Program: 90990
Project: 90990
Buggy source:
public TrackSchemePanel(final TrackSchemeGraph<?,?> graph,final TrackSchemeHighlight highlight,final TrackSchemeSelection selection,final TrackSchemeOptions optional){
  super(new BorderLayout(),false);
  this.graph=graph;
  this.selection=selection;
  options=optional.values;
  graph.addGraphChangeListener(this);
  final int w=options.getWidth();
  final int h=options.getHeight();
  display=new InteractiveDisplayCanvasComponent<ScreenTransform>(w,h,options.getTransformEventHandlerFactory());
  display.addTransformListener(this);
  highlight.addHighlightListener(this);
  selection.addSelectionListener(this);
  graphOverlay=new DefaultTrackSchemeOverlay(highlight,optional);
  display.addOverlayRenderer(graphOverlay);
  display.addOverlayRenderer(new OverlayRenderer(){
    @Override public void setCanvasSize(    final int width,    final int height){
    }
    @Override public void drawOverlays(    final Graphics g){
      checkAnimate();
    }
  }
);
  screenTransform=new ScreenTransform();
  layout=new LineageTreeLayout(graph);
  entityAnimator=new ScreenEntityAnimator();
  painterThread=new PainterThread(this);
  flags=new Flags();
  display.addMouseMotionListener(new MouseOverListener(graphOverlay,highlight));
  final MouseSelectionHandler mouseSelectionHandler=new MouseSelectionHandler(graphOverlay,selection,display);
  display.addHandler(mouseSelectionHandler);
  display.addOverlayRenderer(mouseSelectionHandler);
  xScrollBar=new JScrollBar(JScrollBar.HORIZONTAL);
  yScrollBar=new JScrollBar(JScrollBar.VERTICAL);
  xScrollBar.addAdjustmentListener(new AdjustmentListener(){
    @Override public void adjustmentValueChanged(    final AdjustmentEvent e){
      if (ignoreScrollBarChanges)       return;
      final double s=xScrollBar.getValue() / xScrollScale;
synchronized (screenTransform) {
        screenTransform.shiftLayoutX(s - screenTransform.getMinX());
        display.getTransformEventHandler().setTransform(screenTransform);
      }
      flags.setTransformChanged();
      painterThread.requestRepaint();
    }
  }
);
  yScrollBar.addAdjustmentListener(new AdjustmentListener(){
    @Override public void adjustmentValueChanged(    final AdjustmentEvent e){
      if (ignoreScrollBarChanges)       return;
      final double s=yScrollBar.getValue() / yScrollScale;
synchronized (screenTransform) {
        screenTransform.shiftLayoutY(s - screenTransform.getMinY());
        display.getTransformEventHandler().setTransform(screenTransform);
      }
      flags.setTransformChanged();
      painterThread.requestRepaint();
    }
  }
);
  add(display,BorderLayout.CENTER);
  add(yScrollBar,BorderLayout.EAST);
  final JPanel xScrollPanel=new JPanel(new BorderLayout());
  xScrollPanel.add(xScrollBar,BorderLayout.CENTER);
  final int space=(Integer)UIManager.getDefaults().get("String_Node_Str");
  xScrollPanel.add(Box.createRigidArea(new Dimension(space,0)),BorderLayout.EAST);
  add(xScrollPanel,BorderLayout.SOUTH);
  painterThread.start();
}

Fixed version (ground truth):
public TrackSchemePanel(final TrackSchemeGraph<?,?> graph,final TrackSchemeHighlight highlight,final TrackSchemeSelection selection,final TrackSchemeOptions optional){
  super(new BorderLayout(),false);
  this.graph=graph;
  this.selection=selection;
  options=optional.values;
  graph.addGraphChangeListener(this);
  final int w=options.getWidth();
  final int h=options.getHeight();
  display=new InteractiveDisplayCanvasComponent<ScreenTransform>(w,h,options.getTransformEventHandlerFactory());
  display.addTransformListener(this);
  highlight.addHighlightListener(this);
  selection.addSelectionListener(this);
  graphOverlay=new DefaultTrackSchemeOverlay(graph,highlight,optional);
  display.addOverlayRenderer(graphOverlay);
  display.addOverlayRenderer(new OverlayRenderer(){
    @Override public void setCanvasSize(    final int width,    final int height){
    }
    @Override public void drawOverlays(    final Graphics g){
      checkAnimate();
    }
  }
);
  screenTransform=new ScreenTransform();
  layout=new LineageTreeLayout(graph);
  entityAnimator=new ScreenEntityAnimator();
  painterThread=new PainterThread(this);
  flags=new Flags();
  display.addMouseMotionListener(new MouseOverListener(graphOverlay,highlight));
  final MouseSelectionHandler mouseSelectionHandler=new MouseSelectionHandler(graphOverlay,selection,display);
  display.addHandler(mouseSelectionHandler);
  display.addOverlayRenderer(mouseSelectionHandler);
  xScrollBar=new JScrollBar(JScrollBar.HORIZONTAL);
  yScrollBar=new JScrollBar(JScrollBar.VERTICAL);
  xScrollBar.addAdjustmentListener(new AdjustmentListener(){
    @Override public void adjustmentValueChanged(    final AdjustmentEvent e){
      if (ignoreScrollBarChanges)       return;
      final double s=xScrollBar.getValue() / xScrollScale;
synchronized (screenTransform) {
        screenTransform.shiftLayoutX(s - screenTransform.getMinX());
        display.getTransformEventHandler().setTransform(screenTransform);
      }
      flags.setTransformChanged();
      painterThread.requestRepaint();
    }
  }
);
  yScrollBar.addAdjustmentListener(new AdjustmentListener(){
    @Override public void adjustmentValueChanged(    final AdjustmentEvent e){
      if (ignoreScrollBarChanges)       return;
      final double s=yScrollBar.getValue() / yScrollScale;
synchronized (screenTransform) {
        screenTransform.shiftLayoutY(s - screenTransform.getMinY());
        display.getTransformEventHandler().setTransform(screenTransform);
      }
      flags.setTransformChanged();
      painterThread.requestRepaint();
    }
  }
);
  add(display,BorderLayout.CENTER);
  add(yScrollBar,BorderLayout.EAST);
  final JPanel xScrollPanel=new JPanel(new BorderLayout());
  xScrollPanel.add(xScrollBar,BorderLayout.CENTER);
  final int space=(Integer)UIManager.getDefaults().get("String_Node_Str");
  xScrollPanel.add(Box.createRigidArea(new Dimension(space,0)),BorderLayout.EAST);
  add(xScrollPanel,BorderLayout.SOUTH);
  painterThread.start();
}