BamView.java

    int lstStart = 0;
    int lstEnd = 0;
    int baseAtStartOfView = getBaseAtStartOfView();
    g2.setColor(Color.blue);
    Rectangle r = jspView.getViewport().getViewRect();
    
    for(int i=0; i<readsInView.size(); i++)
    {
      SAMRecord samRecord = readsInView.get(i);
      int offset = getSequenceOffset(samRecord.getReferenceName());

      int recordStart = samRecord.getAlignmentStart()+offset;
      int recordEnd = samRecord.getAlignmentEnd()+offset;
      
      if(lstStart != recordStart || lstEnd != recordEnd)
      { 
        if (!samRecord.getReadPairedFlag() ||  // read is not paired in sequencing
            samRecord.getMateUnmappedFlag() )  // mate is unmapped )  // mate is unmapped 
          g2.setColor(Color.black);
        else
          g2.setColor(Color.blue);
        
        if(maxEnd < recordStart)
        {
          ypos = (getHeight() - scaleHeight)-2;
          maxEnd = recordEnd+2;
        }
        else
          ypos = ypos-2;
      }
      else
        g2.setColor(darkGreen);

      lstStart = recordStart;
      lstEnd   = recordEnd;
      
      if(ypos > r.getMaxY() || ypos < r.getMinY())
        continue;
      drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
    }
  }
  
  /**
   * Draw the reads as lines in vertical stacks. The reads are colour 
   * coded as follows:
   * 
   * blue  - reads are unique and are paired with a mapped mate
   * black - reads are unique and are not paired or have an unmapped mate
   * green - reads are duplicates
   * 
   * @param g2
   * @param seqLength
   * @param pixPerBase
   * @param start
   * @param end
   */
  private void drawStrandStackView(Graphics2D g2, 
                                   int seqLength, 
                                   float pixPerBase, 
                                   int start, 
                                   int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end);   
    BasicStroke stroke = new BasicStroke(
        1.3f,
        BasicStroke.CAP_BUTT, 
        BasicStroke.JOIN_MITER);
    
    int scaleHeight = 15;
    drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));

    int ymid = (getHeight()/ 2);
    // positive strand    
    drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -2, pixPerBase, stroke);
    
    // negative strand
    drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), 2, pixPerBase, stroke);
  }
  
  private void drawStrand(Graphics2D g2, 
                          boolean isStrandNegative, 
                          int scaleHeight,
                          int ymid,
                          int ystep,
                          float pixPerBase,
                          Stroke stroke)
  {
    int ypos = (getHeight() - scaleHeight);
    int maxEnd = 0;
    int lstStart = 0;
    int lstEnd = 0;
    int baseAtStartOfView = getBaseAtStartOfView();
    g2.setColor(Color.blue);
    Rectangle r = jspView.getViewport().getViewRect();
    
    for(int i=0; i<readsInView.size(); i++)
    {
      SAMRecord samRecord = readsInView.get(i);
      
      if( samRecord.getReadNegativeStrandFlag() == isStrandNegative )
      {
        int offset = getSequenceOffset(samRecord.getReferenceName());
        int recordStart = samRecord.getAlignmentStart()+offset;
        int recordEnd   = samRecord.getAlignmentEnd()+offset;
      
        if(lstStart != recordStart || lstEnd != recordEnd)
        { 
          if (!samRecord.getReadPairedFlag() ||   // read is not paired in sequencing
               samRecord.getMateUnmappedFlag() )  // mate is unmapped 
            g2.setColor(Color.black);
          else
            g2.setColor(Color.blue);
        
          if(maxEnd < recordStart)
          {
            ypos = ymid + ystep;
            maxEnd = recordEnd+2;
          }
          else
            ypos = ypos + ystep;
        }
        else
          g2.setColor(darkGreen);

        lstStart = recordStart;
        lstEnd   = recordEnd;
        
        if(ypos > r.getMaxY() || ypos < r.getMinY())
          continue;
        drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
      }
    }
  }
  
