BamView.java

/* JamView
 *
 * created: 2009
 *
 * This file is part of Artemis
 *
 * Copyright(C) 2009  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or(at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
package uk.ac.sanger.artemis.components.alignment;

import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Composite;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Insets;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowFocusListener;
import java.io.File;
import java.util.Collections;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;

import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.JTextField;
import javax.swing.Scrollable;
import javax.swing.SwingConstants;
import javax.swing.UIManager;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;

import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.util.CloseableIterator;

import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SelectionChangeEvent;
import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.SimpleEntryGroup;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryFileDialog;
import uk.ac.sanger.artemis.components.FeatureDisplay;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;

public class BamView extends JPanel
                     implements Scrollable, DisplayAdjustmentListener, SelectionChangeListener
{
  private static final long serialVersionUID = 1L;
  private List<SAMRecord> readsInView;
  private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
  private Vector<String> seqNames = new Vector<String>();
  private String bam;

  private Bases bases;
  private JScrollPane jspView;
  private JScrollBar scrollBar;
  
  private JComboBox combo;
  private boolean isSingle = false;
  private boolean isSNPs = false;
  private boolean isStackView = false;
  private boolean isPairedStackView = false;
  private boolean isCoverage = false;
  
  private FeatureDisplay feature_display;
  private Selection selection;
  private JPanel mainPanel;
  private CoveragePanel coveragePanel;
  private boolean showScale = true;
  private Ruler ruler = new Ruler();
  private int nbasesInView;
  
  private int startBase = -1;
  private int endBase   = -1;
  private int laststart;
  private int lastend;
  private int maxUnitIncrement = 8;
  private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
  private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
  
  private boolean showBaseAlignment = false;
  
  private AlphaComposite translucent = 
    AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
  
  /** Used to colour the frames. */
  private Color lightGrey = new Color(200, 200, 200);
  private Color darkGreen = new Color(0, 150, 0);
  private Color darkOrange = new Color(255,140,0);
  
  private Point lastMousePoint = null;
  private SAMRecord mouseOverSAMRecord = null;
  // record of where a mouse drag starts
  private int dragStart = -1;
  
  private int maxHeight = 800;
  
  private boolean concatSequences = false;
  private int ALIGNMENT_PIX_PER_BASE;
  
  private JPopupMenu popup;

 
  public BamView(String bam, 
                 String reference,
                 int nbasesInView)
  {
    super();
    setBackground(Color.white);
    this.bam = bam;
    this.nbasesInView = nbasesInView;
    
    if(reference != null)
    {
      EntryGroup entryGroup = new SimpleEntryGroup();
      try
      {
        getEntry(reference,entryGroup);
      }
      catch (NoSequenceException e)
      {
        e.printStackTrace();
      }
    }
    
    readHeaderPicard();
    
    // set font size
    //setFont(getFont().deriveFont(12.f));

    //Options.getOptions().getFontUIResource();
    //final javax.swing.plaf.FontUIResource font_ui_resource =
    //  new javax.swing.plaf.FontUIResource(getFont());
    final javax.swing.plaf.FontUIResource font_ui_resource =
      Options.getOptions().getFontUIResource();
    
    Enumeration<Object> keys = UIManager.getDefaults().keys();
    while(keys.hasMoreElements()) 
    {
      Object key = keys.nextElement();
      Object value = UIManager.get(key);
      if(value instanceof javax.swing.plaf.FontUIResource) 
        UIManager.put(key, font_ui_resource);
    }
    
    setFont(Options.getOptions().getFont());
    FontMetrics fm  = getFontMetrics(getFont());
    ALIGNMENT_PIX_PER_BASE = fm.charWidth('M');
    selection = new Selection(null);
    
    MultiLineToolTipUI.initialize();
    setToolTipText("");
  }
  
  public String getToolTipText()
  {
    return ( mouseOverSAMRecord != null ? 
        mouseOverSAMRecord.getReadName() + "\n" + 
        mouseOverSAMRecord.getAlignmentStart() + ".." +
        mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
        mouseOverSAMRecord.getInferredInsertSize() + "\nrname=" +
        mouseOverSAMRecord.getReferenceName(): null);
  }

