap_action = "http://soap.g-language.org/GLANG#codon_mva";\n-\tsoap->encodingStyle = "http://schemas.xmlsoap.org/soap/encoding/";\n-\tsoap_tmp_ns1__codon_USCOREmva._sequence = _sequence;\n-\tsoap_tmp_ns1__codon_USCOREmva._params = _params;\n-\tsoap_begin(soap);\n-\tsoap_serializeheader(soap);\n-\tsoap_serialize_ns1__codon_USCOREmva(soap, &soap_tmp_ns1__codon_USCOREmva);\n-\tif (soap_begin_count(soap))\n-\t\treturn soap->error;\n-\tif (soap->mode & SOAP_IO_LENGTH)\n-\t{\tif (soap_envelope_begin_out(soap)\n-\t\t || soap_putheader(soap)\n-\t\t || soap_body_begin_out(soap)\n-\t\t || soap_put_ns1__codon_USCOREmva(soap, &soap_tmp_ns1__codon_USCOREmva, "ns1:codon_mva", NULL)\n-\t\t || soap_body_end_out(soap)\n-\t\t || soap_envelope_end_out(soap))\n-\t\t\t return soap->error;\n-\t}\n-\tif (soap_end_count(soap))\n-\t\treturn soap->error;\n-\tif (soap_connect(soap, soap_endpoint, soap_action)\n-\t || soap_envelope_begin_out(soap)\n-\t || soap_putheader(soap)\n-\t || soap_body_begin_out(soap)\n-\t || soap_put_ns1__codon_USCOREmva(soap, &soap_tmp_ns1__codon_USCOREmva, "ns1:codon_mva", NULL)\n-\t || soap_body_end_out(soap)\n-\t || soap_envelope_end_out(soap)\n-\t || soap_end_send(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (!_result)\n-\t\treturn soap_closesock(soap);\n-\t*_result = NULL;\n-\tif (soap_begin_recv(soap)\n-\t || soap_envelope_begin_in(soap)\n-\t || soap_recv_header(soap)\n-\t || soap_body_begin_in(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (soap_recv_fault(soap, 1))\n-\t\treturn soap->error;\n-\tsoap_tmp_ns1__codon_USCOREmvaResponse = soap_get_ns1__codon_USCOREmvaResponse(soap, NULL, "", "");\n-\tif (soap->error)\n-\t\treturn soap_recv_fault(soap, 0);\n-\tif (soap_body_end_in(soap)\n-\t || soap_envelope_end_in(soap)\n-\t || soap_end_recv(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (_result && soap_tmp_ns1__codon_USCOREmvaResponse->_result)\n-\t\t*_result = *soap_tmp_ns1__codon_USCOREmvaResponse->_result;\n-\treturn soap_closesock(soap);\n-}\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__P2(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__P2InputParams *_params, char **_result)\n-{\tstruct ns1__P2 soap_tmp_ns1__P2;\n-\tstruct ns1__P2Response *soap_tmp_ns1__P2Response;\n-\tif (!soap_endpoint)\n-\t\tsoap_endpoint = "http://soap.g-language.org/WS/g-language.cgi";\n-\tif (!soap_action)\n-\t\tsoap_action = "http://soap.g-language.org/GLANG#P2";\n-\tsoap->encodingStyle = "http://schemas.xmlsoap.org/soap/encoding/";\n-\tsoap_tmp_ns1__P2._sequence = _sequence;\n-\tsoap_tmp_ns1__P2._params = _params;\n-\tsoap_begin(soap);\n-\tsoap_serializeheader(soap);\n-\tsoap_serialize_ns1__P2(soap, &soap_tmp_ns1__P2);\n-\tif (soap_begin_count(soap))\n-\t\treturn soap->error;\n-\tif (soap->mode & SOAP_IO_LENGTH)\n-\t{\tif (soap_envelope_begin_out(soap)\n-\t\t || soap_putheader(soap)\n-\t\t || soap_body_begin_out(soap)\n-\t\t || soap_put_ns1__P2(soap, &soap_tmp_ns1__P2, "ns1:P2", NULL)\n-\t\t || soap_body_end_out(soap)\n-\t\t || soap_envelope_end_out(soap))\n'..b'tp://soap.g-language.org/GLANG#help";\n-\tsoap->encodingStyle = "http://schemas.xmlsoap.org/soap/encoding/";\n-\tsoap_tmp_ns1__help._keywords = _keywords;\n-\tsoap_begin(soap);\n-\tsoap_serializeheader(soap);\n-\tsoap_serialize_ns1__help(soap, &soap_tmp_ns1__help);\n-\tif (soap_begin_count(soap))\n-\t\treturn soap->error;\n-\tif (soap->mode & SOAP_IO_LENGTH)\n-\t{\tif (soap_envelope_begin_out(soap)\n-\t\t || soap_putheader(soap)\n-\t\t || soap_body_begin_out(soap)\n-\t\t || soap_put_ns1__help(soap, &soap_tmp_ns1__help, "ns1:help", NULL)\n-\t\t || soap_body_end_out(soap)\n-\t\t || soap_envelope_end_out(soap))\n-\t\t\t return soap->error;\n-\t}\n-\tif (soap_end_count(soap))\n-\t\treturn soap->error;\n-\tif (soap_connect(soap, soap_endpoint, soap_action)\n-\t || soap_envelope_begin_out(soap)\n-\t || soap_putheader(soap)\n-\t || soap_body_begin_out(soap)\n-\t || soap_put_ns1__help(soap, &soap_tmp_ns1__help, "ns1:help", NULL)\n-\t || soap_body_end_out(soap)\n-\t || soap_envelope_end_out(soap)\n-\t || soap_end_send(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (!_result)\n-\t\treturn soap_closesock(soap);\n-\t*_result = NULL;\n-\tif (soap_begin_recv(soap)\n-\t || soap_envelope_begin_in(soap)\n-\t || soap_recv_header(soap)\n-\t || soap_body_begin_in(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (soap_recv_fault(soap, 1))\n-\t\treturn soap->error;\n-\tsoap_tmp_ns1__helpResponse = soap_get_ns1__helpResponse(soap, NULL, "", "");\n-\tif (soap->error)\n-\t\treturn soap_recv_fault(soap, 0);\n-\tif (soap_body_end_in(soap)\n-\t || soap_envelope_end_in(soap)\n-\t || soap_end_recv(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (_result && soap_tmp_ns1__helpResponse->_result)\n-\t\t*_result = *soap_tmp_ns1__helpResponse->_result;\n-\treturn soap_closesock(soap);\n-}\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__hydropathy(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, float *_result)\n-{\tstruct ns1__hydropathy soap_tmp_ns1__hydropathy;\n-\tstruct ns1__hydropathyResponse *soap_tmp_ns1__hydropathyResponse;\n-\tif (!soap_endpoint)\n-\t\tsoap_endpoint = "http://soap.g-language.org/WS/g-language.cgi";\n-\tif (!soap_action)\n-\t\tsoap_action = "http://soap.g-language.org/GLANG#hydropathy";\n-\tsoap->encodingStyle = "http://schemas.xmlsoap.org/soap/encoding/";\n-\tsoap_tmp_ns1__hydropathy._sequence = _sequence;\n-\tsoap_begin(soap);\n-\tsoap_serializeheader(soap);\n-\tsoap_serialize_ns1__hydropathy(soap, &soap_tmp_ns1__hydropathy);\n-\tif (soap_begin_count(soap))\n-\t\treturn soap->error;\n-\tif (soap->mode & SOAP_IO_LENGTH)\n-\t{\tif (soap_envelope_begin_out(soap)\n-\t\t || soap_putheader(soap)\n-\t\t || soap_body_begin_out(soap)\n-\t\t || soap_put_ns1__hydropathy(soap, &soap_tmp_ns1__hydropathy, "ns1:hydropathy", NULL)\n-\t\t || soap_body_end_out(soap)\n-\t\t || soap_envelope_end_out(soap))\n-\t\t\t return soap->error;\n-\t}\n-\tif (soap_end_count(soap))\n-\t\treturn soap->error;\n-\tif (soap_connect(soap, soap_endpoint, soap_action)\n-\t || soap_envelope_begin_out(soap)\n-\t || soap_putheader(soap)\n-\t || soap_body_begin_out(soap)\n-\t || soap_put_ns1__hydropathy(soap, &soap_tmp_ns1__hydropathy, "ns1:hydropathy", NULL)\n-\t || soap_body_end_out(soap)\n-\t || soap_envelope_end_out(soap)\n-\t || soap_end_send(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (!_result)\n-\t\treturn soap_closesock(soap);\n-\tsoap_default_float(soap, _result);\n-\tif (soap_begin_recv(soap)\n-\t || soap_envelope_begin_in(soap)\n-\t || soap_recv_header(soap)\n-\t || soap_body_begin_in(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (soap_recv_fault(soap, 1))\n-\t\treturn soap->error;\n-\tsoap_tmp_ns1__hydropathyResponse = soap_get_ns1__hydropathyResponse(soap, NULL, "", "");\n-\tif (soap->error)\n-\t\treturn soap_recv_fault(soap, 0);\n-\tif (soap_body_end_in(soap)\n-\t || soap_envelope_end_in(soap)\n-\t || soap_end_recv(soap))\n-\t\treturn soap_closesock(soap);\n-\tif (_result && soap_tmp_ns1__hydropathyResponse->_result)\n-\t\t*_result = *soap_tmp_ns1__hydropathyResponse->_result;\n-\treturn soap_closesock(soap);\n-}\n-\n-#ifdef __cplusplus\n-}\n-#endif\n-\n-#if defined(__BORLANDC__)\n-#pragma option pop\n-#pragma option pop\n-#endif\n-\n-/* End of soapClient.c */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapClientLib.c
--- a/GEMBASSY-1.0.3/include/soapClientLib.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-/* soapClientLib.c
- Generated by gSOAP 2.8.6 from gae.h
-
-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.
-The generated code is released under one of the following licenses:
-1) GPL or 2) Genivia's license for commercial use.
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
-*/
-
-/** Use this file in your project build instead of the two files soapC.c and soapClient.c. This hides the serializer functions and avoids linking problems when linking multiple clients and servers. */
-
-#ifndef WITH_NOGLOBAL
-#define WITH_NOGLOBAL
-#endif
-#define SOAP_FMAC3 static
-#include "soapC.c"
-#include "soapClient.c"
-
-/* End of soapClientLib.c */

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapH.h
--- a/GEMBASSY-1.0.3/include/soapH.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,7101 +0,0 @@\n-/* soapH.h\n- Generated by gSOAP 2.8.6 from gae.h\n-\n-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-The generated code is released under one of the following licenses:\n-1) GPL or 2) Genivia\'s license for commercial use.\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n-*/\n-\n-#ifndef soapH_H\n-#define soapH_H\n-#include "soapStub.h"\n-#ifdef __cplusplus\n-extern "C" {\n-#endif\n-#ifndef WITH_NOIDREF\n-SOAP_FMAC3 void SOAP_FMAC4 soap_markelement(struct soap*, const void*, int);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_putelement(struct soap*, const void*, const char*, int, int);\n-SOAP_FMAC3 void *SOAP_FMAC4 soap_getelement(struct soap*, int*);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_putindependent(struct soap*);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_getindependent(struct soap*);\n-#endif\n-SOAP_FMAC3 int SOAP_FMAC4 soap_ignore_element(struct soap*);\n-\n-#ifndef SOAP_TYPE_byte\n-#define SOAP_TYPE_byte (3)\n-#endif\n-SOAP_FMAC3 void SOAP_FMAC4 soap_default_byte(struct soap*, char *);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_byte(struct soap*, const char*, int, const char *, const char*);\n-SOAP_FMAC3 char * SOAP_FMAC4 soap_in_byte(struct soap*, const char*, char *, const char*);\n-\n-#ifndef soap_write_byte\n-#define soap_write_byte(soap, data) ( soap_begin_send(soap) || soap_put_byte(soap, data, "byte", NULL) || soap_end_send(soap) )\n-#endif\n-\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_byte(struct soap*, const char *, const char*, const char*);\n-\n-#ifndef soap_read_byte\n-#define soap_read_byte(soap, data) ( soap_begin_recv(soap) || !soap_get_byte(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 char * SOAP_FMAC4 soap_get_byte(struct soap*, char *, const char*, const char*);\n-\n-#ifndef SOAP_TYPE_int\n-#define SOAP_TYPE_int (1)\n-#endif\n-SOAP_FMAC3 void SOAP_FMAC4 soap_default_int(struct soap*, int *);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_int(struct soap*, const char*, int, const int *, const char*);\n-SOAP_FMAC3 int * SOAP_FMAC4 soap_in_int(struct soap*, const char*, int *, const char*);\n-\n-#ifndef soap_write_int\n-#define soap_write_int(soap, data) ( soap_begin_send(soap) || soap_put_int(soap, data, "int", NULL) || soap_end_send(soap) )\n-#endif\n-\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_int(struct soap*, const int *, const char*, const char*);\n-\n-#ifndef soap_read_int\n-#define soap_read_int(soap, data) ( soap_begin_recv(soap) || !soap_get_int(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 int * SOAP_FMAC4 soap_get_int(struct soap*, int *, const char*, const char*);\n-\n-#ifndef SOAP_TYPE_float\n-#define SOAP_TYPE_float (424)\n-#endif\n-SOAP_FMAC3 void SOAP_FMAC4 soap_default_float(struct soap*, float *);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_float(struct soap*, const char*, int, const float *, const char*);\n-SOAP_FMAC3 float * SOAP_FMAC4 soap_in_float(struct soap*, const char*, float *, const char*);\n-\n-#ifndef soap_write_float\n-#define soap_write_float(soap, data) ( soap_begin_send(soap) || soap_put_float(soap, data, "float", NULL) || soap_end_send(soap) )\n-#endif\n-\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_float(struct soap*, const float *, const char*, const char*);\n-\n-#ifndef soap_read_float\n-#define soap_read_float(soap, data) ( soap_begin_recv(soap) || !soap_get_float(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 float * SOAP_FMAC4 soap_get_float(struct soap*, float *, const char*, const char*);\n-\n-#ifndef SOAP_TYPE_double\n-#define SOAP_TYPE_double (13)\n-#endif\n-SOAP_FMAC3 void SOAP_FMAC4 soap_default_double(struct soap*, double *);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_double(struct soap*, const char*, int, const double *, const char*);\n-SOAP_FMAC3 double * SOAP_FMAC4 soap_in_double(struct soap*, const char*, double *, const char*);\n-\n-#ifndef soap_write_double\n-#define soap_write_double(soap, data) ( soap_begin_send(soap) || soap_put_double(soap, data, "double", NULL) || soap_end_send(soap)'..b'utParams(soap, data) ( soap_begin_send(soap) || (soap_serialize_PointerTons1__codon_USCOREmvaInputParams(soap, data), 0) || soap_put_PointerTons1__codon_USCOREmvaInputParams(soap, data, "ns1:codon_mvaInputParams", NULL) || soap_end_send(soap) )\n-#endif\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_PointerTons1__codon_USCOREmvaInputParams(struct soap*, struct ns1__codon_USCOREmvaInputParams *const*, const char*, const char*);\n-\n-#ifndef soap_read_PointerTons1__codon_USCOREmvaInputParams\n-#define soap_read_PointerTons1__codon_USCOREmvaInputParams(soap, data) ( soap_begin_recv(soap) || !soap_get_PointerTons1__codon_USCOREmvaInputParams(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 struct ns1__codon_USCOREmvaInputParams ** SOAP_FMAC4 soap_get_PointerTons1__codon_USCOREmvaInputParams(struct soap*, struct ns1__codon_USCOREmvaInputParams **, const char*, const char*);\n-\n-#ifndef SOAP_TYPE_PointerTostring\n-#define SOAP_TYPE_PointerTostring (75)\n-#endif\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serialize_PointerTostring(struct soap*, char **const*);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_PointerTostring(struct soap*, const char *, int, char **const*, const char *);\n-SOAP_FMAC3 char *** SOAP_FMAC4 soap_in_PointerTostring(struct soap*, const char*, char ***, const char*);\n-\n-#ifndef soap_write_PointerTostring\n-#define soap_write_PointerTostring(soap, data) ( soap_begin_send(soap) || (soap_serialize_PointerTostring(soap, data), 0) || soap_put_PointerTostring(soap, data, "byte", NULL) || soap_end_send(soap) )\n-#endif\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_PointerTostring(struct soap*, char **const*, const char*, const char*);\n-\n-#ifndef soap_read_PointerTostring\n-#define soap_read_PointerTostring(soap, data) ( soap_begin_recv(soap) || !soap_get_PointerTostring(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 char *** SOAP_FMAC4 soap_get_PointerTostring(struct soap*, char ***, const char*, const char*);\n-\n-#ifndef SOAP_TYPE__QName\n-#define SOAP_TYPE__QName (5)\n-#endif\n-\n-#define soap_default__QName(soap, a) soap_default_string(soap, a)\n-\n-\n-#define soap_serialize__QName(soap, a) soap_serialize_string(soap, a)\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out__QName(struct soap*, const char*, int, char*const*, const char*);\n-SOAP_FMAC3 char * * SOAP_FMAC4 soap_in__QName(struct soap*, const char*, char **, const char*);\n-\n-#ifndef soap_write__QName\n-#define soap_write__QName(soap, data) ( soap_begin_send(soap) || (soap_serialize__QName(soap, data), 0) || soap_put__QName(soap, data, "byte", NULL) || soap_end_send(soap) )\n-#endif\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put__QName(struct soap*, char *const*, const char*, const char*);\n-\n-#ifndef soap_read__QName\n-#define soap_read__QName(soap, data) ( soap_begin_recv(soap) || !soap_get__QName(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 char ** SOAP_FMAC4 soap_get__QName(struct soap*, char **, const char*, const char*);\n-\n-#ifndef SOAP_TYPE_string\n-#define SOAP_TYPE_string (4)\n-#endif\n-SOAP_FMAC3 void SOAP_FMAC4 soap_default_string(struct soap*, char **);\n-SOAP_FMAC3 void SOAP_FMAC4 soap_serialize_string(struct soap*, char *const*);\n-SOAP_FMAC3 int SOAP_FMAC4 soap_out_string(struct soap*, const char*, int, char*const*, const char*);\n-SOAP_FMAC3 char * * SOAP_FMAC4 soap_in_string(struct soap*, const char*, char **, const char*);\n-\n-#ifndef soap_write_string\n-#define soap_write_string(soap, data) ( soap_begin_send(soap) || (soap_serialize_string(soap, data), 0) || soap_put_string(soap, data, "byte", NULL) || soap_end_send(soap) )\n-#endif\n-\n-SOAP_FMAC3 int SOAP_FMAC4 soap_put_string(struct soap*, char *const*, const char*, const char*);\n-\n-#ifndef soap_read_string\n-#define soap_read_string(soap, data) ( soap_begin_recv(soap) || !soap_get_string(soap, data, NULL, NULL) || soap_end_recv(soap) )\n-#endif\n-\n-SOAP_FMAC3 char ** SOAP_FMAC4 soap_get_string(struct soap*, char **, const char*, const char*);\n-\n-#ifdef __cplusplus\n-}\n-#endif\n-\n-#endif\n-\n-/* End of soapH.h */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapServer.c
--- a/GEMBASSY-1.0.3/include/soapServer.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4231 +0,0 @@\n-/* soapServer.c\n- Generated by gSOAP 2.8.6 from gae.h\n-\n-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-The generated code is released under one of the following licenses:\n-1) GPL or 2) Genivia\'s license for commercial use.\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n-*/\n-\n-#if defined(__BORLANDC__)\n-#pragma option push -w-8060\n-#pragma option push -w-8004\n-#endif\n-#include "soapH.h"\n-#ifdef __cplusplus\n-extern "C" {\n-#endif\n-\n-SOAP_SOURCE_STAMP("@(#) soapServer.c ver 2.8.6 2013-04-04 13:42:58 GMT")\n-\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_serve(struct soap *soap)\n-{\n-#ifndef WITH_FASTCGI\n-\tunsigned int k = soap->max_keep_alive;\n-#endif\n-\tdo\n-\t{\n-#ifndef WITH_FASTCGI\n-\t\tif (soap->max_keep_alive > 0 && !--k)\n-\t\t\tsoap->keep_alive = 0;\n-#endif\n-\t\tif (soap_begin_serve(soap))\n-\t\t{\tif (soap->error >= SOAP_STOP)\n-\t\t\t\tcontinue;\n-\t\t\treturn soap->error;\n-\t\t}\n-\t\tif (soap_serve_request(soap) || (soap->fserveloop && soap->fserveloop(soap)))\n-\t\t{\n-#ifdef WITH_FASTCGI\n-\t\t\tsoap_send_fault(soap);\n-#else\n-\t\t\treturn soap_send_fault(soap);\n-#endif\n-\t\t}\n-\n-#ifdef WITH_FASTCGI\n-\t\tsoap_destroy(soap);\n-\t\tsoap_end(soap);\n-\t} while (1);\n-#else\n-\t} while (soap->keep_alive);\n-#endif\n-\treturn SOAP_OK;\n-}\n-\n-#ifndef WITH_NOSERVEREQUEST\n-SOAP_FMAC5 int SOAP_FMAC6 soap_serve_request(struct soap *soap)\n-{\n-\tsoap_peek_element(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:codon_mva"))\n-\t\treturn soap_serve_ns1__codon_USCOREmva(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:P2"))\n-\t\treturn soap_serve_ns1__P2(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:w_value"))\n-\t\treturn soap_serve_ns1__w_USCOREvalue(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:splitprintseq"))\n-\t\treturn soap_serve_ns1__splitprintseq(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:median"))\n-\t\treturn soap_serve_ns1__median(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:find_ori_ter"))\n-\t\treturn soap_serve_ns1__find_USCOREori_USCOREter(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:plasmid_map"))\n-\t\treturn soap_serve_ns1__plasmid_USCOREmap(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:sum"))\n-\t\treturn soap_serve_ns1__sum(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:nucleotide_periodicity"))\n-\t\treturn soap_serve_ns1__nucleotide_USCOREperiodicity(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:variance"))\n-\t\treturn soap_serve_ns1__variance(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:amino_info"))\n-\t\treturn soap_serve_ns1__amino_USCOREinfo(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:circular_map"))\n-\t\treturn soap_serve_ns1__circular_USCOREmap(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:togoWS"))\n-\t\treturn soap_serve_ns1__togoWS(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:translate"))\n-\t\treturn soap_serve_ns1__translate(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:phx"))\n-\t\treturn soap_serve_ns1__phx(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:icdi"))\n-\t\treturn soap_serve_ns1__icdi(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:enc"))\n-\t\treturn soap_serve_ns1__enc(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:fop"))\n-\t\treturn soap_serve_ns1__fop(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:bui"))\n-\t\treturn soap_serve_ns1__bui(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:dist_in_cc"))\n-\t\treturn soap_serve_ns1__dist_USCOREin_USCOREcc(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:find_dnaAbox"))\n-\t\treturn soap_serve_ns1__find_USCOREdnaAbox(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:ttest"))\n-\t\treturn soap_serve_ns1__ttest(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:seq2png"))\n-\t\treturn soap_serve_ns1__seq2png(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:amino_counter"))\n-\t\treturn soap_serve_ns1__amino_USCOREcounter(soap);\n-\tif (!soap_match_tag(soap, soap->tag, "ns1:aaui"))\n-\t\treturn soap_serve_ns1__aaui(soap);\n-\tif (!soap_match_tag(soap, '..b'| soap_putheader(soap)\n-\t || soap_body_begin_out(soap)\n-\t || soap_put_ns1__S_USCOREvalueResponse(soap, &soap_tmp_ns1__S_USCOREvalueResponse, "ns1:S_valueResponse", NULL)\n-\t || soap_body_end_out(soap)\n-\t || soap_envelope_end_out(soap)\n-\t || soap_end_send(soap))\n-\t\treturn soap->error;\n-\treturn soap_closesock(soap);\n-}\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_serve_ns1__help(struct soap *soap)\n-{\tstruct ns1__help soap_tmp_ns1__help;\n-\tstruct ns1__helpResponse soap_tmp_ns1__helpResponse;\n-\tchar * soap_tmp_string;\n-\tsoap_default_ns1__helpResponse(soap, &soap_tmp_ns1__helpResponse);\n-\tsoap_tmp_string = NULL;\n-\tsoap_tmp_ns1__helpResponse._result = &soap_tmp_string;\n-\tsoap_default_ns1__help(soap, &soap_tmp_ns1__help);\n-\tsoap->encodingStyle = "http://schemas.xmlsoap.org/soap/encoding/";\n-\tif (!soap_get_ns1__help(soap, &soap_tmp_ns1__help, "ns1:help", NULL))\n-\t\treturn soap->error;\n-\tif (soap_body_end_in(soap)\n-\t || soap_envelope_end_in(soap)\n-\t || soap_end_recv(soap))\n-\t\treturn soap->error;\n-\tsoap->error = ns1__help(soap, soap_tmp_ns1__help._keywords, soap_tmp_ns1__helpResponse._result);\n-\tif (soap->error)\n-\t\treturn soap->error;\n-\tsoap_serializeheader(soap);\n-\tsoap_serialize_ns1__helpResponse(soap, &soap_tmp_ns1__helpResponse);\n-\tif (soap_begin_count(soap))\n-\t\treturn soap->error;\n-\tif (soap->mode & SOAP_IO_LENGTH)\n-\t{\tif (soap_envelope_begin_out(soap)\n-\t\t || soap_putheader(soap)\n-\t\t || soap_body_begin_out(soap)\n-\t\t || soap_put_ns1__helpResponse(soap, &soap_tmp_ns1__helpResponse, "ns1:helpResponse", NULL)\n-\t\t || soap_body_end_out(soap)\n-\t\t || soap_envelope_end_out(soap))\n-\t\t\t return soap->error;\n-\t};\n-\tif (soap_end_count(soap)\n-\t || soap_response(soap, SOAP_OK)\n-\t || soap_envelope_begin_out(soap)\n-\t || soap_putheader(soap)\n-\t || soap_body_begin_out(soap)\n-\t || soap_put_ns1__helpResponse(soap, &soap_tmp_ns1__helpResponse, "ns1:helpResponse", NULL)\n-\t || soap_body_end_out(soap)\n-\t || soap_envelope_end_out(soap)\n-\t || soap_end_send(soap))\n-\t\treturn soap->error;\n-\treturn soap_closesock(soap);\n-}\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_serve_ns1__hydropathy(struct soap *soap)\n-{\tstruct ns1__hydropathy soap_tmp_ns1__hydropathy;\n-\tstruct ns1__hydropathyResponse soap_tmp_ns1__hydropathyResponse;\n-\tfloat soap_tmp_float;\n-\tsoap_default_ns1__hydropathyResponse(soap, &soap_tmp_ns1__hydropathyResponse);\n-\tsoap_default_float(soap, &soap_tmp_float);\n-\tsoap_tmp_ns1__hydropathyResponse._result = &soap_tmp_float;\n-\tsoap_default_ns1__hydropathy(soap, &soap_tmp_ns1__hydropathy);\n-\tsoap->encodingStyle = "http://schemas.xmlsoap.org/soap/encoding/";\n-\tif (!soap_get_ns1__hydropathy(soap, &soap_tmp_ns1__hydropathy, "ns1:hydropathy", NULL))\n-\t\treturn soap->error;\n-\tif (soap_body_end_in(soap)\n-\t || soap_envelope_end_in(soap)\n-\t || soap_end_recv(soap))\n-\t\treturn soap->error;\n-\tsoap->error = ns1__hydropathy(soap, soap_tmp_ns1__hydropathy._sequence, soap_tmp_ns1__hydropathyResponse._result);\n-\tif (soap->error)\n-\t\treturn soap->error;\n-\tsoap_serializeheader(soap);\n-\tsoap_serialize_ns1__hydropathyResponse(soap, &soap_tmp_ns1__hydropathyResponse);\n-\tif (soap_begin_count(soap))\n-\t\treturn soap->error;\n-\tif (soap->mode & SOAP_IO_LENGTH)\n-\t{\tif (soap_envelope_begin_out(soap)\n-\t\t || soap_putheader(soap)\n-\t\t || soap_body_begin_out(soap)\n-\t\t || soap_put_ns1__hydropathyResponse(soap, &soap_tmp_ns1__hydropathyResponse, "ns1:hydropathyResponse", NULL)\n-\t\t || soap_body_end_out(soap)\n-\t\t || soap_envelope_end_out(soap))\n-\t\t\t return soap->error;\n-\t};\n-\tif (soap_end_count(soap)\n-\t || soap_response(soap, SOAP_OK)\n-\t || soap_envelope_begin_out(soap)\n-\t || soap_putheader(soap)\n-\t || soap_body_begin_out(soap)\n-\t || soap_put_ns1__hydropathyResponse(soap, &soap_tmp_ns1__hydropathyResponse, "ns1:hydropathyResponse", NULL)\n-\t || soap_body_end_out(soap)\n-\t || soap_envelope_end_out(soap)\n-\t || soap_end_send(soap))\n-\t\treturn soap->error;\n-\treturn soap_closesock(soap);\n-}\n-\n-#ifdef __cplusplus\n-}\n-#endif\n-\n-#if defined(__BORLANDC__)\n-#pragma option pop\n-#pragma option pop\n-#endif\n-\n-/* End of soapServer.c */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapServerLib.c
--- a/GEMBASSY-1.0.3/include/soapServerLib.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-/* soapServerLib.c
- Generated by gSOAP 2.8.6 from gae.h
-
-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.
-The generated code is released under one of the following licenses:
-1) GPL or 2) Genivia's license for commercial use.
-This program is released under the GPL with the additional exemption that
-compiling, linking, and/or using OpenSSL is allowed.
-*/
-
-/** Use this file in your project build instead of the two files soapC.c and soapServer.c. This hides the serializer functions and avoids linking problems when linking multiple clients and servers. */
-
-#ifndef WITH_NOGLOBAL
-#define WITH_NOGLOBAL
-#endif
-#define SOAP_FMAC3 static
-#include "soapC.c"
-#include "soapServer.c"
-
-/* End of soapServerLib.c */

