[Sashimi-commit] SF.net SVN: sashimi:[6107] trunk/trans_proteomic_pipeline/src/Validation/ PTMProphetParser

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

Revision: 6107
          http://sashimi.svn.sourceforge.net/sashimi/?rev=6107&view=rev
Author:   dshteyn
Date:     2013-02-22 19:17:11 +0000 (Fri, 22 Feb 2013)
Log Message:
-----------
PTMProphet: fix datafile error checking issue.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMpx.cxx
    trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx

Modified: trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMpx.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMpx.cxx	2013-02-22 19:07:43 UTC (rev 6106)
+++ trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMpx.cxx	2013-02-22 19:17:11 UTC (rev 6107)
@@ -227,10 +227,7 @@
     rampScanInfo* scanInfo = NULL;
     rampPeakList* peaks = NULL;
     Peptide* pep = pep_;
-    if (!cramp_->m_scanOffsets) {
-      cerr << "ERROR: cannot read scan in data file " << cramp_->m_filename << " exiting ..." << endl;
-      exit(1);
-    }
+  
     scanInfo = cramp_->getScanHeaderInfo(scan_);
     //read the peaks
     peaks = cramp_->getPeakList(scan_);	    

Modified: trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx	2013-02-22 19:07:43 UTC (rev 6106)
+++ trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx	2013-02-22 19:17:11 UTC (rev 6107)
@@ -173,7 +173,10 @@
 	      delete cramp;
 
 	    cramp = new cRamp(dataFile.c_str());
-
+	    if (!cramp->OK()) {
+	      cerr << "ERROR: cannot read scan in data file " << dataFile << " exiting ..." << endl;
+	      exit(1);
+	    }
 	  }
 
 	  else if (tag->isStart() && 
@@ -387,7 +390,10 @@
 	      delete cramp;
 
 	    cramp = new cRamp(dataFile.c_str());
-
+	    if (!cramp->OK()) {
+	      cerr << "ERROR: cannot read scan in data file " << dataFile << " exiting ..." << endl;
+	      exit(1);
+	    }
 	  }
 
 	  else if (tag->isStart() && 
@@ -699,7 +705,10 @@
 	      delete cramp;
 
 	    cramp = new cRamp(dataFile.c_str());
-
+	    if (!cramp->OK()) {
+	      cerr << "ERROR: cannot read scan in data file " << dataFile << " exiting ..." << endl;
+	      exit(1);
+	    }
 	  }
 
 	  else if (tag->isStart() && 
@@ -975,7 +984,10 @@
 	      delete cramp;
 
 	    cramp = new cRamp(dataFile.c_str());
-
+	    if (!cramp->OK()) {
+	      cerr << "ERROR: cannot read scan in data file " << dataFile << " exiting ..." << endl;
+	      exit(1);
+	    }
 	  }
 
 	  else if (tag->isStart() && 
@@ -1242,7 +1254,10 @@
 	      delete cramp;
 
 	    cramp = new cRamp(dataFile.c_str());
-
+	    if (!cramp->OK()) {
+	      cerr << "ERROR: cannot read scan in data file " << dataFile << " exiting ..." << endl;
+	      exit(1);
+	    }
 	  }
 
 	  else if (tag->isStart() && 
@@ -1522,7 +1537,10 @@
 	      delete cramp;
 
 	    cramp = new cRamp(dataFile.c_str());
-
+	    if (!cramp->OK()) {
+	      cerr << "ERROR: cannot read scan in data file " << dataFile << " exiting ..." << endl;
+	      exit(1);
+	    }
 	  }
 
 	  else if (tag->isStart() && 

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