  /*
  private void readHeader()
  {
    String samtoolCmd = "";
    if(System.getProperty("samtoolDir") != null)
      samtoolCmd = System.getProperty("samtoolDir");
    String cmd[] = { samtoolCmd+File.separator+"samtools",  
			     "view", "-H", bam };
	
    RunSamTools samtools = new RunSamTools(cmd, null, null, null);
	
    if(samtools.getProcessStderr() != null)
      System.out.println(samtools.getProcessStderr());
 
    String header = samtools.getProcessStdout();
    
    StringReader samReader = new StringReader(header);
	BufferedReader buff = new BufferedReader(samReader);
    
	String line;
	try 
	{
	  while((line = buff.readLine()) != null)
	  {
	    if(line.indexOf("LN:") > -1)
	    {
	      String parts[] = line.split("\t");
	      String name = "";
	      int seqLength = 0;
	      for(int i=0; i<parts.length; i++)
	      {
	        if(parts[i].startsWith("LN:"))
	          seqLength = Integer.parseInt( parts[i].substring(3) );
	        else if(parts[i].startsWith("SN:"))
	          name = parts[i].substring(3);
	      }
	      seqLengths.put(name, seqLength);
	      seqNames.add(name);
	    }
	  }
	} 
	catch (IOException e) 
	{
	  e.printStackTrace();
	}
  }

  private void readFromBam(int start, int end)
  {
    String refName = (String) combo.getSelectedItem();
    
    String samtoolCmd = "";
    if(System.getProperty("samtoolDir") != null)
      samtoolCmd = System.getProperty("samtoolDir");
    
	String cmd[] = { samtoolCmd+File.separator+"samtools",  
				     "view", 
				     bam, refName+":"+start+"-"+end };
		
	for(int i=0; i<cmd.length;i++)
	  System.out.print(cmd[i]+" ");
	System.out.println();
	
    if(readsInView == null)
      readsInView = new Vector<SAMRecord>();
    else
      readsInView.clear();
	RunSamTools samtools = new RunSamTools(cmd, null, null, readsInView);
		
	if(samtools.getProcessStderr() != null)
      System.out.println(samtools.getProcessStderr());
	    
	samtools.waitForStdout();
  }*/
  

  private void readHeaderPicard()
  {
    File bamFile = new File(bam);
    File indexFile = new File(bam+".bai");
    final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
    SAMFileHeader header = inputSam.getFileHeader();
    List<SAMSequenceRecord> readGroups = header.getSequenceDictionary().getSequences();
    
    for(int i=0; i<readGroups.size(); i++)
    {
      seqLengths.put(readGroups.get(i).getSequenceName(),
                     readGroups.get(i).getSequenceLength());
      seqNames.add(readGroups.get(i).getSequenceName());
    }
    inputSam.close();
  }
  
  /**
   * Read a SAM or BAM file.
   */
  private void readFromBamPicard(int start, int end)
  {
    // Open the input file.  Automatically detects whether input is SAM or BAM
    // and delegates to a reader implementation for the appropriate format.
    File bamFile = new File(bam);
    File indexFile = new File(bam+".bai");
    final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
    inputSam.setValidationStringency(ValidationStringency.SILENT);
    
    if(readsInView == null)
      readsInView = new Vector<SAMRecord>();
    else
      readsInView.clear();

    if(concatSequences)
    {
      int len = 0;
      int lastLen = 1;
      for(int i=0; i<seqNames.size(); i++)
      {
        int thisLength = seqLengths.get(seqNames.get(i));
        len += thisLength;

        if( (lastLen >= start && lastLen < end) ||
            (len >= start && len < end) ||
            (start >= lastLen && start < len) ||
            (end >= lastLen && end < len) )
        {
          int offset = getSequenceOffset(seqNames.get(i)); 
          int thisStart = start - offset;
          if(thisStart < 1)
            thisStart = 1;
          int thisEnd   = end - offset;
          if(thisEnd > thisLength)
            thisEnd = thisLength;
          
