JamView.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.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.awt.geom.GeneralPath;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.StringReader;
import java.util.Collections;
import java.util.Comparator;
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.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 JamView 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 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;
  
  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 lightBlue = new Color(30,144,255);
  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 int ALIGNMENT_PIX_PER_BASE;
  
  private JPopupMenu popup;
  // use the picard library otherwise call samtools
  public static boolean PICARD = true;

 
  public JamView(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();
      }
    }
    
    if(PICARD)
      readHeaderPicard();
    else
      readHeader();
    
    // 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(): null);
  }
  
  /**
   * Read the BAM/SAM header
   */
  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 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 data from BAM/SAM file for a region.
   * @param start
   * @param end
   * @param pair_sort
   */
  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();
  }
  
  /**
   * 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();
    String refName = (String) combo.getSelectedItem();
    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());
      }
    }
    inputSam.close();
    //System.out.println("readFromBamPicard "+start+".."+end);
  }
  
  /**
   * Override
   */
  protected void paintComponent(Graphics g)
  {
	super.paintComponent(g);
	Graphics2D g2 = (Graphics2D)g;

	mouseOverSAMRecord = null;
	String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);
	float pixPerBase = getPixPerBaseByWidth();
	
    int start;
    final int end;
    
    if(startBase > 0)
      start = startBase;
    else
    {
      double x = jspView.getViewport().getViewRect().getX();
      start = 1 + (int) (getMaxBasesInPanel(seqLength) * ( (float)x / (float)getPreferredSize().getWidth() ));
    }
    
    if(endBase > 0)
      end = endBase;
    else
    {
      int width = jspView.getViewport().getViewRect().width;
      if(jspView.getVerticalScrollBar() != null)
        width += jspView.getVerticalScrollBar().getWidth();
      end   = (int) (start + ((float)width / (float)pixPerBase));
    }

    //System.out.println("paintComponent "+start+".."+end+"       "+startBase+".."+endBase+
    //   "  pixPerBase="+pixPerBase+"  getPreferredSize().getWidth()="+getPreferredSize().getWidth());
    
    if(laststart != start ||
       lastend   != end)
    {
      try
      {
        setCursor(cbusy);

        if(PICARD)
          readFromBamPicard(start, end);
        else
          readFromBam(start, end);

        if(!isStackView || pixPerBase*3 >= 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*3 >= 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()
  {
    String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);
    return ((float)getPreferredSize().getWidth())/(getMaxBasesInPanel(seqLength));
  }
  
  private float getPixPerBaseByBasesInView()
  {
    int width = jspView.getViewport().getViewRect().width;
    if(jspView.getVerticalScrollBar() != null)
      width += jspView.getVerticalScrollBar().getWidth();
    
    return ((float)width)/(float)(nbasesInView); 
  }
  
  private float getMaxBasesInPanel(int seqLength)
  {
    if(feature_display == null)
      return (float)(seqLength);
    else
      return (float)(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();
        int xpos = (refSeqStart-1)*ALIGNMENT_PIX_PER_BASE;
        
        g2.setColor(lightGrey);
        g2.fillRect(xpos, ypos-11, 
            jspView.getViewport().getWidth()+(ALIGNMENT_PIX_PER_BASE*2), 11);
        drawSelectionRange(g2, pixPerBase, start, end);
        g2.setColor(Color.black);
        g2.drawString(refSeq, xpos, ypos);
        
        //for(int i=0;i<refSeq.length(); i++)
        //{
          //xpos = ((refSeqStart-1) + i)*ALIGNMENT_PIX_PER_BASE;
          //g2.drawString(refSeq.substring(i, i+1), xpos, ypos);
        //}
      }
      catch (OutOfRangeException e)
      {
        e.printStackTrace();
      }
    }
    else
      drawSelectionRange(g2, pixPerBase, 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, pixPerBase, 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, pixPerBase, 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, 
                            float pixPerBase, 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();

