--- 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;
-}