  /**
   * Draw the reads as lines in vertical stacks. The reads are colour 
   * coded as follows:
   * 
   * blue  - reads are unique and are paired with a mapped mate
   * black - reads are unique and are not paired or have an unmapped mate
   * green - reads are duplicates
   * 
   * @param g2
   * @param seqLength
   * @param pixPerBase
   * @param start
   * @param end
   */
  private void drawPairedStackView(Graphics2D g2, 
                                   int seqLength, 
                                   float pixPerBase, 
                                   int start, 
                                   int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end);
    if(isShowScale())
      drawScale(g2, start, end, pixPerBase, getHeight());
    
    Vector<PairedRead> pairedReads = new Vector<PairedRead>();
    for(int i=0; i<readsInView.size(); i++)
    {
      SAMRecord samRecord = readsInView.get(i);

      if( !samRecord.getReadPairedFlag() ||  // read is not paired in sequencing
          samRecord.getMateUnmappedFlag() )  // mate is unmapped
        continue;

      SAMRecord samNextRecord = null;      
      if(i < readsInView.size()-1)
      {
        samNextRecord = readsInView.get(++i);
        PairedRead pr = new PairedRead();
        if(samRecord.getReadName().equals(samNextRecord.getReadName()))
        { 
          if(samRecord.getAlignmentStart() < samNextRecord.getAlignmentStart())
          {
            pr.sam1 = samRecord;
            pr.sam2 = samNextRecord;
          }
          else
          {
            pr.sam2 = samRecord;
            pr.sam1 = samNextRecord;
          }
          
        }
        else
        {
          --i;
          pr.sam1 = samRecord;
          pr.sam2 = null;
        }
        pairedReads.add(pr);
      }
    }
    Collections.sort(pairedReads, new PairedReadComparator());
    
    Stroke originalStroke = new BasicStroke (1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND); 
    Stroke stroke =
            new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
    g2.setStroke(stroke);
    
    int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    int ypos = getHeight() - scaleHeight - 3;
    int lastEnd = 0;
    int baseAtStartOfView = getBaseAtStartOfView();
    Rectangle r = jspView.getViewport().getViewRect();
    
    for(int i=0; i<pairedReads.size(); i++)
    {
      PairedRead pr = pairedReads.get(i);
      
      if(pr.sam1.getAlignmentStart() > lastEnd)
      {
        ypos = getHeight() - scaleHeight - 3;
        
        if(pr.sam2 != null)
        {  
          lastEnd = pr.sam2.getAlignmentEnd();
        }
        else
          lastEnd = pr.sam1.getAlignmentEnd();
      }
      else
        ypos = ypos - 3;
      
      if(ypos > r.getMaxY() || ypos < r.getMinY())
        continue;
      
      g2.setStroke(originalStroke);
      g2.setColor(Color.LIGHT_GRAY);
      
      if(pr.sam2 != null)
      {
        drawTranslucentJointedLine(g2, 
                (int)((pr.sam1.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase),
                (int)((pr.sam2.getAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
      }
      else
      {
        if(!pr.sam1.getMateUnmappedFlag() &&
            pr.sam1.getMateReferenceName().equals(pr.sam1.getReferenceName()))
        {
          int prStart;
          
          if(pr.sam1.getAlignmentStart() > pr.sam1.getMateAlignmentStart())
            prStart = pr.sam1.getAlignmentEnd();
          else
            prStart = pr.sam1.getAlignmentStart();
            
          drawTranslucentJointedLine(g2, 
              (int)( (prStart-getBaseAtStartOfView())*pixPerBase),
              (int)( (pr.sam1.getMateAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
        }
      }
      
      if( pr.sam1.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
          ( pr.sam2 != null && pr.sam2.getReadNegativeStrandFlag() ) )
        g2.setColor(Color.red);
      else
        g2.setColor(Color.blue);
      drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView);
      
      if(pr.sam2 != null)
        drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView);
    }
  }
  