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/include/soapStub.h
--- a/GEMBASSY-1.0.3/include/soapStub.h Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3194 +0,0 @@\n-/* soapStub.h\n- Generated by gSOAP 2.8.6 from gae.h\n-\n-Copyright(C) 2000-2011, Robert van Engelen, Genivia Inc. All Rights Reserved.\n-The generated code is released under one of the following licenses:\n-1) GPL or 2) Genivia\'s license for commercial use.\n-This program is released under the GPL with the additional exemption that\n-compiling, linking, and/or using OpenSSL is allowed.\n-*/\n-\n-#ifndef soapStub_H\n-#define soapStub_H\n-#define SOAP_NAMESPACE_OF_ns1\t"http://soap.g-language.org/GLANG"\n-#include "stdsoap2.h"\n-#ifdef __cplusplus\n-extern "C" {\n-#endif\n-\n-/******************************************************************************\\\n- * *\n- * Enumerations *\n- * *\n-\\******************************************************************************/\n-\n-\n-/******************************************************************************\\\n- * *\n- * Types with Custom Serializers *\n- * *\n-\\******************************************************************************/\n-\n-\n-/******************************************************************************\\\n- * *\n- * Classes and Structs *\n- * *\n-\\******************************************************************************/\n-\n-\n-#if 0 /* volatile type: do not declare here, declared elsewhere */\n-\n-#endif\n-\n-#ifndef SOAP_TYPE_ns1__Definition\n-#define SOAP_TYPE_ns1__Definition (7)\n-/* ns1:Definition */\n-struct ns1__Definition\n-{\n-\tchar *entry;\t/* required element of type xsd:string */\n-};\n-#endif\n-\n-#ifndef SOAP_TYPE_ns1__codon_USCOREmvaInputParams\n-#define SOAP_TYPE_ns1__codon_USCOREmvaInputParams (8)\n-/* ns1:codon_mvaInputParams */\n-struct ns1__codon_USCOREmvaInputParams\n-{\n-\tint parameter;\t/* required element of type xsd:int */\n-\tint naxis;\t/* required element of type xsd:int */\n-\tint translate;\t/* required element of type xsd:int */\n-\tint data;\t/* required element of type xsd:int */\n-\tchar *method;\t/* required element of type xsd:string */\n-\tchar *output;\t/* required element of type xsd:string */\n-\tchar *del_USCOREkey;\t/* required element of type xsd:string */\n-};\n-#endif\n-\n-#ifndef SOAP_TYPE_ns1__P2InputParams\n-#define SOAP_TYPE_ns1__P2InputParams (9)\n-/* ns1:P2InputParams */\n-struct ns1__P2InputParams\n-{\n-\tchar *output;\t/* required element of type xsd:string */\n-\tchar *tag;\t/* required element of type xsd:string */\n-};\n-#endif\n-\n-#ifndef SOAP_TYPE_ns1__w_USCOREvalueInputParams\n-#define SOAP_TYPE_ns1__w_USCOREvalueInputParams (10)\n-/* ns1:w_valueInputParams */\n-struct ns1__w_USCOREvalueInputParams\n-{\n-\tchar *include;\t/* required element of type xsd:string */\n-\tchar *output;\t/* required element of type xsd:string */\n-\tchar *exclude;\t/* required element of type xsd:string */\n-\tchar *tag;\t/* required element of type xsd:string */\n-};\n-#endif\n-\n-#ifndef SOAP_TYPE_ns1__find_USCOREori_USCOREterInputParams\n-#define SOAP_TYPE_ns1__find_USCOREori_USCOREterInputParams (11)\n-/* ns1:find_ori_terInputParams */\n-struct ns1__find_USCOREori_USCOREterInputParams\n-{\n-\tint window;\t/* required element of type xsd:int */\n-\tint purine;\t/* required element of type xsd:int */\n-\tint filter;\t/* required element of type xsd:int */\n-\tint keto;\t/* required element of type xsd:int */\n-};\n-#endif\n-\n-#ifndef SOAP_TYPE_ns1__consensus_USCOREzInputParams\n-#define SOAP_TYPE_ns1__consensus_USCOREzInputParams (12)\n-/* ns1:consensus_zInputParams */\n-struct ns1__consensus_USCOREzInputParams\n-{\n-\tint high'..b'uct arrayIn *_array, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__find_USCOREiteron(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__find_USCOREiteronInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__complement(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__mean(struct soap *soap, const char *soap_endpoint, const char *soap_action, struct arrayIn *_array, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__codon_USCOREcounter(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__codon_USCOREcounterInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__entrez(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_database, char *_query, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__palindrome(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__palindromeInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__least_USCOREsquares_USCOREfit(struct soap *soap, const char *soap_endpoint, const char *soap_action, struct arrayIn *_array, struct ns1__least_USCOREsquares_USCOREfitResponse *_param_9);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__dinuc(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__dinucInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__cgr(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__cgrInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__B1(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__B1InputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__B2(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__base_USCOREcounter(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__base_USCOREcounterInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__base_USCOREz_USCOREvalue(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__base_USCOREz_USCOREvalueInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__kmer_USCOREtable(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__kmer_USCOREtableInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__lda_USCOREbias(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__lda_USCOREbiasInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__scs(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__scsInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__leading_USCOREstrand(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__leading_USCOREstrandResponse *_param_10);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__S_USCOREvalue(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, struct ns1__S_USCOREvalueInputParams *_params, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__help(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_keywords, char **_result);\n-\n-SOAP_FMAC5 int SOAP_FMAC6 soap_call_ns1__hydropathy(struct soap *soap, const char *soap_endpoint, const char *soap_action, char *_sequence, float *_result);\n-\n-#ifdef __cplusplus\n-}\n-#endif\n-\n-#endif\n-\n-/* End of soapStub.h */\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/install-sh
--- a/GEMBASSY-1.0.3/install-sh Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,501 +0,0 @@\n-#!/bin/sh\n-# install - install a program, script, or datafile\n-\n-scriptversion=2013-12-25.23; # UTC\n-\n-# This originates from X11R5 (mit/util/scripts/install.sh), which was\n-# later released in X11R6 (xc/config/util/install.sh) with the\n-# following copyright and license.\n-#\n-# Copyright (C) 1994 X Consortium\n-#\n-# Permission is hereby granted, free of charge, to any person obtaining a copy\n-# of this software and associated documentation files (the "Software"), to\n-# deal in the Software without restriction, including without limitation the\n-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n-# sell copies of the Software, and to permit persons to whom the Software is\n-# furnished to do so, subject to the following conditions:\n-#\n-# The above copyright notice and this permission notice shall be included in\n-# all copies or substantial portions of the Software.\n-#\n-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN\n-# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-\n-# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n-#\n-# Except as contained in this notice, the name of the X Consortium shall not\n-# be used in advertising or otherwise to promote the sale, use or other deal-\n-# ings in this Software without prior written authorization from the X Consor-\n-# tium.\n-#\n-#\n-# FSF changes to this file are in the public domain.\n-#\n-# Calling this script install-sh is preferred over install.sh, to prevent\n-# \'make\' implicit rules from creating a file called install from it\n-# when there is no Makefile.\n-#\n-# This script is compatible with the BSD install script, but was written\n-# from scratch.\n-\n-tab=\'\t\'\n-nl=\'\n-\'\n-IFS=" $tab$nl"\n-\n-# Set DOITPROG to "echo" to test this script.\n-\n-doit=${DOITPROG-}\n-doit_exec=${doit:-exec}\n-\n-# Put in absolute file names if you don\'t have them in your path;\n-# or use environment vars.\n-\n-chgrpprog=${CHGRPPROG-chgrp}\n-chmodprog=${CHMODPROG-chmod}\n-chownprog=${CHOWNPROG-chown}\n-cmpprog=${CMPPROG-cmp}\n-cpprog=${CPPROG-cp}\n-mkdirprog=${MKDIRPROG-mkdir}\n-mvprog=${MVPROG-mv}\n-rmprog=${RMPROG-rm}\n-stripprog=${STRIPPROG-strip}\n-\n-posix_mkdir=\n-\n-# Desired mode of installed file.\n-mode=0755\n-\n-chgrpcmd=\n-chmodcmd=$chmodprog\n-chowncmd=\n-mvcmd=$mvprog\n-rmcmd="$rmprog -f"\n-stripcmd=\n-\n-src=\n-dst=\n-dir_arg=\n-dst_arg=\n-\n-copy_on_change=false\n-is_target_a_directory=possibly\n-\n-usage="\\\n-Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE\n- or: $0 [OPTION]... SRCFILES... DIRECTORY\n- or: $0 [OPTION]... -t DIRECTORY SRCFILES...\n- or: $0 [OPTION]... -d DIRECTORIES...\n-\n-In the 1st form, copy SRCFILE to DSTFILE.\n-In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.\n-In the 4th, create DIRECTORIES.\n-\n-Options:\n- --help display this help and exit.\n- --version display version info and exit.\n-\n- -c (ignored)\n- -C install only if different (preserve the last data modification time)\n- -d create directories instead of installing files.\n- -g GROUP $chgrpprog installed files to GROUP.\n- -m MODE $chmodprog installed files to MODE.\n- -o USER $chownprog installed files to USER.\n- -s $stripprog installed files.\n- -t DIRECTORY install into DIRECTORY.\n- -T report an error if DSTFILE is a directory.\n-\n-Environment variables override the default commands:\n- CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG\n- RMPROG STRIPPROG\n-"\n-\n-while test $# -ne 0; do\n- case $1 in\n- -c) ;;\n-\n- -C) copy_on_change=true;;\n-\n- -d) dir_arg=true;;\n-\n- -g) chgrpcmd="$chgrpprog $2"\n- shift;;\n-\n- --help) echo "$usage"; exit $?;;\n-\n- -m) mode=$2\n- case $mode in\n- *\' \''..b'et +f\n- IFS=$oIFS\n-\n- prefixes=\n-\n- for d\n- do\n- test X"$d" = X && continue\n-\n- prefix=$prefix$d\n- if test -d "$prefix"; then\n- prefixes=\n- else\n- if $posix_mkdir; then\n- (umask=$mkdir_umask &&\n- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break\n- # Don\'t fail if two instances are running concurrently.\n- test -d "$prefix" || exit 1\n- else\n- case $prefix in\n- *\\\'*) qprefix=`echo "$prefix" | sed "s/\'/\'\\\\\\\\\\\\\\\\\'\'/g"`;;\n- *) qprefix=$prefix;;\n- esac\n- prefixes="$prefixes \'$qprefix\'"\n- fi\n- fi\n- prefix=$prefix/\n- done\n-\n- if test -n "$prefixes"; then\n- # Don\'t fail if two instances are running concurrently.\n- (umask $mkdir_umask &&\n- eval "\\$doit_exec \\$mkdirprog $prefixes") ||\n- test -d "$dstdir" || exit 1\n- obsolete_mkdir_used=true\n- fi\n- fi\n- fi\n-\n- if test -n "$dir_arg"; then\n- { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&\n- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&\n- { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||\n- test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1\n- else\n-\n- # Make a couple of temp file names in the proper directory.\n- dsttmp=$dstdir/_inst.$$_\n- rmtmp=$dstdir/_rm.$$_\n-\n- # Trap to clean up those temp files at exit.\n- trap \'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret\' 0\n-\n- # Copy the file name to the temp name.\n- (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&\n-\n- # and set any options; do chmod last to preserve setuid bits.\n- #\n- # If any of these fail, we abort the whole thing. If we want to\n- # ignore errors from any of these, just make sure not to ignore\n- # errors from the above "$doit $cpprog $src $dsttmp" command.\n- #\n- { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&\n- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&\n- { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&\n- { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&\n-\n- # If -C, don\'t bother to copy if it wouldn\'t change the file.\n- if $copy_on_change &&\n- old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&\n- new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&\n- set -f &&\n- set X $old && old=:$2:$4:$5:$6 &&\n- set X $new && new=:$2:$4:$5:$6 &&\n- set +f &&\n- test "$old" = "$new" &&\n- $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1\n- then\n- rm -f "$dsttmp"\n- else\n- # Rename the file to the real destination.\n- $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||\n-\n- # The rename failed, perhaps because mv can\'t rename something else\n- # to itself, or perhaps because mv is so ancient that it does not\n- # support -f.\n- {\n- # Now remove or move aside any old file at destination location.\n- # We try this two ways since rm can\'t unlink itself on some\n- # systems and the destination file might be busy for other\n- # reasons. In this case, the final cleanup might fail but the new\n- # file should still install successfully.\n- {\n- test ! -f "$dst" ||\n- $doit $rmcmd -f "$dst" 2>/dev/null ||\n- { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&\n- { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }\n- } ||\n- { echo "$0: cannot unlink or rename $dst" >&2\n- (exit 1); exit 1\n- }\n- } &&\n-\n- # Now rename the file to the real destination.\n- $doit $mvcmd "$dsttmp" "$dst"\n- }\n- fi || exit 1\n-\n- trap \'\' 0\n- fi\n-done\n-\n-# Local variables:\n-# eval: (add-hook \'write-file-hooks \'time-stamp)\n-# time-stamp-start: "scriptversion="\n-# time-stamp-format: "%:y-%02m-%02d.%02H"\n-# time-stamp-time-zone: "UTC"\n-# time-stamp-end: "; # UTC"\n-# End:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/ltmain.sh
--- a/GEMBASSY-1.0.3/ltmain.sh Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,11140 +0,0 @@\n-#! /bin/sh\n-## DO NOT EDIT - This file generated from ./build-aux/ltmain.in\n-## by inline-source v2014-01-03.01\n-\n-# libtool (GNU libtool) 2.4.5\n-# Provide generalized library-building support services.\n-# Written by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996\n-\n-# Copyright (C) 1996-2015 Free Software Foundation, Inc.\n-# This is free software; see the source for copying conditions. There is NO\n-# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n-\n-# GNU Libtool is free software; you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation; either version 2 of the License, or\n-# (at your option) any later version.\n-#\n-# As a special exception to the GNU General Public License,\n-# if you distribute this file as part of a program or library that\n-# is built using GNU Libtool, you may include this file under the\n-# same distribution terms that you use for the rest of that program.\n-#\n-# GNU Libtool is distributed in the hope that it will be useful, but\n-# WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n-# General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n-\n-\n-PROGRAM=libtool\n-PACKAGE=libtool\n-VERSION=2.4.5\n-package_revision=2.4.5\n-\n-\n-## ------ ##\n-## Usage. ##\n-## ------ ##\n-\n-# Run \'./libtool --help\' for help with using this script from the\n-# command line.\n-\n-\n-## ------------------------------- ##\n-## User overridable command paths. ##\n-## ------------------------------- ##\n-\n-# After configure completes, it has a better idea of some of the\n-# shell tools we need than the defaults used by the functions shared\n-# with bootstrap, so set those here where they can still be over-\n-# ridden by the user, but otherwise take precedence.\n-\n-: ${AUTOCONF="autoconf"}\n-: ${AUTOMAKE="automake"}\n-\n-\n-## -------------------------- ##\n-## Source external libraries. ##\n-## -------------------------- ##\n-\n-# Much of our low-level functionality needs to be sourced from external\n-# libraries, which are installed to $pkgauxdir.\n-\n-# Set a version string for this script.\n-scriptversion=2014-01-03.01; # UTC\n-\n-# General shell script boiler plate, and helper functions.\n-# Written by Gary V. Vaughan, 2004\n-\n-# Copyright (C) 2004-2015 Free Software Foundation, Inc.\n-# This is free software; see the source for copying conditions. There is NO\n-# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n-\n-# This program is free software; you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation; either version 3 of the License, or\n-# (at your option) any later version.\n-\n-# As a special exception to the GNU General Public License, if you distribute\n-# this file as part of a program or library that is built using GNU Libtool,\n-# you may include this file under the same distribution terms that you use\n-# for the rest of that program.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNES FOR A PARTICULAR PURPOSE. See the GNU\n-# General Public License for more details.\n-\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n-\n-# Please report bugs or propose patches to gary@gnu.org.\n-\n-\n-## ------ ##\n-## Usage. ##\n-## ------ ##\n-\n-# Evaluate this file near the top of your script to gain access to\n-# the functions and variables defined here:\n-#\n-# . `echo "$0" | ${SED-sed} \'s|[^/]*$||\'`/build-aux/funclib.sh\n-#\n-# If you need to override any of the default environment variable\n-# settings, do that before eva'..b'st -n "$library_names"; then\n-\t # Do each command in the postuninstall commands.\n-\t func_execute_cmds "$postuninstall_cmds" \'$rmforce || exit_status=1\'\n-\t fi\n-\n-\t if test -n "$old_library"; then\n-\t # Do each command in the old_postuninstall commands.\n-\t func_execute_cmds "$old_postuninstall_cmds" \'$rmforce || exit_status=1\'\n-\t fi\n-\t # FIXME: should reinstall the best remaining shared library.\n-\t ;;\n-\t esac\n-\tfi\n-\t;;\n-\n- *.lo)\n-\t# Possibly a libtool object, so verify it.\n-\tif func_lalib_p "$file"; then\n-\n-\t # Read the .lo file\n-\t func_source $dir/$name\n-\n-\t # Add PIC object to the list of files to remove.\n-\t if test -n "$pic_object" && test none != "$pic_object"; then\n-\t func_append rmfiles " $dir/$pic_object"\n-\t fi\n-\n-\t # Add non-PIC object to the list of files to remove.\n-\t if test -n "$non_pic_object" && test none != "$non_pic_object"; then\n-\t func_append rmfiles " $dir/$non_pic_object"\n-\t fi\n-\tfi\n-\t;;\n-\n- *)\n-\tif test clean = "$opt_mode"; then\n-\t noexename=$name\n-\t case $file in\n-\t *.exe)\n-\t func_stripname \'\' \'.exe\' "$file"\n-\t file=$func_stripname_result\n-\t func_stripname \'\' \'.exe\' "$name"\n-\t noexename=$func_stripname_result\n-\t # $file with .exe has already been added to rmfiles,\n-\t # add $file without .exe\n-\t func_append rmfiles " $file"\n-\t ;;\n-\t esac\n-\t # Do a test to see if this is a libtool program.\n-\t if func_ltwrapper_p "$file"; then\n-\t if func_ltwrapper_executable_p "$file"; then\n-\t func_ltwrapper_scriptname "$file"\n-\t relink_command=\n-\t func_source $func_ltwrapper_scriptname_result\n-\t func_append rmfiles " $func_ltwrapper_scriptname_result"\n-\t else\n-\t relink_command=\n-\t func_source $dir/$noexename\n-\t fi\n-\n-\t # note $name still contains .exe if it was in $file originally\n-\t # as does the version of $file that was added into $rmfiles\n-\t func_append rmfiles " $odir/$name $odir/${name}S.$objext"\n-\t if test yes = "$fast_install" && test -n "$relink_command"; then\n-\t func_append rmfiles " $odir/lt-$name"\n-\t fi\n-\t if test "X$noexename" != "X$name"; then\n-\t func_append rmfiles " $odir/lt-$noexename.c"\n-\t fi\n-\t fi\n-\tfi\n-\t;;\n- esac\n- func_show_eval "$RM $rmfiles" \'exit_status=1\'\n- done\n-\n- # Try to remove the $objdir\'s in the directories where we deleted files\n- for dir in $rmdirs; do\n- if test -d "$dir"; then\n-\tfunc_show_eval "rmdir $dir >/dev/null 2>&1"\n- fi\n- done\n-\n- exit $exit_status\n-}\n-\n-if test uninstall = "$opt_mode" || test clean = "$opt_mode"; then\n- func_mode_uninstall ${1+"$@"}\n-fi\n-\n-test -z "$opt_mode" && {\n- help=$generic_help\n- func_fatal_help "you must specify a MODE"\n-}\n-\n-test -z "$exec_cmd" && \\\n- func_fatal_help "invalid operation mode \'$opt_mode\'"\n-\n-if test -n "$exec_cmd"; then\n- eval exec "$exec_cmd"\n- exit $EXIT_FAILURE\n-fi\n-\n-exit $exit_status\n-\n-\n-# The TAGs below are defined such that we never get into a situation\n-# where we disable both kinds of libraries. Given conflicting\n-# choices, we go for a static library, that is the most portable,\n-# since we can\'t tell whether shared libraries were disabled because\n-# the user asked for that or because the platform doesn\'t support\n-# them. This is particularly important on AIX, because we don\'t\n-# support having both static and shared libraries enabled at the same\n-# time on that platform, so we default to a shared-only configuration.\n-# If a disable-shared tag is given, we\'ll fallback to a static-only\n-# configuration. But we\'ll never go from static-only to shared-only.\n-\n-# ### BEGIN LIBTOOL TAG CONFIG: disable-shared\n-build_libtool_libs=no\n-build_old_libs=yes\n-# ### END LIBTOOL TAG CONFIG: disable-shared\n-\n-# ### BEGIN LIBTOOL TAG CONFIG: disable-static\n-build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`\n-# ### END LIBTOOL TAG CONFIG: disable-static\n-\n-# Local Variables:\n-# mode:shell-script\n-# sh-indentation:2\n-# End:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/._libtool.m4

Binary file GEMBASSY-1.0.3/m4/._libtool.m4 has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/._ltoptions.m4

Binary file GEMBASSY-1.0.3/m4/._ltoptions.m4 has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/._ltsugar.m4

Binary file GEMBASSY-1.0.3/m4/._ltsugar.m4 has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/._lt~obsolete.m4

Binary file GEMBASSY-1.0.3/m4/._lt~obsolete.m4 has changed

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/general.m4
--- a/GEMBASSY-1.0.3/m4/general.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,32 +0,0 @@
-AC_DEFUN([CHECK_GENERAL],
-#
-# Handle general setup e.g. documentation directory
-#
-[AC_MSG_CHECKING(if docroot is given)
-AC_ARG_WITH([docroot],
-    [AS_HELP_STRING([--with-docroot=DIR],
-        [root directory path of documentation (defaults to none)])],
-[if test "$withval" != no ; then
-  AC_MSG_RESULT(yes)
-  CPPFLAGS="$CPPFLAGS -DDOC_ROOT=\\\"$withval\\\""
-fi], [
-AC_MSG_RESULT(no)
-])
-]
-
-
-# GCC profiling
-[AC_MSG_CHECKING(if gcc profiling is selected)
-AC_ARG_WITH([gccprofile],
-    [AS_HELP_STRING([--with-gccprofile], [selects profiling])],
-[if test "$withval" != no ; then
-  AC_MSG_RESULT(yes)
-  CFLAGS="$CFLAGS -g -pg"
-  LDFLAGS="$LDFLAGS -pg"
-fi], [
-AC_MSG_RESULT(no)
-])
-
-]
-)
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/hpdf.m4
--- a/GEMBASSY-1.0.3/m4/hpdf.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,89 +0,0 @@
-dnl @synopsis CHECK_HPDF()
-dnl
-dnl This macro searches for an installed libhpdf (libharu) library. If nothing
-dnl was specified when calling configure, it first searches in /usr/local
-dnl and then in /usr. If the --with-hpdf=DIR is specified, it will try
-dnl to find it in DIR/include and DIR/lib.
-dnl
-dnl It defines the symbol PLD_pdf if the library is found.
-dnl
-
-
-AC_DEFUN([CHECK_HPDF],
-#
-# Handle user hints
-#
-[AC_MSG_CHECKING([whether to look for pdf support])
-AC_ARG_WITH([hpdf],
-    [AS_HELP_STRING([--with-hpdf=DIR],
-        [root directory path of hpdf installation @<:@defaults to /usr@:>@])],
-    [if test "$withval" != no ; then
-      AC_MSG_RESULT(yes)
-      ALT_HOME="$withval"
-    else
-      AC_MSG_RESULT([no])
-    fi], [
-    AC_MSG_RESULT([yes])
-    ALT_HOME=/usr
-])
-
-
-#
-# Locate hpdf
-#
-if test -d "${ALT_HOME}"
-then
-
-#
-# Keep a copy if it fails
-#
- ALT_LDFLAGS="$LDFLAGS"
- ALT_CPPFLAGS="$CPPFLAGS"
-
-#
-# Set
-#
-        LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-        CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
-
-#
-# Check for libharu in ALT_HOME
-#
-        AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0, -L${ALT_HOME}/lib)
-#
-#
-# If everything found okay then proceed to include png driver in config.
-#
- if test $CHECK = "1" ; then
-   LIBS="$LIBS -lhpdf"
-
-   case $host_os in
-   solaris*)
- LDFLAGS="$LDFLAGS -R$ALT_HOME/lib"
- ;;
-          esac
-
-   AC_DEFINE([PLD_pdf], [1], [Define to 1 if PDF support is available])
-   AM_CONDITIONAL(AMPDF, true)
-   echo PDF support found
-     if test $ALT_HOME = "/usr" ; then
-   LDFLAGS="$ALT_LDFLAGS"
-   CPPFLAGS="$ALT_CPPFLAGS"
-     fi
- else
-#
-# If not okay then reset FLAGS.
-#
-     AM_CONDITIONAL(AMPDF, false)
-   LDFLAGS="$ALT_LDFLAGS"
-   CPPFLAGS="$ALT_CPPFLAGS"
-   echo "No pdf support (libhpdf) found."
- fi
-
-else
-        if test $withval != "no"; then
- echo "Directory $ALT_HOME does not exist"
- exit 0
-        fi
-fi
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/java.m4
--- a/GEMBASSY-1.0.3/m4/java.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,249 +0,0 @@
-dnl                                            -*- Autoconf -*-
-dnl @synopsis CHECK_JAVA()
-dnl
-dnl Need to specify --with-java and --with-javaos
-dnl @author Alan Bleasby
-dnl
-dnl This macro calls:
-dnl
-dnl   AC_SUBST([JAVA_CFLAGS])
-dnl   AC_SUBST([JAVA_CPPFLAGS])
-dnl   AC_SUBST([JAVA_LDFLAGS])
-dnl
-dnl   AM_CONDITIONAL([JAVA_BUILD], ...)
-dnl
-dnl And sets:
-dnl
-dnl   AC_DEFINE([HAVE_JAVA], ...)
-dnl
-dnl   AC_PATH_PROG([ANT], ...)
-dnl   AC_PATH_PROG([JAR], ...)
-dnl   AC_PATH_PROG([JAVA], ...)
-dnl   AC_PATH_PROG([JAVAC], ...)
-
-AC_DEFUN([CHECK_JAVA],
-[
-  JAVA_CFLAGS=""
-  JAVA_CPPFLAGS=""
-  JAVA_LDFLAGS=""
-
-  have_java="yes"
-  auth_java=""
-
-  AC_MSG_CHECKING([for Java JNI])
-
-  AC_ARG_WITH([java],
-  [AS_HELP_STRING([--with-java@<:@=ARG@:>@],
-  [root directory path of Java installation])],
-  [
-    AC_MSG_RESULT([${withval}])
-    AS_IF([test "x${withval}" = "xno"], [have_java="no"])
-  ],
-  [
-    AC_MSG_RESULT([no])
-    have_java="no"
-  ])
-
-  AS_IF([test "x${have_java}" = "xyes"],
-  [
-    # If specified, the Java JNI include directory has to exist.
-    AS_IF([test -d ${with_java}],
-    [AS_VAR_SET([JAVA_CPPFLAGS], ["-I${withval}"])],
-    [
-      have_java="no"
-      AC_MSG_ERROR([Java include directory ${withval} does not exist])
-    ])
-  ])
-
-  AC_MSG_CHECKING([for Java JNI OS])
-
-  AC_ARG_WITH([javaos],
-  [AS_HELP_STRING([--with-javaos@<:@=ARG@:>@],
-  [root directory path of Java OS include])],
-  [
-    AC_MSG_RESULT([${withval}])
-
-    AS_IF([test "x${withval}" != "xno"],
-    [
-      # If specified, the Java JNI OS include directory has to exist.
-      AS_IF([test "x${have_java}" = "xyes" && test -d ${withval}],
-      [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -I${withval}"])],
-      [
-        have_java="no"
-        AC_MSG_ERROR([Java OS include directory ${withval} does not exist])
-      ])
-    ])
-  ],
-  [
-    AC_MSG_RESULT([no])
-  ])
-
-  # Authorisation type
-
-  AC_MSG_CHECKING([for authorisation type])
-
-  AC_ARG_WITH([auth],
-  [AS_HELP_STRING([--with-auth@<:@=ARG@:>@],
-  [authorisation mechanism for Jemboss server @<:@default=PAM@:>@])],
-  [
-    AS_IF([test "x${withval}" != "xno"],
-    [
-      AC_MSG_RESULT([yes])
-
-      AS_CASE([${withval}],
-      [yes],
-      [
-        auth_java="PAM"
-        AC_CHECK_LIB([pam], [main],
-        [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpam"])])
-      ],
-      [pam],
-      [
-        auth_java="PAM"
-        AC_CHECK_LIB([pam], [main],
-        [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpam"])])
-      ],
-      [shadow],
-      [
-        auth_java="N_SHADOW"
-        AC_CHECK_LIB([crypy], [main],
-        [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lcrypt"])])
-      ],
-      [rshadow],
-      [
-        auth_java="R_SHADOW"
-        AC_CHECK_LIB([crypy], [main],
-        [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lcrypt"])])
-      ],
-      [noshadow],
-      [auth_java="NO_SHADOW"],
-      [rnoshadow],
-      [auth_java="RNO_SHADOW"],
-      [aixshadow],
-      [auth_java="AIX_SHADOW"],
-      [hpuxshadow],
-      [auth_java="HPUX_SHADOW"])
-    ],
-    [AC_MSG_RESULT([no])])
-  ],
-  [AC_MSG_RESULT([no])])
-
-  AS_IF([test -n "${auth_java}"],
-  [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D${auth_java}"])],
-  [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -DNO_AUTH"])])
-
-  # Threading type
-
-  AC_MSG_CHECKING([for threading type])
-
-  AC_ARG_WITH([thread],
-  [AS_HELP_STRING([--with-thread@<:@=ARG@:>@],
-  [thread type @<:@default=linux@:>@])],
-  [
-    AS_IF([test "x${withval}" != "xno"],
-    [
-      AC_MSG_RESULT([yes])
-
-      AS_CASE([${withval}],
-      [yes],
-      [
-        AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        # AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [freebsd],
-      [
-        AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_THREAD_SAFE"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -pthread"])
-        # AS_VAR_APPEND([LIBS], [" -lc_r"])
-      ],
-      [linux],
-      [
-        AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        # AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [solaris],
-      [
-        AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_POSIX_C_SOURCE=199506L"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        # AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [macos],
-      [
-        # AS_VAR_APPEND([JAVA_CPPFLAGS], [""])
-        # AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        # AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [hpux],
-      [
-        AS_VAR_APPEND([JAVA_CFLAGS], [" -Ae +z"])
-        AS_VAR_APPEND([JAVA CPPFLAGS], [" -DNATIVE -D_POSIX_C_SOURCE=199506L"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        # AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [irix],
-      [
-        # AS_VAR_APPEND([JAVA_CFLAGS], [""])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [aix],
-      [
-        AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ],
-      [osf],
-      [
-        AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT -D_OSF_SOURCE"])
-        AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"])
-        AS_VAR_APPEND([LIBS], [" -lpthread"])
-      ])
-    ],
-    [AC_MSG_RESULT([no])])
-  ],
-  [AC_MSG_RESULT([no])])
-
-  # Test for programs ant, jar, java and javac.
-
-  AS_IF([test "x${have_java}" = "xyes"],
-  [
-    AC_PATH_PROG([ANT], [ant], [no])
-    AS_IF([test "x${ANT}" = "xno"], [have_java="no"])
-
-    AC_PATH_PROG([JAR], [jar], [no])
-    AS_IF([test "x${JAR}" = "xno"], [have_java="no"])
-
-    AC_PATH_PROG([JAVA], [java], [no])
-    AS_IF([test "x${JAVA}" = "xno"], [have_java="no"])
-
-    AC_PATH_PROG([JAVAC], [javac], [no])
-    AS_IF([test "x${JAVAC}" = "xno"], [have_java="no"])
-  ])
-
-  AS_IF([test "x${have_java}" = "xyes"],
-  [
-    AC_DEFINE([HAVE_JAVA], [1],
-    [Define to 1 if the Java Native Interface (JNI) is available.])
-
-    ### FIXME: Append -DDEBIAN for the moment.
-    # Debian uses PAM service "ssh" instead of "login", see ajjava.c
-    # This could use AC_DEFINE() if no better option was avialable.
-    # Ultimately, this should be configurable via server configuration
-    # files.
-    AS_IF([test -f "/etc/debian_release" || test -f /etc/debian_version],
-    [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -DDEBIAN"])])
-  ])
-
-  AC_ARG_VAR([ANT], [Path to the Apache Ant make tool])
-  AC_ARG_VAR([JAR], [Path to the Java archive tool])
-  AC_ARG_VAR([JAVA], [Path to the Java application launcher])
-  AC_ARG_VAR([JAVAC], [Path to the Java compiler])
-
-  AC_SUBST([JAVA_CFLAGS])
-  AC_SUBST([JAVA_CPPFLAGS])
-  AC_SUBST([JAVA_LDFLAGS])
-
-  AM_CONDITIONAL([JAVA_BUILD], [test "x${have_java}" = "xyes"])
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/lf_x11.m4
--- a/GEMBASSY-1.0.3/m4/lf_x11.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,78 +0,0 @@
-dnl Copyright (C) 1988 Eleftherios Gkioulekas <lf@amath.washington.edu>
-dnl
-dnl This program is free software; you can redistribute it and/or modify
-dnl it under the terms of the GNU General Public License as published by
-dnl the Free Software Foundation; either version 2 of the License, or
-dnl (at your option) any later version.
-dnl
-dnl This program is distributed in the hope that it will be useful,
-dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
-dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-dnl GNU General Public License for more details.
-dnl
-dnl You should have received a copy of the GNU General Public License
-dnl along with this program; if not, write to the Free Software
-dnl Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
-dnl
-dnl As a special exception to the GNU General Public License, if you
-dnl distribute this file as part of a program that contains a configuration
-dnl script generated by Autoconf, you may include it under the same
-dnl distribution terms that you use for the rest of that program.
-
-
-#-----------------------------------------------------------------------
-# This macro searches for Xlib and when it finds it it adds the
-# appropriate flags to CFLAGS and export the link sequence to
-# the variable XLIB.
-# In your configure.in file add:
-#   LF_PATH_XLIB
-# In your Makefile.am add
-#   program_LDADD = .... $(XLIB)
-#------------------------------------------------------------------------
-#
-# Just added EMBOSS into LF_PATH_XLIB so that on the systems where
-# LF_PATH_XLIB exists there are no duplication errors.
-
-
-AC_DEFUN([LF_EMBOSS_PATH_XLIB],[
-  CFLAGS="$CFLAGS $X_CFLAGS"
-
-case $host_os in
-irix*)
-    XLIB="-lX11 $X_EXTRA_LIBS"
-    ;;
-*)
-    XLIB="$X_LIBS -lX11 $X_EXTRA_LIBS"
-    ;;
-esac
-
-  AC_SUBST([XLIB])
-
-AC_CHECK_HEADER(X11/Xlib.h,
-[
- AC_DEFINE([PLD_xwin], [1], [Define to 1 if X11 support is available])
-],
-[
- echo ""
- echo "X11 graphics have been selected but no X11 header files"
-        echo "have been found."
-        echo ""
-        echo "This error usually happens on Linux/MacOSX distributions"
- echo "where the optional X11 development files have not been installed."
-        echo "On Linux RPM systems this package is usually called something"
-        echo "like xorg-x11-proto-devel whereas on Debian/Ubuntu it may"
-        echo "be called x-dev. On MacOSX installation DVDs the X11 files"
-        echo "can usually be found as an explicitly named optional"
-        echo "installation."
-        echo ""
-        echo "After installing the X11 development files you should do a"
-        echo "'make clean' and perform the configure stage again."
-        echo ""
-        echo "Alternatively, to install EMBOSS without X11 support, you can add"
-        echo "the --without-x switch to the configure command."
- echo ""
-        exit $?
-])
-
-])
-

