Program: 16745
Project: 16745
Buggy source:
public BiojavaJmol(){
  frame=new JFrame();
  JMenuBar menu=MenuCreator.initMenu();
  frame.setJMenuBar(menu);
  frame.addWindowListener(new WindowAdapter(){
    @Override public void windowClosing(    WindowEvent e){
      frame.dispose();
    }
  }
);
  Container contentPane=frame.getContentPane();
  Box vBox=Box.createVerticalBox();
  jmolPanel=new JmolPanel();
  jmolPanel.setPreferredSize(new Dimension(500,500));
  vBox.add(jmolPanel);
  JTextField field=new JTextField();
  field.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  field.setText("String_Node_Str");
  org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener listener=new org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener(jmolPanel,field);
  field.addActionListener(listener);
  field.addMouseListener(listener);
  field.addKeyListener(listener);
  vBox.add(field);
  Box hBox1=Box.createHorizontalBox();
  String[] styles=new String[]{"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"};
  JComboBox style=new JComboBox(styles);
  hBox1.add(new JLabel("String_Node_Str"));
  hBox1.add(style);
  vBox.add(hBox1);
  style.addActionListener(jmolPanel);
  String[] colorModes=new String[]{"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"};
  JComboBox colors=new JComboBox(colorModes);
  colors.addActionListener(jmolPanel);
  hBox1.add(Box.createGlue());
  hBox1.add(new JLabel("String_Node_Str"));
  hBox1.add(colors);
  Box hBox2=Box.createHorizontalBox();
  JButton resetDisplay=new JButton("String_Node_Str");
  resetDisplay.addActionListener(new ActionListener(){
    @Override public void actionPerformed(    ActionEvent e){
      System.out.println("String_Node_Str");
      jmolPanel.executeCmd("String_Node_Str");
    }
  }
);
  hBox2.add(resetDisplay);
  hBox2.add(Box.createGlue());
  JCheckBox toggleSelection=new JCheckBox("String_Node_Str");
  toggleSelection.addItemListener(new ItemListener(){
    @Override public void itemStateChanged(    ItemEvent e){
      boolean showSelection=(e.getStateChange() == ItemEvent.SELECTED);
      if (showSelection) {
        jmolPanel.executeCmd("String_Node_Str");
      }
 else {
        jmolPanel.executeCmd("String_Node_Str");
      }
    }
  }
);
  hBox2.add(toggleSelection);
  hBox2.add(Box.createGlue());
  vBox.add(hBox2);
  contentPane.add(vBox);
  frame.pack();
  frame.setVisible(true);
}

Fixed version (ground truth):
public BiojavaJmol(){
  frame=new JFrame();
  JMenuBar menu=MenuCreator.initMenu();
  frame.setJMenuBar(menu);
  frame.addWindowListener(new WindowAdapter(){
    @Override public void windowClosing(    WindowEvent e){
      frame.dispose();
    }
  }
);
  Container contentPane=frame.getContentPane();
  Box vBox=Box.createVerticalBox();
  jmolPanel=new JmolPanel();
  jmolPanel.setPreferredSize(new Dimension(500,500));
  vBox.add(jmolPanel);
  JTextField field=new JTextField();
  field.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  field.setText("String_Node_Str");
  org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener listener=new org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener(jmolPanel,field);
  field.addActionListener(listener);
  field.addMouseListener(listener);
  field.addKeyListener(listener);
  vBox.add(field);
  Box hBox1=Box.createHorizontalBox();
  hBox1.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  String[] styles=new String[]{"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"};
  JComboBox style=new JComboBox(styles);
  hBox1.add(new JLabel("String_Node_Str"));
  hBox1.add(style);
  vBox.add(hBox1);
  style.addActionListener(jmolPanel);
  String[] colorModes=new String[]{"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"};
  JComboBox colors=new JComboBox(colorModes);
  colors.addActionListener(jmolPanel);
  hBox1.add(Box.createGlue());
  hBox1.add(new JLabel("String_Node_Str"));
  hBox1.add(colors);
  Box hBox2=Box.createHorizontalBox();
  hBox2.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  JButton resetDisplay=new JButton("String_Node_Str");
  resetDisplay.addActionListener(new ActionListener(){
    @Override public void actionPerformed(    ActionEvent e){
      System.out.println("String_Node_Str");
      jmolPanel.executeCmd("String_Node_Str");
    }
  }
);
  hBox2.add(resetDisplay);
  hBox2.add(Box.createGlue());
  JCheckBox toggleSelection=new JCheckBox("String_Node_Str");
  toggleSelection.addItemListener(new ItemListener(){
    @Override public void itemStateChanged(    ItemEvent e){
      boolean showSelection=(e.getStateChange() == ItemEvent.SELECTED);
      if (showSelection) {
        jmolPanel.executeCmd("String_Node_Str");
      }
 else {
        jmolPanel.executeCmd("String_Node_Str");
      }
    }
  }
);
  hBox2.add(toggleSelection);
  hBox2.add(Box.createGlue());
  vBox.add(hBox2);
  contentPane.add(vBox);
  frame.pack();
  frame.setVisible(true);
}