  
  /**
   * Draw a read that apparently has a read mate that is not in view.
   * @param g2
   * @param thisRead
   * @param ypos
   * @param pixPerBase
   * @param originalStroke
   * @param stroke
   */
  private void drawLoneRead(Graphics2D g2, SAMRecord samRecord, int ypos, 
      float pixPerBase, int baseAtStartOfView)
  {
    boolean offTheTop = false;
    int offset = getSequenceOffset(samRecord.getReferenceName());
    int thisStart = samRecord.getAlignmentStart()+offset;
    int thisEnd   = thisStart + samRecord.getReadString().length() -1;
    
    if(ypos <= 0)
    {
      offTheTop = true;
      ypos = samRecord.getReadString().length();
    }
      
    if(Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
    {
      g2.setColor(Color.LIGHT_GRAY);
      
      if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
      {
        int nextStart = 
          (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
        drawTranslucentLine(g2, 
          (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
      }
      else
      {
        int nextStart = 
            (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
        drawTranslucentLine(g2, 
            (int)((thisStart-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, ypos, baseAtStartOfView);
    
    if (isSNPs)
      showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
  }

  
  private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
  {
    g2.setColor(Color.black);
    g2.drawLine( 0, ypos-14,
                 (int)((end - getBaseAtStartOfView())*pixPerBase),   ypos-14);
    int interval = end-start;
    
    if(interval > 256000)
      drawTicks(g2, start, end, pixPerBase, 512000, ypos);
    else if(interval > 64000)
      drawTicks(g2, start, end, pixPerBase, 12800, ypos);
    else if(interval > 16000)
      drawTicks(g2, start, end, pixPerBase, 3200, ypos);
    else if(interval > 4000)
      drawTicks(g2, start, end, pixPerBase, 800, ypos);
    else if(interval > 1000)
      drawTicks(g2, start, end, pixPerBase, 400, ypos);
    else
      drawTicks(g2, start, end, pixPerBase, 100, ypos);
  }
  
  private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division, int ypos)
  {
    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, ypos-14,(int)x, ypos-12);
    }
    
    for(int m=markStart; m<end; m+=division)
    {
      x = (m-getBaseAtStartOfView())*pixPerBase;
      g2.drawString(Integer.toString(m), x, ypos-1);
      g2.drawLine((int)x, ypos-14,(int)x, ypos-11);
      
      sm = m+(division/2);
      
      if(sm < end)
      {
        x = (sm-getBaseAtStartOfView())*pixPerBase;
        g2.drawLine((int)x, ypos-14,(int)x, ypos-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 ypos
   * @param baseAtStartOfView
   */
  private void drawRead(Graphics2D g2, SAMRecord thisRead,
		                float pixPerBase,
		                int ypos,
		                int baseAtStartOfView)
  {
    int offset = getSequenceOffset(thisRead.getReferenceName());

    int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
    int thisEnd   = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
    
    if(highlightSAMRecord != null && 
       highlightSAMRecord.getReadName().equals(thisRead.getReadName()))
     {
       Stroke originalStroke = g2.getStroke();
       Stroke stroke =
         new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
       g2.setStroke(stroke);
       Color c = g2.getColor();
       g2.setColor(Color.black);
       g2.drawLine((int)( thisStart * pixPerBase), ypos,
                   (int)( thisEnd * pixPerBase), ypos);
       g2.setColor(c);
       g2.setStroke(originalStroke);
     }

    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);

      offset = offset - getBaseAtStartOfView();
      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) * pixPerBase), ypos + 2,
                        (int) ((refPos+offset) * 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));
    }
    else
    { 
      topPanel = new JMenuBar();
      frame.setJMenuBar((JMenuBar)topPanel);
    }
    
    if(seqNames.size() > 1)
    {
      int len = 0;
      for(int i=0; i<seqNames.size(); i++)
        len += seqLengths.get(seqNames.get(i));
    
      if(feature_display != null &&
         len == feature_display.getSequenceLength())
        concatSequences = true;
      else if(bases != null &&
          len == bases.getLength() )
        concatSequences = true;
    }

