annotate GEMBASSY-1.0.3/src/gcircularmap.c @ 1:84a17b3fad1f draft

Uploaded

/******************************************************************************
** @source gcircularmap
**
** Draws circular map of the genome
**
** @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 gcircularmap ********************************************************
**
** Draws circular map of the genome
**
******************************************************************************/

int main(int argc, char *argv[])
{
  embInitPV("gcircularmap", argc, argv, "GEMBASSY", "1.0.3");

  struct soap soap;
  struct ns1__circular_USCOREmapInputParams params;

  AjPSeqall seqall;
  AjPSeq    seq;
  AjPStr    inseq    = NULL;
  AjPStr    seqid    = NULL;
  AjBool    accid    = ajFalse;
  AjPFile   outf     = NULL;
  AjPStr    filename = NULL;
  AjPStr    outfname = NULL;
  AjPStr    format   = NULL;

  ajint i;

  char *in0;
  char *result;

  seqall   = ajAcdGetSeqall("sequence");
  filename = ajAcdGetString("goutfile");
  accid    = ajAcdGetBoolean("accid");
  format   = ajAcdGetString("format");

  params.gmap = 0;

  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) == 0)
        {
          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
        }

      if(ajStrGetLen(seqid) == 0)
        {
          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__circular_USCOREmap(
	                                  &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, "svg"))
            {
              if(!gHttpConvertC(result, &outf, ajStrNewC("svg"), 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;
}