Splash.java

    if(gcode_default != null)
    {
      String defS = (String)gcode_default.elementAt(0);
      if(defS.length() < 3)
      {
        try
        {
          int num = Integer.parseInt(defS);
          if(num > 0 && num <= gcodes.length)
            default_code = num-1;
          else
            System.err.println(defS+" is not a valid number");
        }
        catch(NumberFormatException nfe)
        {
          System.err.println(defS+" is not a valid number");
        }
      }
    }
    
    ButtonGroup gcodeGroup = new ButtonGroup();
    geneCode = new JCheckBoxMenuItem[gcodes.length];
    
    for(int i = 0; i< gcodes.length; i++)
    {
      if(gcodes[i].equals("-"))
        continue;

      int ind1; 
      while((ind1 = gcodes[i].indexOf("_")) > -1)
        gcodes[i] = gcodes[i].substring(0,ind1) + " " +
                    gcodes[i].substring(ind1+1,gcodes[i].length());

      String num = Integer.toString(i+1);
      final String gc_name = num+". "+gcodes[i];
      geneCode[i] = new JCheckBoxMenuItem(gc_name);
      gcodeGroup.add(geneCode[i]);
      final int menuNum = i;
      geneCode[i].setActionCommand(num);

      geneCode[i].addItemListener(new ItemListener()
      {
        public void itemStateChanged(ItemEvent event)
        {
          if(geneCode[menuNum].getState())
          {
            geneticCode = gc_name;
            String tab = "translation_table_"+geneCode[menuNum].getActionCommand();
            String startCodons = "start_codons_"+geneCode[menuNum].getActionCommand();

            StringVector options_file_table =
                         Options.getOptions().getOptionValues(tab);

            if(options_file_table != null)
            {
              if(options_file_table.size() == 64) 
              {
                StringBuffer sbuff = new StringBuffer();
                for(int i = 0; i < 64; ++i) 
                  sbuff.append(options_file_table.elementAt(i)+" ");

                Options.getOptions().setGeneticCode(sbuff.toString());
              }
              else
              {
                StringVector table = Options.getOptions().getOptionValues("translation_table_1");

                for(int i = 0; i < options_file_table.size(); ++i)
                {
                  String cod_plus_aa = (String)options_file_table.elementAt(i);
//                System.out.println(cod_plus_aa);
                  final int codon_index = Bases.getIndexOfBase(cod_plus_aa.charAt(0)) * 16 +
                                          Bases.getIndexOfBase(cod_plus_aa.charAt(1)) * 4 +
                                          Bases.getIndexOfBase(cod_plus_aa.charAt(2));

//                System.out.println(cod_plus_aa.substring(3)+"  "+codon_index+"  "+
//                                   table.elementAt(codon_index));
                  table.setElementAt(cod_plus_aa.substring(3), codon_index);
                }
                
                StringBuffer sbuff = new StringBuffer();
                for(int i = 0; i < 64; ++i)
                  sbuff.append(table.elementAt(i)+" ");

                Options.getOptions().setGeneticCode(sbuff.toString());
              }

              options_file_table =
                         Options.getOptions().getOptionValues(startCodons);

              if(options_file_table != null)
              {
                StringBuffer sbuff = new StringBuffer();
                for(int i = 0; i < options_file_table.size(); ++i)
                  sbuff.append(options_file_table.elementAt(i)+" ");
                
                Options.getOptions().setProperty("start_codons",sbuff.toString());
              }
            }
           
            AminoAcidSequence.setGeneCode();
 
            if(helix_canvas != null)
              helix_canvas.repaint();
          }
        }
      });
      options_menu.add(geneCode[i]);

      if(i == default_code)
        geneCode[i].setState(true);
    }
  }
  
  /**
   * Set the Genetic Code number
   * @param geneticCodeValue
   */
  public void setTranslationTable(final String geneticCodeValue)
  {
	for(int i=0;i<geneCode.length;i++)
	{
	  if(geneCode[i] == null)
		continue;

	  if( geneCode[i].getActionCommand().equals(geneticCodeValue) && 
	     !geneCode[i].getState() )
	  {  
		int val = JOptionPane.showConfirmDialog(null, 
		    		"Change translation table to:\n"+
		    		geneCode[i].getText(), 
			    	"Confirm Translation Table Change",
		    		JOptionPane.OK_CANCEL_OPTION);
		if(val == JOptionPane.CANCEL_OPTION)
		  return;
		logger4j.debug("SET GENETIC CODE translationTable="
					+ geneticCodeValue);
	    geneCode[i].setState(true);
		break; 
	  }
	}
  }
  
  /**
   *  Make a new menu item in the given menu, with its label given the
   *  String and add the given ActionListener to it.
   */
  protected static void makeMenuItem(JMenu menu, String name,
                                     ActionListener listener) 
  {
    JMenuItem new_item = new JMenuItem(name);
    menu.add(new_item);
    new_item.addActionListener(listener);
    if(name.equals("Open ..."))
      new_item.setAccelerator(KeyStroke.getKeyStroke
             (KeyEvent.VK_O, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask())); // InputEvent.CTRL_MASK));
  }

  /**
   *  Return a Logger for warnings/errors/messages.
   **/
  protected static Logger getLogger() 
  {
    return logger;
  }

  /**
   *  Return the JComponent that the Splash screen is drawing on.
   **/
  public JComponent getCanvas() 
  {
    return helix_canvas;
  }

  /**
   *  Make the LogViewer visible.
   **/
  public static void showLog() 
  {
    logger.setVisible(true);
  }

  /**
   *  An InputStreamProgressListener used to update the error label with the
   *  current number of chars read.
   **/
  private final InputStreamProgressListener stream_progress_listener =
    new InputStreamProgressListener() {
      public void progressMade(final InputStreamProgressEvent event) 
      {
        final int char_count = event.getCharCount();
        if(char_count == -1) 
          getStatusLabel().setText("");
        else 
          getStatusLabel().setText("chars read so far: " + char_count);
      }

      public void progressMade(String progress)
      {
        getStatusLabel().setText(progress);
      }

    };
}