Program: 58875
Project: 58875
Buggy source:
private void handleAreaTag(){
  String sName="String_Node_Str";
  String sCoords="String_Node_Str";
  String sShape="String_Node_Str";
  String sExternalLink="String_Node_Str";
  for (int iAttributeIndex=0; iAttributeIndex < attributes.getLength(); iAttributeIndex++) {
    sAttributeName=attributes.getLocalName(iAttributeIndex);
    if ("String_Node_Str".equals(sAttributeName)) {
      sAttributeName=attributes.getQName(iAttributeIndex);
    }
    if (sAttributeName.equals("String_Node_Str")) {
      sShape=attributes.getValue(iAttributeIndex);
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      sCoords=attributes.getValue(iAttributeIndex);
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      sExternalLink=attributes.getValue(iAttributeIndex);
      if (sExternalLink.contains("String_Node_Str")) {
        sName=sExternalLink.substring(sExternalLink.lastIndexOf("String_Node_Str") + 5,sExternalLink.length());
      }
    }
  }
  IIDMappingManager genomeIdManager=generalManager.getIDMappingManager();
  Set<Integer> iSetDavidID=(Set<Integer>)genomeIdManager.<String,Integer>getMultiID(EMappingType.BIOCARTA_GENE_ID_2_DAVID,sName);
  if (iSetDavidID == null)   return;
  for (  Integer iDavidId : iSetDavidID) {
    if (iDavidId == null || iDavidId == -1 || iDavidId == 0) {
      generalManager.getLogger().log(Level.FINE,"String_Node_Str" + sName + "String_Node_Str");
      return;
    }
    IGraphItem vertex=pathwayItemManager.createVertexGene(sName,"String_Node_Str",BIOCARTA_EXTERNAL_URL_VERTEX + sExternalLink,"String_Node_Str",iDavidId);
    generalManager.getPathwayItemManager().createVertexRep(currentPathway,vertex,sName,sShape,sCoords);
  }
}

Fixed version (ground truth):
private void handleAreaTag(){
  String sName="String_Node_Str";
  String sCoords="String_Node_Str";
  String sShape="String_Node_Str";
  String sExternalLink="String_Node_Str";
  for (int iAttributeIndex=0; iAttributeIndex < attributes.getLength(); iAttributeIndex++) {
    sAttributeName=attributes.getLocalName(iAttributeIndex);
    if ("String_Node_Str".equals(sAttributeName)) {
      sAttributeName=attributes.getQName(iAttributeIndex);
    }
    if (sAttributeName.equals("String_Node_Str")) {
      sShape=attributes.getValue(iAttributeIndex);
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      sCoords=attributes.getValue(iAttributeIndex);
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      sExternalLink=attributes.getValue(iAttributeIndex);
      if (sExternalLink.contains("String_Node_Str")) {
        sName=sExternalLink.substring(sExternalLink.lastIndexOf("String_Node_Str") + 5,sExternalLink.length());
      }
    }
  }
  IIDMappingManager genomeIdManager=generalManager.getIDMappingManager();
  Set<Integer> iSetDavidID=(Set<Integer>)genomeIdManager.<String,Integer>getMultiID(EMappingType.BIOCARTA_GENE_ID_2_DAVID,sName);
  if (iSetDavidID == null)   return;
  ArrayList<IGraphItem> alVertex=pathwayItemManager.createVertexGene(sName,"String_Node_Str",BIOCARTA_EXTERNAL_URL_VERTEX + sExternalLink,"String_Node_Str",iSetDavidID);
  generalManager.getPathwayItemManager().createVertexRep(currentPathway,alVertex,sName,sShape,sCoords);
}