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

Uploaded

--- a/GEMBASSY-1.0.3/src/gconsensusz.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,188 +0,0 @@
-/******************************************************************************
-** @source gconsensusz
-**
-** Calculate the consensus in givin array of sequences
-**
-** @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 gconsensusz *********************************************************
-**
-** Calculate the consensus in givin array of sequences
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("gconsensusz", argc, argv, "GEMBASSY", "1.0.3");
-
-  struct soap	  soap;
-  struct ns1__consensus_USCOREzInputParams params;
-  struct arrayIn  array_seq;
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  ajint	    high  = 0;
-  double    low   = 0;
-
-  char *result;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  ajint i;
-  ajint size = 0;
-  char **ptr = NULL;
-
-  seqall = ajAcdGetSeqall("sequence");
-  high   = ajAcdGetInt("high");
-  low    = ajAcdGetFloat("low");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  params.high   = high;
-  params.low    = low;
-  params.output = "f";
-
-  array_seq.__ptr = NULL;
-  array_seq.__size = 0;
-
-  ptr = (char**)malloc(sizeof(char*));
-
-  if(!ptr)
-    {
-      ajDie("Error in allocation\n");
-    }
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      ptr = (char**)realloc(ptr, sizeof(char*) * (size + 1));
-
-      if(!ptr)
-	{
-	  ajDie("Error in allocation\n");
-	}
-
-      *(ptr + size) = ajCharNewS(ajSeqGetSeqS(seq));
-
-      ++size;
-    }
-
-  if(size < 2)
-    {
-      AJFREE(*ptr);
-      AJFREE(ptr);
-
-      ajDie("File only has one sequence. Please input more than two.\n");
-    }
-
-  array_seq.__ptr = ptr;
-  array_seq.__size = size;
-
-  soap_init(&soap);
-
-  if(soap_call_ns1__consensus_USCOREz(
-                                     &soap,
-				      NULL,
-				      NULL,
-				     &array_seq,
-				     &params,
-				     &result
-                                     ) == SOAP_OK)
-    {
-      if(plot)
-	{
-	  ajStrAppendC(&title, argv[0]);
-
-	  gpp.title = ajStrNewS(title);
-	  gpp.xlab = ajStrNewC("position");
-	  gpp.ylab = ajStrNewC("consensus");
-
-          if(!gFilebuffURLC(result, &buff))
-            {
-              ajDie("File downloading error from:\n%s\n", result);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-	  ajStrDel(&title);
-	  ajStrDel(&(gpp.xlab));
-	  ajStrDel(&(gpp.ylab));
-	}
-      else
-	{
-	  if(!gFileOutURLC(result, &outf))
-	    {
-              ajDie("File downloading error from:\n%s\n", result);
-              embExitBad();
-	    }
-	}
-    }
-  else
-    {
-      soap_print_fault(&soap, stderr);
-    }
-
-  soap_destroy(&soap);
-  soap_end(&soap);
-  soap_done(&soap);
-  
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-
-  i = 0;
-
-  while(i < size)
-    {
-      AJFREE(*(ptr + i));
-      ++i;
-    }
-
-  AJFREE(ptr);
-
-  embExit();
-
-  return 0;
-}