BamView.java

    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());
    colourByCoverageColour.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;
          logMenuItem.setEnabled(true);
        }
        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);
          logMenuItem.setEnabled(false);
        }
        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);
          logMenuItem.setEnabled(false);
        }
        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();
          logMenuItem.setEnabled(false);
        }
        repaint();
      }
    });
    viewMenu.add(checkBoxStrandStackView);  
    menu.add(viewMenu);
 
    final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNPs");
    // 
    JMenu colourMenu = new JMenu("Colour By");
    colourMenu.add(colourByCoverageColour);
    
    baseQualityColour.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        if(baseQualityColour.isSelected())
        {
          checkBoxSNPs.setSelected(false);
          isSNPs = false;
        }
        repaint();
      }
    });
    colourMenu.add(baseQualityColour);
    menu.add(colourMenu);
    
    //
    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);
    
    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);
    
    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("BamView 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);
        }
      });
    }
    
    menu.add(new JSeparator());
    logMenuItem.setFont(checkIsizeStackView.getFont());
    menu.add(logMenuItem);
    logMenuItem.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        logScale = logMenuItem.isSelected();
        repaint();
      }
    });
    
    JMenuItem filter = new JMenuItem("Filter by Flag...");
    menu.add(filter);
    filter.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        new SAMRecordFilter(BamView.this);
      } 
    });
    menu.add(new JSeparator());
  }
  
  public void setVisible(boolean visible)
  {
    super.setVisible(visible);
    mainPanel.setVisible(visible);
  }
  
  private void setViewportMidPoint()
  {
    Point p = jspView.getViewport().getLocation();
    p.y = (getHeight() - jspView.getViewport().getViewRect().height)/2;
    jspView.getViewport().setViewPosition(p);
  }
  
  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)(mainPanel.getWidth()/pixPerBase);
      jspView.getVerticalScrollBar().setValue(0);
      
      if(ruler == null)
        ruler = new Ruler();
      jspView.setColumnHeaderView(ruler);
      showBaseAlignment = true;
      baseQualityColour.setEnabled(true);
      markInsertions.setEnabled(true);
    }
    else if(jspView != null)
    {
      jspView.setColumnHeaderView(null);
      
      if(!isStrandStackView)
        jspView.getVerticalScrollBar().setValue(
            jspView.getVerticalScrollBar().getMaximum());
      showBaseAlignment = false;
      baseQualityColour.setEnabled(false);
      markInsertions.setEnabled(false);
    }
    
    if(scrollBar != null)
    {
      scrollBar.setValues(startValue, nbasesInView, 1, 
             getMaxBasesInPanel(getSequenceLength()));
      scrollBar.setUnitIncrement(nbasesInView/20);
      scrollBar.setBlockIncrement(nbasesInView);
    }
  }

  
  /**
   * 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);
    }
    
    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 handleCanvasMouseDrag(final MouseEvent event)
  {
    if(event.getButton() == MouseEvent.BUTTON3 || bases == null) 
      return;
    
    highlightSAMRecord = null;
    if(event.getClickCount() > 1)
    {
      getSelection().clear();
      repaint();
      return;  
    }
    
    highlightRange(event, 
        MouseEvent.BUTTON1_DOWN_MASK & MouseEvent.BUTTON2_DOWN_MASK);
  }
  
  /**
   * 
   * @param event
   * @param onmask
   */
  private void highlightRange(MouseEvent event, int onmask)
  {
    int seqLength = getSequenceLength();
    float pixPerBase = getPixPerBaseByWidth();
    int start = (int) ( ( (event.getPoint().getX())/pixPerBase) + getBaseAtStartOfView() );
    
    if(start < 1)
      start = 1;
    if(start > seqLength)
      start = seqLength;
    
    if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
      dragStart = start;
    else if((event.getModifiersEx() & onmask) != onmask)
      dragStart = -1;
    
