BamView.java

			    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.getReadPairedFlag() && 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("\nRead Paired       "+
        (thisSAMRecord.getReadPairedFlag() ? "yes" : "no"), Level.DEBUG);
    if(thisSAMRecord.getReadPairedFlag())
    {
      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);
    
    if(thisSAMRecord.getReadPairedFlag())
      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)
  {
    BamFrame frame = new BamFrame();
    if(args.length == 0 && BamFrame.isMac())
    {
      try
      {
        Thread.sleep(1000);
      }
      catch (InterruptedException e1) {}
      if(frame.getBamFile() != null)
        args = new String[]{ frame.getBamFile() };
    }
      
    List<String> bam = new Vector<String>();
    String reference = null;
    if(args.length == 0)
    {
      System.setProperty("default_directory", System.getProperty("user.dir"));
      FileSelectionDialog fileSelection = new FileSelectionDialog(
          null, true, "BamView", "BAM");
      bam = fileSelection.getFiles(".*\\.bam$");
      reference = fileSelection.getReferenceFile();
      if(reference == null || reference.equals(""))
        reference = null;
      
      if(bam == null || bam.size() < 1)
      {
        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 = 1000;
    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);
  }
}