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/libtool.m4
--- a/GEMBASSY-1.0.3/m4/libtool.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,8364 +0,0 @@\n-# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-\n-#\n-# Copyright (C) 1996-2001, 2003-2015 Free Software Foundation, Inc.\n-# Written by Gordon Matzigkeit, 1996\n-#\n-# This file is free software; the Free Software Foundation gives\n-# unlimited permission to copy and/or distribute it, with or without\n-# modifications, as long as this notice is preserved.\n-\n-m4_define([_LT_COPYING], [dnl\n-# Copyright (C) 2014 Free Software Foundation, Inc.\n-# This is free software; see the source for copying conditions. There is NO\n-# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n-\n-# GNU Libtool is free software; you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation; either version 2 of of the License, or\n-# (at your option) any later version.\n-#\n-# As a special exception to the GNU General Public License, if you\n-# distribute this file as part of a program or library that is built\n-# using GNU Libtool, you may include this file under the same\n-# distribution terms that you use for the rest of that program.\n-#\n-# GNU Libtool is distributed in the hope that it will be useful, but\n-# WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-# GNU General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n-])\n-\n-# serial 58 LT_INIT\n-\n-\n-# LT_PREREQ(VERSION)\n-# ------------------\n-# Complain and exit if this libtool version is less that VERSION.\n-m4_defun([LT_PREREQ],\n-[m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1,\n- [m4_default([$3],\n-\t\t [m4_fatal([Libtool version $1 or higher is required],\n-\t\t 63)])],\n- [$2])])\n-\n-\n-# _LT_CHECK_BUILDDIR\n-# ------------------\n-# Complain if the absolute build directory name contains unusual characters\n-m4_defun([_LT_CHECK_BUILDDIR],\n-[case `pwd` in\n- *\\ * | *\\\t*)\n- AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;;\n-esac\n-])\n-\n-\n-# LT_INIT([OPTIONS])\n-# ------------------\n-AC_DEFUN([LT_INIT],\n-[AC_PREREQ([2.62])dnl We use AC_PATH_PROGS_FEATURE_CHECK\n-AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl\n-AC_BEFORE([$0], [LT_LANG])dnl\n-AC_BEFORE([$0], [LT_OUTPUT])dnl\n-AC_BEFORE([$0], [LTDL_INIT])dnl\n-m4_require([_LT_CHECK_BUILDDIR])dnl\n-\n-dnl Autoconf doesn\'t catch unexpanded LT_ macros by default:\n-m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl\n-m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl\n-dnl aclocal doesn\'t pull ltoptions.m4, ltsugar.m4, or ltversion.m4\n-dnl unless we require an AC_DEFUNed macro:\n-AC_REQUIRE([LTOPTIONS_VERSION])dnl\n-AC_REQUIRE([LTSUGAR_VERSION])dnl\n-AC_REQUIRE([LTVERSION_VERSION])dnl\n-AC_REQUIRE([LTOBSOLETE_VERSION])dnl\n-m4_require([_LT_PROG_LTMAIN])dnl\n-\n-_LT_SHELL_INIT([SHELL=${CONFIG_SHELL-/bin/sh}])\n-\n-dnl Parse OPTIONS\n-_LT_SET_OPTIONS([$0], [$1])\n-\n-# This can be used to rebuild libtool when needed\n-LIBTOOL_DEPS=$ltmain\n-\n-# Always use our own libtool.\n-LIBTOOL=\'$(SHELL) $(top_builddir)/libtool\'\n-AC_SUBST(LIBTOOL)dnl\n-\n-_LT_SETUP\n-\n-# Only expand once:\n-m4_define([LT_INIT])\n-])# LT_INIT\n-\n-# Old names:\n-AU_ALIAS([AC_PROG_LIBTOOL], [LT_INIT])\n-AU_ALIAS([AM_PROG_LIBTOOL], [LT_INIT])\n-dnl aclocal-1.4 backwards compatibility:\n-dnl AC_DEFUN([AC_PROG_LIBTOOL], [])\n-dnl AC_DEFUN([AM_PROG_LIBTOOL], [])\n-\n-\n-# _LT_PREPARE_CC_BASENAME\n-# -----------------------\n-m4_defun([_LT_PREPARE_CC_BASENAME], [\n-# Calculate cc_basename. Skip known compiler wrappers and cross-prefix.\n-func_cc_basename ()\n-{\n- for cc_temp in @S|@*""; do\n- case $cc_temp in\n- compile | *[[\\\\/]]compile | ccache | *[[\\\\/]]ccache ) ;;\n- distcc | *[[\\\\/]]distcc | purify | *[[\\\\/]]purify ) ;;\n- \\-*) ;;\n- *) break;;\n- esac\n- done\n- func_cc_basename_result='..b'r GNU sed and select it if it is found.\n- if "$lt_ac_sed" --version 2>&1 < /dev/null | grep \'GNU\' > /dev/null; then\n- lt_cv_path_SED=$lt_ac_sed\n- break\n- fi\n- while true; do\n- cat conftest.in conftest.in >conftest.tmp\n- mv conftest.tmp conftest.in\n- cp conftest.in conftest.nl\n- echo >>conftest.nl\n- $lt_ac_sed -e \'s/a$//\' < conftest.nl >conftest.out || break\n- cmp -s conftest.out conftest.nl || break\n- # 10000 chars as input seems more than enough\n- test 10 -lt "$lt_ac_count" && break\n- lt_ac_count=`expr $lt_ac_count + 1`\n- if test "$lt_ac_count" -gt "$lt_ac_max"; then\n- lt_ac_max=$lt_ac_count\n- lt_cv_path_SED=$lt_ac_sed\n- fi\n- done\n-done\n-])\n-SED=$lt_cv_path_SED\n-AC_SUBST([SED])\n-AC_MSG_RESULT([$SED])\n-])#AC_PROG_SED\n-])#m4_ifndef\n-\n-# Old name:\n-AU_ALIAS([LT_AC_PROG_SED], [AC_PROG_SED])\n-dnl aclocal-1.4 backwards compatibility:\n-dnl AC_DEFUN([LT_AC_PROG_SED], [])\n-\n-\n-# _LT_CHECK_SHELL_FEATURES\n-# ------------------------\n-# Find out whether the shell is Bourne or XSI compatible,\n-# or has some other useful features.\n-m4_defun([_LT_CHECK_SHELL_FEATURES],\n-[if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then\n- lt_unset=unset\n-else\n- lt_unset=false\n-fi\n-_LT_DECL([], [lt_unset], [0], [whether the shell understands "unset"])dnl\n-\n-# test EBCDIC or ASCII\n-case `echo X|tr X \'\\101\'` in\n- A) # ASCII based system\n- # \\n is not interpreted correctly by Solaris 8 /usr/ucb/tr\n- lt_SP2NL=\'tr \\040 \\012\'\n- lt_NL2SP=\'tr \\015\\012 \\040\\040\'\n- ;;\n- *) # EBCDIC based system\n- lt_SP2NL=\'tr \\100 \\n\'\n- lt_NL2SP=\'tr \\r\\n \\100\\100\'\n- ;;\n-esac\n-_LT_DECL([SP2NL], [lt_SP2NL], [1], [turn spaces into newlines])dnl\n-_LT_DECL([NL2SP], [lt_NL2SP], [1], [turn newlines into spaces])dnl\n-])# _LT_CHECK_SHELL_FEATURES\n-\n-\n-# _LT_PATH_CONVERSION_FUNCTIONS\n-# -----------------------------\n-# Determine what file name conversion functions should be used by\n-# func_to_host_file (and, implicitly, by func_to_host_path). These are needed\n-# for certain cross-compile configurations and native mingw.\n-m4_defun([_LT_PATH_CONVERSION_FUNCTIONS],\n-[AC_REQUIRE([AC_CANONICAL_HOST])dnl\n-AC_REQUIRE([AC_CANONICAL_BUILD])dnl\n-AC_MSG_CHECKING([how to convert $build file names to $host format])\n-AC_CACHE_VAL(lt_cv_to_host_file_cmd,\n-[case $host in\n- *-*-mingw* )\n- case $build in\n- *-*-mingw* ) # actually msys\n- lt_cv_to_host_file_cmd=func_convert_file_msys_to_w32\n- ;;\n- *-*-cygwin* )\n- lt_cv_to_host_file_cmd=func_convert_file_cygwin_to_w32\n- ;;\n- * ) # otherwise, assume *nix\n- lt_cv_to_host_file_cmd=func_convert_file_nix_to_w32\n- ;;\n- esac\n- ;;\n- *-*-cygwin* )\n- case $build in\n- *-*-mingw* ) # actually msys\n- lt_cv_to_host_file_cmd=func_convert_file_msys_to_cygwin\n- ;;\n- *-*-cygwin* )\n- lt_cv_to_host_file_cmd=func_convert_file_noop\n- ;;\n- * ) # otherwise, assume *nix\n- lt_cv_to_host_file_cmd=func_convert_file_nix_to_cygwin\n- ;;\n- esac\n- ;;\n- * ) # unhandled hosts (and "normal" native builds)\n- lt_cv_to_host_file_cmd=func_convert_file_noop\n- ;;\n-esac\n-])\n-to_host_file_cmd=$lt_cv_to_host_file_cmd\n-AC_MSG_RESULT([$lt_cv_to_host_file_cmd])\n-_LT_DECL([to_host_file_cmd], [lt_cv_to_host_file_cmd],\n- [0], [convert $build file names to $host format])dnl\n-\n-AC_MSG_CHECKING([how to convert $build file names to toolchain format])\n-AC_CACHE_VAL(lt_cv_to_tool_file_cmd,\n-[#assume ordinary cross tools, or native build.\n-lt_cv_to_tool_file_cmd=func_convert_file_noop\n-case $host in\n- *-*-mingw* )\n- case $build in\n- *-*-mingw* ) # actually msys\n- lt_cv_to_tool_file_cmd=func_convert_file_msys_to_w32\n- ;;\n- esac\n- ;;\n-esac\n-])\n-to_tool_file_cmd=$lt_cv_to_tool_file_cmd\n-AC_MSG_RESULT([$lt_cv_to_tool_file_cmd])\n-_LT_DECL([to_tool_file_cmd], [lt_cv_to_tool_file_cmd],\n- [0], [convert $build files to toolchain format])dnl\n-])# _LT_PATH_CONVERSION_FUNCTIONS\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/ltoptions.m4
--- a/GEMBASSY-1.0.3/m4/ltoptions.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b"@@ -1,437 +0,0 @@\n-# Helper functions for option handling. -*- Autoconf -*-\n-#\n-# Copyright (C) 2004-2005, 2007-2009, 2011-2015 Free Software\n-# Foundation, Inc.\n-# Written by Gary V. Vaughan, 2004\n-#\n-# This file is free software; the Free Software Foundation gives\n-# unlimited permission to copy and/or distribute it, with or without\n-# modifications, as long as this notice is preserved.\n-\n-# serial 8 ltoptions.m4\n-\n-# This is to help aclocal find these macros, as it can't see m4_define.\n-AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])\n-\n-\n-# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME)\n-# ------------------------------------------\n-m4_define([_LT_MANGLE_OPTION],\n-[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])])\n-\n-\n-# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME)\n-# ---------------------------------------\n-# Set option OPTION-NAME for macro MACRO-NAME, and if there is a\n-# matching handler defined, dispatch to it. Other OPTION-NAMEs are\n-# saved as a flag.\n-m4_define([_LT_SET_OPTION],\n-[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl\n-m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]),\n- _LT_MANGLE_DEFUN([$1], [$2]),\n- [m4_warning([Unknown $1 option '$2'])])[]dnl\n-])\n-\n-\n-# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET])\n-# ------------------------------------------------------------\n-# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.\n-m4_define([_LT_IF_OPTION],\n-[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])])\n-\n-\n-# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET)\n-# -------------------------------------------------------\n-# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME\n-# are set.\n-m4_define([_LT_UNLESS_OPTIONS],\n-[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),\n-\t [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option),\n-\t\t [m4_define([$0_found])])])[]dnl\n-m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3\n-])[]dnl\n-])\n-\n-\n-# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST)\n-# ----------------------------------------\n-# OPTION-LIST is a space-separated list of Libtool options associated\n-# with MACRO-NAME. If any OPTION has a matching handler declared with\n-# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about\n-# the unknown option and exit.\n-m4_defun([_LT_SET_OPTIONS],\n-[# Set options\n-m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),\n- [_LT_SET_OPTION([$1], _LT_Option)])\n-\n-m4_if([$1],[LT_INIT],[\n- dnl\n- dnl Simply set some default values (i.e off) if boolean options were not\n- dnl specified:\n- _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no\n- ])\n- _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no\n- ])\n- dnl\n- dnl If no reference was made to various pairs of opposing options, then\n- dnl we run the default mode handler for the pair. For example, if neither\n- dnl 'shared' nor 'disable-shared' was passed, we enable building of shared\n- dnl archives by default:\n- _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED])\n- _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC])\n- _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC])\n- _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install],\n-\t\t [_LT_ENABLE_FAST_INSTALL])\n- _LT_UNLESS_OPTIONS([LT_INIT], [aix-soname=aix aix-soname=both aix-soname=svr4],\n-\t\t [_LT_WITH_AIX_SONAME([aix])])\n- ])\n-])# _LT_SET_OPTIONS\n-\n-\n-## --------------------------------- ##\n-## Macros to handle LT_INIT options. ##\n-## --------------------------------- ##\n-\n-# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME)\n-# -----------------------------------------\n-m4_define([_LT_MANGLE_DEFUN],\n-[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])])\n-\n-\n-# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE)\n-# -----------------------------------------------\n-m4_define([LT_OPTION_DEFINE],\n-[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl\n-])# LT_OPTION_DEFINE\n-\n-\n-# dlopen\n-# ------\n-LT_OPTION_DEFI"..b'-soname=both\' and `aix-soname=svr4\' LT_INIT options. DEFAULT\n-# is either `aix\', `both\' or `svr4\'. If omitted, it defaults to `aix\'.\n-m4_define([_LT_WITH_AIX_SONAME],\n-[m4_define([_LT_WITH_AIX_SONAME_DEFAULT], [m4_if($1, svr4, svr4, m4_if($1, both, both, aix))])dnl\n-shared_archive_member_spec=\n-case $host,$enable_shared in\n-power*-*-aix[[5-9]]*,yes)\n- AC_MSG_CHECKING([which variant of shared library versioning to provide])\n- AC_ARG_WITH([aix-soname],\n- [AS_HELP_STRING([--with-aix-soname=aix|svr4|both],\n- [shared library versioning (aka "SONAME") variant to provide on AIX, @<:@default=]_LT_WITH_AIX_SONAME_DEFAULT[@:>@.])],\n- [case $withval in\n- aix|svr4|both)\n- ;;\n- *)\n- AC_MSG_ERROR([Unknown argument to --with-aix-soname])\n- ;;\n- esac\n- lt_cv_with_aix_soname=$with_aix_soname],\n- [AC_CACHE_VAL([lt_cv_with_aix_soname],\n- [lt_cv_with_aix_soname=]_LT_WITH_AIX_SONAME_DEFAULT)\n- with_aix_soname=$lt_cv_with_aix_soname])\n- AC_MSG_RESULT([$with_aix_soname])\n- if test aix != "$with_aix_soname"; then\n- # For the AIX way of multilib, we name the shared archive member\n- # based on the bitwidth used, traditionally \'shr.o\' or \'shr_64.o\',\n- # and \'shr.imp\' or \'shr_64.imp\', respectively, for the Import File.\n- # Even when GNU compilers ignore OBJECT_MODE but need \'-maix64\' flag,\n- # the AIX toolchain works better with OBJECT_MODE set (default 32).\n- if test 64 = "${OBJECT_MODE-32}"; then\n- shared_archive_member_spec=shr_64\n- else\n- shared_archive_member_spec=shr\n- fi\n- fi\n- ;;\n-*)\n- with_aix_soname=aix\n- ;;\n-esac\n-\n-_LT_DECL([], [shared_archive_member_spec], [0],\n- [Shared archive member basename, for filename based shared library versioning on AIX])dnl\n-])# _LT_WITH_AIX_SONAME\n-\n-LT_OPTION_DEFINE([LT_INIT], [aix-soname=aix], [_LT_WITH_AIX_SONAME([aix])])\n-LT_OPTION_DEFINE([LT_INIT], [aix-soname=both], [_LT_WITH_AIX_SONAME([both])])\n-LT_OPTION_DEFINE([LT_INIT], [aix-soname=svr4], [_LT_WITH_AIX_SONAME([svr4])])\n-\n-\n-# _LT_WITH_PIC([MODE])\n-# --------------------\n-# implement the --with-pic flag, and support the \'pic-only\' and \'no-pic\'\n-# LT_INIT options.\n-# MODE is either \'yes\' or \'no\'. If omitted, it defaults to \'both\'.\n-m4_define([_LT_WITH_PIC],\n-[AC_ARG_WITH([pic],\n- [AS_HELP_STRING([--with-pic@<:@=PKGS@:>@],\n-\t[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],\n- [lt_p=${PACKAGE-default}\n- case $withval in\n- yes|no) pic_mode=$withval ;;\n- *)\n- pic_mode=default\n- # Look at the argument we got. We use all the common list separators.\n- lt_save_ifs=$IFS; IFS=$IFS$PATH_SEPARATOR,\n- for lt_pkg in $withval; do\n-\tIFS=$lt_save_ifs\n-\tif test "X$lt_pkg" = "X$lt_p"; then\n-\t pic_mode=yes\n-\tfi\n- done\n- IFS=$lt_save_ifs\n- ;;\n- esac],\n- [pic_mode=m4_default([$1], [default])])\n-\n-_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl\n-])# _LT_WITH_PIC\n-\n-LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])])\n-LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])])\n-\n-# Old name:\n-AU_DEFUN([AC_LIBTOOL_PICMODE],\n-[_LT_SET_OPTION([LT_INIT], [pic-only])\n-AC_DIAGNOSE([obsolete],\n-[$0: Remove this warning and the call to _LT_SET_OPTION when you\n-put the \'pic-only\' option into LT_INIT\'s first parameter.])\n-])\n-\n-dnl aclocal-1.4 backwards compatibility:\n-dnl AC_DEFUN([AC_LIBTOOL_PICMODE], [])\n-\n-## ----------------- ##\n-## LTDL_INIT Options ##\n-## ----------------- ##\n-\n-m4_define([_LTDL_MODE], [])\n-LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive],\n-\t\t [m4_define([_LTDL_MODE], [nonrecursive])])\n-LT_OPTION_DEFINE([LTDL_INIT], [recursive],\n-\t\t [m4_define([_LTDL_MODE], [recursive])])\n-LT_OPTION_DEFINE([LTDL_INIT], [subproject],\n-\t\t [m4_define([_LTDL_MODE], [subproject])])\n-\n-m4_define([_LTDL_TYPE], [])\n-LT_OPTION_DEFINE([LTDL_INIT], [installable],\n-\t\t [m4_define([_LTDL_TYPE], [installable])])\n-LT_OPTION_DEFINE([LTDL_INIT], [convenience],\n-\t\t [m4_define([_LTDL_TYPE], [convenience])])\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/ltsugar.m4
--- a/GEMBASSY-1.0.3/m4/ltsugar.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,124 +0,0 @@
-# ltsugar.m4 -- libtool m4 base layer.                         -*-Autoconf-*-
-#
-# Copyright (C) 2004-2005, 2007-2008, 2011-2015 Free Software
-# Foundation, Inc.
-# Written by Gary V. Vaughan, 2004
-#
-# This file is free software; the Free Software Foundation gives
-# unlimited permission to copy and/or distribute it, with or without
-# modifications, as long as this notice is preserved.
-
-# serial 6 ltsugar.m4
-
-# This is to help aclocal find these macros, as it can't see m4_define.
-AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
-
-
-# lt_join(SEP, ARG1, [ARG2...])
-# -----------------------------
-# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
-# associated separator.
-# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
-# versions in m4sugar had bugs.
-m4_define([lt_join],
-[m4_if([$#], [1], [],
-       [$#], [2], [[$2]],
-       [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
-m4_define([_lt_join],
-[m4_if([$#$2], [2], [],
-       [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
-
-
-# lt_car(LIST)
-# lt_cdr(LIST)
-# ------------
-# Manipulate m4 lists.
-# These macros are necessary as long as will still need to support
-# Autoconf-2.59, which quotes differently.
-m4_define([lt_car], [[$1]])
-m4_define([lt_cdr],
-[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
-       [$#], 1, [],
-       [m4_dquote(m4_shift($@))])])
-m4_define([lt_unquote], $1)
-
-
-# lt_append(MACRO-NAME, STRING, [SEPARATOR])
-# ------------------------------------------
-# Redefine MACRO-NAME to hold its former content plus 'SEPARATOR''STRING'.
-# Note that neither SEPARATOR nor STRING are expanded; they are appended
-# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
-# No SEPARATOR is output if MACRO-NAME was previously undefined (different
-# than defined and empty).
-#
-# This macro is needed until we can rely on Autoconf 2.62, since earlier
-# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
-m4_define([lt_append],
-[m4_define([$1],
-    m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
-
-
-
-# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
-# ----------------------------------------------------------
-# Produce a SEP delimited list of all paired combinations of elements of
-# PREFIX-LIST with SUFFIX1 through SUFFIXn.  Each element of the list
-# has the form PREFIXmINFIXSUFFIXn.
-# Needed until we can rely on m4_combine added in Autoconf 2.62.
-m4_define([lt_combine],
-[m4_if(m4_eval([$# > 3]), [1],
-       [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
-[[m4_foreach([_Lt_prefix], [$2],
-      [m4_foreach([_Lt_suffix],
- ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
- [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
-
-
-# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
-# -----------------------------------------------------------------------
-# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
-# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
-m4_define([lt_if_append_uniq],
-[m4_ifdef([$1],
-   [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
- [lt_append([$1], [$2], [$3])$4],
- [$5])],
-   [lt_append([$1], [$2], [$3])$4])])
-
-
-# lt_dict_add(DICT, KEY, VALUE)
-# -----------------------------
-m4_define([lt_dict_add],
-[m4_define([$1($2)], [$3])])
-
-
-# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
-# --------------------------------------------
-m4_define([lt_dict_add_subkey],
-[m4_define([$1($2:$3)], [$4])])
-
-
-# lt_dict_fetch(DICT, KEY, [SUBKEY])
-# ----------------------------------
-m4_define([lt_dict_fetch],
-[m4_ifval([$3],
- m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
-    m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
-
-
-# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
-# -----------------------------------------------------------------
-m4_define([lt_if_dict_fetch],
-[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
- [$5],
-    [$6])])
-
-
-# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
-# --------------------------------------------------------------
-m4_define([lt_dict_filter],
-[m4_if([$5], [], [],
-  [lt_join(m4_quote(m4_default([$4], [[, ]])),
-           lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
-       [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/ltversion.m4
--- a/GEMBASSY-1.0.3/m4/ltversion.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,23 +0,0 @@
-# ltversion.m4 -- version numbers -*- Autoconf -*-
-#
-# Copyright (C) 2004, 2011-2015 Free Software Foundation, Inc.
-# Written by Scott James Remnant, 2004
-#
-# This file is free software; the Free Software Foundation gives
-# unlimited permission to copy and/or distribute it, with or without
-# modifications, as long as this notice is preserved.
-
-# @configure_input@
-
-# serial 4171 ltversion.m4
-# This file is part of GNU Libtool
-
-m4_define([LT_PACKAGE_VERSION], [2.4.5])
-m4_define([LT_PACKAGE_REVISION], [2.4.5])
-
-AC_DEFUN([LTVERSION_VERSION],
-[macro_version='2.4.5'
-macro_revision='2.4.5'
-_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
-_LT_DECL(, macro_revision, 0)
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/lt~obsolete.m4
--- a/GEMBASSY-1.0.3/m4/lt~obsolete.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,99 +0,0 @@
-# lt~obsolete.m4 -- aclocal satisfying obsolete definitions.    -*-Autoconf-*-
-#
-#   Copyright (C) 2004-2005, 2007, 2009, 2011-2015 Free Software
-#   Foundation, Inc.
-#   Written by Scott James Remnant, 2004.
-#
-# This file is free software; the Free Software Foundation gives
-# unlimited permission to copy and/or distribute it, with or without
-# modifications, as long as this notice is preserved.
-
-# serial 5 lt~obsolete.m4
-
-# These exist entirely to fool aclocal when bootstrapping libtool.
-#
-# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN),
-# which have later been changed to m4_define as they aren't part of the
-# exported API, or moved to Autoconf or Automake where they belong.
-#
-# The trouble is, aclocal is a bit thick.  It'll see the old AC_DEFUN
-# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
-# using a macro with the same name in our local m4/libtool.m4 it'll
-# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
-# and doesn't know about Autoconf macros at all.)
-#
-# So we provide this file, which has a silly filename so it's always
-# included after everything else.  This provides aclocal with the
-# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
-# because those macros already exist, or will be overwritten later.
-# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
-#
-# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
-# Yes, that means every name once taken will need to remain here until
-# we give up compatibility with versions before 1.7, at which point
-# we need to keep only those names which we still refer to.
-
-# This is to help aclocal find these macros, as it can't see m4_define.
-AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])])
-
-m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])])
-m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])])
-m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])])
-m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])])
-m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])])
-m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])])
-m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])])
-m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])])
-m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])])
-m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])])
-m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])])
-m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])])
-m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])])
-m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])])
-m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])])
-m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])])
-m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])])
-m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])])
-m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])])
-m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])])
-m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])])
-m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])])
-m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])])
-m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])])
-m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])])
-m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])])
-m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])])
-m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])])
-m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])])
-m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])])
-m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])])
-m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])])
-m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])])
-m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])])
-m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])])
-m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])])
-m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])])
-m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])])
-m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])])
-m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])])
-m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])])
-m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])])
-m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])])
-m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])])
-m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])])
-m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])])
-m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])])
-m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])])
-m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])])
-m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])])
-m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])])
-m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])])
-m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])])
-m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])])
-m4_ifndef([_LT_REQUIRED_DARWIN_CHECKS], [AC_DEFUN([_LT_REQUIRED_DARWIN_CHECKS])])
-m4_ifndef([_LT_AC_PROG_CXXCPP], [AC_DEFUN([_LT_AC_PROG_CXXCPP])])
-m4_ifndef([_LT_PREPARE_SED_QUOTE_VARS], [AC_DEFUN([_LT_PREPARE_SED_QUOTE_VARS])])
-m4_ifndef([_LT_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_PROG_ECHO_BACKSLASH])])
-m4_ifndef([_LT_PROG_F77], [AC_DEFUN([_LT_PROG_F77])])
-m4_ifndef([_LT_PROG_FC], [AC_DEFUN([_LT_PROG_FC])])
-m4_ifndef([_LT_PROG_CXX], [AC_DEFUN([_LT_PROG_CXX])])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/mysql.m4
--- a/GEMBASSY-1.0.3/m4/mysql.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,187 +0,0 @@
-dnl                                            -*- Autoconf -*-
-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html
-#
-# SYNOPSIS
-#
-#   AX_LIB_MYSQL([MINIMUM-VERSION])
-#
-# DESCRIPTION
-#
-#   This macro provides tests of availability of MySQL 'libmysqlclient'
-#   library of particular version or newer.
-#
-#   AX_LIB_MYSQL macro takes only one argument which is optional.
-#   If there is no required version passed, then macro does not run
-#   version test.
-#
-#   The --with-mysql option takes one of three possible values:
-#
-#   no - do not check for MySQL client library
-#
-#   yes - do check for MySQL library in standard locations
-#   (mysql_config should be in the PATH)
-#
-#   path - complete path to mysql_config utility, use this option if
-#   mysql_config can't be found in the PATH
-#
-#   This macro calls:
-#
-#     AC_SUBST([MYSQL_CFLAGS])
-#     AC_SUBST([MYSQL_CPPFLAGS])
-#     AC_SUBST([MYSQL_LDFLAGS])
-#     AC_SUBST([MYSQL_VERSION])
-#
-#   And sets:
-#
-#     HAVE_MYSQL
-#
-# LAST MODIFICATION
-#
-#   2006-07-16
-#   2007-01-09 MKS: mysql_config --cflags may set gcc -fomit-frame-pointers,
-#                   which prevents gdb from displaying stack traces.
-#                   Changed mysql_config --cflags to mysql_config --include
-#   2009-09-23 AJB: Checking for availability of both, include files and
-#                   library files.
-#   2010-06-14 MKS: Added MYSQL_CPPFLAGS
-#   2011-08-01 MKS: Made test constructs more portable
-#
-# COPYLEFT
-#
-#   Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
-#
-#   Copying and distribution of this file, with or without
-#   modification, are permitted in any medium without royalty provided
-#   the copyright notice and this notice are preserved.
-
-AC_DEFUN([AX_LIB_MYSQL],
-[
-  MYSQL_CFLAGS=""
-  MYSQL_CPPFLAGS=""
-  MYSQL_LDFLAGS=""
-  MYSQL_CONFIG=""
-  MYSQL_VERSION=""
-
-  AC_ARG_WITH([mysql],
-  [AS_HELP_STRING([--with-mysql@<:@=ARG@:>@],
-  [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config])],
-  [
-    AS_IF([test "x${withval}" = "xno"],
-    [want_mysql="no"],
-    [test "x${withval}" = "xyes"],
-    [want_mysql="yes"],
-    [
-      want_mysql="yes"
-      MYSQL_CONFIG="${withval}"
-    ])
-  ],
-  [want_mysql="yes"])
-
-  dnl
-  dnl Check MySQL libraries (libmysqlclient)
-  dnl
-
-  AS_IF([test "x${want_mysql}" = "xyes"],
-  [
-    AS_IF([test -z "${MYSQL_CONFIG}" -o test],
-    [AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])])
-
-    AS_IF([test "x${MYSQL_CONFIG}" != "xno"],
-    [
-      AC_MSG_CHECKING([for MySQL libraries])
-
-      MYSQL_CFLAGS="`${MYSQL_CONFIG} --cflags`"
-      MYSQL_CPPFLAGS="`${MYSQL_CONFIG} --include`"
-      MYSQL_LDFLAGS="`${MYSQL_CONFIG} --libs`"
-
-      MYSQL_VERSION=`${MYSQL_CONFIG} --version`
-
-      dnl It isn't enough to just test for mysql_config as Fedora
-      dnl provides it in the mysql RPM even though mysql-devel may
-      dnl not be installed
-
-      EMBCPPFLAGS="${CPPFLAGS}"
-      EMBLDFLAGS="${LDFLAGS}"
-
-      CPPFLAGS="${MYSQL_CPPFLAGS} ${EMBCPPFLAGS}"
-      LDFLAGS="${MYSQL_LDFLAGS} ${EMBLDFLAGS}"
-
-      AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
-                                        #include "mysql.h"]],
-                                      [[mysql_info(NULL)]])],
-        [havemysql="yes"],
-        [havemysql="no"])
-
-      CPPFLAGS="${EMBCPPFLAGS}"
-      LDFLAGS="${EMBLDFLAGS}"
-
-      AS_IF([test "x${havemysql}" = "xyes"],
-      [
-        AC_DEFINE([HAVE_MYSQL], [1],
-        [Define to 1 if MySQL libraries are available.])
-        found_mysql="yes"
-        AC_MSG_RESULT([yes])
-      ],
-      [
-        MYSQL_CFLAGS=""
-        MYSQL_CPPFLAGS=""
-        MYSQL_LDFLAGS=""
-        found_mysql="no"
-        AC_MSG_RESULT([no])
-      ])
-    ],
-    [
-      found_mysql="no"
-    ])
-  ])
-
-  dnl
-  dnl Check if required version of MySQL is available
-  dnl
-
-  mysql_version_req=ifelse([$1], [], [], [$1])
-
-  AS_IF([test "x${found_mysql}" = "xyes" -a -n "${mysql_version_req}"],
-  [
-    AC_MSG_CHECKING([if MySQL version is >= ${mysql_version_req}])
-
-    dnl Decompose required version string of MySQL
-    dnl and calculate its number representation
-
-    mysql_version_req_major=`expr ${mysql_version_req} : '$[[0-9]]*$'`
-    mysql_version_req_minor=`expr ${mysql_version_req} : '[[0-9]]*\.$[[0-9]]*$'`
-    mysql_version_req_micro=`expr ${mysql_version_req} : '[[0-9]]*\.[[0-9]]*\.$[[0-9]]*$'`
-
-    AS_IF([test "x${mysql_version_req_micro}" = "x"],
-    [mysql_version_req_micro="0"])
-
-    mysql_version_req_number=`expr ${mysql_version_req_major} \* 1000000 \
-                             \+ ${mysql_version_req_minor} \* 1000 \
-                             \+ ${mysql_version_req_micro}`
-
-    dnl Decompose version string of installed MySQL
-    dnl and calculate its number representation
-
-    mysql_version_major=`expr ${MYSQL_VERSION} : '$[[0-9]]*$'`
-    mysql_version_minor=`expr ${MYSQL_VERSION} : '[[0-9]]*\.$[[0-9]]*$'`
-    mysql_version_micro=`expr ${MYSQL_VERSION} : '[[0-9]]*\.[[0-9]]*\.$[[0-9]]*$'`
-
-    AS_IF([test "x${mysql_version_micro}" = "x"],
-    [mysql_version_micro="0"])
-
-    mysql_version_number=`expr ${mysql_version_major} \* 1000000 \
-                         \+ ${mysql_version_minor} \* 1000 \
-                         \+ ${mysql_version_micro}`
-
-    mysql_version_check=`expr ${mysql_version_number} \>\= ${mysql_version_req_number}`
-
-    AS_IF([test "x${mysql_version_check}" = "x1"],
-    [AC_MSG_RESULT([yes])],
-    [AC_MSG_RESULT([no])])
-  ])
-
-  AC_SUBST([MYSQL_CFLAGS])
-  AC_SUBST([MYSQL_CPPFLAGS])
-  AC_SUBST([MYSQL_LDFLAGS])
-  AC_SUBST([MYSQL_VERSION])
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/pngdriver.m4
--- a/GEMBASSY-1.0.3/m4/pngdriver.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,145 +0,0 @@
-dnl @synopsis CHECK_PNGDRIVER()
-dnl
-dnl This macro searches for an installed png/gd/zlib library. If nothing
-dnl was specified when calling configure, it searches first in /usr/local
-dnl and then in /usr. If the --with-pngdriver=DIR is specified, it will try
-dnl to find it in DIR/include/zlib.h and DIR/lib/libz.a. If --without-pngdriver
-dnl is specified, the library is not searched at all.
-dnl
-dnl It defines the symbol PLD_png if the librarys are found. You should
-dnl use autoheader to include a definition for this symbol in a config.h
-dnl file.
-dnl
-dnl Sources files should then use something like
-dnl
-dnl   #ifdef PLD_png
-dnl   #include <zlib.h>
-dnl   #endif /* PLD_png */
-dnl
-dnl @author Ian Longden <il@sanger.ac.uk>
-dnl Modified: Alan Bleasby. Corrected library order
-dnl
-
-AC_DEFUN([CHECK_PNGDRIVER],
-#
-# Handle user hints
-#
-[AC_MSG_CHECKING([if png driver is wanted])
-AC_ARG_WITH([pngdriver],
-    [AS_HELP_STRING([--with-pngdriver=@<:@DIR@:>@],
-        [root directory path of png/gd/zlib installation (defaults to /usr)])],
-[if test "$withval" != no ; then
-  AC_MSG_RESULT([yes])
-  ALT_HOME="$withval"
-else
-  AC_MSG_RESULT([no])
-fi], [
-AC_MSG_RESULT([yes])
-ALT_HOME=/usr
-])
-
-
-#
-# Locate png/gd/zlib, if wanted
-#
-if test -d "${ALT_HOME}"
-then
-
-#
-# Keep a copy if it fails
-#
- ALT_LDFLAGS="$LDFLAGS"
- ALT_CPPFLAGS="$CPPFLAGS"
-
-#
-# Set
-#
-        LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-        CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
-
-   ICCHECK=0
-   case $host_os in
-          solaris*)
-         AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv)
-            if test $ICCHECK = "1" ; then
-                LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv"
-            fi
-         LDFLAGS="$LDFLAGS -R$ALT_HOME/lib"
-                ;;
-          esac
-
-
-
-
-
-#
-# Check for zlib in ALT_HOME
-#
-        AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, -L${ALT_HOME}/lib -lz)
-#
-
-#
-# Check for png
-#
- if test $CHECK = "1" ; then
-   AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lz)
- fi
-
-
-
-
-#
-# Check for gd
-#
- if test $CHECK = "1"; then
-   AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lgd -lpng -lz -lm)
-          if test $CHECK = "0"; then
- echo need to upgrade gd for png driver for plplot
-   fi
- fi
-#
-# If everything found okay then proceed to include png driver in config.
-#
- if test $CHECK = "1" ; then
-   LIBS="$LIBS -lgd -lpng -lz -lm"
-
-   if test $ICCHECK = "1" ; then
-   LIBS="$LIBS -liconv"
-   fi
-
-          case $host_os in
-          solaris*)
-       LDFLAGS="$LDFLAGS -R$ALT_HOME/lib"
-              ;;
-          esac
-
-   AC_DEFINE([PLD_png], [1], [Define to 1 is PNG support is available])
-   AM_CONDITIONAL(AMPNG, true)
-   echo PNG libraries found
-     if test $ALT_HOME = "/usr" ; then
-   LDFLAGS="$ALT_LDFLAGS"
-   CPPFLAGS="$ALT_CPPFLAGS"
-     fi
- else
-#
-# If not okay then reset FLAGS.
-#
-     AM_CONDITIONAL(AMPNG, false)
-   LDFLAGS="$ALT_LDFLAGS"
-   CPPFLAGS="$ALT_CPPFLAGS"
-   echo No png driver will be made due to librarys missing/old.
- fi
-#       echo PNG STUFF FOLLOWS!!!
-#       echo CHECK = $CHECK
-#       echo LIBS = $LIBS
-#       echo LDFLAGS = $LDFLAGS
-#       echo CPPFLAGS = $CPPFLAGS
-
-
-else
-        if test $withval != "no"; then
- echo "Directory $ALT_HOME does not exist"
- exit 0
-        fi
-fi
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/postgresql.m4
--- a/GEMBASSY-1.0.3/m4/postgresql.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,184 +0,0 @@
-dnl                                            -*- Autoconf -*-
-##### http://autoconf-archive.cryp.to/ax_lib_postgresql.html
-#
-# SYNOPSIS
-#
-#   AX_LIB_POSTGRESQL([MINIMUM-VERSION])
-#
-# DESCRIPTION
-#
-#   This macro provides tests of availability of PostgreSQL 'libpq'
-#   library of particular version or newer.
-#
-#   AX_LIB_POSTGRESQL macro takes only one argument which is optional.
-#   If there is no required version passed, then macro does not run
-#   version test.
-#
-#   The --with-postgresql option takes one of three possible values:
-#
-#   no - do not check for PostgreSQL client library
-#
-#   yes - do check for PostgreSQL library in standard locations
-#   (pg_config should be in the PATH)
-#
-#   path - complete path to pg_config utility, use this option if
-#   pg_config can't be found in the PATH
-#
-#   This macro calls:
-#
-#     AC_SUBST([POSTGRESQL_CFLAGS])
-#     AC_SUBST([POSTGRESQL_CPPFLAGS])
-#     AC_SUBST([POSTGRESQL_LDFLAGS])
-#     AC_SUBST([POSTGRESQL_VERSION])
-#
-#   And sets:
-#
-#     HAVE_POSTGRESQL
-#
-# LAST MODIFICATION
-#
-#   2006-07-16
-#   2010-05-14 MKS: Added POSTGRESQL_CPPFLAGS
-#   2011-06-21 AJB: Added workaround for Fedora pg_config oddity
-#   2011-08-01 MKS: Changed PG_CONFIG to POSTGRESQL_CONFIG
-#                   Made test constructs more portable
-#
-# COPYLEFT
-#
-#   Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
-#
-#   Copying and distribution of this file, with or without
-#   modification, are permitted in any medium without royalty provided
-#   the copyright notice and this notice are preserved.
-
-AC_DEFUN([AX_LIB_POSTGRESQL],
-[
-  POSTGRESQL_CFLAGS=""
-  POSTGRESQL_CPPFLAGS=""
-  POSTGRESQL_LDFLAGS=""
-  POSTGRESQL_CONFIG=""
-  POSTGRESQL_VERSION=""
-
-  AC_ARG_WITH([postgresql],
-  [AS_HELP_STRING([--with-postgresql@<:=@ARG@:>@],
-  [use PostgreSQL library @<:@default=yes@:>@, optionally specify path to pg_config])],
-  [
-    AS_IF([test "x${withval}" = "xno"],
-    [want_postgresql="no"],
-    [test "x${withval}" = "xyes"],
-    [want_postgresql="yes"],
-    [
-      want_postgresql="yes"
-      POSTGRESQL_CONFIG="${withval}"
-    ])
-  ],
-  [want_postgresql="yes"])
-
-  dnl
-  dnl Check PostgreSQL libraries (libpq)
-  dnl
-
-  AS_IF([test "x${want_postgresql}" = "xyes"],
-  [
-    AS_IF([test -z "${POSTGRESQL_CONFIG}" -o test],
-    [AC_PATH_PROG([POSTGRESQL_CONFIG], [pg_config], [no])])
-
-    AS_IF([test "x${POSTGRESQL_CONFIG}" != "xno"],
-    [
-      AC_MSG_CHECKING([for PostgreSQL libraries])
-
-      POSTGRESQL_CFLAGS="-I`${POSTGRESQL_CONFIG} --includedir`"
-      POSTGRESQL_CPPFLAGS="-I`${POSTGRESQL_CONFIG} --includedir`"
-      POSTGRESQL_LDFLAGS="-L`${POSTGRESQL_CONFIG} --libdir` -lpq"
-
-      POSTGRESQL_VERSION=`${POSTGRESQL_CONFIG} --version | sed -e 's#PostgreSQL ##'`
-
-      dnl It isn't enough to just test for pg_config as Fedora
-      dnl provides it in the postgresql RPM even though postgresql-devel may
-      dnl not be installed
-
-      EMBCPPFLAGS="${CPPFLAGS}"
-      EMBLDFLAGS="${LDFLAGS}"
-
-      CPPFLAGS="${POSTGRESQL_CPPFLAGS} ${EMBCPPFLAGS}"
-      LDFLAGS="${POSTGRESQL_LDFLAGS} ${EMBLDFLAGS}"
-
-      AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
-                                        #include "libpq-fe.h"]],
-                                      [[PQconnectdb(NULL)]])],
-        [havepostgresql="yes"],
-        [havepostgresql="no"])
-
-      CPPFLAGS="${EMBCPPFLAGS}"
-      LDFLAGS="${EMBLDFLAGS}"
-
-      AS_IF([test "x${havepostgresql}" = "xyes"],
-      [
-        AC_DEFINE([HAVE_POSTGRESQL], [1],
-        [Define to 1 if PostgreSQL libraries are available.])
-        found_postgresql="yes"
-        AC_MSG_RESULT([yes])
-      ],
-      [
-        POSTGRESQL_CFLAGS=""
-        POSTGRESQL_CPPFLAGS=""
-        POSTGRESQL_LDFLAGS=""
-        found_postgresql="no"
-        AC_MSG_RESULT([no])
-      ])
-    ],
-    [
-      found_postgresql="no"
-    ])
-  ])
-
-  dnl
-  dnl Check if required version of PostgreSQL is available
-  dnl
-
-  postgresql_version_req=ifelse([$1], [], [], [$1])
-
-  AS_IF([test "x${found_postgresql}" = "xyes" -a -n "${postgresql_version_req}"],
-  [
-    AC_MSG_CHECKING([if PostgreSQL version is >= ${postgresql_version_req}])
-
-    dnl Decompose required version string of PostgreSQL
-    dnl and calculate its number representation
-
-    postgresql_version_req_major=`expr ${postgresql_version_req} : '$[[0-9]]*$'`
-    postgresql_version_req_minor=`expr ${postgresql_version_req} : '[[0-9]]*\.$[[0-9]]*$'`
-    postgresql_version_req_micro=`expr ${postgresql_version_req} : '[[0-9]]*\.[[0-9]]*\.$[[0-9]]*$'`
-
-    AS_IF([test "x${postgresql_version_req_micro}" = "x"],
-    [postgresql_version_req_micro="0"])
-
-    postgresql_version_req_number=`expr ${postgresql_version_req_major} \* 1000000 \
-                                  \+ ${postgresql_version_req_minor} \* 1000 \
-                                  \+ ${postgresql_version_req_micro}`
-
-    dnl Decompose version string of installed PostgreSQL
-    dnl and calculate its number representation
-
-    postgresql_version_major=`expr ${POSTGRESQL_VERSION} : '$[[0-9]]*$'`
-    postgresql_version_minor=`expr ${POSTGRESQL_VERSION} : '[[0-9]]*\.$[[0-9]]*$'`
-    postgresql_version_micro=`expr ${POSTGRESQL_VERSION} : '[[0-9]]*\.[[0-9]]*\.$[[0-9]]*$'`
-
-    AS_IF([test "x${postgresql_version_micro}" = "x"],
-      [postgresql_version_micro="0"])
-
-    postgresql_version_number=`expr ${postgresql_version_major} \* 1000000 \
-                              \+ ${postgresql_version_minor} \* 1000 \
-                              \+ ${postgresql_version_micro}`
-
-    postgresql_version_check=`expr ${postgresql_version_number} \>\= ${postgresql_version_req_number}`
-
-    AS_IF([test "x${postgresql_version_check}" = "x1"],
-    [AC_MSG_RESULT([yes])],
-    [AC_MSG_RESULT([no])])
-  ])
-
-  AC_SUBST([POSTGRESQL_CFLAGS])
-  AC_SUBST([POSTGRESQL_CPPFLAGS])
-  AC_SUBST([POSTGRESQL_LDFLAGS])
-  AC_SUBST([POSTGRESQL_VERSION])
-])

