BamView.java

      g2.setStroke(originalStroke);
      g2.setColor(Color.LIGHT_GRAY);
      
      if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
      {
        int nextStart = 
            (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
        drawTranslucentLine(g2, 
            (int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
      }
      else
      {
        int nextStart = 
            (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
        drawTranslucentLine(g2, 
            (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
      }
    }
    
    if(offTheTop)
      g2.setColor(darkOrange); 
    else if(samRecord.getReadNegativeStrandFlag()) // strand of the query (1 for reverse)
      g2.setColor(Color.red);
    else
      g2.setColor(Color.blue);

 
    drawRead(g2, samRecord, pixPerBase, stroke, ypos);
    
    if (isSNPs)
      showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
  }

  
  private void drawScale(Graphics2D g2, int start, int end, float pixPerBase)
  {
    g2.setColor(Color.black);
    g2.drawLine( 0, getHeight()-14,
                 (int)((end - getBaseAtStartOfView())*pixPerBase),   getHeight()-14);
    int interval = end-start;
    
    if(interval > 256000)
      drawTicks(g2, start, end, pixPerBase, 512000);
    else if(interval > 64000)
      drawTicks(g2, start, end, pixPerBase, 12800);
    else if(interval > 16000)
      drawTicks(g2, start, end, pixPerBase, 3200);
    else if(interval > 4000)
      drawTicks(g2, start, end, pixPerBase, 800);
    else if(interval > 1000)
      drawTicks(g2, start, end, pixPerBase, 400);
    else
      drawTicks(g2, start, end, pixPerBase, 100);
  }
  
  private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division)
  {
    int markStart = (Math.round(start/division)*division);
    
    if(markStart < 1)
      markStart = 1;
    
    int sm = markStart-(division/2);
    float x;
    if(sm > start)
    {
      x = (sm-getBaseAtStartOfView())*pixPerBase;
      g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-12);
    }
    
    for(int m=markStart; m<end; m+=division)
    {
      x = (m-getBaseAtStartOfView())*pixPerBase;
      g2.drawString(Integer.toString(m), x, getHeight()-1);
      g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-11);
      
      sm = m+(division/2);
      
      if(sm < end)
      {
        x = (sm-getBaseAtStartOfView())*pixPerBase;
        g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-12);
      }
      
      if(m == 1)
        m = 0;
    }
  }
  
  /**
   * Draw a y-scale for inferred size (isize) of reads.
   * @param g2
   * @param xScaleHeight
   */
  private void drawYScale(Graphics2D g2, int xScaleHeight)
  {
    g2.setColor(Color.black);
    int maxY = getPreferredSize().height-xScaleHeight;
    
    for(int i=100; i<maxY; i+=100)
    {
      int ypos = getHeight()-i-xScaleHeight;
      g2.drawLine(0, ypos, 2, ypos);
      g2.drawString(Integer.toString(i), 3, ypos);
    }
  }
  
  /**
   * Draw a given read.
   * @param g2
   * @param thisRead
   * @param pixPerBase
   * @param stroke
   * @param ypos
   */
  private void drawRead(Graphics2D g2, SAMRecord thisRead,
		                float pixPerBase, Stroke stroke, int ypos)
  {
    int offset = getSequenceOffset(thisRead.getReferenceName());
    
    int thisStart = thisRead.getAlignmentStart()+offset-getBaseAtStartOfView();
    int thisEnd   = thisRead.getAlignmentEnd()+offset-getBaseAtStartOfView();
    g2.setStroke(stroke);
    g2.drawLine((int)( thisStart * pixPerBase), ypos,
                (int)( thisEnd * pixPerBase), ypos);

    // test if the mouse is over this read
    if(lastMousePoint != null)
    {
      if(lastMousePoint.getY()+2 > ypos && lastMousePoint.getY()-2 < ypos)
      if(lastMousePoint.getX() > thisStart * pixPerBase &&
         lastMousePoint.getX() < thisEnd * pixPerBase)
      {
        mouseOverSAMRecord = thisRead;
      }
    }
    
    if (isSNPs)
      showSNPsOnReads(g2, thisRead, pixPerBase, ypos, offset);
  }
  
  /**
   * Highlight a selected range
   * @param g2
   * @param pixPerBase
   * @param start
   * @param end
   */
  private void drawSelectionRange(Graphics2D g2, float pixPerBase, int start, int end)
  {
    if(getSelection() != null)
    {
      Range selectedRange = getSelection().getSelectionRange();

      if(selectedRange != null)
      {
        int rangeStart = selectedRange.getStart();
        int rangeEnd   = selectedRange.getEnd();
        
        if(end < rangeStart || start > rangeEnd)
          return;
        
        int x = (int) (pixPerBase*(rangeStart-getBaseAtStartOfView()));
        int width = (int) (pixPerBase*(rangeEnd-rangeStart+1));
        
        g2.setColor(Color.pink);
        g2.fillRect(x, 0, width, getHeight());
      }
    }
  }
  
