Program: 56894
Project: 56894
Buggy source:
protected void registerListeners(){
  parentGLCanvas.addMouseListener(new IGLMouseListener(){
    @Override public void mouseWheelMoved(    IMouseEvent mouseEvent){
    }
    @Override public void mouseReleased(    IMouseEvent mouseEvent){
    }
    @Override public void mousePressed(    IMouseEvent mouseEvent){
    }
    @Override public void mouseMoved(    IMouseEvent mouseEvent){
      Point mousePosition=mouseEvent.getRAWPoint();
      if (pathwayRow.getVisibility() != EVisibility.NONE) {
        for (        PathwayMultiFormInfo info : pathwayInfos) {
          if (setWindowActive(mousePosition,info.window))           return;
        }
      }
      if (pathInfo != null && pathInfo.window != null && setWindowActive(mousePosition,pathInfo.window))       return;
      if (setWindowActive(mousePosition,rankingWindow))       return;
      if (setWindowActive(mousePosition,dataMappingWindow))       return;
    }
    private boolean setWindowActive(    Point mousePosition,    GLWindow window){
      Vec2f location=window.getAbsoluteLocation();
      Vec2f size=window.getSize();
      if ((mousePosition.x >= location.x() && mousePosition.x <= location.x() + size.x()) && (mousePosition.y >= location.y() && mousePosition.y <= location.y() + size.y())) {
        windowToSetActive=window;
        return true;
      }
      return false;
    }
    @Override public void mouseExited(    IMouseEvent mouseEvent){
    }
    @Override public void mouseEntered(    IMouseEvent mouseEvent){
    }
    @Override public void mouseDragged(    IMouseEvent mouseEvent){
    }
    @Override public void mouseClicked(    IMouseEvent mouseEvent){
    }
  }
);
  parentGLCanvas.addKeyListener(new IGLKeyListener(){
    @Override public void keyPressed(    IKeyEvent e){
      update(e);
      isControlKeyPressed=e.isControlDown();
    }
    @Override public void keyReleased(    IKeyEvent e){
      isControlKeyPressed=e.isControlDown();
    }
    private void update(    IKeyEvent e){
      boolean isPPressed=e.isKeyDown('p');
      if (isPPressed) {
        ShowPortalsEvent event=new ShowPortalsEvent(!showPortalsButton.isChecked());
        showPortalsButton.setChecked(!showPortalsButton.isChecked());
        event.setEventSpace(pathEventSpace);
        EventPublisher.INSTANCE.triggerEvent(event);
      }
      boolean iswPressed=e.isKeyDown('w');
      if (iswPressed) {
        if (showSrcWindowLinks)         showSrcWindowLinks=false;
 else         showSrcWindowLinks=true;
      }
    }
  }
);
}

Fixed version (ground truth):
protected void registerListeners(){
  parentGLCanvas.addMouseListener(new IGLMouseListener(){
    @Override public void mouseWheelMoved(    IMouseEvent mouseEvent){
    }
    @Override public void mouseReleased(    IMouseEvent mouseEvent){
    }
    @Override public void mousePressed(    IMouseEvent mouseEvent){
    }
    @Override public void mouseMoved(    IMouseEvent mouseEvent){
      Vec2f mousePosition=mouseEvent.getDIPPoint();
      if (pathwayRow.getVisibility() != EVisibility.NONE) {
        for (        PathwayMultiFormInfo info : pathwayInfos) {
          if (setWindowActive(mousePosition,info.window))           return;
        }
      }
      if (pathInfo != null && pathInfo.window != null && setWindowActive(mousePosition,pathInfo.window))       return;
      if (setWindowActive(mousePosition,rankingWindow))       return;
      if (setWindowActive(mousePosition,dataMappingWindow))       return;
    }
    private boolean setWindowActive(    Vec2f mousePosition,    GLWindow window){
      Vec2f location=window.getAbsoluteLocation();
      Vec2f size=window.getSize();
      if ((mousePosition.x() >= location.x() && mousePosition.x() <= location.x() + size.x()) && (mousePosition.y() >= location.y() && mousePosition.y() <= location.y() + size.y())) {
        windowToSetActive=window;
        return true;
      }
      return false;
    }
    @Override public void mouseExited(    IMouseEvent mouseEvent){
    }
    @Override public void mouseEntered(    IMouseEvent mouseEvent){
    }
    @Override public void mouseDragged(    IMouseEvent mouseEvent){
    }
    @Override public void mouseClicked(    IMouseEvent mouseEvent){
    }
  }
);
  parentGLCanvas.addKeyListener(new IGLKeyListener(){
    @Override public void keyPressed(    IKeyEvent e){
      update(e);
      isControlKeyPressed=e.isControlDown();
    }
    @Override public void keyReleased(    IKeyEvent e){
      isControlKeyPressed=e.isControlDown();
    }
    private void update(    IKeyEvent e){
      boolean isPPressed=e.isKeyDown('p');
      if (isPPressed) {
        ShowPortalsEvent event=new ShowPortalsEvent(!showPortalsButton.isChecked());
        showPortalsButton.setChecked(!showPortalsButton.isChecked());
        event.setEventSpace(pathEventSpace);
        EventPublisher.INSTANCE.triggerEvent(event);
      }
      boolean iswPressed=e.isKeyDown('w');
      if (iswPressed) {
        if (showSrcWindowLinks)         showSrcWindowLinks=false;
 else         showSrcWindowLinks=true;
      }
    }
  }
);
}