BamView.java

          null, true, "BamView", "BAM");
      bam = fileSelection.getFiles(BAM_SUFFIX); 
      reference = fileSelection.getReferenceFile();
      if(reference == null || reference.equals(""))
        reference = null;
      
      if(bam == null || bam.size() < 1)
      {
        if(args.length > 0 && args[0].equals("NEW-BAMVIEW"))
          return;
        System.err.println("No files found.");
        System.exit(0);
      }
    }
    else if(!args[0].startsWith("-"))
    {
      for(int i=0; i< args.length; i++)
        bam.add(args[i]);
    }
    int nbasesInView = 2000;
    String chr = null;
    String vw  = null;
    boolean orientation = false;
    boolean covPlot     = false;
    boolean snpPlot     = false;
    int base = 0;
    
    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("-n"))
        nbasesInView = Integer.parseInt(args[++i]);
      else if(args[i].equals("-s"))
        System.setProperty("samtoolDir", args[++i]);
      else if(args[i].equals("-c"))
        chr = args[++i].trim();
      else if(args[i].equals("-b"))
        base = Integer.parseInt(args[++i].trim());
      else if(args[i].equals("-v"))
        vw = args[++i].trim();
      else if(args[i].equals("-o"))
        orientation = true;
      else if(args[i].equals("-pc"))
        covPlot = true;
      else if(args[i].equals("-ps"))
        snpPlot = true;
      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("-n\t number of bases to display in the view (optional)");
        System.out.println("-c\t chromosome name (optional)");
        System.out.println("-v\t view (optional - IS (inferred size), S (stack, default), PS (paired stack), ST (strand), C (coverage))");
        System.out.println("-b\t base position (optional)");
        System.out.println("-o\t show orientation (optional)");
        System.out.println("-pc\t plot coverage (optional)");
        System.out.println("-ps\t plot SNP (optional and only with -r)");
        System.exit(0);
      }
    }

    final BamView view = new BamView(bam, reference, nbasesInView, null, null,
        (JPanel)frame.getContentPane(), frame);
    frame.setTitle("BamView v"+view.getVersion());
    
    if(chr != null)
      view.combo.setSelectedItem(chr);
    if(vw != null)
    {
      if(vw.equalsIgnoreCase("IS"))
        view.cbIsizeStackView.setSelected(true);
      if(vw.equalsIgnoreCase("PS"))
        view.cbPairedStackView.setSelected(true);
      if(vw.equalsIgnoreCase("ST"))
        view.cbStrandStackView.setSelected(true);
      if(vw.equalsIgnoreCase("C"))
        view.cbCoverageView.setSelected(true);
    }
    if(base > 0)
      view.scrollBar.setValue(base);
    if(orientation)
      view.isOrientation = true;
    if(covPlot)
    {
      view.isCoverage = true;
      view.coveragePanel.setVisible(true);
    }
    if(snpPlot)
    {
      view.isSNPplot = true;
      view.snpPanel.setVisible(true);
    }

    // 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){}
    });*/

    frame.pack();

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