Program: 57729
Project: 57729
Buggy source:
/** 
 * Reacts on the elements of the pathway tag. An example pathway tag looks like this: <pathway name="path:map00271" org="map" number="00271" title="Methionine metabolism" image="http://www.genome.jp/kegg/pathway/map/map00271.gif" link="http://www.genome.jp/dbget-bin/show_pathway?map00271">
 */
protected void handlePathwayTag(){
  String name="String_Node_Str";
  String title="String_Node_Str";
  String sImageLink="String_Node_Str";
  String externalLink="String_Node_Str";
  for (int attributeIndex=0; attributeIndex < attributes.getLength(); attributeIndex++) {
    attributeName=attributes.getLocalName(attributeIndex);
    if ("String_Node_Str".equals(attributeName)) {
      attributeName=attributes.getQName(attributeIndex);
    }
    if (attributeName.equals("String_Node_Str")) {
      name=attributes.getValue(attributeIndex);
    }
 else     if (attributeName.equals("String_Node_Str")) {
      title=attributes.getValue(attributeIndex);
    }
 else     if (attributeName.equals("String_Node_Str")) {
      sImageLink=attributes.getValue(attributeIndex);
    }
 else     if (attributeName.equals("String_Node_Str")) {
      externalLink=attributes.getValue(attributeIndex);
    }
  }
  if (title.length() == 0) {
    title="String_Node_Str";
  }
  String pathwayTexturePath=sImageLink.substring(sImageLink.lastIndexOf('/') + 1,sImageLink.length());
  pathwayTexturePath=pathwayTexturePath.replace("String_Node_Str","String_Node_Str");
  currentPathway=pathwayManager.createPathway(PathwayDatabaseType.KEGG,name,title,pathwayTexturePath,externalLink);
  hashKgmlEntryIdToVertexRep.clear();
  hashKgmlNameToVertexRep.clear();
  hashKgmlReactionNameToVertexRep.clear();
  currentEntryId=-1;
  currentReactionName=null;
  currentReactionType=null;
  currentVertices.clear();
  currentVertexGroupRep=null;
}

Fixed version (ground truth):
/** 
 * Reacts on the elements of the pathway tag. An example pathway tag looks like this: <pathway name="path:map00271" org="map" number="00271" title="Methionine metabolism" image="http://www.genome.jp/kegg/pathway/map/map00271.gif" link="http://www.genome.jp/dbget-bin/show_pathway?map00271">
 */
protected void handlePathwayTag(){
  String name="String_Node_Str";
  String title="String_Node_Str";
  String sImageLink="String_Node_Str";
  String externalLink="String_Node_Str";
  for (int attributeIndex=0; attributeIndex < attributes.getLength(); attributeIndex++) {
    attributeName=attributes.getLocalName(attributeIndex);
    if ("String_Node_Str".equals(attributeName)) {
      attributeName=attributes.getQName(attributeIndex);
    }
    if (attributeName.equals("String_Node_Str")) {
      name=attributes.getValue(attributeIndex);
    }
 else     if (attributeName.equals("String_Node_Str")) {
      title=attributes.getValue(attributeIndex);
    }
 else     if (attributeName.equals("String_Node_Str")) {
      sImageLink=attributes.getValue(attributeIndex);
    }
 else     if (attributeName.equals("String_Node_Str")) {
      externalLink=attributes.getValue(attributeIndex);
    }
  }
  if (title.length() == 0) {
    title="String_Node_Str";
  }
  String pathwayTexturePath=sImageLink.substring(sImageLink.lastIndexOf('/') + 1,sImageLink.length());
  pathwayTexturePath=pathwayTexturePath.replace("String_Node_Str","String_Node_Str");
  currentPathway=pathwayManager.createPathway(PathwayDatabaseType.KEGG,name,title,pathwayTexturePath,externalLink);
  hashKgmlEntryIdToVertexRep.clear();
  hashKgmlReactionNameToVertexRep.clear();
  currentEntryId=-1;
  currentReactionName=null;
  currentReactionType=null;
  currentVertices.clear();
  currentVertexGroupRep=null;
}