JamView.java

              * maxUnitIncrement
              - currentPosition;
    }
  }
  
  /**
   * Artemis event notification
   */
  public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
  {
    if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
    {
      laststart = -1;
      lastend = -1;
      this.startBase = event.getStart();
      this.endBase   = event.getEnd();
      
      //int width = event.getEnd()-event.getStart()+1;
      int width = feature_display.getMaxVisibleBases();
      //System.out.println("displayAdjustmentValueChanged() "+event.getStart()+".."+event.getEnd()+"  +width");

      setZoomLevel(width);
      goToBasePosition(event.getStart());
      setDisplay(event.getStart(), event.getEnd(), event);
      repaint();
    }
    else
    {
      setDisplay(event.getStart(), event.getEnd(), event);
      repaint();
    }
  }
  
  public void selectionChanged(SelectionChangeEvent event)
  {
    repaint();
  }
  
  
  
  public static void main(String[] args)
  {
    String bam = args[0];
    int nbasesInView = 1000;
    String reference = null;
    
    for(int i=0;i<args.length; i++)
    {
      if(args[i].equals("-a"))
        bam = args[++i];
      else if(args[i].equals("-r"))
        reference = args[++i];
      else if(args[i].equals("-v"))
        nbasesInView = Integer.parseInt(args[++i]);
      else if(args[i].equals("-s"))
        System.setProperty("samtoolDir", args[++i]);
      else if(args[i].startsWith("-h"))
      { 
        System.out.println("-h\t show help");
        
        System.out.println("-a\t BAM/SAM file to display");
        System.out.println("-r\t reference file (optional)");
        System.out.println("-v\t number of bases to display in the view (optional)");
        /*System.out.println("-s\t samtool directory");*/

        System.exit(0);
      }
    }

    final JamView view = new JamView(bam, reference, nbasesInView);
    JFrame frame = new JFrame("JAM");
    
    // translucent
    //frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f));

    frame.addWindowFocusListener(new WindowFocusListener()
    {
      public void windowGainedFocus(WindowEvent e)
      {
        view.requestFocus();
      }
      public void windowLostFocus(WindowEvent e){}
    });
    
    view.addJamToPanel((JPanel)frame.getContentPane(), frame, false, null);
    frame.pack();

    view.jspView.getVerticalScrollBar().setValue(
        view.jspView.getVerticalScrollBar().getMaximum());
    frame.setVisible(true);
  }


}