Program: 59208
Project: 59208
Buggy source:
protected void buildPathwayDisplayList(){
  String[] strPathwayPaths=new String[3];
  strPathwayPaths[0]="String_Node_Str";
  strPathwayPaths[1]="String_Node_Str";
  strPathwayPaths[2]="String_Node_Str";
  String[] strPathwayTexturePaths=new String[3];
  strPathwayTexturePaths[0]="String_Node_Str";
  strPathwayTexturePaths[1]="String_Node_Str";
  strPathwayTexturePaths[2]="String_Node_Str";
  loadPathwayFromFile(strPathwayPaths[0]);
  loadBackgroundOverlayImage(strPathwayTexturePaths[0]);
  refHashPathwayToZLayerValue.put(refCurrentPathway,fZLayerValue);
  refBasicPathway=refCurrentPathway;
  fZLayerValue+=1.0f;
  loadPathwayFromFile(strPathwayPaths[1]);
  loadBackgroundOverlayImage(strPathwayTexturePaths[1]);
  refHashPathwayToZLayerValue.put(refCurrentPathway,fZLayerValue);
  fZLayerValue+=1.0f;
  loadPathwayFromFile(strPathwayPaths[2]);
  loadBackgroundOverlayImage(strPathwayTexturePaths[2]);
  refHashPathwayToZLayerValue.put(refCurrentPathway,fZLayerValue);
  Iterator<Pathway> iterPathways=refGeneralManager.getSingelton().getPathwayManager().getPathwayIterator();
  Texture refPathwayTexture=null;
  System.out.println("String_Node_Str");
  while (iterPathways.hasNext()) {
    System.out.println("String_Node_Str");
    int iVerticesDiplayListId=gl.glGenLists(1);
    int iEdgeDisplayListId=gl.glGenLists(1);
    iArPathwayNodeDisplayListIDs.add(iVerticesDiplayListId);
    iArPathwayEdgeDisplayListIDs.add(iEdgeDisplayListId);
    refCurrentPathway=iterPathways.next();
    System.out.println("String_Node_Str" + refCurrentPathway.getTitle());
    fZLayerValue=refHashPathwayToZLayerValue.get(refCurrentPathway);
    refPathwayTexture=refHashPathwayToTexture.get(refCurrentPathway);
    fPathwayTextureAspectRatio=(float)refPathwayTexture.getImageWidth() / (float)refPathwayTexture.getImageHeight();
    fScalingFactorX=fPathwayTextureAspectRatio / (float)refPathwayTexture.getImageWidth();
    fScalingFactorY=1.0f / (float)refPathwayTexture.getImageHeight();
    System.out.println("String_Node_Str" + fScalingFactorX);
    System.out.println("String_Node_Str" + fScalingFactorY);
    System.out.println("String_Node_Str" + fPathwayTextureAspectRatio);
    buildEnzymeNodeDisplayList();
    buildHighlightedEnzymeNodeDisplayList();
    buildCompoundNodeDisplayList();
    buildHighlightedCompoundNodeDisplayList();
    buildContainedPathwayNodeDisplayList();
    gl.glNewList(iVerticesDiplayListId,GL.GL_COMPILE);
    extractVertices();
    gl.glEndList();
    gl.glNewList(iEdgeDisplayListId,GL.GL_COMPILE);
    extractEdges();
    gl.glEndList();
  }
}

Fixed version (ground truth):
protected void buildPathwayDisplayList(){
  String[] strPathwayPaths=new String[3];
  strPathwayPaths[0]="String_Node_Str";
  strPathwayPaths[1]="String_Node_Str";
  strPathwayPaths[2]="String_Node_Str";
  String[] strPathwayTexturePaths=new String[3];
  strPathwayTexturePaths[0]="String_Node_Str";
  strPathwayTexturePaths[1]="String_Node_Str";
  strPathwayTexturePaths[2]="String_Node_Str";
  loadPathwayFromFile(strPathwayPaths[0]);
  loadBackgroundOverlayImage(strPathwayTexturePaths[0]);
  refHashPathwayToZLayerValue.put(refCurrentPathway,fZLayerValue);
  refBasicPathway=refCurrentPathway;
  fZLayerValue+=1.0f;
  loadPathwayFromFile(strPathwayPaths[1]);
  loadBackgroundOverlayImage(strPathwayTexturePaths[1]);
  refHashPathwayToZLayerValue.put(refCurrentPathway,fZLayerValue);
  fZLayerValue+=1.0f;
  loadPathwayFromFile(strPathwayPaths[2]);
  loadBackgroundOverlayImage(strPathwayTexturePaths[2]);
  refHashPathwayToZLayerValue.put(refCurrentPathway,fZLayerValue);
  Iterator<Pathway> iterPathways=refHashPathwayToZLayerValue.keySet().iterator();
  Texture refPathwayTexture=null;
  System.out.println("String_Node_Str");
  while (iterPathways.hasNext()) {
    System.out.println("String_Node_Str");
    int iVerticesDiplayListId=gl.glGenLists(1);
    int iEdgeDisplayListId=gl.glGenLists(1);
    iArPathwayNodeDisplayListIDs.add(iVerticesDiplayListId);
    iArPathwayEdgeDisplayListIDs.add(iEdgeDisplayListId);
    refCurrentPathway=iterPathways.next();
    System.out.println("String_Node_Str" + refCurrentPathway.getTitle());
    fZLayerValue=refHashPathwayToZLayerValue.get(refCurrentPathway);
    refPathwayTexture=refHashPathwayToTexture.get(refCurrentPathway);
    fPathwayTextureAspectRatio=(float)refPathwayTexture.getImageWidth() / (float)refPathwayTexture.getImageHeight();
    fScalingFactorX=fPathwayTextureAspectRatio / (float)refPathwayTexture.getImageWidth();
    fScalingFactorY=1.0f / (float)refPathwayTexture.getImageHeight();
    System.out.println("String_Node_Str" + fScalingFactorX);
    System.out.println("String_Node_Str" + fScalingFactorY);
    System.out.println("String_Node_Str" + fPathwayTextureAspectRatio);
    buildEnzymeNodeDisplayList();
    buildHighlightedEnzymeNodeDisplayList();
    buildCompoundNodeDisplayList();
    buildHighlightedCompoundNodeDisplayList();
    gl.glNewList(iVerticesDiplayListId,GL.GL_COMPILE);
    extractVertices();
    gl.glEndList();
    gl.glNewList(iEdgeDisplayListId,GL.GL_COMPILE);
    extractEdges();
    gl.glEndList();
  }
}