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/m4/sgi.m4
--- a/GEMBASSY-1.0.3/m4/sgi.m4 Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,53 +0,0 @@
-AC_DEFUN([CHECK_SGI],
-#
-# Handle SGI compiler flags
-#
-[AC_MSG_CHECKING([for sgiabi])
-AC_ARG_WITH([sgiabi],
-    [AS_HELP_STRING([--with-sgiabi=@<:@ARG@:>@],
-        [SGI compiler flags @<:@default=no@:>@])],
-[if test "$withval" != no ; then
-  AC_MSG_RESULT([yes])
-
-  case $host_os in
-  irix*)
-    if test "$withval" = n32m3 ; then
-      CFLAGS="-n32 -mips3 $CFLAGS"
-      LD="/usr/bin/ld -n32 -mips3 -IPA -L/usr/lib32"
- if test -d /usr/freeware ; then
-          LDFLAGS="-L/usr/freeware/lib32 $LDFLAGS"
-        fi
-    fi
-
-    if test "$withval" = n32m4 ; then
-      CFLAGS="-n32 -mips4 $CFLAGS"
-      LD="/usr/bin/ld -n32 -mips4 -IPA -L/usr/lib32"
- if test -d /usr/freeware ; then
-          LDFLAGS="-L/usr/freeware/lib32 $LDFLAGS"
-        fi
-    fi
-
-    if test "$withval" = 64m3 ; then
-      CFLAGS="-64 -mips3 $CFLAGS"
-      LD="/usr/bin/ld -64 -mips3 -IPA -L/usr/lib64"
- if test -d /usr/freeware ; then
-          LDFLAGS="-L/usr/freeware/lib64 $LDFLAGS"
-        fi
-    fi
-
-    if test "$withval" = 64m4 ; then
-      CFLAGS="-64 -mips4 $CFLAGS"
-      LD="/usr/bin/ld -64 -mips4 -IPA -L/usr/lib64"
- if test -d /usr/freeware ; then
-          LDFLAGS="-L/usr/freeware/lib64 $LDFLAGS"
-        fi
-    fi
-    ;;
-  esac
-
-
-fi], [
-AC_MSG_RESULT([no])
-])
-]
-)

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/missing
--- a/GEMBASSY-1.0.3/missing Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,215 +0,0 @@
-#! /bin/sh
-# Common wrapper for a few potentially missing GNU programs.
-
-scriptversion=2013-10-28.13; # UTC
-
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
-# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-if test $# -eq 0; then
-  echo 1>&2 "Try '$0 --help' for more information"
-  exit 1
-fi
-
-case $1 in
-
-  --is-lightweight)
-    # Used by our autoconf macros to check whether the available missing
-    # script is modern enough.
-    exit 0
-    ;;
-
-  --run)
-    # Back-compat with the calling convention used by older automake.
-    shift
-    ;;
-
-  -h|--h|--he|--hel|--help)
-    echo "\
-$0 [OPTION]... PROGRAM [ARGUMENT]...
-
-Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
-to PROGRAM being missing or too old.
-
-Options:
-  -h, --help      display this help and exit
-  -v, --version   output version information and exit
-
-Supported PROGRAM values:
-  aclocal   autoconf  autoheader   autom4te  automake  makeinfo
-  bison     yacc      flex         lex       help2man
-
-Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
-'g' are ignored when checking the name.
-
-Send bug reports to <bug-automake@gnu.org>."
-    exit $?
-    ;;
-
-  -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
-    echo "missing $scriptversion (GNU Automake)"
-    exit $?
-    ;;
-
-  -*)
-    echo 1>&2 "$0: unknown '$1' option"
-    echo 1>&2 "Try '$0 --help' for more information"
-    exit 1
-    ;;
-
-esac
-
-# Run the given program, remember its exit status.
-"$@"; st=$?
-
-# If it succeeded, we are done.
-test $st -eq 0 && exit 0
-
-# Also exit now if we it failed (or wasn't found), and '--version' was
-# passed; such an option is passed most likely to detect whether the
-# program is present and works.
-case $2 in --version|--help) exit $st;; esac
-
-# Exit code 63 means version mismatch.  This often happens when the user
-# tries to use an ancient version of a tool on a file that requires a
-# minimum version.
-if test $st -eq 63; then
-  msg="probably too old"
-elif test $st -eq 127; then
-  # Program was missing.
-  msg="missing on your system"
-else
-  # Program was found and executed, but failed.  Give up.
-  exit $st
-fi
-
-perl_URL=http://www.perl.org/
-flex_URL=http://flex.sourceforge.net/
-gnu_software_URL=http://www.gnu.org/software
-
-program_details ()
-{
-  case $1 in
-    aclocal|automake)
-      echo "The '$1' program is part of the GNU Automake package:"
-      echo "<$gnu_software_URL/automake>"
-      echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
-      echo "<$gnu_software_URL/autoconf>"
-      echo "<$gnu_software_URL/m4/>"
-      echo "<$perl_URL>"
-      ;;
-    autoconf|autom4te|autoheader)
-      echo "The '$1' program is part of the GNU Autoconf package:"
-      echo "<$gnu_software_URL/autoconf/>"
-      echo "It also requires GNU m4 and Perl in order to run:"
-      echo "<$gnu_software_URL/m4/>"
-      echo "<$perl_URL>"
-      ;;
-  esac
-}
-
-give_advice ()
-{
-  # Normalize program name to check for.
-  normalized_program=`echo "$1" | sed '
-    s/^gnu-//; t
-    s/^gnu//; t
-    s/^g//; t'`
-
-  printf '%s\n' "'$1' is $msg."
-
-  configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
-  case $normalized_program in
-    autoconf*)
-      echo "You should only need it if you modified 'configure.ac',"
-      echo "or m4 files included by it."
-      program_details 'autoconf'
-      ;;
-    autoheader*)
-      echo "You should only need it if you modified 'acconfig.h' or"
-      echo "$configure_deps."
-      program_details 'autoheader'
-      ;;
-    automake*)
-      echo "You should only need it if you modified 'Makefile.am' or"
-      echo "$configure_deps."
-      program_details 'automake'
-      ;;
-    aclocal*)
-      echo "You should only need it if you modified 'acinclude.m4' or"
-      echo "$configure_deps."
-      program_details 'aclocal'
-      ;;
-   autom4te*)
-      echo "You might have modified some maintainer files that require"
-      echo "the 'autom4te' program to be rebuilt."
-      program_details 'autom4te'
-      ;;
-    bison*|yacc*)
-      echo "You should only need it if you modified a '.y' file."
-      echo "You may want to install the GNU Bison package:"
-      echo "<$gnu_software_URL/bison/>"
-      ;;
-    lex*|flex*)
-      echo "You should only need it if you modified a '.l' file."
-      echo "You may want to install the Fast Lexical Analyzer package:"
-      echo "<$flex_URL>"
-      ;;
-    help2man*)
-      echo "You should only need it if you modified a dependency" \
-           "of a man page."
-      echo "You may want to install the GNU Help2man package:"
-      echo "<$gnu_software_URL/help2man/>"
-    ;;
-    makeinfo*)
-      echo "You should only need it if you modified a '.texi' file, or"
-      echo "any other file indirectly affecting the aspect of the manual."
-      echo "You might want to install the Texinfo package:"
-      echo "<$gnu_software_URL/texinfo/>"
-      echo "The spurious makeinfo call might also be the consequence of"
-      echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
-      echo "want to install GNU make:"
-      echo "<$gnu_software_URL/make/>"
-      ;;
-    *)
-      echo "You might have modified some files without having the proper"
-      echo "tools for further handling them.  Check the 'README' file, it"
-      echo "often tells you about the needed prerequisites for installing"
-      echo "this package.  You may also peek at any GNU archive site, in"
-      echo "case some other package contains this missing '$1' program."
-      ;;
-  esac
-}
-
-give_advice "$1" | sed -e '1s/^/WARNING: /' \
-                       -e '2,$s/^/         /' >&2
-
-# Propagate the correct exit status (expected to be 127 for a program
-# not found, 63 for a program that failed due to version mismatch).
-exit $st
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/Makefile.am
--- a/GEMBASSY-1.0.3/src/Makefile.am Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,164 +0,0 @@
-## Process this file with automake to produce Makefile.in
-
-if LOCALLINK
-INCLUDES = -I../include -I../../../nucleus -I../../../ajax/pcre \
- -I../../../ajax/expat -I../../../ajax/zlib \
- -I../../../ajax/core -I../../../ajax/graphics \
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- -I../../../ajax/acd -I../../../plplot -I../gsoap
-else
-INCLUDES = -I../include -I${embprefix}/include -I${embprefix}/include/eplplot -I${embprefix}/include/epcre -I${embprefix}/include/ezlib -I../gsoap
-endif
-
-if ISSHARED
-if ISAIXIA64
-if LOCALLINK
-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../plplot/.libs \
--L../../../ajax/pcre/.libs -L../../../ajax/expat/.libs \
--L../../../ajax/zlib/.libs -L../../../ajax/core/.libs \
--L../../../ajax/graphics/.libs -L../../../ajax/ensembl/.libs \
--L../../../ajax/ajaxdb/.libs -L../../../ajax/acd/.libs \
--L../../../nucleus/.libs \
--lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \
--lezlib -leplplot
-else
-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
--lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre -lezlib -leplplot
-endif
-endif
-endif
-
-AM_CFLAGS =  $(AIX_CFLAGS) $(WARN_CFLAGS) $(DEVWARN_CFLAGS)
-
-## To add programs
-## Add the program binary name to bin_PROGRAMS
-## (using \ as a continuation character for multiple lines)
-##
-## And add a programname_SOURCES line to define the source files
-## to be compiled and linked
-##
-## make will compile and link the program
-## make install will copy the program to the install directory
-
-bin_PROGRAMS = genret \
-               gaaui\
-               gaminoinfo\
-               gb1\
-               gb2\
-               gbasecounter\
-               gbaseentropy\
-               gbaseinformationcontent\
-               gbaserelativeentropy\
-               gbasezvalue\
-        gbui\
-               gcai\
-               gcbi\
-               gcgr\
-               gcircularmap\
-               gcodoncompiler\
-               gconsensusz\
-               gdeltaenc\
-               gdeltagcskew\
-               gdinuc\
-               gdistincc\
-               gdnawalk\
-               genc\
-               gentrez\
-               gew\
-               gfindoriter\
-               gfop\
-               ggcsi\
-               ggcskew\
-               ggcwin\
-               ggeneskew\
-               ggenomicskew\
-               ggenomemap3\
-               gicdi\
-               gkmertable\
-               gldabias\
-               gnucleotideperiodicity\
-        goligomercounter\
-        goligomersearch\
-               gp2\
-               gpalindrome\
-               gphx\
-               gqueryarm\
-               gquerystrand\
-               greporiter\
-               gsvalue\
-               gscs\
-               gseq2png\
-               gseqinfo\
-               gshuffleseq\
-               gsignature\
-               gviewcds\
-               gwvalue
-
-genret_SOURCES                  = genret.c
-gaaui_SOURCES                   = gaaui.c
-gaminoinfo_SOURCES              = gaminoinfo.c
-gb1_SOURCES                     = gb1.c
-gb2_SOURCES                     = gb2.c
-gbasecounter_SOURCES            = gbasecounter.c
-gbaseentropy_SOURCES            = gbaseentropy.c
-gbaseinformationcontent_SOURCES = gbaseinformationcontent.c
-gbaserelativeentropy_SOURCES    = gbaserelativeentropy.c
-gbasezvalue_SOURCES             = gbasezvalue.c
-gbui_SOURCES                    = gbui.c
-gcai_SOURCES                    = gcai.c
-gcbi_SOURCES                    = gcbi.c
-gcgr_SOURCES                    = gcgr.c
-gcircularmap_SOURCES            = gcircularmap.c
-gcodoncompiler_SOURCES          = gcodoncompiler.c
-gconsensusz_SOURCES             = gconsensusz.c
-gdeltaenc_SOURCES               = gdeltaenc.c
-gdeltagcskew_SOURCES            = gdeltagcskew.c
-gdistincc_SOURCES               = gdistincc.c
-gdinuc_SOURCES                  = gdinuc.c
-gdnawalk_SOURCES                = gdnawalk.c
-genc_SOURCES                    = genc.c
-gentrez_SOURCES                 = gentrez.c
-gew_SOURCES                     = gew.c
-gfindoriter_SOURCES             = gfindoriter.c
-gfop_SOURCES                    = gfop.c
-ggcsi_SOURCES                   = ggcsi.c
-ggcwin_SOURCES                  = ggcwin.c
-ggeneskew_SOURCES               = ggeneskew.c
-ggenomicskew_SOURCES            = ggenomicskew.c
-ggenomemap3_SOURCES             = ggenomemap3.c
-gicdi_SOURCES                   = gicdi.c
-gkmertable_SOURCES              = gkmertable.c
-gldabias_SOURCES                = gldabias.c
-gnucleotideperiodicity_SOURCES  = gnucleotideperiodicity.c
-goligomercounter_SOURCES        = goligomercounter.c
-goligomersearch_SOURCES         = goligomersearch.c
-gp2_SOURCES                     = gp2.c
-gpalindrome_SOURCES             = gpalindrome.c
-gphx_SOURCES                    = gphx.c
-gqueryarm_SOURCES               = gqueryarm.c
-gquerystrand_SOURCES            = gquerystrand.c
-greporiter_SOURCES              = greporiter.c
-gsvalue_SOURCES                 = gsvalue.c
-gscs_SOURCES                    = gscs.c
-gseq2png_SOURCES                = gseq2png.c
-gseqinfo_SOURCES                = gseqinfo.c
-gshuffleseq_SOURCES             = gshuffleseq.c
-gsignature_SOURCES              = gsignature.c
-gviewcds_SOURCES                = gviewcds.c
-gwvalue_SOURCES                 = gwvalue.c
-
-if LOCALLINK
-LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
- ../../../ajax/ajaxdb/libajaxdb.la \
- ../../../ajax/ensembl/libensembl.la \
- ../../../ajax/graphics/libajaxg.la \
- ../../../ajax/core/libajax.la \
- ../../../ajax/zlib/libezlib.la \
- ../../../ajax/expat/libeexpat.la \
- ../../../ajax/pcre/libepcre.la \
- ../../../plplot/libeplplot.la \
-        $(XLIB)
-else
-LDADD = -L${embprefix}/lib -L../include -lnucleus -lacd -lajaxdb -lensembl \
-        -lajaxg -lajax -leexpat -lepcre -lezlib -leplplot $(XLIB)
-endif

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/Makefile.in
--- a/GEMBASSY-1.0.3/src/Makefile.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1920 +0,0 @@\n-# Makefile.in generated by automake 1.15 from Makefile.am.\n-# @configure_input@\n-\n-# Copyright (C) 1994-2014 Free Software Foundation, Inc.\n-\n-# This Makefile.in is free software; the Free Software Foundation\n-# gives unlimited permission to copy and/or distribute it,\n-# with or without modifications, as long as this notice is preserved.\n-\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without\n-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A\n-# PARTICULAR PURPOSE.\n-\n-@SET_MAKE@\n-\n-VPATH = @srcdir@\n-am__is_gnu_make = { \\\n- if test -z \'$(MAKELEVEL)\'; then \\\n- false; \\\n- elif test -n \'$(MAKE_HOST)\'; then \\\n- true; \\\n- elif test -n \'$(MAKE_VERSION)\' && test -n \'$(CURDIR)\'; then \\\n- true; \\\n- else \\\n- false; \\\n- fi; \\\n-}\n-am__make_running_with_option = \\\n- case $${target_option-} in \\\n- ?) ;; \\\n- *) echo "am__make_running_with_option: internal error: invalid" \\\n- "target option \'$${target_option-}\' specified" >&2; \\\n- exit 1;; \\\n- esac; \\\n- has_opt=no; \\\n- sane_makeflags=$$MAKEFLAGS; \\\n- if $(am__is_gnu_make); then \\\n- sane_makeflags=$$MFLAGS; \\\n- else \\\n- case $$MAKEFLAGS in \\\n- *\\\\[\\ \\\t]*) \\\n- bs=\\\\; \\\n- sane_makeflags=`printf \'%s\\n\' "$$MAKEFLAGS" \\\n- | sed "s/$$bs$$bs[$$bs $$bs\t]*//g"`;; \\\n- esac; \\\n- fi; \\\n- skip_next=no; \\\n- strip_trailopt () \\\n- { \\\n- flg=`printf \'%s\\n\' "$$flg" | sed "s/$$1.*$$//"`; \\\n- }; \\\n- for flg in $$sane_makeflags; do \\\n- test $$skip_next = yes && { skip_next=no; continue; }; \\\n- case $$flg in \\\n- *=*|--*) continue;; \\\n- -*I) strip_trailopt \'I\'; skip_next=yes;; \\\n- -*I?*) strip_trailopt \'I\';; \\\n- -*O) strip_trailopt \'O\'; skip_next=yes;; \\\n- -*O?*) strip_trailopt \'O\';; \\\n- -*l) strip_trailopt \'l\'; skip_next=yes;; \\\n- -*l?*) strip_trailopt \'l\';; \\\n- -[dEDm]) skip_next=yes;; \\\n- -[JT]) skip_next=yes;; \\\n- esac; \\\n- case $$flg in \\\n- *$$target_option*) has_opt=yes; break;; \\\n- esac; \\\n- done; \\\n- test $$has_opt = yes\n-am__make_dryrun = (target_option=n; $(am__make_running_with_option))\n-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))\n-pkgdatadir = $(datadir)/@PACKAGE@\n-pkgincludedir = $(includedir)/@PACKAGE@\n-pkglibdir = $(libdir)/@PACKAGE@\n-pkglibexecdir = $(libexecdir)/@PACKAGE@\n-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd\n-install_sh_DATA = $(install_sh) -c -m 644\n-install_sh_PROGRAM = $(install_sh) -c\n-install_sh_SCRIPT = $(install_sh) -c\n-INSTALL_HEADER = $(INSTALL_DATA)\n-transform = $(program_transform_name)\n-NORMAL_INSTALL = :\n-PRE_INSTALL = :\n-POST_INSTALL = :\n-NORMAL_UNINSTALL = :\n-PRE_UNINSTALL = :\n-POST_UNINSTALL = :\n-build_triplet = @build@\n-host_triplet = @host@\n-bin_PROGRAMS = genret$(EXEEXT) gaaui$(EXEEXT) gaminoinfo$(EXEEXT) \\\n-\tgb1$(EXEEXT) gb2$(EXEEXT) gbasecounter$(EXEEXT) \\\n-\tgbaseentropy$(EXEEXT) gbaseinformationcontent$(EXEEXT) \\\n-\tgbaserelativeentropy$(EXEEXT) gbasezvalue$(EXEEXT) \\\n-\tgbui$(EXEEXT) gcai$(EXEEXT) gcbi$(EXEEXT) gcgr$(EXEEXT) \\\n-\tgcircularmap$(EXEEXT) gcodoncompiler$(EXEEXT) \\\n-\tgconsensusz$(EXEEXT) gdeltaenc$(EXEEXT) gdeltagcskew$(EXEEXT) \\\n-\tgdinuc$(EXEEXT) gdistincc$(EXEEXT) gdnawalk$(EXEEXT) \\\n-\tgenc$(EXEEXT) gentrez$(EXEEXT) gew$(EXEEXT) \\\n-\tgfindoriter$(EXEEXT) gfop$(EXEEXT) ggcsi$(EXEEXT) \\\n-\tggcskew$(EXEEXT) ggcwin$(EXEEXT) ggeneskew$(EXEEXT) \\\n-\tggenomicskew$(EXEEXT) ggenomemap3$(EXEEXT) gicdi$(EXEEXT) \\\n-\tgkmertable$(EXEEXT) gldabias$(EXEEXT) \\\n-\tgnucleotideperiodicity$(EXEEXT) goligomercounter$(EXEEXT) \\\n-\tgoligomersearch$(EXEEXT) gp2$(EXEEXT) gpalindrome$(EXEEXT) \\\n-\tgphx$(EXEEXT) gqueryarm$(EXEEXT) gquerystrand$(EXEEXT) \\\n-\tgreporiter$(EXEEXT) gsvalue$(EXEEXT) gscs$(EXEEXT) \\\n-\tgseq2png$(EXEEXT) gseqinfo$(EXEEXT) gshuffleseq$(EXEEXT) \\\n-\tgsignature$(EXEEXT) gviewcds$(EXEEXT) gwvalue$(EXEEXT)\n-subdir = src\n-ACLOCAL_M4 = $(top_srcdir)/'..b'-\t if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \\\n-\t if test -d $$d/$$file; then \\\n-\t dir=`echo "/$$file" | sed -e \'s,/[^/]*$$,,\'`; \\\n-\t if test -d "$(distdir)/$$file"; then \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \\\n-\t cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \\\n-\t find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \\;; \\\n-\t fi; \\\n-\t cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \\\n-\t else \\\n-\t test -f "$(distdir)/$$file" \\\n-\t || cp -p $$d/$$file "$(distdir)/$$file" \\\n-\t || exit 1; \\\n-\t fi; \\\n-\tdone\n-check-am: all-am\n-check: check-am\n-all-am: Makefile $(PROGRAMS) config.h\n-installdirs:\n-\tfor dir in "$(DESTDIR)$(bindir)"; do \\\n-\t test -z "$$dir" || $(MKDIR_P) "$$dir"; \\\n-\tdone\n-install: install-am\n-install-exec: install-exec-am\n-install-data: install-data-am\n-uninstall: uninstall-am\n-\n-install-am: all-am\n-\t@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am\n-\n-installcheck: installcheck-am\n-install-strip:\n-\tif test -z \'$(STRIP)\'; then \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t install; \\\n-\telse \\\n-\t $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \\\n-\t install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \\\n-\t "INSTALL_PROGRAM_ENV=STRIPPROG=\'$(STRIP)\'" install; \\\n-\tfi\n-mostlyclean-generic:\n-\n-clean-generic:\n-\n-distclean-generic:\n-\t-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)\n-\t-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)\n-\n-maintainer-clean-generic:\n-\t@echo "This command is intended for maintainers to use"\n-\t@echo "it deletes files that may require special tools to rebuild."\n-clean: clean-am\n-\n-clean-am: clean-binPROGRAMS clean-generic clean-libtool mostlyclean-am\n-\n-distclean: distclean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-distclean-am: clean-am distclean-compile distclean-generic \\\n-\tdistclean-hdr distclean-tags\n-\n-dvi: dvi-am\n-\n-dvi-am:\n-\n-html: html-am\n-\n-html-am:\n-\n-info: info-am\n-\n-info-am:\n-\n-install-data-am:\n-\n-install-dvi: install-dvi-am\n-\n-install-dvi-am:\n-\n-install-exec-am: install-binPROGRAMS\n-\n-install-html: install-html-am\n-\n-install-html-am:\n-\n-install-info: install-info-am\n-\n-install-info-am:\n-\n-install-man:\n-\n-install-pdf: install-pdf-am\n-\n-install-pdf-am:\n-\n-install-ps: install-ps-am\n-\n-install-ps-am:\n-\n-installcheck-am:\n-\n-maintainer-clean: maintainer-clean-am\n-\t-rm -rf ./$(DEPDIR)\n-\t-rm -f Makefile\n-maintainer-clean-am: distclean-am maintainer-clean-generic\n-\n-mostlyclean: mostlyclean-am\n-\n-mostlyclean-am: mostlyclean-compile mostlyclean-generic \\\n-\tmostlyclean-libtool\n-\n-pdf: pdf-am\n-\n-pdf-am:\n-\n-ps: ps-am\n-\n-ps-am:\n-\n-uninstall-am: uninstall-binPROGRAMS\n-\n-.MAKE: all install-am install-strip\n-\n-.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \\\n-\tclean-binPROGRAMS clean-generic clean-libtool cscopelist-am \\\n-\tctags ctags-am distclean distclean-compile distclean-generic \\\n-\tdistclean-hdr distclean-libtool distclean-tags distdir dvi \\\n-\tdvi-am html html-am info info-am install install-am \\\n-\tinstall-binPROGRAMS install-data install-data-am install-dvi \\\n-\tinstall-dvi-am install-exec install-exec-am install-html \\\n-\tinstall-html-am install-info install-info-am install-man \\\n-\tinstall-pdf install-pdf-am install-ps install-ps-am \\\n-\tinstall-strip installcheck installcheck-am installdirs \\\n-\tmaintainer-clean maintainer-clean-generic mostlyclean \\\n-\tmostlyclean-compile mostlyclean-generic mostlyclean-libtool \\\n-\tpdf pdf-am ps ps-am tags tags-am uninstall uninstall-am \\\n-\tuninstall-binPROGRAMS\n-\n-.PRECIOUS: Makefile\n-\n-\n-# Tell versions [3.59,3.63) of GNU make to not export all variables.\n-# Otherwise a system limit (for SysV at least) may be exceeded.\n-.NOEXPORT:\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/config.h.in
--- a/GEMBASSY-1.0.3/src/config.h.in Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,202 +0,0 @@
-/* src/config.h.in.  Generated from configure.in by autoheader.  */
-
-/* Define if building universal (internal helper macro) */
-#undef AC_APPLE_UNIVERSAL_BUILD
-
-/* Define to 1 to compile all deprecated functions */
-#undef AJ_COMPILE_DEPRECATED
-
-/* Define to 1 to compile deprecated functions used in book texts for 6.2.0 */
-#undef AJ_COMPILE_DEPRECATED_BOOK
-
-/* Define to 1 to collect AJAX library usage statistics. */
-#undef AJ_SAVESTATS
-
-/* Define to 1 if the `getpgrp' function requires zero arguments. */
-#undef GETPGRP_VOID
-
-/* Define to 1 if you have the <dirent.h> header file, and it defines `DIR'.
-   */
-#undef HAVE_DIRENT_H
-
-/* Define to 1 if you have the <dlfcn.h> header file. */
-#undef HAVE_DLFCN_H
-
-/* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */
-#undef HAVE_DOPRNT
-
-/* Define to 1 if you have the `erand48' function. */
-#undef HAVE_ERAND48
-
-/* Define to 1 if you have the `fork' function. */
-#undef HAVE_FORK
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if the Java Native Interface (JNI) is available. */
-#undef HAVE_JAVA
-
-/* Define to 1 if you have the `curl' library (-lcurl). */
-#undef HAVE_LIBCURL
-
-/* Define to 1 if you have the `m' library (-lm). */
-#undef HAVE_LIBM
-
-/* Define to 1 if you have the `mcheck' function. */
-#undef HAVE_MCHECK
-
-/* Define to 1 if you have the `memmove' function. */
-#undef HAVE_MEMMOVE
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Define to 1 if MySQL libraries are available. */
-#undef HAVE_MYSQL
-
-/* Define to 1 if you have the <ndir.h> header file, and it defines `DIR'. */
-#undef HAVE_NDIR_H
-
-/* Define to 1 if PostgreSQL libraries are available. */
-#undef HAVE_POSTGRESQL
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the `strchr' function. */
-#undef HAVE_STRCHR
-
-/* Define to 1 if you have the `strdup' function. */
-#undef HAVE_STRDUP
-
-/* Define to 1 if you have the `strftime' function. */
-#undef HAVE_STRFTIME
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the `strstr' function. */
-#undef HAVE_STRSTR
-
-/* Define to 1 if you have the <sys/dir.h> header file, and it defines `DIR'.
-   */
-#undef HAVE_SYS_DIR_H
-
-/* Define to 1 if you have the <sys/ndir.h> header file, and it defines `DIR'.
-   */
-#undef HAVE_SYS_NDIR_H
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <TargetConfig.h> header file. */
-#undef HAVE_TARGETCONFIG_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Define to 1 if you have the `vfork' function. */
-#undef HAVE_VFORK
-
-/* Define to 1 if you have the <vfork.h> header file. */
-#undef HAVE_VFORK_H
-
-/* Define to 1 if you have the `vprintf' function. */
-#undef HAVE_VPRINTF
-
-/* Define to 1 if `fork' works. */
-#undef HAVE_WORKING_FORK
-
-/* Define to 1 if `vfork' works. */
-#undef HAVE_WORKING_VFORK
-
-/* Set to 1 if HPUX 64bit ptrs on 32 bit m/c */
-#undef HPUX64PTRS
-
-/* Define to the sub-directory where libtool stores uninstalled libraries. */
-#undef LT_OBJDIR
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Define to 1 if PDF support is available */
-#undef PLD_pdf
-
-/* Define to 1 is PNG support is available */
-#undef PLD_png
-
-/* Define to 1 if X11 support is available */
-#undef PLD_xwin
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* Define to 1 if your <sys/time.h> declares `struct tm'. */
-#undef TM_IN_SYS_TIME
-
-/* Version number of package */
-#undef VERSION
-
-/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
-   significant byte first (like Motorola and SPARC, unlike Intel). */
-#if defined AC_APPLE_UNIVERSAL_BUILD
-# if defined __BIG_ENDIAN__
-#  define WORDS_BIGENDIAN 1
-# endif
-#else
-# ifndef WORDS_BIGENDIAN
-#  undef WORDS_BIGENDIAN
-# endif
-#endif
-
-/* Define to 1 if the X Window System is missing or not being used. */
-#undef X_DISPLAY_MISSING
-
-/* Set to 2 for open args */
-#undef _FORTIFY_SOURCE
-
-/* Define to empty if `const' does not conform to ANSI C. */
-#undef const
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-#undef inline
-#endif
-
-/* Define to `int' if <sys/types.h> does not define. */
-#undef pid_t
-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-#undef size_t
-
-/* Define as `fork' if `vfork' does not work. */
-#undef vfork