  /**
   * Draw a translucent line
   * @param g2
   * @param start
   * @param end
   * @param ypos
   */
  private void drawTranslucentLine(Graphics2D g2, int start, int end, int ypos)
  {
    Composite origComposite = g2.getComposite();
    g2.setComposite(translucent);
    g2.drawLine(start, ypos, end, ypos);
    g2.setComposite(origComposite);
  }
  
  /**
   * Draw a translucent line
   * @param g2
   * @param start
   * @param end
   * @param ypos
   */
  private void drawTranslucentJointedLine(Graphics2D g2, int start, int end, int ypos)
  {
    Composite origComposite = g2.getComposite();
    g2.setComposite(translucent);
    
    int mid = (int) ((end-start)/2.f)+start;
    //g2.drawLine(start, ypos, end, ypos);
    g2.drawLine(start, ypos, mid, ypos-5);
    g2.drawLine(mid, ypos-5, end, ypos);
    g2.setComposite(origComposite);
  }
  
  /**
   * Display the SNPs for the given read.
   * @param g2
   * @param thisRead
   * @param pixPerBase
   * @param ypos
   */
  private void showSNPsOnReads(Graphics2D g2, SAMRecord thisRead,
                               float pixPerBase, int ypos, int offset)
  {
    int thisStart = thisRead.getAlignmentStart();
    int thisEnd   = thisRead.getAlignmentEnd();
    
    // use alignment blocks of the contiguous alignment of
    // subsets of read bases to a reference sequence
    List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
    try
    {
      char[] refSeq = bases.getSubSequenceC(
          new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
      byte[] readSeq = thisRead.getReadBases();

      Color col = g2.getColor();
      g2.setColor(Color.red);

      for(int i=0; i<blocks.size(); i++)
      {
        AlignmentBlock block = blocks.get(i);
        for(int j=0; j<block.getLength(); j++)
        {
          int readPos = block.getReadStart()-1+j;
          int refPos  = block.getReferenceStart()+j;

          if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
          {
            g2.drawLine((int) ((refPos+offset-getBaseAtStartOfView()) * pixPerBase), ypos + 2,
                        (int) ((refPos+offset-getBaseAtStartOfView()) * pixPerBase), ypos - 2);
          }
        }
        
      }

      g2.setColor(col);
    }
    catch (OutOfRangeException e)
    {
      e.printStackTrace();
    }
  }
  
  /**
   * Add the alignment view to the supplied <code>JPanel</code> in
   * a <code>JScrollPane</code>.
   * @param mainPanel  panel to add the alignment to
   * @param autohide automatically hide the top panel containing the buttons
   */
  public void addJamToPanel(final JPanel mainPanel,
                            final JFrame frame,
                            final boolean autohide,
                            final FeatureDisplay feature_display)
  {
    this.mainPanel = mainPanel;
    final JComponent topPanel;
    if(feature_display != null)
    {
      this.feature_display = feature_display;
      this.selection = feature_display.getSelection();
      topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
      
      if(seqNames.size() > 1)
      {
        int len = 0;
        for(int i=0; i<seqNames.size(); i++)
          len += seqLengths.get(seqNames.get(i));
      
        if(len == feature_display.getSequenceLength())
          concatSequences = true;
      }
    }
    else
    { 
      topPanel = new JMenuBar();
      frame.setJMenuBar((JMenuBar)topPanel);
    }

