[Sashimi-commit] SF.net SVN: sashimi:[6048] branches/4-6/trans_proteomic_pipeline/src/ Visualization/InteractParser/InteractParser.cxx

[<ds...@us...>]

Revision: 6048
          http://sashimi.svn.sourceforge.net/sashimi/?rev=6048&view=rev
Author:   dshteyn
Date:     2013-01-31 22:54:18 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
InteractParser: fix segfault on unknown enzyme.  Auto update ntt and nmc info based on sample_enzyme tag when recognized.

Modified Paths:
--------------
    branches/4-6/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx

Modified: branches/4-6/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
===================================================================
--- branches/4-6/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx	2013-01-31 22:51:14 UTC (rev 6047)
+++ branches/4-6/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx	2013-01-31 22:54:18 UTC (rev 6048)
@@ -565,9 +565,14 @@
 	  
 	  if (tag->isStart() && 
 	      !strcmp(tag->getName(), "sample_enzyme")) {
-	    if (enzyme_ == NULL) {
-	      enzyme_ = (new ProteolyticEnzymeFactory())->getProteolyticEnzyme(tag->getAttributeValue("name")); 
+	    if ((enzyme_ = (new ProteolyticEnzymeFactory())->getProteolyticEnzyme(tag->getAttributeValue("name")))  == NULL) {
+	      cerr << "ERROR: Unrecognized enzyme " << tag->getAttributeValue("name") << " - please specify enzyme with -E option" << endl;
+	      exit(1);
 	    }
+	    else if (enz_ == NULL) {
+	       enz_ = new char[strlen(tag->getAttributeValue("name"))+1];
+	       strcpy(enz_,   tag->getAttributeValue("name"));
+	    }
 	    enzyme_->writePepXMLTags(fout);
 	    skip_tag = True;
 	  }

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.