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gaaui.c
--- a/GEMBASSY-1.0.3/src/gaaui.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,147 +0,0 @@
-/******************************************************************************
-** @source gaaui
-**
-** Calculates various indeces of amino acid usage
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gaaui ****************************************************************
-**
-** Calculates various indeces of amino acid usage
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gaaui", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/aaui/output=f/tag=gene", base, restid);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gaminoinfo.c
--- a/GEMBASSY-1.0.3/src/gaminoinfo.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,121 +0,0 @@
-/******************************************************************************
-** @source gaminoinfo
-**
-** Prints out basic amino acid sequence statistics
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gaminoinfo ***********************************************************
-**
-** Prints out basic amino acid sequence statisctics
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gaminoinfo", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr    tmpname = NULL;
-  AjPSeqout tmpout  = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/amino_info", base, restid);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gb1.c
--- a/GEMBASSY-1.0.3/src/gb1.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,160 +0,0 @@
-/******************************************************************************
-** @source gb1
-**
-** Calculate strand bias of bacterial genome using B1 index
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gb1 ******************************************************************
-**
-** Calculate strand bias of bacterial genome using B1 index
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gb1", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr method = NULL;
-
-  AjPFile outf = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  method = ajAcdGetSelectSingle("method");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/B1/method=%S", base, restid, method);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S B1: %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&method);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gb2.c
--- a/GEMBASSY-1.0.3/src/gb2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,155 +0,0 @@
-/******************************************************************************
-** @source gb2
-**
-** Calculate strand bias of bacterial genome using B2 index
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gb2 ******************************************************************
-**
-** Calculate strand bias of bacterial genome using B2 index
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gb2", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile outf = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                    "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/B2", base, restid);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S B2: %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gbasecounter.c
--- a/GEMBASSY-1.0.3/src/gbasecounter.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,159 +0,0 @@
-/******************************************************************************
-** @source gbasecounter
-**
-** Creates a position weight matrix of oligomers around start codon
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gbasecounter *********************************************************
-**
-** Creates a position weight matrix of oligomers around start codon
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gbasecounter", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjPStr position   = NULL;
-  ajint PatLen     = 0;
-  ajint upstream   = 0;
-  ajint downstream = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  position   = ajAcdGetSelectSingle("position");
-  PatLen     = ajAcdGetInt("patlen");
-  upstream   = ajAcdGetInt("upstream");
-  downstream = ajAcdGetInt("downstream");
-  accid      = ajAcdGetBoolean("accid");
-  outf       = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/base_counter/position=%S/PatLen=%d"
-                  "upstream=%d/downstream=%d/output=f/tag=gene",
-                  base, restid, position, PatLen, upstream, downstream);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gbaseentropy.c
--- a/GEMBASSY-1.0.3/src/gbaseentropy.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,205 +0,0 @@
-/******************************************************************************
-** @source gbaseentropy
-**
-** Calculates and graphs the sequence conservation using Shanon uncertainty
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gbaseentropy *******************************************************
-**
-** Calculates and graphs the sequence conservation using Shanon uncertainty
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gbaseentropy", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjPStr position   = 0;
-  ajint  PatLen     = 0;
-  ajint  upstream   = 0;
-  ajint  downstream = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  position   = ajAcdGetSelectSingle("position");
-  PatLen     = ajAcdGetInt("patlen");
-  upstream   = ajAcdGetInt("upstream");
-  downstream = ajAcdGetInt("downstream");
-  accid      = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/base_entropy/position=%S/PatLen=%d/"
-                  "upstream=%d/downstream=%d/output=f/tag=gene", base, restid,
-                  position, PatLen, upstream, downstream);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("position");
-          gpp.ylab = ajStrNewC("entropy");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gbaseinformationcontent.c
--- a/GEMBASSY-1.0.3/src/gbaseinformationcontent.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,205 +0,0 @@
-/******************************************************************************
-** @source gbaseinformationcontent
-**
-** Calculates and graphs the sequence conservation using information content
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gbaseinformationcontent **********************************************
-**
-** Calculates and graphs the sequence conservation using information content
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gbaseinformationcontent", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjPStr position   = 0;
-  ajint  PatLen     = 0;
-  ajint  upstream   = 0;
-  ajint  downstream = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  position   = ajAcdGetSelectSingle("position");
-  PatLen     = ajAcdGetInt("patlen");
-  upstream   = ajAcdGetInt("upstream");
-  downstream = ajAcdGetInt("downstream");
-  accid      = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/base_information_content/position=%S/"
-                  "PatLen=%d/upstream=%d/downstream=%d/output=f/tag=gene",
-                  base, restid, position, PatLen, upstream, downstream);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("position");
-          gpp.ylab = ajStrNewC("information content");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gbaserelativeentropy.c
--- a/GEMBASSY-1.0.3/src/gbaserelativeentropy.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,207 +0,0 @@
-/******************************************************************************
-** @source gbaserelativeentropy
-**
-** Calculates and graphs the sequence conservation using Kullback-Leibler
-** divergence (relative entropy)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gbaserelativeentropy *************************************************
-**
-** Calculates and graphs the sequence conservation using Kullback-Leibler
-** divergence (relative entropy)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gbaserelativeentropy", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjPStr position   = 0;
-  ajint  PatLen     = 0;
-  ajint  upstream   = 0;
-  ajint  downstream = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  position   = ajAcdGetSelectSingle("position");
-  PatLen     = ajAcdGetInt("patlen");
-  upstream   = ajAcdGetInt("upstream");
-  downstream = ajAcdGetInt("downstream");
-  accid      = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/base_relative_entropy/position=%S/"
-                  "PatLen=%d/upstream=%d/downstream=%d/output=f/tag=gene",
-                  base, restid, position, PatLen, upstream, downstream);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("position");
-          gpp.ylab = ajStrNewC("relative entropy");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gbasezvalue.c
--- a/GEMBASSY-1.0.3/src/gbasezvalue.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,162 +0,0 @@
-/******************************************************************************
-** @source gbasezvalue
-**
-** Extracts conserved oligomers per position using Z-score
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gbasezvalue ********************************************************
-**
-** Extracts conserved oligomers per position using Z-score
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gbasezvalue", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjPStr position   = NULL;
-  ajint limit      = 0;
-  ajint  PatLen     = 0;
-  ajint  upstream   = 0;
-  ajint  downstream = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  position   = ajAcdGetSelectSingle("position");
-  limit      = ajAcdGetInt("limit");
-  PatLen     = ajAcdGetInt("patlen");
-  upstream   = ajAcdGetInt("upstream");
-  downstream = ajAcdGetInt("downstream");
-  accid      = ajAcdGetBoolean("accid");
-  outf       = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/base_z_value/position=%S/PatLen=%d"
-                  "upstream=%d/downstream=%d/limit=%d/output=f/tag=gene",
-                  base, restid, position, PatLen, upstream, downstream, limit);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gbui.c
--- a/GEMBASSY-1.0.3/src/gbui.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,165 +0,0 @@
-/******************************************************************************
-** @source gbui
-**
-** Calculates base usage indices for protein-coding sequences
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gbui ****************************************************************
-**
-** Calculates base usage indices for protein-coding sequences
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gbui", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr position  = NULL;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  position  = ajAcdGetListSingle("position");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  if(ajStrMatchC(position, "all"))
-    {
-      ajStrDel(&position);
-      position = ajStrNew();
-    }
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/bui/translate=%d/position=%S/"
-                  "delkey=%S/output=f/tag=gene", base, restid, translate,
-                  position, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gcai.c
--- a/GEMBASSY-1.0.3/src/gcai.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,161 +0,0 @@
-/******************************************************************************
-** @source gcai
-**
-** Calculate codon adaptation index for each gene
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gcai *****************************************************************
-**
-** Calculate codon adaptation index for each gene
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gcai", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr wabsent   = NULL;
-  AjBool tai       = ajFalse;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  wabsent   = ajAcdGetString("wabsent");
-  tai       = ajAcdGetBoolean("tai");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  if(ajStrPrefixC(wabsent, "-"))
-    {
-      ajStrAssignC(&wabsent, "-");
-    }
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/cai/translate=%d/wabsent=%S/"
-                  "tai=%d/output=f/tag=gene", base, restid, translate,
-                  wabsent, tai);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gtaiFileOutURLS(url, &outf, tai))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gcbi.c
--- a/GEMBASSY-1.0.3/src/gcbi.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,155 +0,0 @@
-/******************************************************************************
-** @source gcbi
-**
-** Calculates the codon bias index
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gcbi *****************************************************************
-**
-** Calculates the codon bias index
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gcbi", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/cbi/translate=%d/delkey=%S/"
-                  "output=f/tag=gene", base, restid, translate, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gcgr.c
--- a/GEMBASSY-1.0.3/src/gcgr.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,164 +0,0 @@
-/******************************************************************************
-** @source gcgr
-**
-** Create a Chaos Game Representation of a given sequence
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gcgr ****************************************************************
-**
-** Create a Chaos Game Representation of a given sequence
-**
-*****************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gcgr", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__cgrInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  ajint     width    = 0;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  width    = ajAcdGetInt("width");
-  filename = ajAcdGetString("goutfile");
-  format   = ajAcdGetString("format");
-
-  params.width = width;
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      soap_init(&soap);
-
-      inseq = NULL;
-
-      ajStrAppendC(&inseq, ">");
-      ajStrAppendS(&inseq, ajSeqGetAccS(seq));
-      ajStrAppendC(&inseq, "\n");
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0) {
-        ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-      }
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__cgr(
-                           &soap,
-     NULL,
-     NULL,
-     in0,
-    &params,
-    &result
-                           ) == SOAP_OK)
- {
-          ++i;
-
-   outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-   outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "png"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-   ajStrDel(&outfname);
- }
-      else
- {
-   soap_print_fault(&soap, stderr);
- }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gcircularmap.c
--- a/GEMBASSY-1.0.3/src/gcircularmap.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,186 +0,0 @@
-/******************************************************************************
-** @source gcircularmap
-**
-** Draws circular map of the genome
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gcircularmap ********************************************************
-**
-** Draws circular map of the genome
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gcircularmap", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__circular_USCOREmapInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  AjBool    accid    = ajFalse;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  filename = ajAcdGetString("goutfile");
-  accid    = ajAcdGetBoolean("accid");
-  format   = ajAcdGetString("format");
-
-  params.gmap = 0;
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      soap_init(&soap);
-
-      soap.send_timeout = 0;
-      soap.recv_timeout = 0;
-
-      inseq = NULL;
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid || !gFormatGenbank(seq, &inseq))
-        {
-          if(!accid)
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID:%S\n", seqid);
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-
-          ajStrAssignS(&inseq, seqid);
-        }
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__circular_USCOREmap(
-                                   &soap,
-    NULL,
-    NULL,
-    in0,
-   &params,
-   &result
-                                          ) == SOAP_OK)
- {
-          ++i;
-
-          outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-          outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "svg"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("svg"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-          ajStrDel(&outfname);
- }
-      else
- {
-   soap_print_fault(&soap, stderr);
- }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gcodoncompiler.c
--- a/GEMBASSY-1.0.3/src/gcodoncompiler.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,163 +0,0 @@
-/******************************************************************************
-** @source gcodoncompiler
-**
-** Calculate various kinds of amino acid and codon usage data
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gcodoncompiler ******************************************************
-**
-** Calculate various kinds of amino acid and codon usage data
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gcodoncompiler", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate  = ajFalse;
-  AjBool startcodon = ajFalse;
-  AjBool stopcodon  = ajFalse;
-  AjPStr delkey     = NULL;
-  AjPStr data       = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  translate  = ajAcdGetBoolean("translate");
-  startcodon = ajAcdGetBoolean("startcodon");
-  stopcodon  = ajAcdGetBoolean("stopcodon");
-  delkey     = ajAcdGetString("delkey");
-  data       = ajAcdGetListSingle("data");
-  accid      = ajAcdGetBoolean("accid");
-  outf       = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                    "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/codon_compiler//translate=%d/"
-                  "startcodon=%d/stopcodon=%d/delkey=%S/data=%S/output=f/",
-                  base, restid, translate, startcodon, stopcodon, delkey, data);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&delkey);
-  ajStrDel(&data);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gconsensusz.c
--- a/GEMBASSY-1.0.3/src/gconsensusz.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,188 +0,0 @@
-/******************************************************************************
-** @source gconsensusz
-**
-** Calculate the consensus in givin array of sequences
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gconsensusz *********************************************************
-**
-** Calculate the consensus in givin array of sequences
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gconsensusz", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap   soap;
-  struct ns1__consensus_USCOREzInputParams params;
-  struct arrayIn  array_seq;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  ajint     high  = 0;
-  double    low   = 0;
-
-  char *result;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  ajint i;
-  ajint size = 0;
-  char **ptr = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  high   = ajAcdGetInt("high");
-  low    = ajAcdGetFloat("low");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  params.high   = high;
-  params.low    = low;
-  params.output = "f";
-
-  array_seq.__ptr = NULL;
-  array_seq.__size = 0;
-
-  ptr = (char**)malloc(sizeof(char*));
-
-  if(!ptr)
-    {
-      ajDie("Error in allocation\n");
-    }
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      ptr = (char**)realloc(ptr, sizeof(char*) * (size + 1));
-
-      if(!ptr)
- {
-   ajDie("Error in allocation\n");
- }
-
-      *(ptr + size) = ajCharNewS(ajSeqGetSeqS(seq));
-
-      ++size;
-    }
-
-  if(size < 2)
-    {
-      AJFREE(*ptr);
-      AJFREE(ptr);
-
-      ajDie("File only has one sequence. Please input more than two.\n");
-    }
-
-  array_seq.__ptr = ptr;
-  array_seq.__size = size;
-
-  soap_init(&soap);
-
-  if(soap_call_ns1__consensus_USCOREz(
-                                     &soap,
-       NULL,
-       NULL,
-      &array_seq,
-      &params,
-      &result
-                                     ) == SOAP_OK)
-    {
-      if(plot)
- {
-   ajStrAppendC(&title, argv[0]);
-
-   gpp.title = ajStrNewS(title);
-   gpp.xlab = ajStrNewC("position");
-   gpp.ylab = ajStrNewC("consensus");
-
-          if(!gFilebuffURLC(result, &buff))
-            {
-              ajDie("File downloading error from:\n%s\n", result);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-   ajStrDel(&title);
-   ajStrDel(&(gpp.xlab));
-   ajStrDel(&(gpp.ylab));
- }
-      else
- {
-   if(!gFileOutURLC(result, &outf))
-     {
-              ajDie("File downloading error from:\n%s\n", result);
-              embExitBad();
-     }
- }
-    }
-  else
-    {
-      soap_print_fault(&soap, stderr);
-    }
-
-  soap_destroy(&soap);
-  soap_end(&soap);
-  soap_done(&soap);
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  i = 0;
-
-  while(i < size)
-    {
-      AJFREE(*(ptr + i));
-      ++i;
-    }
-
-  AJFREE(ptr);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gdeltaenc.c
--- a/GEMBASSY-1.0.3/src/gdeltaenc.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,157 +0,0 @@
-/******************************************************************************
-** @source gdeltaenc
-**
-** Calculate the codon usage bias related to translation optimization
-** (delta enc)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gdeltaenc **********************************************************
-**
-** Calculate the codon usage bias related to translation optimization
-** (delta enc)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gdeltaenc", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-  AjPFilebuff tmp = NULL;
-
-  AjPStr line = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                    "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/delta_enc/", base, restid);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S DELTA-ENC %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gdeltagcskew.c
--- a/GEMBASSY-1.0.3/src/gdeltagcskew.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,164 +0,0 @@
-/******************************************************************************
-** @source gdeltagcskew
-**
-** Calculates strand bias of bacterial genome using delta GC skew index
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gdeltagcskew ********************************************************
-**
-** Calculates strand bias of bacterial genome using delta GC skew index
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gdeltagcskew", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool at     = 0;
-  AjBool purine = 0;
-  AjBool keto   = 0;
-  AjPStr method = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-  AjPFilebuff tmp = NULL;
-
-  AjPStr line = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  at     = ajAcdGetBoolean("at");
-  purine = ajAcdGetBoolean("purine");
-  keto   = ajAcdGetBoolean("keto");
-  method = ajAcdGetSelectSingle("method");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/delta_gcskew/", base, restid);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S DELTA-GCskew %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gdinuc.c
--- a/GEMBASSY-1.0.3/src/gdinuc.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,165 +0,0 @@
-/******************************************************************************
-** @source gdinuc
-**
-** Calculates dinucleotide usage
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gdinuc ***************************************************************
-**
-** Calculates dinucleotide usage
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gdinuc", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr position  = NULL;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  position  = ajAcdGetListSingle("position");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  if(ajStrMatchCaseC(position, "all"))
-    {
-      ajStrDel(&position);
-      position = ajStrNew();
-    }
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/dinuc/translate=%d/position=%S/"
-                  "delkey=%S/output=f/tag=gene", base, restid, translate,
-                  position, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&position);
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gdistincc.c
--- a/GEMBASSY-1.0.3/src/gdistincc.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,194 +0,0 @@
-/******************************************************************************
-** @source gdistincc
-**
-** Calculates distance betwwen two loci in cirular chromosomes
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Support sequences without features
-** @modified 2015/2/7   Remove negative distance bug
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-
-/* @prog gdistincc **********************************************************
-**
-** Calculates distance betwwen two loci in cirular chromosomes
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gdistincc", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq;
-
-  AjBool accid = ajFalse;
-  AjPStr seqid  = NULL;
-  AjPStr restid = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  ajint first;
-  ajint second;
-
-  AjPFile     outfile = NULL;
-  AjPFile     tmpfile = NULL;
-  AjPStr      tmpname = NULL;
-  AjPStr      fstname = NULL;
-  AjPFilebuff tmp     = NULL;
-  AjPStr      line    = NULL;
-  AjPSeqout   tmpout  = NULL;
-
-  seqall  = ajAcdGetSeqall("sequence");
-  first   = ajAcdGetInt("first");
-  second  = ajAcdGetInt("second");
-  accid   = ajAcdGetBoolean("accid");
-  outfile = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  gAssignUniqueName(&fstname);
-  ajStrAppendC(&fstname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = ajStrNew();
-
-      tmpout = ajSeqoutNew();
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              if(!ajSeqoutOpenFilename(tmpout, fstname))
-                {
-                  embExitBad();
-                }
-
-              ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-              ajSeqoutWriteSeq(tmpout, seq);
-              ajSeqoutClose(tmpout);
-              ajSeqoutDel(&tmpout);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, fstname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(fstname);
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      if(second >= 0)
-        {
-          ajFmtPrintS(&url, "http://%S/%S/dist_in_cc/%d/%d",
-                      base, restid, first, second);
-        }
-      else
-        {
-          ajFmtPrintS(&url, "http://%S/%S/dist_in_cc/%d",
-                      base, restid, first);
-        }
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      if(second >= 0)
-        {
-          ajFmtPrintF(outfile, "Sequence: %S Position1: %d Position2: %d "
-                      "Distance %S\n", seqid, first, line);
-        }
-      else
-        {
-          ajFmtPrintF(outfile, "Sequence: %S Position1: %d Distance %S\n",
-                      seqid, first, line);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-    }
-
-  ajFileClose(&outfile);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gdnawalk.c
--- a/GEMBASSY-1.0.3/src/gdnawalk.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,163 +0,0 @@
-/******************************************************************************
-** @source gdnawalk
-**
-** Draws DNA Walk map of the genome
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gdnawalk *************************************************************
-**
-** Draws DNA Walk map of the genome
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gdnawalk", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__dnawalkInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  filename = ajAcdGetString("goutfile");
-  format   = ajAcdGetString("format");
-
-  params.gmap = 0;
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      soap_init(&soap);
-
-      soap.send_timeout = 0;
-      soap.recv_timeout = 0;
-
-      inseq = NULL;
-
-      ajStrAppendC(&inseq, ">");
-      ajStrAppendS(&inseq, ajSeqGetAccS(seq));
-      ajStrAppendC(&inseq, "\n");
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__dnawalk(
-                        &soap,
-         NULL,
-         NULL,
-         in0,
-        &params,
-        &result
-                               ) == SOAP_OK)
- {
-          ++i;
-
-          outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-          outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "png"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-          ajStrDel(&outfname);
-        }
-      else
-        {
-          soap_print_fault(&soap, stderr);
-        }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/genc.c
--- a/GEMBASSY-1.0.3/src/genc.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,153 +0,0 @@
-/******************************************************************************
-** @source genc
-**
-** Calculate the effective number of codons (Nc)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog genc *****************************************************************
-**
-** Calculate the effective number of codons (Nc)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("genc", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/enc/translate=%d/delkey=%S/"
-                  "output=f/tag=gene", base, restid, translate, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&seqid);
-
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/genret.c
--- a/GEMBASSY-1.0.3/src/genret.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,302 +0,0 @@\n-/******************************************************************************\n-** @source genret\n-**\n-** Retrieves various gene related infomration from genome flatfile\n-**\n-** @author Copyright (C) 2012 Hidetoshi Itaya\n-** @version 1.0.3\n-** @modified 2012/1/20 Hidetoshi Itaya Created!\n-** @modified 2013/6/16 Revision 1\n-** @modified 2015/2/7 Refactor\n-** @@\n-**\n-** This program is free software; you can redistribute it and/or\n-** modify it under the terms of the GNU General Public License\n-** as published by the Free Software Foundation; either version 2\n-** of the License, or (at your option) any later version.\n-**\n-** This program is distributed in the hope that it will be useful,\n-** but WITHOUT ANY WARRANTY; without even the implied warranty of\n-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-** GNU General Public License for more details.\n-**\n-** You should have received a copy of the GNU General Public License\n-** along with this program; if not, write to the Free Software\n-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\n-******************************************************************************/\n-\n-#include "emboss.h"\n-#include "glibs.h"\n-\n-\n-\n-\n-/* @prog genret ***************************************************************\n-**\n-** Retrieves various gene related infomration from genome flatfile\n-**\n-******************************************************************************/\n-\n-int main(int argc, char *argv[])\n-{\n- embInitPV("genret", argc, argv, "GEMBASSY", "1.0.3");\n-\n- AjPSeqall seqall;\n- AjPSeq seq = NULL;\n- AjPStr inseq = NULL;\n- AjPStr gene = NULL;\n- AjPStr access = NULL;\n- AjBool accid = ajTrue;\n- AjPStr argument = NULL;\n- AjPFile outfile = NULL;\n-\n- AjPStr seqid = NULL;\n- AjPStr restid = NULL;\n-\n- AjBool valid = ajFalse;\n- AjBool isseq = ajFalse;\n- AjBool isgbk = ajFalse;\n-\n- AjPFilebuff buff = NULL;\n- AjPFile tmpfile = NULL;\n- AjPStr tmpname = NULL;\n-\n- AjPStr regexstr = NULL;\n- AjPStrTok token = NULL;\n- AjPRegexp regex = NULL;\n-\n- AjPStr url = NULL;\n- AjPStr base = NULL;\n- AjPStr head = NULL;\n- AjPStr line = NULL;\n-\n- seqall = ajAcdGetSeqall("sequence");\n- access = ajAcdGetString("access");\n- gene = ajAcdGetString("gene");\n- argument = ajAcdGetString("argument");\n- accid = ajAcdGetBoolean("accid");\n- outfile = ajAcdGetOutfile("outfile");\n-\n- if(\n- ajStrMatchC(access, "translation") ||\n- ajStrMatchC(access, "get_exon") ||\n- ajStrMatchC(access, "get_exons") ||\n- ajStrMatchC(access, "get_cdsseq") ||\n- ajStrMatchC(access, "get_gbkseq") ||\n- ajStrMatchC(access, "get_geneseq") ||\n- ajStrMatchC(access, "get_intron") ||\n- ajStrMatchC(access, "getseq") ||\n- ajStrMatchC(access, "seq") ||\n- ajStrMatchC(access, "around_startcodon") ||\n- ajStrMatchC(access, "around_stopcodon") ||\n- ajStrMatchC(access, "before_startcodon") ||\n- ajStrMatchC(access, "before_stopcodon") ||\n- ajStrMatchC(access, "after_startcodon") ||\n- ajStrMatchC(access, "after_stopcodon")\n- )\n- {\n- isseq = ajTrue;\n- }\n- else if(ajStrMatchC(access, "annotate") ||\n- ajStrMatchC(access, "output"))\n- {\n- isgbk = ajTrue;\n- }\n- else\n- {\n- ajFmtPrintF(outfile, "gene,%S\\n", access);\n- }\n-\n- base = ajStrNewC("rest.g-language.org");\n-\n- ajStrExchangeCC(&argument, " ", "/");\n- ajStrExchangeCC(&argument, ",", "/");\n- ajStrExchangeCC(&argument, "\\t", "/");\n- ajStrExchangeCC(&argument, "\\r", "/");\n- ajStrExchangeCC(&argument, "\\n", "/");\n-\n- if(ajStrMatchC(gene, "*"))\n- {\n- ajStrInsertK(&gene, 0, \'.\');\n- }\n-\n- if(ajStrPrefixC(gene, "@") || ajStrPrefixC(gene, "list::"))\n- {\n- ajStrExchangeCC(&gene, "@", "");\n- ajStrExchangeCC(&gene, "list::", "");\n- ajStrAssignS(&tmpname, gene);\n-\n- tmpfile = ajFileNewInNameS(tmpname);\n-\n- if(!tmpfile)\n- {\n- ajDie("List fil'..b'= ajStrNew();\n-\n- while(ajReadline(tmpfile, &line))\n- {\n- ajStrAppendS(&gene, line);\n- }\n-\n- ajFileClose(&tmpfile);\n- ajStrDel(&tmpname);\n- ajStrDel(&line);\n- }\n-\n- tmpname = ajStrNew();\n- gAssignUniqueName(&tmpname);\n-\n- while(ajSeqallNext(seqall, &seq))\n- {\n- inseq = ajStrNew();\n-\n- if(!accid)\n- {\n- if(gFormatGenbank(seq, &inseq))\n- {\n- tmpfile = ajFileNewOutNameS(tmpname);\n-\n- if(!tmpfile)\n- {\n- ajDie("Output file (%S) open error\\n", tmpname);\n- }\n-\n- ajFmtPrintF(tmpfile, "%S", inseq);\n-\n- ajFileClose(&tmpfile);\n-\n- ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);\n-\n- gFilePostSS(url, tmpname, &restid);\n-\n- ajStrDel(&url);\n-\n- ajSysFileUnlinkS(tmpname);\n- }\n- else\n- {\n- ajWarn("Sequence does not have features\\n"\n- "Proceeding with sequence accession ID\\n");\n- accid = ajTrue;\n- }\n- }\n-\n-\n- ajStrAssignS(&seqid, ajSeqGetAccS(seq));\n-\n- if(ajStrGetLen(seqid) == 0)\n- {\n- ajStrAssignS(&seqid, ajSeqGetNameS(seq));\n- }\n-\n- if(ajStrGetLen(seqid) == 0)\n- {\n- ajWarn("No valid header information\\n");\n- }\n-\n- if(accid)\n- {\n- ajStrAssignS(&restid, seqid);\n- if(ajStrGetLen(seqid) == 0)\n- {\n- ajDie("Cannot proceed without header with -accid\\n");\n- }\n-\n- if(!gValID(seqid))\n- {\n- ajDie("Invalid accession ID:%S, exiting\\n", seqid);\n- }\n- }\n-\n- url = ajStrNew();\n-\n- if(isgbk)\n- {\n- ajFmtPrintS(&url, "http://%S/%S/%S", base, restid, access);\n- }\n- else\n- {\n- ajFmtPrintS(&url, "http://%S/%S/*/%S/%S", base, restid, access, argument);\n- }\n-\n- if(!gFilebuffURLS(url, &buff))\n- {\n- ajDie("GET error from %S\\n", url);\n- }\n-\n- while(ajBuffreadLine(buff, &line))\n- {\n- if(isgbk){\n- ajFmtPrintF(outfile, "%S", line);\n- continue;\n- }\n-\n- ajStrRemoveLastNewline(&line);\n-\n- regex = ajRegCompC("^>");\n-\n- if(ajRegExec(regex, line))\n- {\n- head = ajStrNew();\n-\n- ajStrAssignS(&head, line);\n- ajStrTrimStartC(&head, ">");\n-\n- valid = ajFalse;\n-\n- token = ajStrTokenNewC(ajStrNewS(gene), " ,\\t\\r\\n");\n-\n- while(ajStrTokenNextParse(token, &regexstr))\n- {\n- if(ajStrGetLen(regexstr))\n- {\n- regex = ajRegComp(regexstr);\n-\n- if(ajRegExec(regex, line))\n- {\n- valid = ajTrue;\n- if(ajStrIsAlnum(regexstr))\n- {\n- ajStrExchangeSC(&gene, regexstr, "");\n- }\n- }\n-\n- ajRegFree(&regex);\n- }\n- }\n- }\n- else\n- {\n- if(valid)\n- {\n- if(isseq)\n- {\n- ajStrFmtWrap(&line, 60);\n- ajFmtPrintF(outfile, ">%S\\n%S\\n", head, line);\n- }\n- else\n- {\n- ajFmtPrintF(outfile, "%S,%S\\n", head, line);\n- }\n-\n- valid = ajFalse;\n- }\n- }\n- }\n-\n- ajFileClose(&outfile);\n-\n- ajStrDel(&restid);\n- ajStrDel(&seqid);\n- ajStrDel(&inseq);\n- }\n-\n- ajSeqallDel(&seqall);\n- ajSeqDel(&seq);\n- ajStrDel(&access);\n- ajStrDel(&gene);\n-\n- embExit();\n-}\n'