    // auto hide top panel
    final JCheckBox buttonAutoHide = new JCheckBox("Hide", autohide);
    buttonAutoHide.setToolTipText("Auto-Hide");
    final MouseMotionListener mouseMotionListener = new MouseMotionListener()
    {
      public void mouseDragged(MouseEvent event)
      {
        handleCanvasMouseDragOrClick(event);
      }
      
      public void mouseMoved(MouseEvent e)
      {
        lastMousePoint = e.getPoint();
        
        int thisHgt = HEIGHT;
        if (thisHgt < 5)
          thisHgt = 15;

        int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
        if (y < thisHgt)
        {
          topPanel.setVisible(true);
        }
        else
        {
          if (buttonAutoHide.isSelected())
            topPanel.setVisible(false);
        }
        mainPanel.repaint();
        mainPanel.revalidate();
      }
    };
    addMouseMotionListener(mouseMotionListener);

    combo = new JComboBox(seqNames);
    combo.setEditable(false);
    combo.addItemListener(new ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        laststart = -1;
        lastend = -1;
        setZoomLevel(BamView.this.nbasesInView);
      }
    });
    topPanel.add(combo);

    if(feature_display == null)
    {
      final JTextField baseText = new JTextField(8);
      JButton goTo = new JButton("GoTo:");
      goTo.setToolTipText("Go to base position");
      goTo.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          try
          {
            int basePosition = Integer.parseInt(baseText.getText());
            scrollBar.setValue(basePosition);
          }
          catch (NumberFormatException nfe)
          {
            JOptionPane.showMessageDialog(BamView.this,
                "Expecting a base number!", "Number Format",
                JOptionPane.WARNING_MESSAGE);
          }
        }
      });
      topPanel.add(goTo);
      topPanel.add(baseText);

      JButton zoomIn = new JButton("-");
      Insets ins = new Insets(1,1,1,1);
      zoomIn.setMargin(ins);
      zoomIn.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
        }
      });
      topPanel.add(zoomIn);

      JButton zoomOut = new JButton("+");
      zoomOut.setMargin(ins);
      zoomOut.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          if (showBaseAlignment)
            return;
          setZoomLevel((int) (BamView.this.nbasesInView * .9));
        }
      });
      topPanel.add(zoomOut);
    }
    
    topPanel.add(buttonAutoHide);

    mainPanel.setPreferredSize(new Dimension(900, 400));
    
    jspView = new JScrollPane(this, 
        JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
        JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);

    setDisplay(1, nbasesInView, null);
    mainPanel.setLayout(new BorderLayout());

    if(topPanel instanceof JPanel)
      mainPanel.add(topPanel, BorderLayout.NORTH);
    mainPanel.add(jspView, BorderLayout.CENTER);
    
    JPanel bottomPanel = new JPanel(new BorderLayout());
    
    
    coveragePanel = new CoveragePanel(this);
    bottomPanel.add(coveragePanel, BorderLayout.CENTER);

    if(feature_display == null)
    {
      scrollBar = new JScrollBar(JScrollBar.HORIZONTAL, 1, nbasesInView, 1,
          getMaxBasesInPanel(getSequenceLength()));
      scrollBar.setUnitIncrement(nbasesInView/20);
      scrollBar.addAdjustmentListener(new AdjustmentListener()
      {
        public void adjustmentValueChanged(AdjustmentEvent e)
        {
          repaint();
        }
      });
      bottomPanel.add(scrollBar, BorderLayout.SOUTH);
    }

    mainPanel.add(bottomPanel, BorderLayout.SOUTH);
    coveragePanel.setPreferredSize(new Dimension(900, 100));
    coveragePanel.setVisible(false);
    
    jspView.getVerticalScrollBar().setValue(
        jspView.getVerticalScrollBar().getMaximum());
    jspView.getVerticalScrollBar().setUnitIncrement(maxUnitIncrement);
    
    if(feature_display == null)
    {
      addKeyListener(new KeyAdapter()
      {
        public void keyPressed(final KeyEvent event)
        {
          switch (event.getKeyCode())
          {
          case KeyEvent.VK_UP:
            setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
            break;
          case KeyEvent.VK_DOWN:
            if (showBaseAlignment)
              break;
            setZoomLevel((int) (BamView.this.nbasesInView * .9));
            break;
          default:
            break;
          }
        }
      });
    }

    addMouseListener(new PopupListener());
    setFocusable(true);
    requestFocusInWindow();
    addFocusListener(new FocusListener()
    {
      public void focusGained(FocusEvent fe){}
      public void focusLost(FocusEvent fe){}
    });
  }

  
  private void createViewMenu(JComponent view)
  {
    JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
    checkBoxSingle.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        repaint();
        isSingle = !isSingle;
      }
    });
    view.add(checkBoxSingle);

    JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNPs");
    checkBoxSNPs.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        if (isSNPs && bases == null)
        {
          JOptionPane.showMessageDialog(null,
              "No reference sequence supplied to identify SNPs.", "SNPs",
              JOptionPane.INFORMATION_MESSAGE);
        }
        isSNPs = !isSNPs;
        repaint();
      }
    });
    view.add(checkBoxSNPs);
    
    final JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
    final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
    
    checkBoxStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isStackView = !isStackView;
        
        if(isStackView)
        {
          isPairedStackView = !isStackView;
          checkBoxPairedStackView.setSelected(!isStackView);
        }
        repaint();
      }
    });
    view.add(checkBoxStackView);
    

    checkBoxPairedStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isPairedStackView = !isPairedStackView;
        
        if(isPairedStackView)
        {
          isStackView = !isPairedStackView;
          checkBoxStackView.setSelected(!isPairedStackView);
        }
        repaint();
      }
    });
    view.add(checkBoxPairedStackView);
    
    
    JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
    checkBoxCoverage.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        isCoverage = !isCoverage;
        coveragePanel.setVisible(isCoverage);
        repaint();
      }
    });
    view.add(checkBoxCoverage);
    view.add(new JSeparator());
    
    JMenu maxHeightMenu = new JMenu("Plot Height");
    view.add(maxHeightMenu);
    
    final String hgts[] = 
       {"500", "800", "1000", "1500", "2500", "5000"};
    
    ButtonGroup bgroup = new ButtonGroup();
    for(int i=0; i<hgts.length; i++)
    {
      final String hgt = hgts[i];
      final JCheckBoxMenuItem maxHeightMenuItem = new JCheckBoxMenuItem(hgt);
      bgroup.add(maxHeightMenuItem);
      maxHeightMenuItem.setSelected(hgts[i].equals(Integer.toString(maxHeight)));
      maxHeightMenu.add(maxHeightMenuItem);
      maxHeightMenuItem.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          if(maxHeightMenuItem.isSelected())
            maxHeight = Integer.parseInt(hgt);
          int start = getBaseAtStartOfView();
          setDisplay(start, nbasesInView+start, null);
        }
      });
    }
  }
  
  public void setVisible(boolean visible)
  {
    super.setVisible(visible);
    mainPanel.setVisible(visible);
  }
  
  private int getBaseAtStartOfView()
  {
    if(feature_display != null)
      return feature_display.getForwardBaseAtLeftEdge();
    else
      return scrollBar.getValue();
  }
  
  /**
   * Set the panel size based on the number of bases visible
   * and repaint.
   * @param nbasesInView
   */
  private void setZoomLevel(final int nbasesInView)
  {
    int startValue = getBaseAtStartOfView();
    this.nbasesInView = nbasesInView;
    float pixPerBase = getPixPerBaseByWidth(); 

    if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
    {
      pixPerBase = ALIGNMENT_PIX_PER_BASE;
      this.nbasesInView = (int)(getPreferredSize().getWidth()/pixPerBase);
      jspView.getVerticalScrollBar().setValue(0);
      jspView.setColumnHeaderView(ruler);
      showBaseAlignment = true;
    }
    else if(jspView != null)
    {
      jspView.setColumnHeaderView(null);
      jspView.getVerticalScrollBar().setValue(
          jspView.getVerticalScrollBar().getMaximum());
      showBaseAlignment = false;
    }
    
    if(scrollBar != null)
    {
      scrollBar.setValues(startValue, nbasesInView, 1, 
             getMaxBasesInPanel(getSequenceLength()));
      scrollBar.setUnitIncrement(nbasesInView/20);
    }
  }
  

  
  /**
   * Set the start and end base positions to display.
   * @param start
   * @param end
   * @param event
   */
  public void setDisplay(int start,
                         int end,
                         DisplayAdjustmentEvent event)
  {
    this.startBase = start;
    this.endBase   = end;
    this.nbasesInView = end-start+1;
    lastMousePoint = null;

    float pixPerBase;
    if(jspView.getViewport().getViewRect().width > 0)
      pixPerBase = getPixPerBaseByWidth();
    else
    {
      if(feature_display == null)
        pixPerBase = 1000.f/(float)(end-start+1);
      else
        pixPerBase = feature_display.getWidth()/(float)(end-start+1);
    }

    if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
    {
      pixPerBase = ALIGNMENT_PIX_PER_BASE;
      jspView.getVerticalScrollBar().setValue(0);
      jspView.setColumnHeaderView(ruler);
      showBaseAlignment = true;
    }
    else if(jspView != null)
    {
      jspView.setColumnHeaderView(null);
      showBaseAlignment = false;
    }
    