    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;
        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), xpos*ALIGNMENT_PIX_PER_BASE, ypos);
      }
    }
    
    if(lastMousePoint != null)
    {
      int xstart = (blocks.get(0).getReferenceStart()-1)*ALIGNMENT_PIX_PER_BASE;
      int xend   = (blocks.get(0).getReferenceStart()-1+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()*pixPerBase), 
                     (int)(samNextRecord.getAlignmentStart()*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, start, pixPerBase, 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()*pixPerBase),
                    (int)(pr.sam2.getAlignmentStart()*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*pixPerBase),
              (int)(pr.sam1.getMateAlignmentStart()*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 thisStart = samRecord.getAlignmentStart()-1;
    int thisEnd   = thisStart + samRecord.getReadString().length();
    
    if(ypos <= 0)
    {
      offTheTop = true;
      ypos = samRecord.getReadString().length();
    }
      
    if(Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
    {
      g2.setStroke(originalStroke);
      g2.setColor(Color.LIGHT_GRAY);
      
      if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
      {
        int nextStart = (int) ((samRecord.getMateAlignmentStart()-1)*pixPerBase);
        drawTranslucentLine(g2, 
            (int)(thisStart*pixPerBase), nextStart, ypos);
      }
      else
      {
        int nextStart = (int) ((samRecord.getMateAlignmentStart()-1)*pixPerBase);
        drawTranslucentLine(g2, 
            (int)(thisEnd*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, stroke, ypos);
    
    if (isSNPs)
      showSNPsOnReads(g2, samRecord, pixPerBase, ypos);
  }

  
  private void drawScale(Graphics2D g2, int start, int end, float pixPerBase)
  {
    g2.setColor(Color.black);
    g2.drawLine( (int)(start*pixPerBase), getHeight()-14,
                 (int)(end*pixPerBase),   getHeight()-14);
    int interval = end-start;
    
    if(interval > 256000)
      drawTicks(g2, start, end, pixPerBase, 512000);
    else if(interval > 64000)
      drawTicks(g2, start, end, pixPerBase, 12800);
    else if(interval > 16000)
      drawTicks(g2, start, end, pixPerBase, 3200);
    else if(interval > 4000)
      drawTicks(g2, start, end, pixPerBase, 800);
    else if(interval > 1000)
      drawTicks(g2, start, end, pixPerBase, 400);
    else
      drawTicks(g2, start, end, pixPerBase, 100);
  }
  
  private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division)
  {
    int markStart = (Math.round(start/division)*division);
    
    if(markStart < 1)
      markStart = 1;
    
    int sm = markStart-(division/2);
    
    if(sm > start)
      g2.drawLine((int)(sm*pixPerBase), getHeight()-14,(int)(sm*pixPerBase), getHeight()-12);
    
    for(int m=markStart; m<end; m+=division)
    {
      g2.drawString(Integer.toString(m), m*pixPerBase, getHeight()-1);
      g2.drawLine((int)(m*pixPerBase), getHeight()-14,(int)(m*pixPerBase), getHeight()-11);
      
      sm = m+(division/2);
      
      if(sm < end)
        g2.drawLine((int)(sm*pixPerBase), getHeight()-14,(int)(sm*pixPerBase), getHeight()-12);
      
      if(m == 1)
        m = 0;
    }
  }
  
  /**
   * Draw a y-scale for inferred size (isize) of reads.
   * @param g2
   * @param start
   * @param pixPerBase
   * @param xScaleHeight
   */
  private void drawYScale(Graphics2D g2, int start, float pixPerBase, int xScaleHeight)
  {
    g2.setColor(Color.black);
    int maxY = getPreferredSize().height-xScaleHeight;
    int xpos = (int) (pixPerBase*start);
    
    for(int i=100; i<maxY; i+=100)
    {
      int ypos = getHeight()-i-xScaleHeight;
      g2.drawLine(xpos, ypos, xpos+2, ypos);
      g2.drawString(Integer.toString(i), xpos+3, ypos);
    }
  }
  
  /**
   * Draw a given read.
   * @param g2
   * @param thisRead
   * @param pixPerBase
   * @param stroke
   * @param ypos
   */
  private void drawRead(Graphics2D g2, SAMRecord thisRead,
		                float pixPerBase, Stroke stroke, int ypos)
  {
    int thisStart = thisRead.getAlignmentStart()-1;
    int thisEnd   = thisRead.getAlignmentEnd()-1;
    g2.setStroke(stroke);
    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);
  }
  
  /**
   * 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-1));
        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 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, thisEnd), Bases.FORWARD);
      byte[] readSeq = thisRead.getReadBases();

      Color col = g2.getColor();
      g2.setColor(Color.red);

      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) * pixPerBase), ypos + 2,
                        (int) ((refPos) * 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);
    }

    // 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)
      {
        handleCanvasMouseDragOrClick(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(JamView.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());
            goToBasePosition(basePosition);
          }
          catch (NumberFormatException nfe)
          {
            JOptionPane.showMessageDialog(JamView.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)
        {
          int startBase = getBaseAtStartOfView();
          setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
          goToBasePosition(startBase);
        }
      });
      topPanel.add(zoomIn);