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gentrez.c
--- a/GEMBASSY-1.0.3/src/gentrez.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,108 +0,0 @@
-/******************************************************************************
-** @source gentrez
-**
-** Search NCBI Entrez in G-language Shell
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gentrez **************************************************************
-**
-** Search NCBI Entrez in G-language Shell
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gentrez", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-
-  AjPStr database = NULL;
-  AjPStr query    = NULL;
-
-  char *in0;
-  char *in1;
-  char *result;
-
-  AjPFile outf = NULL;
-
-  database = ajAcdGetString("database");
-  query    = ajAcdGetString("query");
-  outf     = ajAcdGetOutfile("outfile");
-
-  in0 = ajCharNewS(database);
-  in1 = ajCharNewS(query);
-
-  soap_init(&soap);
-
-  if(soap_call_ns1__entrez(
-                          &soap,
-    NULL,
-    NULL,
-    in0,
-    in1,
-   &result
-   ) == SOAP_OK)
-    {
-      if(result)
-        {
-          ajFmtPrintF(outf, "%s", result);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "No results found.\n");
-        }
-    }
-  else
-    {
-      soap_print_fault(&soap, stderr);
-    }
-
-  soap_destroy(&soap);
-  soap_end(&soap);
-  soap_done(&soap);
-
-  ajFileClose(&outf);
-
-  AJFREE(in0);
-  AJFREE(in1);
-
-  ajStrDel(&database);
-  ajStrDel(&query);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gew.c
--- a/GEMBASSY-1.0.3/src/gew.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,155 +0,0 @@
-/******************************************************************************
-** @source gew
-**
-** Calculate a measure of synonymous codon usage evenness (Ew)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3   Revision 1
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gew ******************************************************************
-**
-** Calculate a measure of synonymous codon usage evenness (Ew)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gew", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/Ew/translate=%d/delkey=%S/"
-                  "output=f/tag=gene", base, restid, translate, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gfindoriter.c
--- a/GEMBASSY-1.0.3/src/gfindoriter.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,167 +0,0 @@
-/******************************************************************************
-** @source gfindoriter
-**
-** Predict the replication origin and terminus in bacterial genomes
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gfindoriter ********************************************************
-**
-** Predict the replication origin and terminus in bacterial genomes
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gfindoriter", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-
-  ajint window  = 0;
-  AjBool purine  = 0;
-  AjBool keto    = 0;
-  ajint lowpass = 0;
-
-  AjPStr ori = NULL;
-  AjPStr ter = NULL;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr      tmpname = NULL;
-  AjPSeqout   tmpout  = NULL;
-  AjPFilebuff tmpbuff = NULL;
-
-  AjPStr tmp  = NULL;
-  AjPStr line = NULL;
-
-  AjPRegexp regex;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  window = ajAcdGetInt("window");
-  lowpass = ajAcdGetInt("lowpass");
-  purine = ajAcdGetBoolean("purine");
-  keto   = ajAcdGetBoolean("keto");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/find_ori_ter/window=%d/lowpass=%d/"
-                  "purine=%d/keto=%d/", base, restid, window, lowpass,
-                  purine, keto);
-
-      if(!gFilebuffURLS(url, &tmpbuff))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      regex = ajRegCompC("([0-9]+)$");
-
-      while(ajBuffreadLine(tmpbuff, &line))
-        {
-          if(ajRegExec(regex, line))
-            {
-              if(ajRegSubI(regex, 0, &tmp))
-                {
-                  if(ajStrGetLen(ori) == 0)
-                    {
-                      ajStrAssignS(&ori, tmp);
-                    }
-                  else if(ajStrGetLen(ter) == 0)
-                    {
-                      ajStrAssignS(&ter, tmp);
-                    }
-                }
-            }
-        }
-
-      ajFmtPrintF(outf, "Sequence: %S Origin: %S Terminus: %S\n",
-                  seqid, ori, ter);
-
-      ajStrDel(&tmp);
-      ajStrDel(&ori);
-      ajStrDel(&ter);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&seqid);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gfop.c
--- a/GEMBASSY-1.0.3/src/gfop.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,153 +0,0 @@
-/******************************************************************************
-** @source gfop
-**
-** Calculate the frequency of optimal codons (Fop)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gfop *****************************************************************
-**
-** Calculate the frequency of optimal codons (Fop)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gfop", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/fop/translate=%d/output=f/tag=gene",
-                  base, restid, translate);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/ggcsi.c
--- a/GEMBASSY-1.0.3/src/ggcsi.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,192 +0,0 @@
-/******************************************************************************
-** @source ggcsi
-**
-** GC Skew Index: an index for strand-specific mutational bias
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog ggcsi ****************************************************************
-**
-** GC Skew Index: an index for strand-specific mutational bias
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggcsi", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq   = NULL;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  ajint window  = 0;
-  AjBool at      = 0;
-  AjBool purine  = 0;
-  AjBool keto    = 0;
-  AjBool pval    = 0;
-  AjPStr version = NULL;
-
-  AjPStr      tmpname = NULL;
-  AjPSeqout   tmpout  = NULL;
-  AjPFilebuff tmpbuff = NULL;
-
-  AjPStr tmp   = NULL;
-  AjPStr parse = NULL;
-  AjPStr gcsi  = NULL;
-  AjPStr sa    = NULL;
-  AjPStr dist  = NULL;
-  AjPStr z     = NULL;
-  AjPStr p     = NULL;
-
-  AjPStrTok handle  = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall  = ajAcdGetSeqall("sequence");
-  window  = ajAcdGetInt("window");
-  at      = ajAcdGetBoolean("at");
-  purine  = ajAcdGetBoolean("purine");
-  keto    = ajAcdGetBoolean("keto");
-  pval    = ajAcdGetBoolean("pval");
-  version = ajAcdGetSelectSingle("gcsi");
-  outf    = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/gcsi/window=%d/at=%d/purine=%d/"
-                  "keto=%d/p=%d/version=%d/", base, restid, window, at, purine,
-                  keto, pval, version);
-
-      if(!gFilebuffURLS(url, &tmpbuff))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmpbuff, &tmp);
-
-      parse = ajStrNew();
-      gcsi  = ajStrNew();
-      sa    = ajStrNew();
-      dist  = ajStrNew();
-      z     = ajStrNew();
-      p     = ajStrNew();
-
-      ajStrRemoveLastNewline(&tmp);
-
-      handle = ajStrTokenNewC(tmp, ",");
-
-      while (ajStrTokenNextParse(handle, &parse))
-        {
-          if (ajStrIsFloat(parse))
-            {
-              if(!ajStrGetLen(gcsi))
-                ajStrAssignS(&gcsi, parse);
-              else if(!ajStrGetLen(sa))
-                ajStrAssignS(&sa, parse);
-              else if(!ajStrGetLen(dist))
-                ajStrAssignS(&dist, parse);
-              else if(!ajStrGetLen(z))
-                ajStrAssignS(&z, parse);
-              else if(!ajStrGetLen(p))
-                ajStrAssignS(&p, parse);
-            }
-        }
-
-      tmp = ajFmtStr("Sequence: %S GCSI: %S SA: %S DIST: %S",
-                     seqid, gcsi, sa, dist);
-
-      if(pval)
-        tmp = ajFmtStr("%S Z: %S P: %S", tmp, z, p);
-
-      ajFmtPrintF(outf, "%S\n", tmp);
-
-      ajStrDel(&tmp);
-      ajStrDel(&parse);
-      ajStrDel(&gcsi);
-      ajStrDel(&sa);
-      ajStrDel(&dist);
-      ajStrDel(&z);
-      ajStrDel(&p);
-
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&seqid);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/ggcskew.c
--- a/GEMBASSY-1.0.3/src/ggcskew.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,178 +0,0 @@
-/******************************************************************************
-** @source ggcskew
-**
-** Calculates the GC skew of the input sequence
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog ggcskew **************************************************************
-**
-** Calculates the GC skew of the input sequence
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggcskew", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq      = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr    tmpname = NULL;
-  AjPSeqout tmpout  = NULL;
-
-  ajint window     = 0;
-  ajint slide      = 0;
-  AjBool cumulative = 0;
-  AjBool at         = 0;
-  AjBool purine     = 0;
-  AjBool keto       = 0;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  window     = ajAcdGetInt("window");
-  slide      = ajAcdGetInt("slide");
-  cumulative = ajAcdGetBoolean("cumulative");
-  at         = ajAcdGetBoolean("at");
-  purine     = ajAcdGetBoolean("purine");
-  keto       = ajAcdGetBoolean("keto");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/gcskew/window=%d/slide=%d/cumulative=%d/"
-                  "at=%d/purine=%d/keto=%d/output=f/", base, restid, window,
-                  slide, cumulative, at, purine, keto);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("location");
-          gpp.ylab = ajStrNewC("GC skew");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/ggcwin.c
--- a/GEMBASSY-1.0.3/src/ggcwin.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,173 +0,0 @@
-/******************************************************************************
-** @source ggcwin
-**
-** Calculates the GC content along the given genome
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog ggcwin ***************************************************************
-**
-** Calculates the GC content along the given genome
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggcwin", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq      = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr    tmpname = NULL;
-  AjPSeqout tmpout  = NULL;
-
-  ajint  window = 0;
-  AjBool at     = 0;
-  AjBool purine = 0;
-  AjBool keto   = 0;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  window = ajAcdGetInt("window");
-  at     = ajAcdGetBoolean("at");
-  purine = ajAcdGetBoolean("purine");
-  keto   = ajAcdGetBoolean("keto");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/gcwin/window=%d/at=%d/purine=%d/"
-                  "keto=%d/output=f/", base, restid, window, at, purine, keto);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("location");
-          gpp.ylab = ajStrNewC("GC content");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/ggeneskew.c
--- a/GEMBASSY-1.0.3/src/ggeneskew.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,208 +0,0 @@
-/******************************************************************************
-** @source ggeneskew
-**
-** Calculate the gene strand bias of the given genome
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog ggeneskew ************************************************************
-**
-** Calculate the gene strand bias of the given genome
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggeneskew", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint window     = 0;
-  ajint slide      = 0;
-  AjBool cumulative = ajFalse;
-  AjBool gc3        = ajFalse;
-  AjPStr basetype   = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  window     = ajAcdGetInt("window");
-  slide      = ajAcdGetInt("slide");
-  cumulative = ajAcdGetBoolean("cumulative");
-  gc3        = ajAcdGetBoolean("gctri");
-  basetype   = ajAcdGetSelectSingle("base");
-  accid      = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  if(ajStrMatchC(base, "none"))
-    basetype = ajStrNewC("");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajFmtError("Sequence does not have features\n"
-                         "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/geneskew/window=%d/slide=%d/"
-                  "cumulative=%d/gc3=%d/base=%S/output=f/tag=gene",
-                  base, restid, window, slide, cumulative, gc3, basetype);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("gene skew");
-          gpp.ylab = ajStrNewC("bp");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/ggenomemap3.c
--- a/GEMBASSY-1.0.3/src/ggenomemap3.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,191 +0,0 @@
-/******************************************************************************
-** @source ggenomemap3
-**
-** Draws the map of the genome (Version 3)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7  Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog ggenomemap3 **********************************************************
-**
-** Draws the map of the genome (Version 3)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggenomemap3", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__genome_USCOREmap3InputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  ajint     width;
-  ajint     height;
-  AjBool    accid    = ajFalse;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  width    = ajAcdGetInt("width");
-  height   = ajAcdGetInt("height");
-  filename = ajAcdGetString("goutfile");
-  accid    = ajAcdGetBoolean("accid");
-  format   = ajAcdGetString("format");
-
-  params.width  = width;
-  params.height = height;
-  params.gmap   = 0;
-  params.datafilename = "";
-  params.output = "g";
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-
-      soap_init(&soap);
-
-      soap.send_timeout = 0;
-      soap.recv_timeout = 0;
-
-      inseq = NULL;
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(!ajStrGetLen(seqid))
-        ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-
-      if(!ajStrGetLen(seqid))
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid || !gFormatGenbank(seq, &inseq))
-        {
-          if(!accid)
-            ajWarn("Sequence does not have features\n"
-                   "Proceeding with sequence accession ID:%S\n", seqid);
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-
-          ajStrAssignS(&inseq, seqid);
-        }
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__genome_USCOREmap3(
-                                          &soap,
-   NULL,
-   NULL,
-   in0,
-                                          &params,
-                                          &result
-                                          ) == SOAP_OK)
- {
-          ++i;
-
-          outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-          outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "png"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-          ajStrDel(&outfname);
-        }
-      else
-        {
-          soap_print_fault(&soap, stderr);
-        }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/ggenomicskew.c
--- a/GEMBASSY-1.0.3/src/ggenomicskew.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,219 +0,0 @@
-/******************************************************************************
-** @source ggenomicskew
-**
-** Calculates the GC skew in different regions of the given genome
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog ggenomicskew *********************************************************
-**
-** Calculates the GC skew in different regions of the given genome
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggenomicskew", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint divide = 0;
-  AjBool at    = ajFalse;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-  AjPPStr     names = NULL;
-
-  ajint i;
-
-  seqall = ajAcdGetSeqall("sequence");
-  divide = ajAcdGetInt("divide");
-  at     = ajAcdGetBoolean("at");
-  accid  = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while (ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajFmtError("Sequence does not have features\n"
-                         "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/genomicskew/divide=%d/at=%d/"
-                  "output=f/tag=gene", base, restid, divide, at);
-      if(plot)
-        {
-          if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
-            ajDie("Error in memory allocation, exiting\n");
-          }
-
-          names[0] = NULL;
-          names[1] = ajStrNewC("whole genome");
-          names[2] = ajStrNewC("coding region");
-          names[3] = ajStrNewC("intergenic region");
-          names[4] = ajStrNewC("codon third position");
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("location");
-          gpp.ylab = ajStrNewC("GC skew");
-          gpp.names = names;
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          i = 0;
-          while(names[i])
-            {
-              AJFREE(names[i]);
-              ++i;
-            }
-
-          AJFREE(names);
-
-          ajStrDel(&title);
-          ajStrDel(&(gpp.title));
-          ajStrDel(&(gpp.xlab));
-          ajStrDel(&(gpp.ylab));
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gicdi.c
--- a/GEMBASSY-1.0.3/src/gicdi.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,157 +0,0 @@
-/******************************************************************************
-** @source gicdi
-**
-** Calculates the intrinsic codon deviation index
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gicdi ****************************************************************
-**
-** Calculates the intrinsic codon deviation index
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gicdi", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/icdi/translate=%d/delkey=%S/"
-                  "output=f/tag=gene", base, restid, translate, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gkmertable.c
--- a/GEMBASSY-1.0.3/src/gkmertable.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,164 +0,0 @@
-/******************************************************************************
-** @source gkmertable
-**
-** Create an image showing all k-mer abundance within a sequence
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gkmertable ***********************************************************
-**
-** Create an image showing all k-mer abundance within a sequence
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gkmertable", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__kmer_USCOREtableInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  ajint     k        = 0;
-  AjBool    accid    = ajFalse;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  k        = ajAcdGetInt("k");
-  filename = ajAcdGetString("goutfile");
-  format   = ajAcdGetString("format");
-
-  params.k = k;
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-
-      soap_init(&soap);
-
-      inseq = NULL;
-
-      ajStrAppendC(&inseq, ">");
-      ajStrAppendS(&inseq, ajSeqGetAccS(seq));
-      ajStrAppendC(&inseq, "\n");
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__kmer_USCOREtable(
-                                        &soap,
-                                         NULL,
-                                         NULL,
-                                         in0,
-                                        &params,
-                                        &result
-                                        ) == SOAP_OK)
- {
-          ++i;
-
-          outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-          outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "png"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-          ajStrDel(&outfname);
-        }
-      else
- {
-   soap_print_fault(&soap, stderr);
- }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gldabias.c
--- a/GEMBASSY-1.0.3/src/gldabias.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,163 +0,0 @@
-/******************************************************************************
-** @source gldabias
-**
-** Calculate strand bias of bacterial genome using linear discriminant
-** analysis (LDA)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gldabias ************************************************************
-**
-** Calculate strand bias of bacterial genome using linear discriminant
-** analysis (LDA)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gldabias", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint coefficients = 0;
-  AjPStr variable = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall       = ajAcdGetSeqall("sequence");
-  coefficients = ajAcdGetInt("coefficients");
-  variable     = ajAcdGetSelectSingle("variable");
-  accid        = ajAcdGetBoolean("accid");
-  outf         = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                    "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/lda_bias/coefficients=%d/variable=%S",
-                  base, restid, coefficients, variable);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S LDA-BIAS: %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gnucleotideperiodicity.c
--- a/GEMBASSY-1.0.3/src/gnucleotideperiodicity.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,194 +0,0 @@
-/******************************************************************************
-** @source gnucleotideperiodicity
-**
-** Checks the periodicity of certain oligonucleotides
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "../include/glibs.h"
-
-
-
-
-/* @prog gnucleotideperiodicity ***********************************************
-**
-** Checks the periodicity of certain oligonucleotides
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gnucleotideperiodicity", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint  window     = 0;
-  AjPStr nucleotide = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  window     = ajAcdGetInt("window");
-  nucleotide = ajAcdGetString("nucleotide");
-  accid      = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajFmtError("Sequence does not have features\n"
-                         "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/nucleotide_periodicity/output=f/gmap=0/"
-                  "nucleotide=%S/window=%d", base, restid, nucleotide, window);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("window");
-          gpp.ylab = ajStrNewC("value");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/goligomercounter.c
--- a/GEMBASSY-1.0.3/src/goligomercounter.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,142 +0,0 @@
-/******************************************************************************
-** @source goligomercounter
-**
-** Counts the number of given oligomers in a sequence
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3   Revision 1
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog goligomercounter ****************************************************
-**
-** Counts the number of given oligomers in a sequence
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("goligomercounter", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    oligomer = NULL;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  ajint window = 0;
-
-  AjPFile outf = NULL;
-
-  AjPStr    tmpname = NULL;
-  AjPSeqout tmpout  = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  oligomer = ajAcdGetString("oligomer");
-  window   = ajAcdGetInt("window");
-  outf     = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/oligomer_counter/%S",
-                  base, restid, oligomer);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S Oligomer: %S Number: %S\n",
-                  seqid, oligomer, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&oligomer);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/goligomersearch.c
--- a/GEMBASSY-1.0.3/src/goligomersearch.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,142 +0,0 @@
-/******************************************************************************
-** @source goligomersearch
-**
-** Counts the number of given oligomers in a sequence
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog goligomersearch ******************************************************
-**
-** Counts the number of given oligomers in a sequence
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("goligomersearch", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    oligomer = NULL;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr _return = NULL;
-
-  AjPStr    tmpname = NULL;
-  AjPSeqout tmpout  = NULL;
-
-  AjPFilebuff tmp  = NULL;
-  AjPStr      line = NULL;
-
-  AjPFile outfile = NULL;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  oligomer = ajAcdGetString("oligomer");
-  _return  = ajAcdGetSelectSingle("return");
-  outfile  = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/oligomer_search/%S/return=%S",
-                  base, restid, oligomer, _return);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outfile, "Sequence: %S Oligomer: %S Return: %S\n",
-                  seqid, oligomer, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outfile);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&oligomer);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gp2.c
--- a/GEMBASSY-1.0.3/src/gp2.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,147 +0,0 @@
-/******************************************************************************
-** @source gp2
-**
-**
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gp2 ******************************************************************
-**
-** Predict highly expressed gene
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gp2", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/P2/output=f/tag=gene", base, restid);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gpalindrome.c
--- a/GEMBASSY-1.0.3/src/gpalindrome.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,131 +0,0 @@
-/******************************************************************************
-** @source gpalindrome
-**
-** Searches palindrome sequences
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gpalindrome **********************************************************
-**
-** Searches palindrome sequences
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gpalindrome", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__palindromeInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-  AjPStr    seqid = NULL;
-  ajint     shortest = 0;
-  ajint     loop = 0;
-  AjBool    gtmatch = 0;
-
-  char *in0;
-  char *result;
-
-  AjPFile outf = NULL;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  shortest = ajAcdGetInt("shortest");
-  loop     = ajAcdGetInt("loop");
-  gtmatch  = ajAcdGetBoolean("gtmatch");
-  outf     = ajAcdGetOutfile("outfile");
-
-  params.shortest = shortest;
-  params.loop     = loop;
-  params.gtmatch  = gtmatch;
-  params.output   = "f";
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      soap_init(&soap);
-
-      inseq = NULL;
-
-      ajStrAppendC(&inseq, ">");
-      ajStrAppendS(&inseq, ajSeqGetNameS(seq));
-      ajStrAppendC(&inseq, "\n");
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__palindrome(
-   &soap,
-                                   NULL,
-                                   NULL,
-    in0,
-                                  &params,
-                                  &result
-   ) == SOAP_OK)
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-
-          if(!gFileOutURLC(result, &outf))
-            {
-              ajDie("File downloading error from:\n%s\n", result);
-              embExitBad();
-            }
-        }
-      else
-        {
-          soap_print_fault(&soap, stderr);
-        }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&seqid);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gphx.c
--- a/GEMBASSY-1.0.3/src/gphx.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,156 +0,0 @@
-/******************************************************************************
-** @source gphx
-**
-** Identify predict highly expressed gene
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gphx *****************************************************************
-**
-** Identify predict highly expressed gene
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gphx", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/phx/translate=%d/delkey=%S/"
-                  "output=f/tag=gene", base, restid, translate, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gqueryarm.c
--- a/GEMBASSY-1.0.3/src/gqueryarm.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,159 +0,0 @@
-/******************************************************************************
-** @source gqueryarm
-**
-** Get the replication arm name (left or right) from the given position
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gqueryarm ***********************************************************
-**
-** Get the replication arm name (left or right) from the given position
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gqueryarm", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  ajint position = 0;
-
-  AjPFile outf = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  position = ajAcdGetInt("position");
-  accid    = ajAcdGetBoolean("accid");
-  outf     = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/query_arm/%d/", base, restid, position);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S Arm: %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gquerystrand.c
--- a/GEMBASSY-1.0.3/src/gquerystrand.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,162 +0,0 @@
-/******************************************************************************
-** @source gquerystrand
-**
-** Get the strand name (leading or lagging) from the given position
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gquerystrand *********************************************************
-**
-** Get the strand name (leading or lagging) from the given position
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gquerystrand", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  ajint position  = 0;
-  AjPStr direction = 0;
-
-  AjPFile outf = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  position  = ajAcdGetInt("position");
-  direction = ajAcdGetSelectSingle("direction");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/query_strand/%d/direction=%S/", base,
-                  restid, position, direction);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S Strand: %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/greporiter.c
--- a/GEMBASSY-1.0.3/src/greporiter.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,191 +0,0 @@
-/******************************************************************************
-** @source greporiter
-**
-** Get the positions of replication origin and terminus
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog greporiter *********************************************************
-**
-** Get the positions of replication origin and terminus
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("greporiter", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq  = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjBool oriloc = 0;
-  AjBool gcskew = 0;
-  AjBool dbonly = 0;
-  ajint difthreshold = 0;
-
-  AjPFile outf = NULL;
-
-  AjPFile     tmpfile = NULL;
-  AjPStr      tmpname = NULL;
-  AjPStr      fstname = NULL;
-  AjPFilebuff tmp     = NULL;
-  AjPStr      line    = NULL;
-  AjPSeqout   tmpout  = NULL;
-
-  AjPRegexp regex;
-
-  AjPStr    ori    = NULL;
-  AjPStr    ter    = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  difthreshold = ajAcdGetInt("difthreshold");
-  oriloc = ajAcdGetBoolean("oriloc");
-  gcskew = ajAcdGetBoolean("gcskew");
-  dbonly = ajAcdGetBoolean("dbonly");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  gAssignUniqueName(&fstname);
-  ajStrAppendC(&fstname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = ajStrNew();
-
-      tmpout = ajSeqoutNew();
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              if(!ajSeqoutOpenFilename(tmpout, fstname))
-                {
-                  embExitBad();
-                }
-
-              ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-              ajSeqoutWriteSeq(tmpout, seq);
-              ajSeqoutClose(tmpout);
-              ajSeqoutDel(&tmpout);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, fstname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(fstname);
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/rep_ori_ter/oriloc=%d/gcskew=%d/"
-                  "difthreshold=%d/dbonly=%d/",  base, restid, oriloc, gcskew,
-                  difthreshold, dbonly);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      regex = ajRegCompC("([0-9]+),([0-9]+)");
-
-      if(ajRegExec(regex, line)) {
-        if(ajRegSubI(regex, 1, &ori), ajRegSubI(regex, 2, &ter)) {
-          ajFmtPrint("%S Origin: %S Terminus %S\n", seqid, ori, ter);
-        }
-      }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gscs.c
--- a/GEMBASSY-1.0.3/src/gscs.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,157 +0,0 @@
-/******************************************************************************
-** @source gscs
-**
-** Calculates the scaled chi-square
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gscs *****************************************************************
-**
-** Calculates the scaled chi-square
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gscs", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool translate = ajFalse;
-  AjPStr delkey    = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall    = ajAcdGetSeqall("sequence");
-  translate = ajAcdGetBoolean("translate");
-  delkey    = ajAcdGetString("delkey");
-  accid     = ajAcdGetBoolean("accid");
-  outf      = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/scs/translate=%d/delkey=%S/"
-                  "output=f/tag=gene", base, restid, translate, delkey);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  ajStrDel(&delkey);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gseq2png.c
--- a/GEMBASSY-1.0.3/src/gseq2png.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,171 +0,0 @@
-/******************************************************************************
-** @source gseq2png
-**
-** Converts a sequence to PNG image
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gseq2png *************************************************************
-**
-** Converts a sequence to PNG image
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gseq2png", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__seq2pngInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  ajint     width    = 0;
-  ajint     window   = 0;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    tempname = NULL;
-  AjPStr    appname  = NULL;
-  AjPStr    convert  = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  window   = ajAcdGetInt("window");
-  width    = ajAcdGetInt("width");
-  filename = ajAcdGetString("goutfile");
-  format   = ajAcdGetString("format");
-
-  appname = ajStrNewC("convert");
-
-  params.window = window;
-  params.width  = width;
-  params.output = "g";
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      soap_init(&soap);
-
-      inseq = NULL;
-
-      ajStrAppendC(&inseq, ">");
-      ajStrAppendS(&inseq, ajSeqGetNameS(seq));
-      ajStrAppendC(&inseq, "\n");
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__seq2png(
-        &soap,
-                                NULL,
-                                NULL,
-         in0,
-                               &params,
-                               &result
-        ) == SOAP_OK)
-        {
-          ++i;
-
-          outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-          outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "png"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-          ajStrDel(&outfname);
-        }
-      else
-        {
-          soap_print_fault(&soap, stderr);
-        }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gseqinfo.c
--- a/GEMBASSY-1.0.3/src/gseqinfo.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,127 +0,0 @@
-/******************************************************************************
-** @source gseqinfo
-**
-** Prints out basic nucleotide sequence statistics
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gseqinfo *************************************************************
-**
-** Prints out basic nucleotide sequence statistics
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gseqinfo", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq  = NULL;
-
-  AjPStr ori = NULL;
-  AjPStr ter = NULL;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPStr      tmpname = NULL;
-  AjPSeqout   tmpout  = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  outf = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/seqinfo/", base, restid);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gshuffleseq.c
--- a/GEMBASSY-1.0.3/src/gshuffleseq.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,114 +0,0 @@
-/******************************************************************************
-** @source gshuffleseq
-**
-** Create randomized sequence with conserved k-mer composition
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   RESTify
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "soapH.h"
-#include "GLANGSoapBinding.nsmap"
-#include "soapClient.c"
-#include "soapC.c"
-#include "../gsoap/stdsoap2.c"
-#include "glibs.h"
-
-
-
-
-/* @prog gshuffleseq **********************************************************
-**
-** Create randomized sequence with conserved k-mer composition
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gshuffleseq", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__shuffleseqInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeqout seqout;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-  ajint     k = 0;
-
-  char *in0;
-  char *result;
-
-  seqall = ajAcdGetSeqall("sequence");
-  k      = ajAcdGetInt("k");
-  seqout = ajAcdGetSeqout("outseq");
-
-  params.k = k;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-
-      soap_init(&soap);
-
-      inseq = NULL;
-
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__shuffleseq(
-   &soap,
-                                   NULL,
-                                   NULL,
-    in0,
-                                  &params,
-                                  &result
-   ) == SOAP_OK)
-        {
-          ajCharFmtUpper(result);
-          ajSeqAssignSeqC(seq, result);
-          ajSeqoutWriteSeq(seqout, seq);
-        }
-      else
-        {
-          soap_print_fault(&soap, stderr);
-        }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&inseq);
-  }
-
-  ajSeqoutClose(seqout);
-  ajSeqoutDel(&seqout);
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gsignature.c
--- a/GEMBASSY-1.0.3/src/gsignature.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,156 +0,0 @@
-/******************************************************************************
-** @source gsignature
-**
-** Calculate oligonucleotide usage (genomic signature)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gsignature ***********************************************************
-**
-** Calculate oligonucleotide usage (genomic signature)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gsignature", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint wordlength = 0;
-  AjBool bothstrand = ajFalse;
-  AjBool oe         = ajFalse;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  wordlength = ajAcdGetInt("wordlength");
-  bothstrand = ajAcdGetBoolean("bothstrand");
-  oe     = ajAcdGetBoolean("oe");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/signature/wordlength=%d/bothstrand=%d/"
-                  "oe=%d/output=f/tag=gene", base, restid, wordlength,
-                  bothstrand, oe);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gsvalue.c
--- a/GEMBASSY-1.0.3/src/gsvalue.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,159 +0,0 @@
-/******************************************************************************
-** @source gsvalue
-**
-** Calculate the strength of selected codon usage bias
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gsvalue **************************************************************
-**
-** Calculate the strength of selected codon usage bias
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gsvalue", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  AjBool sharp = ajFalse;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFilebuff tmp = NULL;
-  AjPStr     line = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  sharp  = ajAcdGetBoolean("sharp");
-  accid  = ajAcdGetBoolean("accid");
-  outf   = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                     "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-  ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-  if(ajStrGetLen(seqid) == 0)
-    {
-      ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-    }
-
-  if(ajStrGetLen(seqid) == 0)
-    {
-      ajWarn("No valid header information\n");
-    }
-
-  if(accid)
-    {
-      ajStrAssignS(&restid, seqid);
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajDie("Cannot proceed without header with -accid\n");
-        }
-
-      if(!gValID(seqid))
-        {
-          ajDie("Invalid accession ID:%S, exiting\n", seqid);
-        }
-    }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/S_value/sharp=%d/output=f/tag=gene",
-                  base, restid, sharp);
-
-      if(!gFilebuffURLS(url, &tmp))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmp, &line);
-
-      ajStrRemoveSetC(&line, "\n");
-
-      ajFmtPrintF(outf, "Sequence: %S S-value: %S\n", seqid, line);
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gviewcds.c
--- a/GEMBASSY-1.0.3/src/gviewcds.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,216 +0,0 @@
-/******************************************************************************
-** @source gviewcds
-**
-** Displays a graph of nucleotide contents around start and stop codons
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gviewcds ************************************************************
-**
-** Displays a graph of nucleotide contents around start and stop codons
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gviewcds", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint length = 0;
-  ajint gap = 0;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-  AjPPStr     names = NULL;
-
-  ajint i;
-
-  seqall = ajAcdGetSeqall("sequence");
-  length = ajAcdGetInt("length");
-  gap    = ajAcdGetInt("gap");
-  accid  = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajFmtError("Sequence does not have features\n"
-                         "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/view_cds/length=%d/gap=%d/"
-                  "output=f/tag=gene", base, restid, length, gap);
-
-      if(plot)
-        {
-          if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
-            ajDie("Error in memory allocation, exiting\n");
-          }
-
-          names[0] = NULL;
-          names[1] = ajStrNewC("A");
-          names[2] = ajStrNewC("T");
-          names[3] = ajStrNewC("G");
-          names[4] = ajStrNewC("C");
-
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("position");
-          gpp.ylab = ajStrNewC("percentage");
-          gpp.names = names;
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          i = 0;
-          while(names[i])
-            {
-              AJFREE(names[i]);
-              ++i;
-            }
-
-          AJFREE(names);
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&seqid);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 GEMBASSY-1.0.3/src/gwvalue.c
--- a/GEMBASSY-1.0.3/src/gwvalue.c Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,154 +0,0 @@
-/******************************************************************************
-** @source gwvalue
-**
-** Calculate the 'relative adaptiveness of each codon' (W)
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog gwvalue *************************************************************
-**
-** Calculate the 'relative adaptiveness of each codon' (W)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gwvalue", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq   = NULL;
-
-  AjPStr include = NULL;
-  AjPStr exclude = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall  = ajAcdGetSeqall("sequence");
-  include = ajAcdGetString("include");
-  exclude = ajAcdGetString("exclude");
-  accid   = ajAcdGetBoolean("accid");
-
-  outf = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              tmpfile = ajFileNewOutNameS(tmpname);
-              if(!tmpfile)
-                {
-                  ajDie("Output file (%S) open error\n", tmpname);
-                }
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajWarn("Sequence does not have features\n"
-                    "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/w_value/include=%S/exclude=%S/output=f",
-                  base, restid, include, exclude);
-
-      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-      if(!gFileOutURLS(url, &outf))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf-master.zip

Binary file glang-galaxy-conf-master.zip has changed

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/HEAD Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,1 @@
+ref: refs/heads/master

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/config
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/config Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,13 @@
+[core]
+ repositoryformatversion = 0
+ filemode = true
+ bare = false
+ logallrefupdates = true
+ ignorecase = true
+ precomposeunicode = true
+[remote "origin"]
+ url = https://github.com/ktnyt/glang-galaxy-conf.git
+ fetch = +refs/heads/*:refs/remotes/origin/*
+[branch "master"]
+ remote = origin
+ merge = refs/heads/master

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/description
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/description Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,1 @@
+Unnamed repository; edit this file 'description' to name the repository.

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/applypatch-msg.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/applypatch-msg.sample Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,15 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message taken by
+# applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit. The hook is
+# allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "applypatch-msg".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/commit-msg" &&
+ exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
+:

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/commit-msg.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/commit-msg.sample Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message.
+# Called by "git commit" with one argument, the name of the file
+# that has the commit message. The hook should exit with non-zero
+# status after issuing an appropriate message if it wants to stop the
+# commit. The hook is allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "commit-msg".
+
+# Uncomment the below to add a Signed-off-by line to the message.
+# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
+# hook is more suited to it.
+#
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^$.*>$.*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
+
+# This example catches duplicate Signed-off-by lines.
+
+test "" = "$(grep '^Signed-off-by: ' "$1" |
+ sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || {
+ echo >&2 Duplicate Signed-off-by lines.
+ exit 1
+}

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/post-update.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/post-update.sample Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# An example hook script to prepare a packed repository for use over
+# dumb transports.
+#
+# To enable this hook, rename this file to "post-update".
+
+exec git update-server-info

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/pre-applypatch.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/pre-applypatch.sample Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,14 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed
+# by applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-applypatch".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/pre-commit" &&
+ exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
+:

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/pre-commit.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/pre-commit.sample Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,49 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed.
+# Called by "git commit" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-commit".
+
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+ against=HEAD
+else
+ # Initial commit: diff against an empty tree object
+ against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+# If you want to allow non-ASCII filenames set this variable to true.
+allownonascii=$(git config --bool hooks.allownonascii)
+
+# Redirect output to stderr.
+exec 1>&2
+
+# Cross platform projects tend to avoid non-ASCII filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$allownonascii" != "true" ] &&
+ # Note that the use of brackets around a tr range is ok here, (it's
+ # even required, for portability to Solaris 10's /usr/bin/tr), since
+ # the square bracket bytes happen to fall in the designated range.
+ test $(git diff --cached --name-only --diff-filter=A -z $against |
+   LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
+then
+ cat <<\EOF
+Error: Attempt to add a non-ASCII file name.
+
+This can cause problems if you want to work with people on other platforms.
+
+To be portable it is advisable to rename the file.
+
+If you know what you are doing you can disable this check using:
+
+  git config hooks.allownonascii true
+EOF
+ exit 1
+fi
+
+# If there are whitespace errors, print the offending file names and fail.
+exec git diff-index --check --cached $against --

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/pre-push.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/pre-push.sample Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,53 @@
+#!/bin/sh
+
+# An example hook script to verify what is about to be pushed.  Called by "git
+# push" after it has checked the remote status, but before anything has been
+# pushed.  If this script exits with a non-zero status nothing will be pushed.
+#
+# This hook is called with the following parameters:
+#
+# $1 -- Name of the remote to which the push is being done
+# $2 -- URL to which the push is being done
+#
+# If pushing without using a named remote those arguments will be equal.
+#
+# Information about the commits which are being pushed is supplied as lines to
+# the standard input in the form:
+#
+#   <local ref> <local sha1> <remote ref> <remote sha1>
+#
+# This sample shows how to prevent push of commits where the log message starts
+# with "WIP" (work in progress).
+
+remote="$1"
+url="$2"
+
+z40=0000000000000000000000000000000000000000
+
+while read local_ref local_sha remote_ref remote_sha
+do
+ if [ "$local_sha" = $z40 ]
+ then
+ # Handle delete
+ :
+ else
+ if [ "$remote_sha" = $z40 ]
+ then
+ # New branch, examine all commits
+ range="$local_sha"
+ else
+ # Update to existing branch, examine new commits
+ range="$remote_sha..$local_sha"
+ fi
+
+ # Check for WIP commit
+ commit=`git rev-list -n 1 --grep '^WIP' "$range"`
+ if [ -n "$commit" ]
+ then
+ echo >&2 "Found WIP commit in $local_ref, not pushing"
+ exit 1
+ fi
+ fi
+done
+
+exit 0

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/pre-rebase.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/pre-rebase.sample Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,169 @@
+#!/bin/sh
+#
+# Copyright (c) 2006, 2008 Junio C Hamano
+#
+# The "pre-rebase" hook is run just before "git rebase" starts doing
+# its job, and can prevent the command from running by exiting with
+# non-zero status.
+#
+# The hook is called with the following parameters:
+#
+# $1 -- the upstream the series was forked from.
+# $2 -- the branch being rebased (or empty when rebasing the current branch).
+#
+# This sample shows how to prevent topic branches that are already
+# merged to 'next' branch from getting rebased, because allowing it
+# would result in rebasing already published history.
+
+publish=next
+basebranch="$1"
+if test "$#" = 2
+then
+ topic="refs/heads/$2"
+else
+ topic=`git symbolic-ref HEAD` ||
+ exit 0 ;# we do not interrupt rebasing detached HEAD
+fi
+
+case "$topic" in
+refs/heads/??/*)
+ ;;
+*)
+ exit 0 ;# we do not interrupt others.
+ ;;
+esac
+
+# Now we are dealing with a topic branch being rebased
+# on top of master.  Is it OK to rebase it?
+
+# Does the topic really exist?
+git show-ref -q "$topic" || {
+ echo >&2 "No such branch $topic"
+ exit 1
+}
+
+# Is topic fully merged to master?
+not_in_master=`git rev-list --pretty=oneline ^master "$topic"`
+if test -z "$not_in_master"
+then
+ echo >&2 "$topic is fully merged to master; better remove it."
+ exit 1 ;# we could allow it, but there is no point.
+fi
+
+# Is topic ever merged to next?  If so you should not be rebasing it.
+only_next_1=`git rev-list ^master "^$topic" ${publish} | sort`
+only_next_2=`git rev-list ^master           ${publish} | sort`
+if test "$only_next_1" = "$only_next_2"
+then
+ not_in_topic=`git rev-list "^$topic" master`
+ if test -z "$not_in_topic"
+ then
+ echo >&2 "$topic is already up-to-date with master"
+ exit 1 ;# we could allow it, but there is no point.
+ else
+ exit 0
+ fi
+else
+ not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"`
+ /usr/bin/perl -e '
+ my $topic = $ARGV[0];
+ my $msg = "* $topic has commits already merged to public branch:\n";
+ my (%not_in_next) = map {
+ /^([0-9a-f]+) /;
+ ($1 => 1);
+ } split(/\n/, $ARGV[1]);
+ for my $elem (map {
+ /^([0-9a-f]+) (.*)$/;
+ [$1 => $2];
+ } split(/\n/, $ARGV[2])) {
+ if (!exists $not_in_next{$elem->[0]}) {
+ if ($msg) {
+ print STDERR $msg;
+ undef $msg;
+ }
+ print STDERR " $elem->[1]\n";
+ }
+ }
+ ' "$topic" "$not_in_next" "$not_in_master"
+ exit 1
+fi
+
+exit 0
+
+################################################################
+
+This sample hook safeguards topic branches that have been
+published from being rewound.
+
+The workflow assumed here is:
+
+ * Once a topic branch forks from "master", "master" is never
+   merged into it again (either directly or indirectly).
+
+ * Once a topic branch is fully cooked and merged into "master",
+   it is deleted.  If you need to build on top of it to correct
+   earlier mistakes, a new topic branch is created by forking at
+   the tip of the "master".  This is not strictly necessary, but
+   it makes it easier to keep your history simple.
+
+ * Whenever you need to test or publish your changes to topic
+   branches, merge them into "next" branch.
+
+The script, being an example, hardcodes the publish branch name
+to be "next", but it is trivial to make it configurable via
+$GIT_DIR/config mechanism.
+
+With this workflow, you would want to know:
+
+(1) ... if a topic branch has ever been merged to "next".  Young
+    topic branches can have stupid mistakes you would rather
+    clean up before publishing, and things that have not been
+    merged into other branches can be easily rebased without
+    affecting other people.  But once it is published, you would
+    not want to rewind it.
+
+(2) ... if a topic branch has been fully merged to "master".
+    Then you can delete it.  More importantly, you should not
+    build on top of it -- other people may already want to
+    change things related to the topic as patches against your
+    "master", so if you need further changes, it is better to
+    fork the topic (perhaps with the same name) afresh from the
+    tip of "master".
+
+Let's look at this example:
+
+    o---o---o---o---o---o---o---o---o---o "next"
+   /       /           /           /
+ /   a---a---b A     /           /
+ /   /               /           /
+        /   /   c---c---c---c B         /
+       /   /   /             \         /
+      /   /   /   b---b C     \       /
+     /   /   /   /             \     /
+    ---o---o---o---o---o---o---o---o---o---o---o "master"
+
+
+A, B and C are topic branches.
+
+ * A has one fix since it was merged up to "next".
+
+ * B has finished.  It has been fully merged up to "master" and "next",
+   and is ready to be deleted.
+
+ * C has not merged to "next" at all.
+
+We would want to allow C to be rebased, refuse A, and encourage
+B to be deleted.
+
+To compute (1):
+
+ git rev-list ^master ^topic next
+ git rev-list ^master        next
+
+ if these match, topic has not merged in next at all.
+
+To compute (2):
+
+ git rev-list master..topic
+
+ if this is empty, it is fully merged to "master".