    Dimension d = new Dimension();
    d.setSize(nbasesInView*pixPerBase, maxHeight);
    setPreferredSize(d);
    
    if(event == null)
    {
      this.startBase = -1;
      this.endBase   = -1;
    }
  }
  
  /**
   * Return an Artemis entry from a file 
   * @param entryFileName
   * @param entryGroup
   * @return
   * @throws NoSequenceException
   */
  private Entry getEntry(final String entryFileName, final EntryGroup entryGroup) 
                   throws NoSequenceException
  {
    final Document entry_document = DocumentFactory.makeDocument(entryFileName);
    final EntryInformation artemis_entry_information =
      Options.getArtemisEntryInformation();
    
    //System.out.println(entryFileName);
    final uk.ac.sanger.artemis.io.Entry new_embl_entry =
      EntryFileDialog.getEntryFromFile(null, entry_document,
                                       artemis_entry_information,
                                       false);

    if(new_embl_entry == null)  // the read failed
      return null;

    Entry entry = null;
    try
    {
      if(entryGroup.getSequenceEntry() != null)
        bases = entryGroup.getSequenceEntry().getBases();
      
      if(bases == null)
      {
        entry = new Entry(new_embl_entry);
        bases = entry.getBases();
      }
      else
        entry = new Entry(bases,new_embl_entry);
      
      entryGroup.add(entry);
    } 
    catch(OutOfRangeException e) 
    {
      new MessageDialog(null, "read failed: one of the features in " +
          entryFileName + " has an out of range " +
                        "location: " + e.getMessage());
    }
    return entry;
  }
  
  private boolean isShowScale()
  {
    return showScale;
  }

  public void setShowScale(boolean showScale)
  {
    this.showScale = showScale;
  }
  
  public JScrollPane getJspView()
  {
    return jspView;
  }
  
  public void setBases(Bases bases)
  {
    this.bases = bases;
  }
  
  /**
   * Remove JScrollPane border
   */
  public void removeBorder()
  {
    Border empty = new EmptyBorder(0,0,0,0);
    jspView.setBorder(empty);
  }
  
  /**
   *  Handle a mouse drag event on the drawing canvas.
   **/
  private void handleCanvasMouseDragOrClick(final MouseEvent event)
  {
    if(event.isShiftDown() || event.getButton() == MouseEvent.BUTTON3
        || bases == null) 
      return;
    
    if(event.getClickCount() > 1)
    {
      getSelection().clear();
      repaint();
      return;  
    }
    
    int onmask = MouseEvent.BUTTON1_DOWN_MASK;  
    int seqLength = getSequenceLength();
    float pixPerBase = getPixPerBaseByWidth();
    int start = (int) ( ( (event.getPoint().getX())/pixPerBase) + getBaseAtStartOfView() );
    
    if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
      dragStart = start;
    else if((event.getModifiersEx() & onmask) != onmask)
      dragStart = -1;

    if(start < 1)
      start = 1;
    if(start > seqLength)
      start = seqLength;
    
    MarkerRange drag_range;
    try
    {
      if(dragStart < 0)
        drag_range = new MarkerRange (bases.getForwardStrand(), start, start);
      else
        drag_range = new MarkerRange (bases.getForwardStrand(), dragStart, start);
      getSelection().setMarkerRange(drag_range);
      repaint();
    }
    catch (OutOfRangeException e)
    {
      e.printStackTrace();
    }
  }
  
  private Selection getSelection()
  {
    return selection;
  }
  
  public List<SAMRecord> getReadsInView()
  {
    return readsInView;
  }
  
  /**
   * 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 = 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(getPreferredSize().width, 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;

      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
  {
    public void mouseClicked(MouseEvent e)
    {
      BamView.this.requestFocus();
      handleCanvasMouseDragOrClick(e);
    }
    
    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);
        }
        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("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);
  }


}