      JButton zoomOut = new JButton("+");
      zoomOut.setMargin(ins);
      zoomOut.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          if (showBaseAlignment)
            return;
          int startBase = getBaseAtStartOfView();
          setZoomLevel((int) (JamView.this.nbasesInView * .9));
          goToBasePosition(startBase);
        }
      });
      topPanel.add(zoomOut);
    }
    
    topPanel.add(buttonAutoHide);

    mainPanel.setPreferredSize(new Dimension(900, 400));
    
    jspView = new JScrollPane(this, 
        JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
        JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);

    setDisplay(1, nbasesInView, null);
    mainPanel.setLayout(new BorderLayout());

    if(topPanel instanceof JPanel)
      mainPanel.add(topPanel, BorderLayout.NORTH);
    mainPanel.add(jspView, BorderLayout.CENTER);
    
    coveragePanel = new CoveragePanel();
    mainPanel.add(coveragePanel, BorderLayout.SOUTH);
    coveragePanel.setPreferredSize(new Dimension(900, 100));
    coveragePanel.setVisible(false);
    
    jspView.getVerticalScrollBar().setValue(
        jspView.getVerticalScrollBar().getMaximum());

    if(feature_display == null)
    {
      addKeyListener(new KeyAdapter()
      {
        public void keyPressed(final KeyEvent event)
        {
          switch (event.getKeyCode())
          {
          case KeyEvent.VK_UP:
            int startBase = getBaseAtStartOfView();
            setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
            goToBasePosition(startBase);
            break;
          case KeyEvent.VK_DOWN:
            if (showBaseAlignment)
              break;
            startBase = getBaseAtStartOfView();
            setZoomLevel((int) (JamView.this.nbasesInView * .9));
            goToBasePosition(startBase);
            break;
          default:
            break;
          }
        }
      });
    }

    addMouseListener(new PopupListener());
    setFocusable(true);
    requestFocusInWindow();
    addFocusListener(new FocusListener()
    {
      public void focusGained(FocusEvent fe){}
      public void focusLost(FocusEvent fe){}
    });
  }
  
  private void createViewMenu(JComponent view)
  {
    JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
    checkBoxSingle.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        repaint();
        isSingle = !isSingle;
      }
    });
    view.add(checkBoxSingle);

    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;
        repaint();
      }
    });
    view.add(checkBoxSNPs);
    
    final JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
    final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
    
    checkBoxStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isStackView = !isStackView;
        
        if(isStackView)
        {
          isPairedStackView = !isStackView;
          checkBoxPairedStackView.setSelected(!isStackView);
        }
        repaint();
      }
    });
    view.add(checkBoxStackView);
    

    checkBoxPairedStackView.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        laststart = -1;
        lastend = -1;
        isPairedStackView = !isPairedStackView;
        
        if(isPairedStackView)
        {
          isStackView = !isPairedStackView;
          checkBoxStackView.setSelected(!isPairedStackView);
        }
        repaint();
      }
    });
    view.add(checkBoxPairedStackView);
    
    
    JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
    checkBoxCoverage.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        isCoverage = !isCoverage;
        coveragePanel.setVisible(isCoverage);
        repaint();
      }
    });
    view.add(checkBoxCoverage);
    view.add(new JSeparator());
    
    JMenu maxHeightMenu = new JMenu("Plot Height");
    view.add(maxHeightMenu);
    
    final String hgts[] = 
       {"500", "800", "1000", "1500", "2500", "5000"};
    
    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 int getBaseAtStartOfView()
  {
    String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);
    double x = jspView.getViewport().getViewRect().getX();
    return (int) (getMaxBasesInPanel(seqLength) * ( x / getWidth())) + 1;
  }
  
  /**
   * Set the panel size based on the number of bases visible
   * and repaint.
   * @param nbasesInView
   */
  private void setZoomLevel(final int nbasesInView)
  {
    this.nbasesInView = nbasesInView;

    //System.out.println("setZoomLevel "+nbasesInView+"  "+getBaseAtStartOfView());
    String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);
    float pixPerBase = getPixPerBaseByBasesInView(); 

    if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
    {
      pixPerBase = ALIGNMENT_PIX_PER_BASE;
      jspView.getVerticalScrollBar().setValue(0);
      jspView.setColumnHeaderView(ruler);
      showBaseAlignment = true;
    }
    else if(jspView != null)
    {
      jspView.setColumnHeaderView(null);
      jspView.getVerticalScrollBar().setValue(
          jspView.getVerticalScrollBar().getMaximum());
      showBaseAlignment = false;
    }
    
