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

Uploaded

--- a/GEMBASSY-1.0.3/src/gkmertable.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,164 +0,0 @@
-/******************************************************************************
-** @source gkmertable
-**
-** Create an image showing all k-mer abundance within a 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   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 gkmertable ***********************************************************
-**
-** Create an image showing all k-mer abundance within a sequence
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gkmertable", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap soap;
-  struct ns1__kmer_USCOREtableInputParams params;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq    = NULL;
-  AjPStr    seqid    = NULL;
-  ajint     k        = 0;
-  AjBool    accid    = ajFalse;
-  AjPFile   outf     = NULL;
-  AjPStr    filename = NULL;
-  AjPStr    outfname = NULL;
-  AjPStr    format   = NULL;
-
-  ajint i;
-
-  char *in0;
-  char *result;
-
-  seqall   = ajAcdGetSeqall("sequence");
-  k        = ajAcdGetInt("k");
-  filename = ajAcdGetString("goutfile");
-  format   = ajAcdGetString("format");
-
-  params.k = k;
-
-  i = 0;
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-
-      soap_init(&soap);
-
-      inseq = NULL;
-
-      ajStrAppendC(&inseq, ">");
-      ajStrAppendS(&inseq, ajSeqGetAccS(seq));
-      ajStrAppendC(&inseq, "\n");
-      ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      in0 = ajCharNewS(inseq);
-
-      if(soap_call_ns1__kmer_USCOREtable(
-                                        &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;
-}