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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/gcircularmap.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,186 @@
+/******************************************************************************
+** @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;
+}