--- a/GEMBASSY-1.0.3/src/ggenomemap3.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-/******************************************************************************
-** @source ggenomemap3
-**
-** Draws the map of the genome (Version 3)
-**
-** @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 ggenomemap3 **********************************************************
-**
-** Draws the map of the genome (Version 3)
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggenomemap3", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__genome_USCOREmap3InputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  ajint     width;
-  ajint     height;
-  AjBool    accid    = ajFalse;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  width    = ajAcdGetInt("width");
-  height   = ajAcdGetInt("height");
-  filename = ajAcdGetString("goutfile");
-  accid    = ajAcdGetBoolean("accid");
-  format   = ajAcdGetString("format");
-
-  params.width  = width;
-  params.height = height;
-  params.gmap   = 0;
-  params.datafilename = "";
-  params.output = "g";
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-
-      soap_init(&soap);
-
-      soap.send_timeout = 0;
-      soap.recv_timeout = 0;
-
-      inseq = NULL;
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(!ajStrGetLen(seqid))
-        ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-
-      if(!ajStrGetLen(seqid))
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid || !gFormatGenbank(seq, &inseq))
-        {
-          if(!accid)
-            ajWarn("Sequence does not have features\n"
-                   "Proceeding with sequence accession ID:%S\n", seqid);
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-
-          ajStrAssignS(&inseq, seqid);
-        }
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__genome_USCOREmap3(
-                                          &soap,
-					  NULL,
-					  NULL,
-					  in0,
-                                          &params,
-                                          &result
-                                          ) == SOAP_OK)
-	{
-          ++i;
-
-          outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
-                                        filename,
-                                        i,
-                                        format));
-
-          outf = ajFileNewOutNameS(outfname);
-
-          if(!outf)
-            {
-              ajDie("File open error\n");
-            }
-
-          if(!ajStrMatchC(format, "png"))
-            {
-              if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-          else
-            {
-              if(!gHttpGetBinC(result, &outf))
-                {
-                  ajDie("File downloading error from:\n%s\n", result);
-                }
-              else
-                {
-                  ajFmtPrint("Created %S\n", outfname);
-                }
-            }
-
-          ajStrDel(&outfname);
-        }
-      else
-        {
-          soap_print_fault(&soap, stderr);
-        }
-
-      soap_destroy(&soap);
-      soap_end(&soap);
-      soap_done(&soap);
-
-      AJFREE(in0);
-
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  ajStrDel(&filename);
-
-  embExit();
-
-  return 0;
-}