diff GEMBASSY-1.0.3/src/gconsensusz.c @ 0:8300eb051bea draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/gconsensusz.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,188 @@
+/******************************************************************************
+** @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;
+}