[Debichem-commits] [SCM] massXpert mass spectrometry suite: debian packaging branch, debian, updated. upstream/3.2.0-1-g5564507

[Filippo Rusconi (Debian Maintainer)]

The following commit has been merged in the debian branch:
commit 0c7b5222cf19ddd6059e6e4576420859d5d3275c
Author: Filippo Rusconi (Debian Maintainer) <rusconi-debian at laposte.net>
Date:   Thu Nov 26 20:51:08 2009 +0100

    Fixed a bug causing a crash in corner polymer cleavage cases.

diff --git a/lib/cleaver.cpp b/lib/cleaver.cpp
index 915726e..59cd1a9 100644
--- a/lib/cleaver.cpp
+++ b/lib/cleaver.cpp
@@ -196,7 +196,7 @@ namespace massXpert
       
 	int index = -1;
       
-	while(1)
+	while (1)
 	  {
 	    index = findCleaveMotif(*cleaveMotif, index + 1);
 	  
@@ -301,7 +301,7 @@ namespace massXpert
   int 
   Cleaver::findCleaveMotif(CleaveMotif &cleaveMotif, int index)
   {
-    bool noGood;
+    bool noGood = false;
 
     int firstIndex = 0;
   
@@ -334,70 +334,83 @@ namespace massXpert
     if (codeList.size() == 0)
       return -1;
   
-    Q_ASSERT(index < mp_polymer->size());
-    Q_ASSERT(index >= 0);
-  
-
+    if (index < 0)
+      return -1;
+    
+    if (index >= mp_polymer->size())
+      return -1;
+        
     // Seed the routine by setting 'first' to the first motif in the
-    // codeList(in our example this is "Lys").
+    // codeList (in our example this is "Lys").
 
     QString firstCode = codeList.first();
   
-    // And now iterate(starting from 'index') in the polymer sequence's
-    // list of monomers in search for a monomer having the proper code
-    //("Lys").
+    // And now iterate (starting from 'index') in the polymer
+    // sequence's list of monomers in search for a monomer having the
+    // proper code ("Lys").
   
     int iterIndex = index;
  
-    while(iterIndex < monomerList.size())
+    while (iterIndex < monomerList.size())
       {
 	const Monomer *monomer = monomerList.at(iterIndex);
-      
-	if(monomer->code() == firstCode)
+
+	if (monomer->code() != firstCode)
 	  {
-	    firstIndex = iterIndex;
-	    noGood = false;
-	  
-	    for (int iter = 1; iter < codeList.size(); ++iter)
+	    // The currently iterated code is not the one we
+	    // search. So go one code further in the sequence.
+	    
+	    ++iterIndex;
+	    continue;
+	  }
+	
+	// If we are here, then that means that we actually found on
+	// monomer code in the sequence that matches the one we are
+	// looking for.
+	
+	firstIndex = iterIndex;
+	noGood = false;
+	
+	// Now that we have anchored our search at firstIndex in the
+	// polymer sequence, continue with next monomer and check if
+	// it matches the next monomer in the motif we are looking
+	// for.
+  
+	for (int iter = 1; iter < codeList.size(); ++iter)
+	  {
+	    if (iterIndex + iter >= mp_polymer->size())
 	      {
-		if(iterIndex + iter >= mp_polymer->size())
-		  {
-		    noGood = true;
-		    break;
-		  }
+		noGood = true;
+		break;
+	      }
 	      
-		QString nextCode = codeList.at(iter);
+	    QString nextCode = codeList.at(iter);
 	      
-		monomer = monomerList.at(iterIndex + iter);
-
-		if(monomer->code() == nextCode)
-		  continue;
-		else
-		  {
-		    noGood = true;
-		    break;
-		  }
-	      }
-	    // End of
-	    // for (int iter = 1; iter < codeList.size(); ++iter)
+	    monomer = monomerList.at(iterIndex + iter);
 
-	    if (noGood)
-	      {
-		++iterIndex;
-		continue;
-	      }
+	    if (monomer->code() == nextCode)
+	      continue;
 	    else
 	      {
-		return firstIndex;
+		noGood = true;
+		break;
 	      }
 	  }
 	// End of
-	// if (monomer->code() == firstCode)
+	// for (int iter = 1; iter < codeList.size(); ++iter)
 
-	++iterIndex;
+	if (noGood)
+	  {
+	    ++iterIndex;
+	    continue;
+	  }
+	else
+	  {
+	    return firstIndex;
+	  }
       }
     // End of 
-    // while(iterIndex < monomerList.size())
+    // while (iterIndex < monomerList.size())
 		  
     return -1;
   }

-- 
massXpert mass spectrometry suite: debian packaging