diff GEMBASSY-1.0.3/src/goligomercounter.c @ 2:8947fca5f715 draft default tip

Uploaded

--- 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;
-}