BamView.java

    {
      laststart = -1;
      lastend = -1;
      this.startBase = event.getStart();
      this.endBase   = event.getEnd();

      int width = feature_display.getMaxVisibleBases();
      setZoomLevel(width);
      repaint();
    }
    else
    {
      setDisplay(event.getStart(), 
          event.getStart()+feature_display.getMaxVisibleBases(), event);
      repaint();
    }
  }
  
  public void selectionChanged(SelectionChangeEvent event)
  {
    repaint();
  }
  
  private class Ruler extends JPanel
  {
    private static final long serialVersionUID = 1L;
    int start;
    int end;

    public Ruler()
    {
      super();
      setPreferredSize(new Dimension(mainPanel.getWidth(), 15));
      setBackground(Color.white);
      setFont(getFont().deriveFont(11.f));
    }

    public void paintComponent(Graphics g)
    {
      super.paintComponent(g);
      Graphics2D g2 = (Graphics2D)g;
      drawBaseScale(g2, start, end, 12);
    }

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

      if(end > getSequenceLength())
        end = getSequenceLength();
      
      for(int i=startMark; i<end; i+=10)
      {
        int xpos = (i-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);
      }
    }
  }
  
  /**
  * Popup menu listener
  */
  class PopupListener extends MouseAdapter
  {
	JMenuItem gotoMateMenuItem;
    public void mouseClicked(MouseEvent e)
    {
      BamView.this.requestFocus();
      
      if(e.getClickCount() > 1)
        getSelection().clear(); 
      else if(e.getButton() == MouseEvent.BUTTON1)
        highlightSAMRecord = mouseOverSAMRecord;
      else
        highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
      repaint();
    }
    
    public void mousePressed(MouseEvent e)
    {
      maybeShowPopup(e);
    }

    public void mouseReleased(MouseEvent e)
    {
      dragStart = -1;
      maybeShowPopup(e);
    }

    private void maybeShowPopup(MouseEvent e)
    {
      if(e.isPopupTrigger())
      {
        if(popup == null)
        {
          popup = new JPopupMenu();
          createViewMenu(popup);
        }
        
        if(gotoMateMenuItem != null)
          popup.remove(gotoMateMenuItem);
        
        if( mouseOverSAMRecord != null && 
            mouseOverSAMRecord.getReadPairedFlag() &&
           !mouseOverSAMRecord.getMateUnmappedFlag() )
        {
          final SAMRecord thisSAMRecord = mouseOverSAMRecord;
          gotoMateMenuItem = new JMenuItem("Go to mate of : "+
              thisSAMRecord.getReadName());
          gotoMateMenuItem.addActionListener(new ActionListener()
          {
			public void actionPerformed(ActionEvent e) 
			{
			  String name = thisSAMRecord.getMateReferenceName();
			  if(name.equals("="))
			    name = thisSAMRecord.getReferenceName();
			  int offset = getSequenceOffset(name);
			  if(feature_display != null)
			    feature_display.makeBaseVisible(
			        thisSAMRecord.getMateAlignmentStart()+offset);
			  else
			    scrollBar.setValue(
			        thisSAMRecord.getMateAlignmentStart()+offset-
			        (nbasesInView/2));
			  
			  highlightSAMRecord = thisSAMRecord; 
			}  
          });
          popup.add(gotoMateMenuItem);
        }
        popup.show(e.getComponent(),
                e.getX(), e.getY());
      }
    }
  }
  
  class PairedRead
  {
    SAMRecord sam1;
    SAMRecord sam2;
  }
  
  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 BamView view = new BamView(bam, reference, nbasesInView);
    JFrame frame = new JFrame("BamView");
    
    // 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);
  }


}