--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/goligomercounter.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,142 @@
+/******************************************************************************
+** @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;
+}