          System.out.println("READ "+seqNames.get(i)+"  "+thisStart+".."+thisEnd);
          iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd);
        }
        lastLen = len;
      }
    }
    else
    {
      String refName = (String) combo.getSelectedItem();
      iterateOverBam(inputSam, refName, start, end);
    }
    
    inputSam.close();
    //System.out.println("readFromBamPicard "+start+".."+end);
  }
  
  /**
   * Iterate over BAM file and load into the <code>List</code> of
   * <code>SAMRecord</code>.
   * @param inputSam
   * @param refName
   * @param start
   * @param end
   */
  private void iterateOverBam(final SAMFileReader inputSam, 
                              String refName, int start, int end)
  {
    CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
    while ( it.hasNext() )
    {
      try
      {
        SAMRecord samRecord = it.next();
        readsInView.add(samRecord);
      }
      catch(Exception e)
      {
        System.out.println(e.getMessage());
      }
    }
    it.close();
  }

  private int getSequenceLength()
  {
    if(concatSequences)
    {
      int len = 0;
      for(int i=0; i<seqNames.size(); i++)
        len += seqLengths.get(seqNames.get(i));
      return len;
    }
    else
      return seqLengths.get((String) combo.getSelectedItem());
  }
  
  protected int getSequenceOffset(String refName)
  {
    if(!concatSequences)
      return 0;
    int offset = 0;
    for(int i=0; i<combo.getItemCount(); i++)
    {
      String thisSeqName = (String) combo.getItemAt(i);
      if(refName.equals(thisSeqName))
        return offset;
      
      offset += seqLengths.get(combo.getItemAt(i));
    }
    return offset;
  }
  
  /**
   * Override
   */
  protected void paintComponent(Graphics g)
  {
	super.paintComponent(g);
	Graphics2D g2 = (Graphics2D)g;

	mouseOverSAMRecord = null;
    int seqLength = getSequenceLength();
	float pixPerBase = getPixPerBaseByWidth();
	
    int start;
    int end;
    
    if(startBase > 0)
      start = startBase;
    else
      start = getBaseAtStartOfView();
    
    if(endBase > 0)
      end = endBase;
    else
    {
      end   = start + nbasesInView - 1;
      if(end > seqLength)
        end = seqLength;
    }


    //System.out.println(start+".."+end+" " +
    //		"sequence length = "+getSequenceLength()+
    //		" pixPerBase="+pixPerBase);
    
      
    if(laststart != start ||
       lastend   != end)
    {
      setCursor(cbusy);
      try
      {
        readFromBamPicard(start, end);
        if(!isStackView || pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
          Collections.sort(readsInView, new SAMRecordComparator());

        setCursor(cdone);
      }
      catch(OutOfMemoryError ome)
      {
        JOptionPane.showMessageDialog(this, "Out of Memory");
        return;
      }
    }
    
    laststart = start;
    lastend   = end;
	if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
	  drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
	else
	{
	  if(isStackView)  
	    drawStackView(g2, seqLength, pixPerBase, start, end);
	  else if(isPairedStackView)
	    drawPairedStackView(g2, seqLength, pixPerBase, start, end);
	  else
	    drawLineView(g2, seqLength, pixPerBase, start, end);
	  if(isCoverage)
	  {
	    coveragePanel.setStartAndEnd(start, end);
	    coveragePanel.setPixPerBase(pixPerBase);
	    coveragePanel.repaint();
	  }
	}
  }
  
  
  private float getPixPerBaseByWidth()
  {
    return (float)( getPreferredSize().getWidth() /nbasesInView);
  }
  
  
  private int getMaxBasesInPanel(int seqLength)
  {
    if(feature_display == null)
      return seqLength+nbasesInView/3;
    else
      return seqLength+nbasesInView;
  }
  