    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();
    }
  }
  
  /**
   * Get the colour for the given read given to it by the coverage plot.
   * @param samRecord
   * @return
   */
  private Color getColourByCoverageColour(SAMRecord samRecord)
  {
    LineAttributes lines[] = CoveragePanel.getLineAttributes(bamList.size());
    int fileIndex = 0;
    if(bamList.size()>1)
      fileIndex = (Integer) samRecord.getAttribute("FL");
    return lines[fileIndex].getLineColour(); 
  }
  
  private Selection getSelection()
  {
    return selection;
  }
  
  protected List<SAMRecord> getReadsInView()
  {
    return readsInView;
  }
  
  protected int getBasesInView()
  {
    return nbasesInView;
  }
  
  private String getVersion()
  {
    final ClassLoader cl = this.getClass().getClassLoader();
    try
    {
      String line;
      InputStream in = cl.getResourceAsStream("etc/versions");
      BufferedReader reader = new BufferedReader(new InputStreamReader(in));
      while((line = reader.readLine()) != null)
      {
        if(line.startsWith("BamView"))
          return line.substring( "BamView".length() ).trim();
      }
      reader.close();
      in.close();
    }
    catch (Exception ex)
    {
    }
    return null;
  }
  
  /**
   * Artemis event notification
   */
  public void displayAdjustmentValueChanged(final DisplayAdjustmentEvent event)
  {
    if(!asynchronous)
    {
      // if not asynchronous
      displayAdjustmentWork(event);
      return;
    }
    
    SwingWorker worker = new SwingWorker()
    {
      public Object construct()
      {
        try
        {
          Thread.sleep(500);
        }
        catch (InterruptedException e)
        {
          e.printStackTrace();
        }
        
        if(event.getStart() != ((FeatureDisplay)event.getSource()).getForwardBaseAtLeftEdge())
        {
          waitingFrame.showWaiting("waiting...", mainPanel);
          return null;
        }
      
        displayAdjustmentWork(event);
        waitingFrame.setVisible(false);
        return null;
      }
    };
    worker.start();
  }
  
  /**
   * Carry out the display agjustment event action.
   * @param event
   */
  private void displayAdjustmentWork(final DisplayAdjustmentEvent event)
  {
    if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
    {
      laststart = -1;
      lastend = -1;
      BamView.this.startBase = event.getStart();
      BamView.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;
	JMenuItem showDetails;
	
    public void mouseClicked(MouseEvent e)
    {
      if(e.isPopupTrigger() ||
         e.getButton() == MouseEvent.BUTTON3)
        return;
      
      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();
          createMenus(popup);
        }
        
        if(gotoMateMenuItem != null)
          popup.remove(gotoMateMenuItem);

        if(showDetails != null)
          popup.remove(showDetails);
        
        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);
        }  
          
        if( mouseOverSAMRecord != null)
        {
          final SAMRecord thisSAMRecord = mouseOverSAMRecord;
          showDetails = new JMenuItem("Show details of : "+
              thisSAMRecord.getReadName());
          showDetails.addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e) 
            {
              FileViewer viewDetail = new FileViewer(thisSAMRecord.getReadName(), true, false);
              appendToDetailView(thisSAMRecord, viewDetail);
            }  
          });
          popup.add(showDetails);
        }
        popup.show(e.getComponent(),
                e.getX(), e.getY());
      }
    }
  }
  
  private void appendToDetailView(SAMRecord thisSAMRecord, FileViewer viewDetail)
  {
    viewDetail.appendString("Read Name             "+thisSAMRecord.getReadName()+"\n", Level.INFO);
    viewDetail.appendString("Coordinates           "+thisSAMRecord.getAlignmentStart()+".."+
                                                     thisSAMRecord.getAlignmentEnd()+"\n", Level.DEBUG);
    viewDetail.appendString("Length                "+thisSAMRecord.getReadLength()+"\n", Level.DEBUG);
    viewDetail.appendString("Reference Name        "+thisSAMRecord.getReferenceName()+"\n", Level.DEBUG);
    viewDetail.appendString("Inferred Size         "+thisSAMRecord.getInferredInsertSize()+"\n", Level.DEBUG);
    viewDetail.appendString("Mapping Quality       "+thisSAMRecord.getMappingQuality()+"\n", Level.DEBUG);
    
