--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/ggcskew.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,178 @@
+/******************************************************************************
+** @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;
+}