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/prepare-commit-msg.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/prepare-commit-msg.sample Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,36 @@
+#!/bin/sh
+#
+# An example hook script to prepare the commit log message.
+# Called by "git commit" with the name of the file that has the
+# commit message, followed by the description of the commit
+# message's source.  The hook's purpose is to edit the commit
+# message file.  If the hook fails with a non-zero status,
+# the commit is aborted.
+#
+# To enable this hook, rename this file to "prepare-commit-msg".
+
+# This hook includes three examples.  The first comments out the
+# "Conflicts:" part of a merge commit.
+#
+# The second includes the output of "git diff --name-status -r"
+# into the message, just before the "git status" output.  It is
+# commented because it doesn't cope with --amend or with squashed
+# commits.
+#
+# The third example adds a Signed-off-by line to the message, that can
+# still be edited.  This is rarely a good idea.
+
+case "$2,$3" in
+  merge,)
+    /usr/bin/perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
+
+# ,|template,)
+#   /usr/bin/perl -i.bak -pe '
+#      print "\n" . `git diff --cached --name-status -r`
+# if /^#/ && $first++ == 0' "$1" ;;
+
+  *) ;;
+esac
+
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^$.*>$.*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/hooks/update.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/hooks/update.sample Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,128 @@
+#!/bin/sh
+#
+# An example hook script to blocks unannotated tags from entering.
+# Called by "git receive-pack" with arguments: refname sha1-old sha1-new
+#
+# To enable this hook, rename this file to "update".
+#
+# Config
+# ------
+# hooks.allowunannotated
+#   This boolean sets whether unannotated tags will be allowed into the
+#   repository.  By default they won't be.
+# hooks.allowdeletetag
+#   This boolean sets whether deleting tags will be allowed in the
+#   repository.  By default they won't be.
+# hooks.allowmodifytag
+#   This boolean sets whether a tag may be modified after creation. By default
+#   it won't be.
+# hooks.allowdeletebranch
+#   This boolean sets whether deleting branches will be allowed in the
+#   repository.  By default they won't be.
+# hooks.denycreatebranch
+#   This boolean sets whether remotely creating branches will be denied
+#   in the repository.  By default this is allowed.
+#
+
+# --- Command line
+refname="$1"
+oldrev="$2"
+newrev="$3"
+
+# --- Safety check
+if [ -z "$GIT_DIR" ]; then
+ echo "Don't run this script from the command line." >&2
+ echo " (if you want, you could supply GIT_DIR then run" >&2
+ echo "  $0 <ref> <oldrev> <newrev>)" >&2
+ exit 1
+fi
+
+if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
+ echo "usage: $0 <ref> <oldrev> <newrev>" >&2
+ exit 1
+fi
+
+# --- Config
+allowunannotated=$(git config --bool hooks.allowunannotated)
+allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
+denycreatebranch=$(git config --bool hooks.denycreatebranch)
+allowdeletetag=$(git config --bool hooks.allowdeletetag)
+allowmodifytag=$(git config --bool hooks.allowmodifytag)
+
+# check for no description
+projectdesc=$(sed -e '1q' "$GIT_DIR/description")
+case "$projectdesc" in
+"Unnamed repository"* | "")
+ echo "*** Project description file hasn't been set" >&2
+ exit 1
+ ;;
+esac
+
+# --- Check types
+# if $newrev is 0000...0000, it's a commit to delete a ref.
+zero="0000000000000000000000000000000000000000"
+if [ "$newrev" = "$zero" ]; then
+ newrev_type=delete
+else
+ newrev_type=$(git cat-file -t $newrev)
+fi
+
+case "$refname","$newrev_type" in
+ refs/tags/*,commit)
+ # un-annotated tag
+ short_refname=${refname##refs/tags/}
+ if [ "$allowunannotated" != "true" ]; then
+ echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
+ echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
+ exit 1
+ fi
+ ;;
+ refs/tags/*,delete)
+ # delete tag
+ if [ "$allowdeletetag" != "true" ]; then
+ echo "*** Deleting a tag is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ refs/tags/*,tag)
+ # annotated tag
+ if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1
+ then
+ echo "*** Tag '$refname' already exists." >&2
+ echo "*** Modifying a tag is not allowed in this repository." >&2
+ exit 1
+ fi
+ ;;
+ refs/heads/*,commit)
+ # branch
+ if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then
+ echo "*** Creating a branch is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ refs/heads/*,delete)
+ # delete branch
+ if [ "$allowdeletebranch" != "true" ]; then
+ echo "*** Deleting a branch is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ refs/remotes/*,commit)
+ # tracking branch
+ ;;
+ refs/remotes/*,delete)
+ # delete tracking branch
+ if [ "$allowdeletebranch" != "true" ]; then
+ echo "*** Deleting a tracking branch is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ *)
+ # Anything else (is there anything else?)
+ echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
+ exit 1
+ ;;
+esac
+
+# --- Finished
+exit 0

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/index

Binary file glang-galaxy-conf/.git/index has changed

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/info/exclude
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/info/exclude Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,6 @@
+# git ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/logs/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/logs/HEAD Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,1 @@
+0000000000000000000000000000000000000000 15b59968544b39bd91d994c15fce1ce128640ae8 ktnyt <t11080hi@sfc.keio.ac.jp> 1435309734 +0900 clone: from https://github.com/ktnyt/glang-galaxy-conf.git

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/logs/refs/heads/master
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/logs/refs/heads/master Fri Jun 26 05:21:44 2015 -0400

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/logs/refs/remotes/origin/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/logs/refs/remotes/origin/HEAD Fri Jun 26 05:21:44 2015 -0400

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/objects/pack/pack-b41a2d653204b7aeb8a4d508d75e178a2be83735.idx

Binary file glang-galaxy-conf/.git/objects/pack/pack-b41a2d653204b7aeb8a4d508d75e178a2be83735.idx has changed

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/objects/pack/pack-b41a2d653204b7aeb8a4d508d75e178a2be83735.pack

Binary file glang-galaxy-conf/.git/objects/pack/pack-b41a2d653204b7aeb8a4d508d75e178a2be83735.pack has changed

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/packed-refs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/packed-refs Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,2 @@
+# pack-refs with: peeled fully-peeled
+15b59968544b39bd91d994c15fce1ce128640ae8 refs/remotes/origin/master

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/refs/heads/master
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/refs/heads/master Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,1 @@
+15b59968544b39bd91d994c15fce1ce128640ae8

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/.git/refs/remotes/origin/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/.git/refs/remotes/origin/HEAD Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,1 @@
+ref: refs/remotes/origin/master

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/LICENSE Fri Jun 26 05:21:44 2015 -0400

b'@@ -0,0 +1,339 @@\n+GNU GENERAL PUBLIC LICENSE\n+ Version 2, June 1991\n+\n+ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>\n+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+ Preamble\n+\n+ The licenses for most software are designed to take away your\n+freedom to share and change it. By contrast, the GNU General Public\n+License is intended to guarantee your freedom to share and change free\n+software--to make sure the software is free for all its users. This\n+General Public License applies to most of the Free Software\n+Foundation\'s software and to any other program whose authors commit to\n+using it. (Some other Free Software Foundation software is covered by\n+the GNU Lesser General Public License instead.) You can apply it to\n+your programs, too.\n+\n+ When we speak of free software, we are referring to freedom, not\n+price. Our General Public Licenses are designed to make sure that you\n+have the freedom to distribute copies of free software (and charge for\n+this service if you wish), that you receive source code or can get it\n+if you want it, that you can change the software or use pieces of it\n+in new free programs; and that you know you can do these things.\n+\n+ To protect your rights, we need to make restrictions that forbid\n+anyone to deny you these rights or to ask you to surrender the rights.\n+These restrictions translate to certain responsibilities for you if you\n+distribute copies of the software, or if you modify it.\n+\n+ For example, if you distribute copies of such a program, whether\n+gratis or for a fee, you must give the recipients all the rights that\n+you have. You must make sure that they, too, receive or can get the\n+source code. And you must show them these terms so they know their\n+rights.\n+\n+ We protect your rights with two steps: (1) copyright the software, and\n+(2) offer you this license which gives you legal permission to copy,\n+distribute and/or modify the software.\n+\n+ Also, for each author\'s protection and ours, we want to make certain\n+that everyone understands that there is no warranty for this free\n+software. If the software is modified by someone else and passed on, we\n+want its recipients to know that what they have is not the original, so\n+that any problems introduced by others will not reflect on the original\n+authors\' reputations.\n+\n+ Finally, any free program is threatened constantly by software\n+patents. We wish to avoid the danger that redistributors of a free\n+program will individually obtain patent licenses, in effect making the\n+program proprietary. To prevent this, we have made it clear that any\n+patent must be licensed for everyone\'s free use or not licensed at all.\n+\n+ The precise terms and conditions for copying, distribution and\n+modification follow.\n+\n+ GNU GENERAL PUBLIC LICENSE\n+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION\n+\n+ 0. This License applies to any program or other work which contains\n+a notice placed by the copyright holder saying it may be distributed\n+under the terms of this General Public License. The "Program", below,\n+refers to any such program or work, and a "work based on the Program"\n+means either the Program or any derivative work under copyright law:\n+that is to say, a work containing the Program or a portion of it,\n+either verbatim or with modifications and/or translated into another\n+language. (Hereinafter, translation is included without limitation in\n+the term "modification".) Each licensee is addressed as "you".\n+\n+Activities other than copying, distribution and modification are not\n+covered by this License; they are outside its scope. The act of\n+running the Program is not restricted, and the output from the Program\n+is covered only if its contents constitute a work based on the\n+Program (ind'..b'RIGHT HOLDERS AND/OR OTHER PARTIES\n+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED\n+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF\n+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS\n+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE\n+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,\n+REPAIR OR CORRECTION.\n+\n+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR\n+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,\n+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING\n+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED\n+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY\n+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER\n+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE\n+POSSIBILITY OF SUCH DAMAGES.\n+\n+ END OF TERMS AND CONDITIONS\n+\n+ How to Apply These Terms to Your New Programs\n+\n+ If you develop a new program, and you want it to be of the greatest\n+possible use to the public, the best way to achieve this is to make it\n+free software which everyone can redistribute and change under these terms.\n+\n+ To do so, attach the following notices to the program. It is safest\n+to attach them to the start of each source file to most effectively\n+convey the exclusion of warranty; and each file should have at least\n+the "copyright" line and a pointer to where the full notice is found.\n+\n+ {description}\n+ Copyright (C) {year} {fullname}\n+\n+ This program is free software; you can redistribute it and/or modify\n+ it under the terms of the GNU General Public License as published by\n+ the Free Software Foundation; either version 2 of the License, or\n+ (at your option) any later version.\n+\n+ This program is distributed in the hope that it will be useful,\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+ GNU General Public License for more details.\n+\n+ You should have received a copy of the GNU General Public License along\n+ with this program; if not, write to the Free Software Foundation, Inc.,\n+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.\n+\n+Also add information on how to contact you by electronic and paper mail.\n+\n+If the program is interactive, make it output a short notice like this\n+when it starts in an interactive mode:\n+\n+ Gnomovision version 69, Copyright (C) year name of author\n+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w\'.\n+ This is free software, and you are welcome to redistribute it\n+ under certain conditions; type `show c\' for details.\n+\n+The hypothetical commands `show w\' and `show c\' should show the appropriate\n+parts of the General Public License. Of course, the commands you use may\n+be called something other than `show w\' and `show c\'; they could even be\n+mouse-clicks or menu items--whatever suits your program.\n+\n+You should also get your employer (if you work as a programmer) or your\n+school, if any, to sign a "copyright disclaimer" for the program, if\n+necessary. Here is a sample; alter the names:\n+\n+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program\n+ `Gnomovision\' (which makes passes at compilers) written by James Hacker.\n+\n+ {signature of Ty Coon}, 1 April 1989\n+ Ty Coon, President of Vice\n+\n+This General Public License does not permit incorporating your program into\n+proprietary programs. If your program is a subroutine library, you may\n+consider it more useful to permit linking proprietary applications with the\n+library. If this is what you want to do, use the GNU Lesser General\n+Public License instead of this License.\n\\ No newline at end of file\n'

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/README.md Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,4 @@
+glang-galaxy-conf
+=================
+
+Galaxy tool configurations for GEMBASSY, KBWS, and Perl Snippet Executer

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/acdgalaxy.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/acdgalaxy.pl Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,194 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+
+my $progname = shift;
+$progname =~ s/\.acd$//g;
+my $progfile = "/usr/local/share/EMBOSS/acd/$progname.acd";
+open my $acdfh, "<", $progfile;
+open my $xmlfh, ">", "$progname.xml";
+
+my $tool;
+my $description;
+my $command;
+my @params;
+my @args;
+my $help;
+my $plot = 0+`grep -c 'toggle: plot' $progfile`;
+my $pngout = 0+`grep -c 'string: format' $progfile`;
+
+while(<$acdfh>) {
+    chomp;
+    if(/\s*application\s*:\s*\w+\s*\[\s*$/../^\s*\]\s*$/) {
+        if(/\s*application\s*:\s*(\w+)\s*\[\s*$/) {
+            $tool = qq(<tool id="EMBOSS: $1" name="$1" version="1.0.2">);
+        }
+
+        if(/\s*documentation:\s*"([^"]+)"?\s*/) {
+            my $tmp = $1;
+            if(/\s*documentation:\s*".+"\s*/) {
+                $description = qq(  <description>$tmp</description>);
+            } else {
+                while(<$acdfh>) {
+                    if(/\s*(.*)"/) {
+                        $tmp.= " $1";
+                        last;
+                    } elsif(/\s*(.*)\s*/) {
+                        $tmp .= " $1";
+                    }
+                }
+                $description = qq(  <description>$tmp</description>);
+            }
+        }
+    }
+
+    if(/\s*section\s*:\s*advanced\s*\[/../\s*endsection:\s*advanced/) {
+        if(/\s*section\s*:\s*advanced\s*\[/../\]/ or /\s*endsction:\s*advanced/) {
+            next;
+        }
+
+        if(/\s*\w+\s*:\s*\w+\s*\[/../\s*\]/) {
+            if(/\s*(\w+)\s*:\s*(\w+)\s*\[/) {
+                my ($type, $name) = ($1, $2);
+                my $information;
+                my $default;
+                my @values;
+
+                next if $name eq "accid";
+                next if $name eq "plot";
+
+                push @args, $name;
+
+                while(<$acdfh>) {
+                    chomp;
+                    if(/\]/) {
+                        last;
+                    }
+                    if(/\s*information:\s*"([^"]+)"?\s*/) {
+                        my $tmp = $1;
+                        if(/\s*information:\s*".+"\s*/) {
+                            $information = $tmp;
+                        } else {
+                            while(<$acdfh>) {
+                                if(/\s*(.*)"/) {
+                                    $tmp.= " $1";
+                                    last;
+                                } elsif(/\s*(.*)\s*/) {
+                                    $tmp .= " $1";
+                                }
+                            }
+                            $information = $tmp;
+                        }
+                    }
+
+                    if(/\s*default:\s*"(.+)"\s*/) {
+                        $default = $1;
+                    }
+
+                    if(/\s*values:\s*"(.+)"\s*/) {
+                        @values = split ";", $1;
+                    }
+                }
+                #print "$type\t$name\t$information";
+                #print "\t$default" if defined $default;
+                #print "\n";
+                my $param;
+
+                if($default) {
+                    $default = "yes" if $default eq "Y";
+                    $default = "no"  if $default eq "N";
+                    $default = "[^ACDEFGHIKLMNPQRSTVWYacgtU]" if $name eq "delkey";
+                } else {
+                    $default = "";
+                }
+
+                if($type eq "boolean") {
+                    $param = <<EOS;
+    <param name="$name" type="select" value="$default">
+      <label>$information</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+EOS
+                }
+
+                if($type =~ /(integer)|(float)|(string)/) {
+                    $type =~ s/string/text/g;
+                    $param = <<EOS;
+    <param name="$name" size="4" type="$type" value="$default">
+      <label>$information</label>
+    </param>
+EOS
+                }
+
+                if($type =~ /selection/) {
+                    my $vals = join "\n", map{
+                        "      <option value=\"$_\">". ucfirst($_) ."</option>"
+                    }@values;
+                    $param = <<EOS
+    <param name="$name" type="select" value="$default">
+      <label>$information</label>
+$vals
+    </param>
+EOS
+                }
+
+                print "$type: $name\n";
+                if($param && length $param) {
+                    chomp($param);
+                    push @params, $param;
+                }
+            }
+        }
+    }
+}
+close $acdfh;
+
+my $args = join(" ", map{"-$_ \$$_"}@args);
+
+my $paramstr = "";
+foreach my $param (@params) {
+    $paramstr .= "$param\n";
+}
+
+my $outputs;
+
+if($plot) {
+    $command = "<command interpreter=\"perl\">gembassy_calcandplot_wrapper.pl $progname -sequence \$input1 $args -auto \$out_file1 \$out_file2</command>";
+    $outputs = <<EOS;
+    <data format="csv" name="out_file1" label="\${tool.name} data for \${input1.name}" />
+    <data format="png" name="out_file2" label="\${tool.name} plot for \${input1.name}" />
+EOS
+} elsif($pngout) {
+    $command = "<command interpreter=\"perl\">emboss_single_outputfile_wrapper.pl $progname -sequence \$input1 -format png -goutfile \$out_file1 -auto $args</command>";
+    $outputs = <<EOS;
+    <data format="png" name="out_file1" label="\${tool.name} for \${input1.name}" />
+EOS
+} else {
+    $command = "<command>$progname -sequence \$input1 $args -auto -outfile \$out_file1</command>";
+    printf(STDERR "Enter output data format of $progname (1: txt 2: csv): ");
+    chomp(my $format = <>);
+    $format = $format == 1 ? "txt" : "csv";
+    $outputs = <<EOS;
+    <data format="$format" name="out_file1" label="\${tool.name} for \${input1.name}" />
+EOS
+}
+chomp $outputs;
+
+print $xmlfh <<EOS;
+$tool
+$description
+  $command
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+$paramstr
+  </inputs>
+  <outputs>
+$outputs
+  </outputs>
+</tool>
+EOS
+
+close $xmlfh;

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/emboss_format_corrector.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/emboss_format_corrector.py Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,53 @@
+#EMBOSS format corrector
+
+import operator
+#from galaxy import datatypes
+
+#Properly set file formats after job run
+def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
+#Properly set file formats before job run
+#def exec_before_job(trans, inp_data, out_data, param_dict,tool):
+    #why isn't items an ordered list?
+    items = out_data.items()
+    #lets sort it ourselves....
+    items = sorted(items, key=operator.itemgetter(0))
+    #items is now sorted...
+
+    #normal filetype correction
+    data_count=1
+    for name, data in items:
+        outputType = param_dict.get( 'out_format'+str(data_count), None )
+        #print "data_count",data_count, "name", name, "outputType", outputType
+        if outputType !=None:
+            if outputType == 'ncbi':
+                outputType = "fasta"
+            elif outputType == 'excel':
+                outputType = "tabular"
+            elif outputType == 'text':
+                outputType = "txt"
+            data = app.datatypes_registry.change_datatype(data, outputType)
+            app.model.context.add( data )
+            app.model.context.flush()
+        data_count+=1
+
+    #html filetype correction
+    data_count=1
+    for name, data in items:
+        wants_plot = param_dict.get( 'html_out'+str(data_count), None )
+        ext = "html"
+        if wants_plot == "yes":
+            data = app.datatypes_registry.change_datatype(data, ext)
+            app.model.context.add( data )
+            app.model.context.flush()
+        data_count+=1
+
+    #png file correction
+    data_count=1
+    for name, data in items:
+        wants_plot = param_dict.get( 'plot'+str(data_count), None )
+        ext = "png"
+        if wants_plot == "yes":
+            data = app.datatypes_registry.change_datatype(data, ext)
+            app.model.context.add( data )
+            app.model.context.flush()
+        data_count+=1

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/emboss_single_outputfile_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/emboss_single_outputfile_wrapper.pl Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,27 @@
+#! /usr/bin/perl -w
+use strict;
+use File::Copy;
+
+my $cmd_string = join (" ",@ARGV);
+my $results = `$cmd_string`;
+my @files = split("\n",$results);
+my $fileNameOut = $ARGV[6];
+my ($drive, $outputDir, $file) = File::Spec->splitpath( $fileNameOut );
+my $destination = $fileNameOut;
+
+foreach my $thisLine (@files)
+  {
+      if ($thisLine =~ /Created /)
+        {
+            $thisLine =~ /[\w|\.]+$/;
+            $thisLine =$&;
+            #print "outfile: $thisLine\n";
+            #there is only one file to move, so we can quit after finding it
+            move($drive.$outputDir.$thisLine,$fileNameOut);
+            exit(1);
+        }
+      else
+        {
+            print $thisLine,"\n";
+        }
+  }

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gaaui.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gaaui.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gaaui" name="gaaui" version="1.0.2">
+  <description>Calculates various indece of amino acid usage</description>
+  <command>gaaui -sequence $input1 -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gaminoinfo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gaminoinfo.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gaminoinfo" name="gaminoinfo" version="1.0.2">
+  <description>Prints out basic amino acid sequence statistics</description>
+  <command>gaminoinfo -sequence $input1 -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gb1.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gb1.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,18 @@
+<tool id="EMBOSS: gb1" name="gb1" version="1.0.2">
+  <description>Calculates strand bias of bacterial genome using B1 index</description>
+  <command>gb1 -sequence $input1 -method $method -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="method" type="select" value="rocha">
+      <label>Choose method of 'lobry' or 'rocha'</label>
+      <option value="lobry">Lobry</option>
+      <option value="rocha">Rocha</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gb2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gb2.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gb2" name="gb2" version="1.0.2">
+  <description>Calculates strand bias of bacterial genome using B2 index</description>
+  <command>gb2 -sequence $input1  -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gbasecounter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gbasecounter.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,27 @@
+<tool id="EMBOSS: gbasecounter" name="gbasecounter" version="1.0.2">
+  <description>Creates a position weight matrix of oligomers around start codon</description>
+  <command>gbasecounter -sequence $input1 -position $position -patlen $patlen -upstream $upstream -downstream $downstream -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="position" type="select" value="start">
+      <label>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</label>
+      <option value="start">Start</option>
+      <option value="end">End</option>
+    </param>
+    <param name="patlen" size="4" type="integer" value="3">
+      <label>Length of oligomer to count</label>
+    </param>
+    <param name="upstream" size="4" type="integer" value="30">
+      <label>Length upstream of specified position to create PWM</label>
+    </param>
+    <param name="downstream" size="4" type="integer" value="30">
+      <label>Length downstream of specified position to create PWM</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gbaseentropy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gbaseentropy.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,28 @@
+<tool id="EMBOSS: gbaseentropy" name="gbaseentropy" version="1.0.2">
+  <description>Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl gbaseentropy -sequence $input1 -position $position -patlen $patlen -upstream $upstream -downstream $downstream -auto -noaccid $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="position" type="select" value="start">
+      <label>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</label>
+      <option value="start">Start</option>
+      <option value="end">End</option>
+    </param>
+    <param name="patlen" size="4" type="integer" value="3">
+      <label>Length of oligomer to count</label>
+    </param>
+    <param name="upstream" size="4" type="integer" value="30">
+      <label>Length upstream of specified position to create PWM</label>
+    </param>
+    <param name="downstream" size="4" type="integer" value="30">
+      <label>Length downstream of specified position to create PWM</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gbaseinformationcontent.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gbaseinformationcontent.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,28 @@
+<tool id="EMBOSS: gbaseinformationcontent" name="gbaseinformationcontent" version="1.0.2">
+  <description>Calculates and graphs the sequence conservation using information content</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl gbaseinformationcontent -sequence $input1 -position $position -upstream $upstream -downstream $downstream -patlen $patlen -auto -noaccid $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="position" type="select" value="start">
+      <label>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</label>
+      <option value="start">Start</option>
+      <option value="end">End</option>
+    </param>
+    <param name="upstream" size="4" type="integer" value="30">
+      <label>Length upstream of specified position to create PWM</label>
+    </param>
+    <param name="downstream" size="4" type="integer" value="30">
+      <label>Length downstream of specified position to create PWM</label>
+    </param>
+    <param name="patlen" size="4" type="integer" value="3">
+      <label>Length of oligomer to count</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gbaserelativeentropy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gbaserelativeentropy.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,28 @@
+<tool id="EMBOSS: gbaserelativeentropy" name="gbaserelativeentropy" version="1.0.2">
+  <description>Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy)</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl gbaserelativeentropy -sequence $input1 -position $position -patlen $patlen -upstream $upstream -downstream $downstream -auto -noaccid $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="position" type="select" value="start">
+      <label>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</label>
+      <option value="start">Start</option>
+      <option value="end">End</option>
+    </param>
+    <param name="patlen" size="4" type="integer" value="3">
+      <label>Length of oligomer to count</label>
+    </param>
+    <param name="upstream" size="4" type="integer" value="30">
+      <label>Length upstream of specified position to create PWM</label>
+    </param>
+    <param name="downstream" size="4" type="integer" value="30">
+      <label>Length downstream of specified position to create PWM</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gbasezvalue.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gbasezvalue.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,30 @@
+<tool id="EMBOSS: gbasezvalue" name="gbasezvalue" version="1.0.2">
+  <description>Extracts conserved oligomers per position using Z-score</description>
+  <command>gbasezvalue -sequence $input1 -limit $limit -position $position -patlen $patlen -upstream $upstream -downstream $downstream -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="limit" size="4" type="integer" value="5">
+      <label>Rank threshold for showing the conserved oligomer</label>
+    </param>
+    <param name="position" type="select" value="start">
+      <label>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</label>
+      <option value="start">Start</option>
+      <option value="end">End</option>
+    </param>
+    <param name="patlen" size="4" type="integer" value="3">
+      <label>Length of oligomer to count</label>
+    </param>
+    <param name="upstream" size="4" type="integer" value="30">
+      <label>Length upstream of specified position to create PWM</label>
+    </param>
+    <param name="downstream" size="4" type="integer" value="30">
+      <label>Length downstream of specified position to create PWM</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gbui.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gbui.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,23 @@
+<tool id="EMBOSS: gbui" name="gbui" version="1.0.2">
+  <description>Calculates base usage indices for protein-coding sequences</description>
+  <command>gbui -sequence $input1 -translate $translate -position $position -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param name="translate" type="select" value="no">
+    <label>Include when translating using standard codon table</label>
+    <option value="no">No</option>
+    <option value="yes">Yes</option>
+  </param>
+  <param name="position" type="select" value="all">
+    <option value="all">Assess overall base usage of the gene</option>
+    <option value="1">Assess overall base at 1st position of codons</option>
+    <option value="2">Assess overall base at 2nd position of codons</option>
+    <option value="3">Assess overall base at 3rd position of codons</option>
+  </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gcai.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gcai.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,21 @@
+<tool id="EMBOSS: gcai" name="gcai" version="1.0.2">
+  <description>Calculates codon adaptation index for each gene</description>
+  <command>gcai -sequence $input1 -translate $translate -wabsent $wabsent -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translating using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="wabsent" size="4" type="text" value="-1">
+      <label>W value of codons absent from a reference set to negative when excludes such codons from the calculation</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gcbi.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gcbi.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,17 @@
+<tool id="EMBOSS: gcbi" name="gcbi" version="1.0.2">
+  <description>Calculates the codon bias index (CBI)</description>
+  <command>gcbi -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translating using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gcgr.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gcgr.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,16 @@
+<tool id="EMBOSS: gcgr" name="gcgr" version="1.0.2">
+  <description>Creates a Chaos Game Representation of a given sequence</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl gcgr -sequence $input1 -format png -goutfile $out_file1 -auto -noaccid -width $width</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="width" size="4" type="integer" value="1024">
+      <label>Width of image</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gcircularmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gcircularmap.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gcircularmap" name="gcircularmap" version="1.0.2">
+  <description>Draws circular map of the genome</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl gcircularmap -sequence $input1 -format png -goutfile $out_file1 -auto -noaccid </command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gcodoncompiler.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gcodoncompiler.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,44 @@
+<tool id="EMBOSS: gcodoncompiler" name="gcodoncompiler" version="1.0.2">
+  <description>Calculates various kinds of amino acid and codon usage data</description>
+  <command>gcodoncompiler -sequence $input1 -translate $translate -startcodon $startcodon -stopcodon $stopcodon -data $data -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include to translate using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="startcodon" type="select" value="no">
+      <label>Include to include start codon</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="stopcodon" type="select" value="no">
+      <label>Include to include stop codon</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="data" type="select" value="R0">
+      <label>Kinds of codon usage data. R* hypothesizes amino acids which are not present in the gene</label>
+      <option value="A0">Absolute amino acid frequency ('AA')</option>
+      <option value="A1">Relative amino acid frequency ('RAAU')</option>
+      <option value="C0">Absolute codon frequency ('AF')</option>
+      <option value="C1">Relative codon frequency in a complete sequence</option>
+      <option value="C2">Relative codon frequency in each amino acid ('RF')</option>
+      <option value="C3">Relative synonymous codon usage ('RSCU')</option>
+      <option value="C4">Relative adaptiveness; i.e., ratio to maximum of minor codon (W)</option>
+      <option value="C5">Maximum (1) or minor (0) codonAbsolute codon frequency ('AF')</option>
+      <option value="R0">Absolute codon frequency</option>
+      <option value="R1">Relative codon frequency in a complete sequence</option>
+      <option value="R2">Relative codon frequency in each amino acid ('RF')</option>
+      <option value="R3">Relative synonymous codon usage ('RSCU')</option>
+      <option value="R4">Relative adaptiveness; i.e., ratio to maximum of minor codon (W)</option>
+      <option value="R5">Maximum (1) or minor (0) codon</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gconsensusz.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gconsensusz.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,20 @@
+<tool id="EMBOSS: gconsensusz" name="gconsensusz" version="1.0.2">
+  <description>Calculates consensus in given array of sequences</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl gconsensusz -sequence $input1 -high $high -low $low -auto $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="high" size="4" type="integer" value="1">
+      <label>Z value greater than which is significant</label>
+    </param>
+    <param name="low" size="4" type="float" value="0.2">
+      <label>Z value less than which is insignificant</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gdeltaenc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gdeltaenc.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,12 @@
+<tool id="EMBOSS: gdeltaenc" name="gdeltaenc" version="1.0.2">
+  <description>Calculates the codon usage bias related to translation optimization (delta ENC)</description>
+  <command>gdeltaenc -sequence $input1 -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gdeltagcskew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gdeltagcskew.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,34 @@
+<tool id="EMBOSS: gdeltagcskew" name="gdeltagcskew" version="1.0.2">
+  <description>Calculates strand bias of bacterial genome using delta GC skew index</description>
+  <command>gdeltagcskew -sequence $input1 -at $at -purine $purine -keto $keto -method $method -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="at" type="select" value="no">
+      <label>Include when observing AT skew instead of GC skew </label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="purine" type="select" value="no">
+      <label>Include when observing purine (AG/TC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select" value="no">
+      <label>Include when observing keto (TG/AC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="method" type="select" value="degenerate">
+      <label>Choose the nucleotides to use 'degenerate', 'gc3', or 'all'</label>
+      <option value="degenerate">Degenerate</option>
+      <option value="gc3">Gc3</option>
+      <option value="all">All</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gdinuc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gdinuc.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,24 @@
+<tool id="EMBOSS: gdinuc" name="gdinuc" version="1.0.2">
+  <description>Calculates dinucleotide usage </description>
+  <command>gdinuc -sequence $input1 -translate $translate -position $position -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translates using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="position" type="select" value="all">
+      <label>Codon position or reading frame</label>
+      <option value="all">Assess all codon positions</option>
+      <option value="12">Assess the reading frame 1-2</option>
+      <option value="23">Assess the reading frame 2-3</option>
+      <option value="31">Assess the reading frame 3-1</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gdistincc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gdistincc.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,18 @@
+<tool id="EMBOSS: gdistincc" name="gdistincc" version="1.0.2">
+  <description>Calculates the distance between two loci in circular chromosomes</description>
+  <command>gdistincc -sequence $input1 -second $second -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param name="first" size="8" type="integer" value="0">
+    <label>Position to find the distance</label>
+  </param>
+  <param name="second" size="8" type="integer" value="-1">
+    <label>If the second position is negative, position of replication origin is used</label>
+  </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gdnawalk.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gdnawalk.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gdnawalk" name="gdnawalk" version="1.0.2">
+  <description>Draws DNA Walk map of the genome</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl gdnawalk -sequence $input1 -format png -goutfile $out_file1 -auto </command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gembassy_calcandplot_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gembassy_calcandplot_wrapper.pl Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,31 @@
+#! /usr/bin/perl -w
+use strict;
+use File::Copy;
+
+my $png_outfile = pop(@ARGV);
+my $csv_outfile = pop(@ARGV);
+
+my $csv_cmd = join(" ", (@ARGV, "-noplot -outfile $csv_outfile"));
+my $png_cmd = join(" ", (@ARGV, "-plot -graph png -goutfile $png_outfile"));
+
+my $csv_results = `$csv_cmd`;
+my $png_results = `$png_cmd`;
+my @files = split("\n", $png_results);
+my ($drive, $outputDir, $file) = File::Spec->splitpath( $png_outfile );
+
+foreach my $thisLine (@files)
+  {
+      if ($thisLine =~ /Created /)
+        {
+            $thisLine =~ /[\w|\.]+$/;
+            $thisLine = $&;
+            #print "outfile: $thisLine\n";
+            #there is only one file to move, so we can quit after finding it
+            move($drive.$outputDir.$thisLine, $png_outfile);
+            exit(1);
+        }
+      else
+        {
+            print $thisLine, "\n";
+        }
+  }

