[Sashimi-commit] SF.net SVN: sashimi:[5104] trunk/trans_proteomic_pipeline/src/Parsers/ RefreshParser/RefreshParser.cxx

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

Revision: 5104
          http://sashimi.svn.sourceforge.net/sashimi/?rev=5104&view=rev
Author:   dshteyn
Date:     2010-08-11 00:29:21 +0000 (Wed, 11 Aug 2010)

Log Message:
-----------
Error out rather than crash when sample_enzyme tag is absent.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx

Modified: trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx	2010-08-10 23:44:51 UTC (rev 5103)
+++ trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx	2010-08-11 00:29:21 UTC (rev 5104)
@@ -352,12 +352,13 @@
 	    }
 	    else {
 	      //already listed
-			delete [] nextenz;
+	      delete [] nextenz;
 	      enzyme_index_ = enzIdx;
 	      if(use_default_min_ntt_)
 		min_num_tol_term_ = 0;
 	    }
 	  }
+	  
 	  if(enzyme_data) {
 	    if(tag->isEnd() && ! strcmp(tag->getName(), "sample_enzyme")) {
 	      (*enzyme_digestions_)[enzyme_index_]->fixSpecificity();
@@ -366,7 +367,7 @@
 	    else if(strcmp(tag->getName(), "sample_enzyme")) {
 	      (*enzyme_digestions_)[enzyme_index_]->enterSpecificity(tag);
 	    }
-
+	    
 	  }
 
 
@@ -757,6 +758,10 @@
 		   else
 		     next = result[nextlen]; // next aa
 
+		   if (enzyme_digestions_->size() == 0) {
+		     cerr << "ERROR: <sample_enzyme> tag was not found in the pep.xml file." << endl;
+		     exit(1);
+		   }
 
 		   int new_ntt = (*enzyme_digestions_)[((interact_data_line_t *)
 							uniq_interact_data[this_index])->enzyme_ind]->
@@ -1080,7 +1085,7 @@
   //  interact_data_line->min_num_enz_term = min_num_tol_term_;
   //HENRY: Check the presence of num_tol_term before doing this -- otherwise
   // it seg-faults for some OMSSA files.
-  if (hit_tag->getAttributeValue("num_tol_term")) {
+  if (hit_tag->getAttributeValue("num_tol_term") && use_default_min_ntt_) {
     interact_data_line->min_num_enz_term = atoi( hit_tag->getAttributeValue("num_tol_term") );
   } else {
     interact_data_line->min_num_enz_term = min_num_tol_term_;
@@ -1561,7 +1566,7 @@
         char* next_descr = new char[strlen(interact_line->db_ref)+strlen(interact_line->db_ref) + strlen(database)+100];
         sprintf(next_descr, "originally identified as %s in database %s", interact_line->db_ref, database);
         search_hit->setAttributeValue("protein_descr", (XMLEscape(next_descr)).c_str());
-        delete next_descr;
+        delete [] next_descr;
       }
       
       tags->insertAtEnd(search_hit);


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