diff GEMBASSY-1.0.3/src/gpalindrome.c @ 0:8300eb051bea draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/gpalindrome.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,131 @@
+/******************************************************************************
+** @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;
+}