    if(thisSAMRecord.getProperPairFlag() && !thisSAMRecord.getMateUnmappedFlag())
    {
      viewDetail.appendString("Mate Reference Name   "+thisSAMRecord.getMateReferenceName()+"\n", Level.DEBUG);
      viewDetail.appendString("Mate Start Coordinate "+thisSAMRecord.getMateAlignmentStart()+"\n", Level.DEBUG);
      viewDetail.appendString("Strand (read/mate)    "+
        (thisSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
        (thisSAMRecord.getMateNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
    }
    else
    {
      viewDetail.appendString("Strand (read)         "+
          (thisSAMRecord.getReadNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
    }
    
    viewDetail.appendString("\n\nCigar String          "+thisSAMRecord.getCigarString(), Level.DEBUG);
    
    viewDetail.appendString("\n\nFlags:", Level.INFO);
    viewDetail.appendString("\nDuplicate Read    "+
        (thisSAMRecord.getDuplicateReadFlag() ? "yes" : "no"), Level.DEBUG);
    viewDetail.appendString("\nFirst of Pair     "+
        (thisSAMRecord.getFirstOfPairFlag() ? "yes" : "no"), Level.DEBUG);
    viewDetail.appendString("\nMate Unmapped     "+
        (thisSAMRecord.getMateUnmappedFlag() ? "yes" : "no"), Level.DEBUG);  
    viewDetail.appendString("\nProper Pair       "+
        (thisSAMRecord.getProperPairFlag() ? "yes" : "no"), Level.DEBUG);
    viewDetail.appendString("\nRead Fails Vendor\nQuality Check     "+
        (thisSAMRecord.getReadFailsVendorQualityCheckFlag() ? "yes" : "no"), Level.DEBUG);
    viewDetail.appendString("\nRead Unmapped     "+
        (thisSAMRecord.getReadUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
    viewDetail.appendString("\nSecond Of Pair    "+
        (thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
    
    viewDetail.appendString("\n\nRead Bases:\n", Level.INFO);
    viewDetail.appendString(new String(thisSAMRecord.getReadBases()), Level.DEBUG);
  }

  protected SAMRecordFlagPredicate getSamRecordFlagPredicate()
  {
    return samRecordFlagPredicate;
  }

  protected void setSamRecordFlagPredicate(
      SAMRecordFlagPredicate samRecordFlagPredicate)
  {
    laststart = -1;
    lastend = -1;
    this.samRecordFlagPredicate = samRecordFlagPredicate;
  }
  
  protected SAMRecordMapQPredicate getSamRecordMapQPredicate()
  {
    return samRecordMapQPredicate;
  }

  protected void setSamRecordMapQPredicate(
      SAMRecordMapQPredicate samRecordMapQPredicate)
  {
    laststart = -1;
    lastend = -1;
    this.samRecordMapQPredicate = samRecordMapQPredicate;
  }
  
  class PairedRead
  {
    SAMRecord sam1;
    SAMRecord sam2;
  }
  
  public static void main(String[] args)
  {
    List<String> bam = new Vector<String>();;
    String reference = null;
    if(args.length == 0)
    {
      FileSelectionDialog fileSelection = new FileSelectionDialog(null, true);
      bam = fileSelection.getBamFiles();
      reference = fileSelection.getReferenceFile();
      if(reference == null || reference.equals(""))
        reference = null;
    }
    else if(!args[0].startsWith("-"))
    {
      for(int i=0; i< args.length; i++)
        bam.add(args[i]);
    }
    int nbasesInView = 1000;

    for(int i=0;i<args.length; i++)
    {
      if(args[i].equals("-a"))
      {
        while(i < args.length-1 && !args[++i].startsWith("-"))
        {
          String filename = args[i];
          if(FileSelectionDialog.isListOfFiles(filename))
            bam.addAll(FileSelectionDialog.getListOfFiles(filename));
          else
            bam.add(filename);
        }
        --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 v"+view.getVersion());
    
    // 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);
  }
}