    // 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)
      {
        handleCanvasMouseDrag(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();
  }

  
  private void createMenus(JComponent menu)
  {   
    JMenu viewMenu = new JMenu("Views");
    ButtonGroup group = new ButtonGroup();
    final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
    final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
    final JCheckBoxMenuItem checkIsizeStackView = new JCheckBoxMenuItem("Inferred Size View", true);
    checkBoxStackView.setFont(checkIsizeStackView.getFont());
    baseQualityColour.setFont(checkIsizeStackView.getFont());
    markInsertions.setFont(checkIsizeStackView.getFont());
    
    group.add(checkBoxStackView);
    group.add(checkBoxPairedStackView);
    group.add(checkBoxStrandStackView);
    group.add(checkIsizeStackView);
    
    checkIsizeStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        
        if(checkIsizeStackView.isSelected())
        {
          isStackView = false;
          isPairedStackView = false;
          isStrandStackView = false;
        }
        repaint();
      }
    });
    viewMenu.add(checkIsizeStackView);
    
    
    checkBoxStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isStackView = !isStackView;
        
        if(isStackView)
        {
          isPairedStackView = !isStackView;
          isStrandStackView = !isStackView;
          checkBoxPairedStackView.setSelected(!isStackView);
          checkBoxStrandStackView.setSelected(!isStackView);
        }
        repaint();
      }
    });
    viewMenu.add(checkBoxStackView);
    

    checkBoxPairedStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isPairedStackView = !isPairedStackView;
        
        if(isPairedStackView)
        {
          isStackView = !isPairedStackView;
          isStrandStackView = !isPairedStackView;
          checkBoxStackView.setSelected(!isPairedStackView);
          checkBoxStrandStackView.setSelected(!isPairedStackView);
        }
        repaint();
      }
    });
    viewMenu.add(checkBoxPairedStackView);
    
    checkBoxStrandStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isStrandStackView = !isStrandStackView;
        
        if(isStrandStackView)
        {
          isStackView = !isStrandStackView;
          isPairedStackView = !isStrandStackView;
          checkBoxStackView.setSelected(!isStrandStackView);
          checkBoxPairedStackView.setSelected(!isStrandStackView);
          setViewportMidPoint();
        }
        repaint();
      }
    });
    viewMenu.add(checkBoxStrandStackView);  
    menu.add(viewMenu);
 
    JMenu showMenu = new JMenu("Show");
    JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
    checkBoxSingle.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        repaint();
        isSingle = !isSingle;
      }
    });
    showMenu.add(checkBoxSingle);

    final 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;
        
        if(isSNPs)
          baseQualityColour.setSelected(false);
        repaint();
      }
    });
    showMenu.add(checkBoxSNPs);
 
    baseQualityColour.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        if(baseQualityColour.isSelected())
        {
          checkBoxSNPs.setSelected(false);
          isSNPs = false;
        }
        repaint();
      }
    });
    showMenu.add(baseQualityColour);
    
    markInsertions.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        repaint();
      }
    });
    showMenu.add(markInsertions);
    showMenu.add(new JSeparator());
    
    JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
    checkBoxCoverage.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        isCoverage = !isCoverage;
        coveragePanel.setVisible(isCoverage);
        repaint();
      }
    });
    showMenu.add(checkBoxCoverage);
    menu.add(showMenu);
    
    if(feature_display != null)
    {
      final JCheckBoxMenuItem checkBoxSync =
        new JCheckBoxMenuItem("Asynchronous", asynchronous);
      checkBoxSync.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          asynchronous = checkBoxSync.isSelected();
        }
      });
      menu.add(checkBoxSync);
    }
    
    menu.add(new JSeparator());

    JMenu maxHeightMenu = new JMenu("Plot Height");
    menu.add(maxHeightMenu);

    final String hgts[] =
       {"500", "800", "1000", "1500", "2500", "5000", "50000"};
    
    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 void setViewportMidPoint()
  {
    Point p = jspView.getViewport().getLocation();