  /**
   * Draw the zoomed-in base view.
   * @param g2
   * @param seqLength
   * @param pixPerBase
   * @param start
   * @param end
   */
  private void drawBaseAlignment(Graphics2D g2, 
                                 int seqLength, 
                                 float pixPerBase, 
                                 final int start, 
                                 final int end)
  {
    ruler.start = start;
    ruler.end = end;
    ruler.repaint();
    
    int ypos = 0;

    String refSeq = null;
    int refSeqStart = start;
    if(bases != null)
    {
      // draw the reference sequence
      ypos+=11;

      try
      {
        int seqEnd = end+2;
        if(seqEnd > bases.getLength())
          seqEnd = bases.getLength();

        if(refSeqStart < 1)
          refSeqStart = 1;
        refSeq = 
          bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
        
        g2.setColor(lightGrey);
        g2.fillRect(0, ypos-11, getPreferredSize().width, 11);
        drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
        g2.setColor(Color.black);
        g2.drawString(refSeq, 0, ypos);
      }
      catch (OutOfRangeException e)
      {
        e.printStackTrace();
      }
    }
    else
      drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);

    
    boolean drawn[] = new boolean[readsInView.size()];
    for(int i=0; i<readsInView.size(); i++)
      drawn[i] = false;
    
    for(int i=0; i<readsInView.size(); i++)
    {
      if (!drawn[i])
      {
        SAMRecord thisRead = readsInView.get(i);
        ypos+=11;

        drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
        drawn[i] = true;
        
        int thisEnd = thisRead.getAlignmentEnd();
        if(thisEnd == 0)
          thisEnd = thisRead.getAlignmentStart()+thisRead.getReadLength();
        
        for(int j=i+1; j<readsInView.size(); j++)
        {
          if (!drawn[j])
          {
            SAMRecord nextRead = readsInView.get(j);
            if(nextRead.getAlignmentStart() > thisEnd+1)
            {
              drawSequence(g2, nextRead, ypos, refSeq, refSeqStart);
              drawn[j] = true;
              thisEnd = nextRead.getAlignmentEnd();
              if(thisEnd == 0)
                thisEnd = nextRead.getAlignmentStart()+nextRead.getReadLength();
            }
          }
        }
      }
    }
    
    if(ypos > getHeight())
    {
      Dimension d = getPreferredSize();
      d.setSize(getPreferredSize().getWidth(), ypos);
      setPreferredSize(d);
      revalidate();
    }
  }

  
  /**
   * Draw the query sequence
   * @param g2
   * @param read
   * @param pixPerBase
   * @param ypos
   */
  private void drawSequence(Graphics2D g2, SAMRecord samRecord, 
                            int ypos, String refSeq, int refSeqStart)
  {
    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);
    
    Color col = g2.getColor();
    int xpos;
    int len = 0;
    String readSeq = samRecord.getReadString();
    int offset = getSequenceOffset(samRecord.getReferenceName());
    
    List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
    for(int i=0; i<blocks.size(); i++)
    {
      AlignmentBlock block = blocks.get(i);
      len += block.getLength();
      for(int j=0; j<block.getLength(); j++)
      {
        int readPos = block.getReadStart()-1+j;
        xpos  = block.getReferenceStart()-1+j+offset;
        int refPos = xpos-refSeqStart+1;
        
        if(isSNPs && refSeq != null && refPos > 0 && refPos < refSeq.length())
        { 
          if(readSeq.charAt(readPos) != refSeq.charAt(refPos))
            g2.setColor(Color.red);
          else
            g2.setColor(col);
        }
        
        g2.drawString(readSeq.substring(readPos, readPos+1), 
                      refPos*ALIGNMENT_PIX_PER_BASE, ypos);
      }
    }
    
    if(lastMousePoint != null)
    {
      int refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
      int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
      int xend   = (refPos+len)*ALIGNMENT_PIX_PER_BASE;

      if(lastMousePoint.getY() > ypos-11 && lastMousePoint.getY() < ypos)
      if(lastMousePoint.getX() > xstart &&
         lastMousePoint.getX() < xend)
      {
        mouseOverSAMRecord = samRecord;    
      }
    }
  }
  
