JamView.java

    private void drawBaseScale(Graphics2D g2, int start, int end, int ypos)
    {
      int startMark = (((int)(start/10))*10)+1;

      for(int i=startMark; i<end; i+=10)
      {
        int xpos = (i-1-start)*ALIGNMENT_PIX_PER_BASE;
        g2.drawString(Integer.toString(i), xpos, ypos);
        
        xpos+=(ALIGNMENT_PIX_PER_BASE/2);
        g2.drawLine(xpos, ypos+1, xpos, ypos+5);
      }
    }
  }
  
  class SAMRecordComparator implements Comparator<Object>
  {
    public int compare(Object o1, Object o2) 
    {
      SAMRecord pr1 = (SAMRecord) o1;
      SAMRecord pr2 = (SAMRecord) o2;
      
      int cmp = pr1.getReadName().compareTo(pr2.getReadName());
      
      if(cmp == 0)
      {
        if(pr1.getAlignmentStart() < pr2.getAlignmentStart())
          return -1;
        else
          return 1;
      }
      return cmp;
    }
  }


  public Dimension getPreferredScrollableViewportSize()
  {
    return getPreferredSize();
  }

  public int getScrollableBlockIncrement(Rectangle visibleRect,
      int orientation, int direction)
  {
    if (orientation == SwingConstants.HORIZONTAL)
      return visibleRect.width - maxUnitIncrement;
    else 
      return visibleRect.height - maxUnitIncrement;
  }

  public boolean getScrollableTracksViewportHeight()
  {
    return false;
  }

  public boolean getScrollableTracksViewportWidth()
  {
    return false;
  }

  public int getScrollableUnitIncrement(Rectangle visibleRect, int orientation,
                                        int direction)
  {
  //Get the current position.
    int currentPosition = 0;
    if (orientation == SwingConstants.HORIZONTAL) 
        currentPosition = visibleRect.x;
    else 
        currentPosition = visibleRect.y;

    //Return the number of pixels between currentPosition
    //and the nearest tick mark in the indicated direction.
    if (direction < 0)
    {
      int newPosition = currentPosition -
                        (currentPosition / maxUnitIncrement)
                         * maxUnitIncrement;
      return (newPosition == 0) ? maxUnitIncrement : newPosition;
    } 
    else 
    {
      return ((currentPosition / maxUnitIncrement) + 1)
              * maxUnitIncrement
              - currentPosition;
    }
  }
  
  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");
    
    frame.addWindowFocusListener(new WindowFocusListener()
    {
      public void windowGainedFocus(WindowEvent e)
      {
        view.requestFocus();
      }
      public void windowLostFocus(WindowEvent e){}
    });
    
    view.addJamToPanel((JPanel)frame.getContentPane());
    frame.pack();

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