    Dimension d = new Dimension();
    d.setSize((getMaxBasesInPanel(seqLength)*pixPerBase), maxHeight);
    setPreferredSize(d);
    revalidate();
  }
  
  /**
   * Set the ViewPort so it starts at the given base position.
   * @param base
   */
  private void goToBasePosition(int base)
  {
    Point p = jspView.getViewport().getViewPosition();
    String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);
    
    float width = (float) getPreferredSize().getWidth();
    
    p.x = Math.round(width*((float)(base-1)/(getMaxBasesInPanel(seqLength))));
    //System.out.println("goToBasePosition "+base);
    jspView.getViewport().setViewPosition(p);
  }
  
  /**
   * 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;
    
    String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);

    float pixPerBase;
    if(jspView.getViewport().getViewRect().width > 0)
      pixPerBase = this.getPixPerBaseByWidth(); // getPixPerBaseByBasesInView();
    else
    {
      if(feature_display == null)
        pixPerBase = 1000.f/(float)(end-start+1);
      else
        pixPerBase = feature_display.getWidth()/(float)(end-start+1);
    }

    if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
    {
      pixPerBase = ALIGNMENT_PIX_PER_BASE;
      jspView.getVerticalScrollBar().setValue(0);
      jspView.setColumnHeaderView(ruler);
      showBaseAlignment = true;
    }
    else if(jspView != null)
    {
      jspView.setColumnHeaderView(null);
      showBaseAlignment = false;
    }
    
    Dimension d = new Dimension();
    d.setSize((getMaxBasesInPanel(seqLength)*pixPerBase), maxHeight);
    
    //System.out.println("setDisplay() "+d.getWidth());
    setPreferredSize(d);
    goToBasePosition(startBase);
    
    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 handleCanvasMouseDragOrClick(final MouseEvent event)
  {
    if(event.isShiftDown()) 
      return;

    if(event.getClickCount() > 1)
    {
      getSelection().clear();
      repaint();
      return;  
    }
    
    int onmask = MouseEvent.BUTTON1_DOWN_MASK;
    
    String refName = (String) combo.getSelectedItem();
    int seqLength = seqLengths.get(refName);
    float pixPerBase = getPixPerBaseByWidth();
    int start = (int) ( (event.getPoint().getX()/pixPerBase) + 1.f );
    
    if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
      dragStart = start;
    else if((event.getModifiersEx() & onmask) != onmask)
      dragStart = -1;

    if(start < 1)
      start = 1;
    if(start > seqLength)
      start = seqLength;
    
    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();
    }
  }
  
  private Selection getSelection()
  {
    return selection;
  }
  
  private class CoveragePanel extends JPanel
  {
	private static final long serialVersionUID = 1L;

    private int start;
	private int end;
	private float pixPerBase;
    
    public CoveragePanel()
    {
      super();
      setBackground(Color.white);
    }
    
	/**
	 * Override
	 */
	protected void paintComponent(Graphics g)
	{
	  super.paintComponent(g);
	  Graphics2D g2 = (Graphics2D)g;
	  
	  if(readsInView == null)
	    return;
	  
	  int windowSize = 10;
	  int nBins = Math.round((end-start+1.f)/windowSize);
	  int coverage[] = new int[nBins];
	  for(int i=0; i<coverage.length; i++)
	    coverage[i] = 0;
	  
	  int max = 0;
	  for(int i=0; i<readsInView.size(); i++)
	  {
	    SAMRecord thisRead = readsInView.get(i);
	    int length = thisRead.getReadLength();
	    
	    for(int j=0; j<length;j++)
	    {
	      int bin = 
	        Math.round(((thisRead.getAlignmentStart()-start) + j) / windowSize);

	      if(bin < 0 || bin > coverage.length-1)
	        continue;   
	      coverage[bin]+=1;
	      if(coverage[bin] > max)
	        max = coverage[bin];
	    }
	  }
	  
	  g2.setColor(lightBlue);
	  GeneralPath shape = new GeneralPath();
	  shape.moveTo(0,getHeight());
	  for(int i=0; i<coverage.length; i++)
	  {
	    float xpos = ((i*(windowSize)) - windowSize/2.f)*pixPerBase;
	    shape.lineTo(xpos,
	        getHeight() - (((float)coverage[i]/(float)max)*getHeight()));
	  }

	  shape.lineTo(getWidth(),getHeight());
	  g2.fill(shape);