  /**
   * Draw zoomed-out view.
   * @param g2
   * @param seqLength
   * @param pixPerBase
   * @param start
   * @param end
   */
  private void drawLineView(Graphics2D g2, int seqLength, float pixPerBase, int start, int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end);
    if(isShowScale())
      drawScale(g2, start, end, pixPerBase);
    
    Stroke originalStroke =
      new BasicStroke (1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND); 
    Stroke stroke =
      new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
    int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    for(int i=0; i<readsInView.size(); i++)
    {
      SAMRecord samRecord = readsInView.get(i);
      SAMRecord samNextRecord = null;      

      if( !samRecord.getReadPairedFlag() ||  // read is not paired in sequencing
          samRecord.getMateUnmappedFlag() )  // mate is unmapped
      {
        if(isSingle)
        {
          int ypos = (getHeight() - scaleHeight) - samRecord.getReadString().length();
          g2.setColor(Color.orange);
          drawRead(g2, samRecord, pixPerBase, stroke, ypos);
        }
        continue;
      }

      int ypos = (getHeight() - scaleHeight) - ( Math.abs(samRecord.getInferredInsertSize()) );
      if(i < readsInView.size()-1)
      {
        samNextRecord = readsInView.get(++i);

        if(samRecord.getReadName().equals(samNextRecord.getReadName()))
        { 
          // draw connection between paired reads
          if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() && 
              (samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
          {
            g2.setStroke(originalStroke);
            g2.setColor(Color.LIGHT_GRAY);

            drawTranslucentLine(g2, 
                   (int)((samRecord.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase), 
                   (int)((samNextRecord.getAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
          }
          
          if( samRecord.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
              samNextRecord.getReadNegativeStrandFlag() )
            g2.setColor(Color.red);
          else
            g2.setColor(Color.blue);
          
          drawRead(g2, samRecord, pixPerBase, stroke, ypos);
          drawRead(g2, samNextRecord, pixPerBase, stroke, ypos);
        }
        else
        {
          drawLoneRead(g2, samRecord, ypos, pixPerBase, originalStroke, stroke);
          i--;
        }
      }
      else
      {
        drawLoneRead(g2, samRecord, ypos, pixPerBase, originalStroke, stroke);
      }
    }
    
    drawYScale(g2, scaleHeight);
  }
  
  /**
   * 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 drawStackView(Graphics2D g2, 
                             int seqLength, 
                             float pixPerBase, 
                             int start, 
                             int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end);
    if(isShowScale())
      drawScale(g2, start, end, pixPerBase);
    
    BasicStroke stroke = new BasicStroke(
        1.3f,
        BasicStroke.CAP_BUTT, 
        BasicStroke.JOIN_MITER);
    
    int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    int ypos = (getHeight() - scaleHeight);
    int maxEnd = 0;
    int lstStart = 0;
    int lstEnd = 0;
    
    g2.setColor(Color.blue);
    for(int i=0; i<readsInView.size(); i++)
    {
      SAMRecord samRecord = readsInView.get(i);

      int recordStart = samRecord.getAlignmentStart();
      int recordEnd = samRecord.getAlignmentEnd();
      
      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;
      drawRead(g2, samRecord, pixPerBase, stroke, ypos);
    }
  }
  
  
  /**
   * 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);
    
    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);
    int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    int ypos = getHeight() - scaleHeight - 3;
    int lastEnd = 0;
    
    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;
      
      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())
        {
          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, stroke, ypos);
      
      if(pr.sam2 != null)
        drawRead(g2, pr.sam2, pixPerBase, stroke, ypos);
    }
  }
  
  
  /**
   * 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, Stroke originalStroke, Stroke stroke)
  {
    boolean offTheTop = false;
    int offset = getSequenceOffset(samRecord.getReferenceName());
    int thisStart = samRecord.getAlignmentStart()-1+offset;
    int thisEnd   = thisStart + samRecord.getReadString().length();
    
    if(ypos <= 0)
    {
      offTheTop = true;
      ypos = samRecord.getReadString().length();
    }