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/genc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/genc.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,17 @@
+<tool id="EMBOSS: genc" name="genc" version="1.0.2">
+  <description>Calculates the effective number of codons (Nc)</description>
+  <command>genc -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translates using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/genret.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/genret.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,22 @@
+<tool id="EMBOSS: genret" name="genret" version="1.0.2">
+  <description>Retrieves various gene features from genome flatfile</description>
+  <command>genret -sequence $input1 -gene '$gene' -access '$access' -argument '$argument' -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param name="gene" area="True" size="8x5" type="text">
+    <label>List of gene name(s) to report</label>
+  </param>
+  <param name="access" size="20" type="text">
+    <label>Name of feature to access</label>
+  </param>
+  <param name="argument" size="20" type="text">
+    <label>Extra arguments to pass to method</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/genret_file.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/genret_file.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,22 @@
+<tool id="EMBOSS: genret-file" name="genret-file" version="1.0.2">
+  <description>Retrieves various gene features from genome flatfile</description>
+  <command>genret -sequence $input1 -gene '@$gene' -access '$access' -argument '$argument' -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param format="data" name="gene" type="data">
+    <label>List of gene name(s) to report</label>
+  </param>
+  <param name="access" size="8" type="text">
+    <label>Name of feature to access</label>
+  </param>
+  <param name="argument" size="20" type="text">
+    <label>Extra arguments to pass to method</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gentrez.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gentrez.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,15 @@
+<tool id="EMBOSS: gentrez" name="gentrez" version="1.0.2">
+  <description>Searches NCBI Entrez</description>
+  <command>gentrez -database $database -query '$query'0 -auto -outfile $out_file1</command>
+  <inputs>
+    <param name="database" type="text">
+      <label>NCBI database to search</label>
+    </param>
+    <param name="query" type="text">
+      <label>Query to search</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="Search ${database.value} for ${query.value}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gew.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,17 @@
+<tool id="EMBOSS: gew" name="gew" version="1.0.2">
+  <description>Calculates a measure of synonymous codon usage evenness (Ew)</description>
+  <command>gew -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translates using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gfindoriter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gfindoriter.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,29 @@
+<tool id="EMBOSS: gfindoriter" name="gfindoriter" version="1.0.2">
+  <description>Predicts the replication origin and terminus in bacterial genomes</description>
+  <command>gfindoriter -sequence $input1 -window $window -purine $purine -keto $keto -lowpass $lowpass -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="window" size="4" type="integer" value="4096">
+      <label>Number of windows to use for Fat Fourier Transform. Only active when -lowpass option is specified. Value must be the power of two</label>
+    </param>
+    <param name="purine" type="select" value="no">
+      <label>Use purine skew for calculation</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select" value="no">
+      <label>Use keto skew for calculation</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="lowpass" size="4" type="integer" value="95">
+      <label>Lowpass filter strength in percent. Typically 95 or 99 works best</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gfop.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gfop.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,18 @@
+<tool id="EMBOSS: gfop" name="gfop" version="1.0.2">
+  <description>Calculates the frequency of optimal codons (Fop)</description>
+  <command>gfop -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translates using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggcsi.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggcsi.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,41 @@
+<tool id="EMBOSS: ggcsi" name="ggcsi" version="1.0.2">
+  <description>GC Skew Index: an index for strand-specific mutational bias</description>
+  <command>ggcsi -sequence $input1 -gcsi $gcsi -window $window -purine $purine -keto $keto -at $at -pval $pval -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="gcsi" type="select" value="2">
+      <label>GCSI version to use</label>
+      <option value="1">1</option>
+      <option value="2">2</option>
+    </param>
+    <param name="window" size="4" type="integer" value="4096">
+      <label>Number of windows. Must be a power of 2</label>
+    </param>
+    <param name="purine" type="select" value="no">
+      <label>Use purine skew for calculation</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select" value="no">
+      <label>Use keto skew for calculation</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="at" type="select" value="no">
+      <label>Use AT skew for calculation</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="pval" type="select" value="no">
+      <label>Calculate p-value when GCSI version 2 is selected</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggcskew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggcskew.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,40 @@
+<tool id="EMBOSS: ggcskew" name="ggcskew" version="1.0.2">
+  <description>Calculates and plots the GC skew of the input sequence</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl ggcskew -sequence $input1 -window $window -slide $slide -cumulative $cumulative -at $at -purine $purine -keto $keto -auto $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="window" size="4" type="integer" value="10000">
+      <label>Window size to observe</label>
+    </param>
+    <param name="slide" size="4" type="integer" value="10000">
+      <label>Window slide size</label>
+    </param>
+    <param name="cumulative" type="select" value="no">
+      <label>Include to calculate cumulative skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="at" type="select" value="no">
+      <label>Include for observing AT skew instead of GC skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="purine" type="select" value="no">
+      <label>Include for observing purine (AG/TC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select" value="no">
+      <label>Include for observing keto (TG/AC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggcskew_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggcskew_plot.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,38 @@
+<tool id="EMBOSS: ggcskew_plot" name="ggcskew_plot" version="1.0.2">
+  <description>Calculates and plots the GC skew of the input sequence</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl ggcskew -sequence $input1 -graph png -goutfile $out_file1 -window $window -slide $slide -cumulative $cumulative -at $at -purine $purine -keto $keto -plot -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="window" size="4" type="integer" value="10000">
+      <label>Window size to observe</label>
+    </param>
+    <param name="slide" size="4" type="integer" value="10000">
+      <label>Window slide size</label>
+    </param>
+    <param name="cumulative" type="select">
+      <label>Include to calculate cumulative skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="at" type="select">
+      <label>Include for observing AT skew instead of GC skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="purine" type="select">
+      <label>Include for observing purine (AG/TC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select">
+      <label>Include for observing keto (TG/AC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggcskew_template.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggcskew_template.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,39 @@
+<tool id="EMBOSS: ggcskew" name="ggcskew" version="1.0.2">
+  <description>Calculates and plots the GC skew of the input sequence</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl ggcskew -sequence $input1 -window $window -slide $slide -cumulative $cumulative -at $at -purine $purine -keto $keto -auto $out_file1 $out_file2</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="window" size="4" type="integer" value="10000">
+      <label>Window size to observe</label>
+    </param>
+    <param name="slide" size="4" type="integer" value="10000">
+      <label>Window slide size</label>
+    </param>
+    <param name="cumulative" type="select" value="yes">
+      <label>Include to calculate cumulative skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="at" type="select">
+      <label>Include for observing AT skew instead of GC skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="purine" type="select">
+      <label>Include for observing purine (AG/TC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select">
+      <label>Include for observing keto (TG/AC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}"/>
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}"/>
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggcwin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggcwin.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,32 @@
+<tool id="EMBOSS: ggcwin" name="ggcwin" version="1.0.2">
+  <description>Calculates and plots the GC content along the given genome</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl ggcwin -sequence $input1 -window $window -at $at -purine $purine -keto $keto -auto $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="window" size="4" type="integer" value="10000">
+      <label>Window size to observe</label>
+    </param>
+    <param name="at" type="select" value="no">
+      <label>Include for observing AT skew instead of GC skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="purine" type="select" value="no">
+      <label>Include for observing purine (AG/TC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="keto" type="select" value="no">
+      <label>Include for observing keto (TG/AC) skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggeneskew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggeneskew.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,38 @@
+<tool id="EMBOSS: ggeneskew" name="ggeneskew" version="1.0.2">
+  <description>Calculates and plots the gene strand bias of the given genome</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl ggeneskew -sequence $input1 -window $window -slide $slide -cumulative $cumulative -base $base -gctri $gctri -auto -noaccid $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="window" size="4" type="integer" value="10000">
+      <label>Window size to observe</label>
+    </param>
+    <param name="slide" size="4" type="integer" value="10000">
+      <label>Window slide size</label>
+    </param>
+    <param name="cumulative" type="select" value="no">
+      <label>Input 1 to calculate cumulative skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="base" type="select" value="none">
+      <label>Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews</label>
+      <option value="none">None</option>
+      <option value="gc">Gc</option>
+      <option value="at">At</option>
+      <option value="purine">Purine</option>
+      <option value="keto">Keto</option>
+    </param>
+    <param name="gctri" type="select" value="no">
+      <label>Include to use only the third codon positions</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggenomemap3.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggenomemap3.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: ggenomemap3" name="ggenomemap3" version="1.0.2">
+  <description>Draws the map of the genome (version 3)</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl ggenomemap3 -sequence $input1 -format png -goutfile $out_file1 -auto -noaccid -width $width -height $height</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="width" size="4" type="integer" value="8192">
+      <label>Image width</label>
+    </param>
+    <param name="height" size="4" type="integer" value="8192">
+      <label>Image height</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/ggenomicskew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/ggenomicskew.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,22 @@
+<tool id="EMBOSS: ggenomicskew" name="ggenomicskew" version="1.0.2">
+  <description>Calculates and plots the GC skew in different regions of the given genome</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl ggenomicskew -sequence $input1 -divide $divide -at $at -auto $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="divide" size="4" type="integer" value="250">
+      <label>Window to divide into</label>
+    </param>
+    <param name="at" type="select" value="no">
+      <label>Include when observing AT skew instead of GC skew</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gicdi.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gicdi.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,17 @@
+<tool id="EMBOSS: gicdi" name="gicdi" version="1.0.2">
+  <description>Calculates the intrinsic codon deviation index (ICDI)</description>
+  <command>gicdi -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translating using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gkmertable.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gkmertable.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,16 @@
+<tool id="EMBOSS: gkmertable" name="gkmertable" version="1.0.2">
+  <description>Creates an image showing all k-mer abundance within a sequence</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl gkmertable -sequence $input1 -format png -goutfile $out_file1 -auto -k $k</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="k" size="4" type="integer" value="6">
+      <label>Length of oligomer</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gldabias.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gldabias.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,23 @@
+<tool id="EMBOSS: gldabias" name="gldabias" version="1.0.2">
+  <description>Calculates strand bias of bacterial genome using linear discriminant analysis (LDA)</description>
+  <command>gldabias -sequence $input1 -coefficients $coefficients -variable $variable -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="coefficients" size="4" type="integer" value="0">
+      <label>Show LDA coefficients</label>
+    </param>
+    <param name="variable" type="select" value="codon">
+      <label>Data to use for LDA. Either 'base', 'codonbase', 'codon', or 'amino'</label>
+      <option value="base">Base</option>
+      <option value="codonbase">Codonbase</option>
+      <option value="codon">Codon</option>
+      <option value="amino">Amino</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gnucleotideperiodicity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gnucleotideperiodicity.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,20 @@
+<tool id="EMBOSS: gnucleotideperiodicity" name="gnucleotideperiodicity" version="1.0.2">
+  <description>Checks the periodicity of certain oligonucleotides</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl gnucleotideperiodicity -sequence $input1 -window $window -nucleotide $nucleotide -auto -noaccid $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="window" size="4" type="integer" value="50">
+      <label>Window size to seek periodicity</label>
+    </param>
+    <param name="nucleotide" size="4" type="text" value="aa">
+      <label>Nucleotide to search</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/goligomercounter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/goligomercounter.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: goligomercounter" name="goligomercounter" version="1.0.2">
+  <description>Counts the number of given oligomers in a sequence</description>
+  <command>goligomercounter -sequence $input1 -oligomer $oligomer -window $window -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param name="oligomer" size="8" type="text" value="">
+    <label>Oligomer to count</label>
+  </param>
+  <param name="window" size="4" type="integer" value="">
+    <label>Int window size</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/goligomersearch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/goligomersearch.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,20 @@
+<tool id="EMBOSS: goligomersearch" name="goligomersearch" version="1.0.2">
+  <description>Searches oligomers in given sequence</description>
+  <command>goligomersearch -sequence $input1 -return $return -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="return" type="select" value="position">
+      <label>'position' to return list of positions where oligomers are found, 'oligo' to return list of oligomers found ordered by positions, 'both' to return a hash with positions as keys and oligomers as values, 'distribution' to return four values about the distribution of given oligomer</label>
+      <option value="position">Position</option>
+      <option value="oligo">Oligo</option>
+      <option value="both">Both</option>
+      <option value="distribution">Distribution</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gp2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gp2.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gp2" name="gp2" version="1.0.2">
+  <description>Calculates the P2 index of each gene</description>
+  <command>gp2 -sequence $input1  -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gpalindrome.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gpalindrome.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,24 @@
+<tool id="EMBOSS: gpalindrome" name="gpalindrome" version="1.0.2">
+  <description>Searches palindrome sequences</description>
+  <command>gpalindrome -sequence $input1 -shortest $shortest -loop $loop -gtmatch $gtmatch -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="shortest" size="4" type="integer" value="4">
+      <label>Shortest palindrome to search</label>
+    </param>
+    <param name="loop" size="4" type="integer" value="">
+      <label>Longest stem loop to allow</label>
+    </param>
+    <param name="gtmatch" type="select" value="">
+      <label>If 1, allows g-t match</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gphx.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gphx.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,17 @@
+<tool id="EMBOSS: gphx" name="gphx" version="1.0.2">
+  <description>Identifies predicted highly expressed gene</description>
+  <command>gphx -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translating using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gqueryarm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gqueryarm.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,15 @@
+<tool id="EMBOSS: gqueryarm" name="gqueryarm" version="1.0.2">
+  <description>Gets the replication arm name (left or right) from the given position</description>
+  <command>gqueryarm -sequence $input1  -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param name="position" type="integer" value="">
+    <label>Position to query</label>
+  </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gquerystrand.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gquerystrand.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,20 @@
+<tool id="EMBOSS: gquerystrand" name="gquerystrand" version="1.0.2">
+  <description>Gets the strand name (leading or lagging) from the given position</description>
+  <command>gquerystrand -sequence $input1 -direction $direction -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+  <param name="position" type="integer" value="0">
+    <label>Position to query</label>
+  </param>
+  <param name="direction" type="select" value="direct">
+    <label>Strand of the querying position either 'direct' or 'complement'</label>
+    <option value="direct">Direct</option>
+    <option value="complement">Complement</option>
+  </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/greporiter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/greporiter.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,31 @@
+<tool id="EMBOSS: greporiter" name="greporiter" version="1.0.2">
+  <description>Gets the positions of replication origin and terminus</description>
+  <command>greporiter -sequence $input1 -oriloc $oriloc -gcskew $gcskew -difthreshold $difthreshold -dbonly $dbonly -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="oriloc" type="select" value="no">
+      <label>Include Oriloc for prediction</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="gcskew" type="select" value="no">
+      <label>Include to use GC skew shift-point for prediction</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="difthreshold" size="4" type="integer" value="">
+      <label>Distance between the GC skew shift point and predicted dif site expressed as the precentage of genome size, used as a threshold to retrieve dif sequence from the database</label>
+    </param>
+    <param name="dbonly" type="select" value="no">
+      <label>Include to only use values available in databases and to suppress prediction</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gscs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gscs.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,17 @@
+<tool id="EMBOSS: gscs" name="gscs" version="1.0.2">
+  <description>Calculates the scaled chi-square</description>
+  <command>gscs -sequence $input1 -translate $translate -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="translate" type="select" value="no">
+      <label>Include when translates using standard codon table</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gseq2png.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gseq2png.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: gseq2png" name="gseq2png" version="1.0.2">
+  <description>Converts a sequence to PNG image</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl gseq2png -sequence $input1 -format png -goutfile $out_file1 -auto -width $width -window $window</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="width" size="4" type="integer" value="640">
+      <label>Width of the image</label>
+    </param>
+    <param name="window" size="4" type="integer" value="20">
+      <label>Window size of a sequence to represent each pixel</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gseqinfo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gseqinfo.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: gseqinfo" name="gseqinfo" version="1.0.2">
+  <description>Prints out basic nucleotide sequence statistics</description>
+  <command>gseqinfo -sequence $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gshuffleseq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gshuffleseq.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,16 @@
+<tool id="EMBOSS: gshuffleseq" name="gshuffleseq" version="1.0.2">
+  <description>Creates randomized sequence with conserved k-mer composition</description>
+  <command>gshuffleseq -sequence $input1 -k $k -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="k" size="4" type="integer" value="1">
+      <label>Sequence k-mer to preserve composition</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gsignature.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gsignature.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,26 @@
+<tool id="EMBOSS: gsignature" name="gsignature" version="1.0.2">
+  <description>Calculates oligonucleotide usage (genomic signature)</description>
+  <command>gsignature -sequence $input1 -wordlength $wordlength -bothstrand $bothstrand -oe $oe -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="wordlength" size="4" type="integer" value="2">
+      <label>Word length</label>
+    </param>
+    <param name="bothstrand" type="select" value="yes">
+      <label>Include to use both strands direct used otherwise</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="oe" type="select" value="yes">
+      <label>Include to use O/E value observed values used otherwise</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gsvalue.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gsvalue.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,18 @@
+<tool id="EMBOSS: gsvalue" name="gsvalue" version="1.0.2">
+  <description>Calculates the strength of selected codon usage bias (S)</description>
+  <command>gsvalue -sequence $input1 -sharp $sharp -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="sharp" type="select" value="no">
+      <label>Include to use the 40 genes used by Sharp instead of ribosomal proteins</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gviewcds.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gviewcds.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,20 @@
+<tool id="EMBOSS: gviewcds" name="gviewcds" version="1.0.2">
+  <description>Displays a graph of nucleotide contents around start and stop codons</description>
+  <command interpreter="perl">gembassy_calcandplot_wrapper.pl gviewcds -sequence $input1 -length $length -gap $gap -auto -noaccid $out_file1 $out_file2</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="length" size="4" type="integer" value="100">
+      <label>Length in bases to show around start/stop codons</label>
+    </param>
+    <param name="gap" size="4" type="integer" value="3">
+      <label>Gap shown in graph in between start/stop codon neighbors</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
+    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/gembassy/gwvalue.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/gembassy/gwvalue.xml Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: gwvalue" name="gwvalue" version="1.0.2">
+  <description>Calculates the 'relative adaptiveness of each codon' (W)</description>
+  <command>gwvalue -sequence $input1 -include $include -exclude $exclude -auto -noaccid -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="include" size="4" type="text" value="ribosomal.*protein">
+      <label>Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al.</label>
+    </param>
+    <param name="exclude" size="4" type="text" value="[Mm]itochondrial">
+      <label>Regular expression to exclude genes from a reference set</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/acdgalaxy.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/acdgalaxy.pl Fri Jun 26 05:21:44 2015 -0400

[

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/emboss_single_outputfile_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/emboss_single_outputfile_wrapper.pl Fri Jun 26 05:21:44 2015 -0400

[

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/gembassy_calcandplot_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/gembassy_calcandplot_wrapper.pl Fri Jun 26 05:21:44 2015 -0400

[

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kblast.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kblast.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,75 @@
+<tool id="EMBOSS: kblast" name="kblast" version="1.0.2">
+  <description>Search similar sequences in public repositories using BLAST</description>
+  <command>kblast -seqall $input1 -database $database -program $program -server $server -format $format -eval $eval -qfilter $qfilter -opengap $opengap -extendgap $extendgap -dropoff $dropoff -penalty $penalty -reward $reward -numdescriptions $numdescriptions -numalignments $numalignments -threshold $threshold -g $g -matrix $matrix -wordsize $wordsize -dbsize $dbsize -k $k -searchsp $searchsp -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="database" size="4" type="text" value="swissprot">
+      <label>database name about target for your search</label>
+    </param>
+    <param name="program" size="4" type="text" value="auto">
+      <label>blast program name. 'auto' (infer suitable program from your sequence), 'blastn', 'blastp' or 'blastx'</label>
+    </param>
+    <param name="server" size="4" type="text" value="">
+      <label>specify web server for your search. 'NCBI', 'EBI' or 'DDBJ'</label>
+    </param>
+    <param name="format" size="4" type="text" value="0">
+      <label>blast report format. 0 : normal BLAST report 8 : tabulark 1: ID listk 2: ID list separated by conmma</label>
+    </param>
+    <param name="eval" size="4" type="text" value="10.0">
+      <label>Expectation value</label>
+    </param>
+    <param name="qfilter" size="4" type="text" value="T">
+      <label></label>
+    </param>
+    <param name="opengap" size="4" type="integer" value="-1">
+      <label>cost to open a gap</label>
+    </param>
+    <param name="extendgap" size="4" type="integer" value="-1">
+      <label>cost to extend a gap</label>
+    </param>
+    <param name="dropoff" size="4" type="text" value="0">
+      <label>X dropoff value for gapped alignment (in bits)</label>
+    </param>
+    <param name="penalty" size="4" type="integer" value="-3">
+      <label>penalty for a nucleotide mismatch (blastn only)</label>
+    </param>
+    <param name="reward" size="4" type="integer" value="1">
+      <label>reward for a nucleotide match (blastn only)</label>
+    </param>
+    <param name="numdescriptions" size="4" type="integer" value="500">
+      <label>show one-line descriptions for this number of database sequences</label>
+    </param>
+    <param name="numalignments" size="4" type="integer" value="250">
+      <label>number of database sequence to show alignments for (B)</label>
+    </param>
+    <param name="threshold" size="4" type="integer" value="0">
+      <label>threshold for extending hits, default if zero for each program</label>
+    </param>
+    <param name="g" type="select" value="no">
+      <label>perform gapped alignment</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="matrix" size="4" type="text" value="BLOSUM62">
+      <label>matrix</label>
+    </param>
+    <param name="wordsize" size="4" type="integer" value="0">
+      <label>word size, default if zero for each program</label>
+    </param>
+    <param name="dbsize" size="4" type="float" value="0">
+      <label>effective size of the database</label>
+    </param>
+    <param name="k" size="4" type="integer" value="0">
+      <label>number of best hits from a region to keep</label>
+    </param>
+    <param name="searchsp" size="4" type="float" value="0">
+      <label>effective length of the search space</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kcentroidfold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kcentroidfold.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: kcentroidfold" name="kcentroidfold" version="1.0.2">
+  <description>Predicts RNA 2D structure using CentroidFold</description>
+  <command>kcentroidfold -seqall $input1 -engine $engine -gamma $gamma -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="engine" size="4" type="text" value="CONTRAfold">
+      <label>specify the inference engine. 'CONTRAfold', 'McCaskill', 'pfold' or 'AUX'</label>
+    </param>
+    <param name="gamma" size="4" type="integer" value="4">
+      <label>weight of base pairs (2^-5 ~ 2^10)</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kclique.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kclique.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kclique" name="kclique" version="1.0.2">
+  <description>Largest clique program using clique</description>
+  <command>kclique -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kcontml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kcontml.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kcontml" name="kcontml" version="1.0.2">
+  <description>Gene frequency and continuous character Maximum Likelihood using contml</description>
+  <command>kcontml -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnacomp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnacomp.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnacomp" name="kdnacomp" version="1.0.2">
+  <description>DNA compatibility algorithm using dnacomp</description>
+  <command>kdnacomp -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnadist.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnadist.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnadist" name="kdnadist" version="1.0.2">
+  <description>Nucleic acid sequence Distance Matrix program using dnadist</description>
+  <command>kdnadist -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnainvar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnainvar.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnainvar" name="kdnainvar" version="1.0.2">
+  <description>Nucleic acid sequence Invariants method using dnainvar</description>
+  <command>kdnainvar -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnaml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnaml.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnaml" name="kdnaml" version="1.0.2">
+  <description>Estimates nucleotide phylogeny by maximum likelihood using dnaml</description>
+  <command>kdnaml -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnamlk.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnamlk.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnamlk" name="kdnamlk" version="1.0.2">
+  <description>Estimates nucleotide phylogeny by maximum likelihood using dnamlk</description>
+  <command>kdnamlk -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnapars.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnapars.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnapars" name="kdnapars" version="1.0.2">
+  <description>DNA parsimony algorithm using dnapars</description>
+  <command>kdnapars -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdnapenny.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdnapenny.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdnapenny" name="kdnapenny" version="1.0.2">
+  <description>Penny algorithm for DNA using dnapenny</description>
+  <command>kdnapenny -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdollop.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdollop.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdollop" name="kdollop" version="1.0.2">
+  <description>Dollo and polymorphism parsimony algorithm using dollop</description>
+  <command>kdollop -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kdolpenny.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kdolpenny.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kdolpenny" name="kdolpenny" version="1.0.2">
+  <description>Penny algorithm Dollo or polymorphism using dolpenny</description>
+  <command>kdolpenny -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kfetchbatch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kfetchbatch.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: kfetchbatch" name="kfetchbatch" version="1.0.2">
+  <description>Fetch a set of entries in a defined format and style</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl kfetchbatch -seqall $input1 -format png -goutfile $out_file1 -auto -format $format -style $style</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="format" size="4" type="text" value="default">
+      <label>Output data format. 'default', 'annot', 'embl', 'emblxml-1.1', 'emblxml-1.2', 'fasta', 'insdxml', 'seqxml' or 'entrysize'</label>
+    </param>
+    <param name="style" size="4" type="text" value="raw">
+      <label>Output data style. 'raw' or 'html'</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kfetchdata.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kfetchdata.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: kfetchdata" name="kfetchdata" version="1.0.2">
+  <description>Fetch an entry in a defined format and style</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl kfetchdata -seqall $input1 -format png -goutfile $out_file1 -auto -format $format -style $style</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="format" size="4" type="text" value="default">
+      <label>Output data format. 'default', 'annot', 'embl', 'emblxml-1.1', emblxml-1.2', 'fasta', 'insdxml', 'seqxml' or 'entrysize'</label>
+    </param>
+    <param name="style" size="4" type="text" value="raw">
+      <label>Output data style. 'raw' or 'html'</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kfitch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kfitch.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kfitch" name="kfitch" version="1.0.2">
+  <description>Fitch-Margoliash and Least-Squares Distance Methods using fitch</description>
+  <command>kfitch -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kgendist.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kgendist.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kgendist" name="kgendist" version="1.0.2">
+  <description>Compute genetic distances from gene frequencies using gendist</description>
+  <command>kgendist -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kgenemarkhmm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kgenemarkhmm.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,26 @@
+<tool id="EMBOSS: kgenemarkhmm" name="kgenemarkhmm" version="1.0.2">
+  <description>Finds genes in prokaryotic genomes using GeneMarkhmm</description>
+  <command>kgenemarkhmm -seqall $input1 -title $title -list $list -rbs $rbs -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="title" size="4" type="text" value="">
+      <label>Your job title</label>
+    </param>
+    <param name="list" type="select" value="no">
+      <label>Show list about species of prediction models</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="rbs" type="select" value="yes">
+      <label>Use RBS model if available</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kglimmer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kglimmer.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: kglimmer" name="kglimmer" version="1.0.2">
+  <description>Finds genes in prokaryotic genomes using Glimmer</description>
+  <command>kglimmer -seqall $input1 -topology $topology -gencode $gencode -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="topology" size="4" type="text" value="circular">
+      <label>Genome topology ('circular' or 'linear')</label>
+    </param>
+    <param name="gencode" size="4" type="integer" value="11">
+      <label>Genetic code. '11': Bacteria or Archaea, '4': Mycoplasma/Spiroplasma</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kkalign.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kkalign.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,28 @@
+<tool id="EMBOSS: kkalign" name="kkalign" version="1.0.2">
+  <description>Multiple sequence alignment using Kalign</description>
+  <command>kkalign -seqall $input1 -moltype $moltype -gpo $gpo -gpe $gpe -tgpe $tgpe -bonus $bonus -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="moltype" size="4" type="text" value="auto">
+      <label>Molecular (sequence) type. 'auto' (auto detection by input sequence), 'N'(nucleotide) or 'P'(protein)</label>
+    </param>
+    <param name="gpo" size="4" type="float" value="">
+      <label>gap creation penalty</label>
+    </param>
+    <param name="gpe" size="4" type="float" value="">
+      <label>gap extension penalty</label>
+    </param>
+    <param name="tgpe" size="4" type="float" value="">
+      <label>terminal gap penalty</label>
+    </param>
+    <param name="bonus" size="4" type="float" value="">
+      <label>bonus score</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kkitsch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kkitsch.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kkitsch" name="kkitsch" version="1.0.2">
+  <description>Fitch-Margoliash method with contemporary tips using kitsch</description>
+  <command>kkitsch -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kmafft.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kmafft.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,44 @@
+<tool id="EMBOSS: kmafft" name="kmafft" version="1.0.2">
+  <description>Multiple sequence alignment using MAFFT</description>
+  <command>kmafft -seqall $input1 -strategy $strategy -outorder $outorder -opengap $opengap -ep $ep -scorematrix $scorematrix -homologs $homologs -showhomologs $showhomologs -numhomologs $numhomologs -threshold $threshold -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="strategy" size="4" type="text" value="auto">
+      <label>Calculation strategy.</label>
+    </param>
+    <param name="outorder" size="4" type="text" value="aligned">
+      <label>Output order. 'input': same as input, 'aligned': aligned</label>
+    </param>
+    <param name="opengap" size="4" type="float" value="1.53">
+      <label>Gap opening penalty (1.0 - 3.0)</label>
+    </param>
+    <param name="ep" size="4" type="float" value="0.0">
+      <label>Offset value (0.0 - 1.0)</label>
+    </param>
+    <param name="scorematrix" size="4" type="text" value="">
+      <label>Scoring matrix. Protein seq:    'BLOSUM30', 'BLOSUM45', 'BLOSUM62'(default), 'BLOSUM80', 'JTT100' or 'JTT200' Nucleotide seq: '1PAM', '20PAM' or '200PAM'(default)</label>
+    </param>
+    <param name="homologs" type="select" value="no">
+      <label>Collects homologs from SwissProt by BLAST and performs profile-based alignments.</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="showhomologs" type="select" value="no">
+      <label>Show homologs  sequence</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="numhomologs" size="4" type="integer" value="50">
+      <label>Number of homologs sequences</label>
+    </param>
+    <param name="threshold" size="4" type="float" value="1e-10">
+      <label>Threshold of homologs sequences</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kmix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kmix.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kmix" name="kmix" version="1.0.2">
+  <description>Mixed parsimony algorithm using mix</description>
+  <command>kmix -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kmuscle.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kmuscle.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kmuscle" name="kmuscle" version="1.0.2">
+  <description>Multiple sequence alignment using MUSCLE</description>
+  <command>kmuscle -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kneighbor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kneighbor.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kneighbor" name="kneighbor" version="1.0.2">
+  <description>Phylogenies from distance matrix by N-J or UPGMA method using neighbor</description>
+  <command>kneighbor -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kpathwayprojector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kpathwayprojector.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kpathwayprojector" name="kpathwayprojector" version="1.0.2">
+  <description>Mapping experimental data on PathwayProjector</description>
+  <command>kpathwayprojector -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kpenny.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kpenny.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kpenny" name="kpenny" version="1.0.2">
+  <description>Penny algorithm, branch-and-bound using penny</description>
+  <command>kpenny -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kphobius.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kphobius.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,16 @@
+<tool id="EMBOSS: kphobius" name="kphobius" version="1.0.2">
+  <description>Predicts transmembrance topology and signal peptides using Phobius</description>
+  <command>kphobius -seqall $input1 -outputformat $outputformat -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="outputformat" size="4" type="text" value="grp">
+      <label>The output format: 'long', 'short', 'raw' or 'grp'</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kprotdist.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kprotdist.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kprotdist" name="kprotdist" version="1.0.2">
+  <description>Protein distance algorithm using protdist</description>
+  <command>kprotdist -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kprotpars.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kprotpars.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kprotpars" name="kprotpars" version="1.0.2">
+  <description>Protein parsimony algorithm using protpars</description>
+  <command>kprotpars -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kpsort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kpsort.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,19 @@
+<tool id="EMBOSS: kpsort" name="kpsort" version="1.0.2">
+  <description>Predicts protein localization for PSORT</description>
+  <command>kpsort -seqall $input1 -org $org -title $title -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="org" size="4" type="text" value="anmal">
+      <label>Source for input sequence organisms. 'Gram-positive bacterium', 'Gram-negative bacterium', 'yeast', 'animal' or 'plant'</label>
+    </param>
+    <param name="title" size="4" type="text" value="MYSEQ">
+      <label>Title for your job</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kpsort2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kpsort2.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kpsort2" name="kpsort2" version="1.0.2">
+  <description>Predicts protein localization for PSORT2</description>
+  <command>kpsort2 -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kpsortb.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kpsortb.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,16 @@
+<tool id="EMBOSS: kpsortb" name="kpsortb" version="1.0.2">
+  <description>Predicts protein localization for PSORT B</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl kpsortb -seqall $input1 -format png -goutfile $out_file1 -auto -format $format</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="format" size="4" type="text" value="normal">
+      <label>Psortb output format ('normal', 'long' and 'short')</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/krestml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/krestml.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: krestml" name="krestml" version="1.0.2">
+  <description>Restriction site maximum Likelihood method utilizinig restml</description>
+  <command>krestml -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/krnafold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/krnafold.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,37 @@
+<tool id="EMBOSS: krnafold" name="krnafold" version="1.0.2">
+  <description>Predicts secondary structure of single starnd RNA or DNA using RNAfold</description>
+  <command>krnafold -seqall $input1 -noclosegu $noclosegu -nolp $nolp -dangling $dangling -param $param -tmp $tmp -circ $circ -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="noclosegu" type="select" value="no">
+      <label>no GU pairs at the end of helices</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="nolp" type="select" value="yes">
+      <label>avoid isolated base pairs</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="dangling" size="4" type="text" value="d2">
+      <label>Dangling end options</label>
+    </param>
+    <param name="param" size="4" type="text" value="rna">
+      <label>Energy Parameters</label>
+    </param>
+    <param name="tmp" size="4" type="integer" value="37">
+      <label>rescale energy parameters to given temperature (C)</label>
+    </param>
+    <param name="circ" type="select" value="no">
+      <label>assume RNA molecule to be circular</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kseqboot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kseqboot.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kseqboot" name="kseqboot" version="1.0.2">
+  <description>Bootstrapped sequences algorithm using seqboot</description>
+  <command>kseqboot -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kssearch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kssearch.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,66 @@
+<tool id="EMBOSS: kssearch" name="kssearch" version="1.0.2">
+  <description>Search similar sequences in public repositories using SSEARCH</description>
+  <command>kssearch -seqall $input1 -moltype $moltype -histogram $histogram -nucleotide $nucleotide -topstrand $topstrand -bottomstrand $bottomstrand -gapopen $gapopen -gapext $gapext -scores $scores -alignments $alignments -ktup $ktup -matrix $matrix -eupper $eupper -elower $elower -dbrange $dbrange -seqrange $seqrange -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="moltype" size="4" type="text" value="">
+      <label>molecular type</label>
+    </param>
+    <param name="histogram" type="select" value="">
+      <label>Display histogram</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="nucleotide" type="select" value="">
+      <label>your query is nucleotide or not(protein)</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="topstrand" type="select" value="">
+      <label>Nucleotide sequence strand to use for seqrch (top)</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="bottomstrand" type="select" value="">
+      <label>Nucleotide sequence strand to use for seqrch (bottom)</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="gapopen" size="4" type="integer" value="">
+      <label>Score for the initiation of a gap</label>
+    </param>
+    <param name="gapext" size="4" type="integer" value="">
+      <label>Score for each base/residue in a gap</label>
+    </param>
+    <param name="scores" size="4" type="integer" value="">
+      <label>Maximum number of scores displayed in the output</label>
+    </param>
+    <param name="alignments" size="4" type="integer" value="">
+      <label>Maximum number of alignments displayed in the output</label>
+    </param>
+    <param name="ktup" size="4" type="integer" value="">
+      <label>Word size to use for sequence comparisons</label>
+    </param>
+    <param name="matrix" size="4" type="text" value="">
+      <label>Scoring matrix to be used in the search</label>
+    </param>
+    <param name="eupper" size="4" type="float" value="">
+      <label>Upper E-value threshold</label>
+    </param>
+    <param name="elower" size="4" type="float" value="">
+      <label>Lower E-value threshold</label>
+    </param>
+    <param name="dbrange" size="4" type="text" value="">
+      <label>Range of sequence lengths in search database to include in search</label>
+    </param>
+    <param name="seqrange" size="4" type="text" value="">
+      <label>Region of the query sequence to use for the search</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/ktcoffee.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/ktcoffee.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: ktcoffee" name="ktcoffee" version="1.0.2">
+  <description>Multiple sequence alignment using T-COFFEE</description>
+  <command>ktcoffee -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/ktrnascan_se.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/ktrnascan_se.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,64 @@
+<tool id="EMBOSS: ktrnascan_se" name="ktrnascan_se" version="1.0.2">
+  <description>Finds tRNA genes using tRNAscan-SE</description>
+  <command>ktrnascan_se -seqall $input1 -title $title -mode $mode -source $source -gcode $gcode -pesudogene $pesudogene -origin $origin -ace $ace -codons $codons -fpos $fpos -breakdown $breakdown -covescore $covescore -euparams $euparams -euscore $euscore -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+    <param name="title" size="4" type="text" value="">
+      <label>Title of your job</label>
+    </param>
+    <param name="mode" size="4" type="text" value="Default">
+      <label>Search mode</label>
+    </param>
+    <param name="source" size="4" type="text" value="Mixed (general tRNA model)">
+      <label>Training data set</label>
+    </param>
+    <param name="gcode" size="4" type="text" value="Universal">
+      <label>Genetic Code for tRNA Isotype Prediction</label>
+    </param>
+    <param name="pesudogene" type="select" value="">
+      <label>Disable pseudo gene checking</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="origin" type="select" value="">
+      <label>Show origin of first-pass hits</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="ace" type="select" value="">
+      <label>Display results in ACeDB format</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="codons" type="select" value="">
+      <label>Show codons instead of tRNA anticodons</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="fpos" type="select" value="">
+      <label>Show false positives from tRNAscan/EufindtRNA</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="breakdown" type="select" value="">
+      <label>Show primary and secondary structure components to Cove scores</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="covescore" size="4" type="text" value="">
+      <label>Cove score cutoff</label>
+    </param>
+    <param name="euparams" size="4" type="text" value="Default">
+      <label>EufindtRNA search parameters</label>
+    </param>
+    <param name="euscore" size="4" type="text" value="">
+      <label>Intermediate score cutoff</label>
+    </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kweblogo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kweblogo.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kweblogo" name="kweblogo" version="1.0.2">
+  <description>Generation of sequence logos using WebLogo</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl kweblogo -seqall $input1 -format png -goutfile $out_file1 -auto </command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/kbws/kwolfpsort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/kwolfpsort.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,13 @@
+<tool id="EMBOSS: kwolfpsort" name="kwolfpsort" version="1.0.2">
+  <description>Predicts protein localization for WoLF PSORT</description>
+  <command>kwolfpsort -seqall $input1  -auto -outfile $out_file1</command>
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/snippets/perl_snippet_file.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/snippets/perl_snippet_file.pl Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,29 @@
+#!/usr/bin/env perl
+use warnings;
+
+my $scriptname = shift;
+my $outname = shift;
+open SCR, "<", $scriptname;
+open OUT, ">", $outname;
+open STDOUT, ">", shift;
+open STDERR, ">", shift;
+
+my $open = "";
+my @files;
+for(my $i = 0; @ARGV; $i++) {
+    my $fn = shift;
+    push @files, $fn;
+    $open .= qq(open IN$i, "<", "$fn";\n);
+}
+
+my $script = join("", <SCR>);
+
+if($script =~ /(open)|(system)|(`.+`)|([$@%]ENV)/smg) {
+    printf(STDERR "Found vulnerable code (open, system, backticks) in given script.");
+    exit(1);
+}
+
+eval("$open$script");
+
+close SCR;
+close OUT;

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/snippets/perl_snippet_file.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/snippets/perl_snippet_file.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,25 @@
+<tool id="perl_snippet_file" name="Perl Snippet File" version="1.0.0">
+  <description>Runs given perl script file</description>
+  <command interpreter="perl">
+    perl_snippet_file.pl
+    $input
+    $out_file1
+    $out_file2
+    $out_file3
+    #for $add in $add_inputs
+      #set $add_input = $add.add_input
+      $add_input
+    #end for
+  </command>
+  <inputs>
+    <param format="txt" name="input" type="data" label="Script to Run" />
+    <repeat name="add_inputs" title="Additional Input Files">
+      <param format="txt" name="add_input" type="data" label="Additional File" />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" label="Perl snippet output" />
+    <data format="input" name="out_file2" label="Perl snippet stdout" />
+    <data format="input" name="out_file3" label="Perl snippet stderr" />
+  </outputs>
+</tool>

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/snippets/perl_snippet_text.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/snippets/perl_snippet_text.pl Fri Jun 26 05:21:44 2015 -0400

[

@@ -0,0 +1,26 @@
+#!/usr/bin/env perl
+use warnings;
+
+my $script = shift;
+open OUT, ">", shift;
+open STDOUT, ">", shift;
+open STDERR, ">", shift;
+
+print OUT $script, "\n";
+
+my $open = "";
+my @files;
+for(my $i = 0; @ARGV; $i++) {
+    my $fn = shift;
+    push @files, $fn;
+    $open .= qq(open IN$i, "<", "$fn";\n);
+}
+
+if($script =~ /(open)|(system)|(`.+`)|([$@%]ENV)/smg) {
+    printf(STDERR "Found vulnerable code (open, system, backticks) in given script.");
+    exit(1);
+}
+
+eval("$open$script");
+
+close OUT;

diff -r 84a17b3fad1f -r 8947fca5f715 glang-galaxy-conf/snippets/perl_snippet_text.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/snippets/perl_snippet_text.xml Fri Jun 26 05:21:44 2015 -0400

@@ -0,0 +1,25 @@
+<tool id="perl_snippet_text" name="Perl Snippet Text" version="1.0.0">
+  <description>Runs given perl script text</description>
+  <command interpreter="perl">
+    perl_snippet_text.pl
+    '$input'
+    $out_file1
+    $out_file2
+    $out_file3
+    #for $add in $add_inputs
+      #set $add_input = $add.add_input
+      $add_input
+    #end for
+  </command>
+  <inputs>
+    <param name="input" area="True" size="25x80" type="text" label="Script to Run" />
+    <repeat name="add_inputs" title="Additional Input Files">
+      <param format="txt" name="add_input" type="data" label="Additional File" />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" label="Perl snippet output" />
+    <data format="txt" name="out_file2" label="Perl snippet stdout" />
+    <data format="txt" name="out_file3" label="Perl snippet stderr" />
+  </outputs>
+</tool>