	  String maxStr = Integer.toString(max);
	  FontMetrics fm = getFontMetrics(getFont());
	  g2.setColor(Color.black);
	  g2.drawString(maxStr, getWidth()-fm.stringWidth(maxStr), fm.getHeight());
	}
	
	protected void setStartAndEnd(int start, int end)
	{
	  this.start = start;
	  this.end = end;
	}

	public void setPixPerBase(float pixPerBase)
	{
	  this.pixPerBase = pixPerBase;
	}
  }
  
  private class Ruler extends JPanel
  {
    private static final long serialVersionUID = 1L;
    int start;
    int end;

    public Ruler()
    {
      super();
      setPreferredSize(new Dimension(getPreferredSize().width, 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;

      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
  {
    public void mouseClicked(MouseEvent e)
    {
      JamView.this.requestFocus();
      handleCanvasMouseDragOrClick(e);
    }
    
    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();
          createViewMenu(popup);
        }
        popup.show(e.getComponent(),
                e.getX(), e.getY());
      }
    }
  }
 
  class SAMRecordComparator implements Comparator<Object>
  {
    public int compare(Object o1, Object o2) 
    {
      SAMRecord pr1 = (SAMRecord) o1;
      SAMRecord pr2 = (SAMRecord) o2;
      
      int cmp = pr1.getReadName().compareTo(pr2.getReadName());
      if(cmp == 0)
      {
        if(pr1.getAlignmentStart() < pr2.getAlignmentStart())
          return -1;
        else
          return 1;
      }   
      return cmp;
    }
  }
  
  
  class PairedReadComparator implements Comparator<Object>
  {
    public int compare(Object o1, Object o2) 
    {
      PairedRead pr1 = (PairedRead) o1;
      PairedRead pr2 = (PairedRead) o2;
      
      int start1 = pr1.sam1.getAlignmentStart();
      if(pr1.sam1.getAlignmentEnd() < start1)
        start1 = pr1.sam1.getAlignmentEnd();
      
      int start2 = pr2.sam1.getAlignmentStart();
      if(pr2.sam1.getAlignmentEnd() < start2)
        start2 = pr1.sam1.getAlignmentEnd();
        
      return start1-start2;
    }
  }
  
  class PairedRead
  {
    SAMRecord sam1;
    SAMRecord sam2;
  }


  public Dimension getPreferredScrollableViewportSize()
  {
    return getPreferredSize();
  }

  public int getScrollableBlockIncrement(Rectangle visibleRect,
      int orientation, int direction)
  {
    if (orientation == SwingConstants.HORIZONTAL)
      return visibleRect.width - maxUnitIncrement;
    else 
      return visibleRect.height - maxUnitIncrement;
  }

  public boolean getScrollableTracksViewportHeight()
  {
    return false;
  }

  public boolean getScrollableTracksViewportWidth()
  {
    return false;
  }

  public int getScrollableUnitIncrement(Rectangle visibleRect, int orientation,
                                        int direction)
  {
  //Get the current position.
    int currentPosition = 0;
    if (orientation == SwingConstants.HORIZONTAL) 
        currentPosition = visibleRect.x;
    else 
        currentPosition = visibleRect.y;

    //Return the number of pixels between currentPosition
    //and the nearest tick mark in the indicated direction.
    if (direction < 0)
    {
      int newPosition = currentPosition -
                        (currentPosition / maxUnitIncrement)
                         * maxUnitIncrement;
      return (newPosition == 0) ? maxUnitIncrement : newPosition;
    } 
    else 
    {
      return ((currentPosition / maxUnitIncrement) + 1)
              * maxUnitIncrement
              - currentPosition;
    }
  }
  
  /**
   * Artemis event notification
   */
  public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
  {
    if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
    {
      laststart = -1;
      lastend = -1;
      this.startBase = event.getStart();
      this.endBase   = event.getEnd();
      
      //int width = event.getEnd()-event.getStart()+1;
      int width = feature_display.getMaxVisibleBases();
      //System.out.println("displayAdjustmentValueChanged() "+event.getStart()+".."+event.getEnd()+"  +width");

      setZoomLevel(width);
      goToBasePosition(event.getStart());
      setDisplay(event.getStart(), event.getEnd(), event);
      repaint();
    }
    else
    {
      setDisplay(event.getStart(), event.getEnd(), event);
      repaint();
    }
  }
  
  public void selectionChanged(SelectionChangeEvent event)
  {
    repaint();
  }
  
  
  public static void main(String[] args)
  {
    String bam = args[0];
    int nbasesInView = 1000;
    String reference = null;
    
    for(int i=0;i<args.length; i++)
    {
      if(args[i].equals("-a"))
        bam = args[++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 JamView view = new JamView(bam, reference, nbasesInView);
    JFrame frame = new JFrame("JAM");
    
    // 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);
  }


}