Program: 59231
Project: 59231
Buggy source:
public void initView(){
class PathwayMarqueeHandler extends BasicMarqueeHandler {
    public boolean isForceMarqueeEvent(    MouseEvent event){
      if (SwingUtilities.isLeftMouseButton(event) && event.getClickCount() == 1)       return true;
 else       return super.isForceMarqueeEvent(event);
    }
    public void mousePressed(    final MouseEvent event){
      DefaultGraphCell clickedCell=(DefaultGraphCell)refPathwayGraph.getFirstCellForLocation(event.getX(),event.getY());
      if (clickedCell == null) {
        for (int iUndoCount=0; iUndoCount < iNeighbourhoodUndoCount; iUndoCount++) {
          refUndoManager.undo(refGraphLayoutCache);
        }
        bNeighbourhoodShown=false;
        return;
      }
      if (clickedCell.getUserObject() == null) {
        super.mousePressed(event);
        return;
      }
      final String sUrl=((PathwayVertex)clickedCell.getUserObject()).getVertexLink();
      if (sUrl == "String_Node_Str") {
        super.mousePressed(event);
        return;
      }
      String sSearchPattern="String_Node_Str";
      String sPathwayFilePath;
      if (sUrl.contains((CharSequence)sSearchPattern)) {
        int iFilePathStartIndex=sUrl.lastIndexOf(sSearchPattern) + sSearchPattern.length();
        sPathwayFilePath=sUrl.substring(iFilePathStartIndex);
        sPathwayFilePath=sPathwayFilePath.replaceFirst("String_Node_Str","String_Node_Str");
        System.out.println("String_Node_Str" + sPathwayFilePath);
        int iPathwayIdIndex=sUrl.lastIndexOf("String_Node_Str") + 5;
        System.out.println("String_Node_Str" + iPathwayIdIndex);
        iPathwayId=StringConversionTool.convertStringToInt(sUrl.substring(iPathwayIdIndex,iPathwayIdIndex + 3),0);
        refGeneralManager.getSingelton().getLoggerManager().logMsg("String_Node_Str" + iPathwayId);
        loadPathwayFromFile("String_Node_Str" + sPathwayFilePath);
        bNeighbourhoodShown=false;
      }
 else {
        final IViewManager tmpViewManager=refGeneralManager.getSingelton().getViewGLCanvasManager();
        refEmbeddedFrameComposite.getDisplay().asyncExec(new Runnable(){
          public void run(){
            ((HTMLBrowserViewRep)tmpViewManager.getItem(iHTMLBrowserId)).setUrl(sUrl);
          }
        }
);
        if (bNeighbourhoodShown == true) {
          for (int iUndoCount=0; iUndoCount < iNeighbourhoodUndoCount; iUndoCount++) {
            refUndoManager.undo(refGraphLayoutCache);
          }
          iNeighbourhoodUndoCount=0;
          bNeighbourhoodShown=false;
        }
        showNeighbourhood(clickedCell,iNeighbourhoodDistance);
        bNeighbourhoodShown=true;
      }
      super.mousePressed(event);
    }
  }
  refGraphModel=new DefaultGraphModel();
  refGraphLayoutCache=new GraphLayoutCache(refGraphModel,new GPCellViewFactory(),true);
  refPathwayGraph=new JGraph(refGraphModel,refGraphLayoutCache);
  refPathwayGraph.setCloneable(true);
  refPathwayGraph.setMarqueeHandler(new PathwayMarqueeHandler());
  refUndoManager=new GraphUndoManager();
  refGraphModel.addUndoableEditListener(refUndoManager);
}

Fixed version (ground truth):
public void initView(){
class PathwayMarqueeHandler extends BasicMarqueeHandler {
    public boolean isForceMarqueeEvent(    MouseEvent event){
      if (SwingUtilities.isLeftMouseButton(event) && event.getClickCount() == 1)       return true;
 else       return super.isForceMarqueeEvent(event);
    }
    public void mousePressed(    final MouseEvent event){
      DefaultGraphCell clickedCell=(DefaultGraphCell)refPathwayGraph.getFirstCellForLocation(event.getX(),event.getY());
      if (clickedCell == null) {
        for (int iUndoCount=0; iUndoCount < iNeighbourhoodUndoCount; iUndoCount++) {
          refUndoManager.undo(refGraphLayoutCache);
        }
        iNeighbourhoodUndoCount=0;
        bNeighbourhoodShown=false;
        return;
      }
      if (clickedCell.getUserObject() == null) {
        super.mousePressed(event);
        return;
      }
      if (!clickedCell.getUserObject().getClass().getSimpleName().equals("String_Node_Str")) {
        super.mousePressed(event);
        return;
      }
      final String sUrl=((PathwayVertex)clickedCell.getUserObject()).getVertexLink();
      if (sUrl == "String_Node_Str") {
        super.mousePressed(event);
        return;
      }
      String sSearchPattern="String_Node_Str";
      String sPathwayFilePath;
      if (sUrl.contains((CharSequence)sSearchPattern)) {
        int iFilePathStartIndex=sUrl.lastIndexOf(sSearchPattern) + sSearchPattern.length();
        sPathwayFilePath=sUrl.substring(iFilePathStartIndex);
        sPathwayFilePath=sPathwayFilePath.replaceFirst("String_Node_Str","String_Node_Str");
        System.out.println("String_Node_Str" + sPathwayFilePath);
        int iPathwayIdIndex=sUrl.lastIndexOf("String_Node_Str") + 5;
        System.out.println("String_Node_Str" + iPathwayIdIndex);
        iPathwayId=StringConversionTool.convertStringToInt(sUrl.substring(iPathwayIdIndex,iPathwayIdIndex + 3),0);
        refGeneralManager.getSingelton().getLoggerManager().logMsg("String_Node_Str" + iPathwayId);
        loadPathwayFromFile("String_Node_Str" + sPathwayFilePath);
        bNeighbourhoodShown=false;
      }
 else {
        final IViewManager tmpViewManager=refGeneralManager.getSingelton().getViewGLCanvasManager();
        refEmbeddedFrameComposite.getDisplay().asyncExec(new Runnable(){
          public void run(){
            ((HTMLBrowserViewRep)tmpViewManager.getItem(iHTMLBrowserId)).setUrl(sUrl);
          }
        }
);
        if (bNeighbourhoodShown == true) {
          for (int iUndoCount=0; iUndoCount < iNeighbourhoodUndoCount; iUndoCount++) {
            refUndoManager.undo(refGraphLayoutCache);
          }
          iNeighbourhoodUndoCount=0;
          bNeighbourhoodShown=false;
        }
        showNeighbourhood(clickedCell,iNeighbourhoodDistance);
        bNeighbourhoodShown=true;
      }
      super.mousePressed(event);
    }
  }
  refGraphModel=new DefaultGraphModel();
  refGraphLayoutCache=new GraphLayoutCache(refGraphModel,new GPCellViewFactory(),true);
  refPathwayGraph=new JGraph(refGraphModel,refGraphLayoutCache);
  refPathwayGraph.setCloneable(true);
  refPathwayGraph.setMarqueeHandler(new PathwayMarqueeHandler());
  refUndoManager=new GraphUndoManager();
  refGraphModel.addUndoableEditListener(refUndoManager);
}