BamView.java

/* BamView
 *
 * 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.Component;
import java.awt.Composite;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
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.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.image.BufferedImage;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.lang.management.ManagementFactory;
import java.lang.management.MemoryMXBean;
import java.lang.reflect.Field;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;

import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButton;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.JTextField;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;

import org.apache.log4j.Level;

import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.sam.BuildBamIndex;
import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMException;
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.FeatureVector;
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.circular.TextFieldInt;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryEdit;
import uk.ac.sanger.artemis.components.EntryFileDialog;
import uk.ac.sanger.artemis.components.FeatureDisplay;
import uk.ac.sanger.artemis.components.FileViewer;
import uk.ac.sanger.artemis.components.IndexReferenceEvent;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.NonModalDialog;
import uk.ac.sanger.artemis.components.SequenceComboBox;
import uk.ac.sanger.artemis.components.SwingWorker;
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.FTPSeekableStream;
import uk.ac.sanger.artemis.util.OutOfRangeException;

public class BamView extends JPanel
                     implements DisplayAdjustmentListener, SelectionChangeListener
{
  private static final long serialVersionUID = 1L;

  private List<BamViewRecord> readsInView;
  private Hashtable<String, SAMFileReader> samFileReaderHash = new Hashtable<String, SAMFileReader>();

  private HashMap<String, Integer> seqLengths = new HashMap<String, Integer>();
  private HashMap<String, Integer> offsetLengths;
  private Vector<String> seqNames = new Vector<String>();
  protected List<String> bamList;
  protected List<Short> hideBamList = new Vector<Short>();

  private SAMRecordPredicate samRecordFlagPredicate;
  private SAMRecordMapQPredicate samRecordMapQPredicate;

  private SAMRecordFilter filterFrame;

  private Bases bases;
  private JScrollPane jspView;
  private JScrollBar scrollBar;
  
  private SequenceComboBox combo;
  private boolean isOrientation = false;
  private boolean isSingle = false;
  private boolean isSNPs = false;
  
  private boolean isCoverage = false;
  private boolean isSNPplot = false;
  
  private EntryEdit entry_edit;
  private FeatureDisplay feature_display;
  private Selection selection;
  private JPanel mainPanel = new JPanel();
  private CoveragePanel coveragePanel;
  private SnpPanel snpPanel;

  private boolean logScale = false;
  private Ruler ruler;
  private int nbasesInView;
  
  private int startBase = -1;
  private int endBase   = -1;
  private int laststart;
  private int lastend;

  private boolean asynchronous = true;
  private boolean showBaseAlignment = false;
  
  private JMenu bamFilesMenu = new JMenu("BAM files");
  private JCheckBoxMenuItem logMenuItem = new JCheckBoxMenuItem("Use Log Scale", logScale);
  
  private JCheckBoxMenuItem cbStackView = new JCheckBoxMenuItem("Stack", true);
  private JCheckBoxMenuItem cbPairedStackView = new JCheckBoxMenuItem("Paired Stack");
  private JCheckBoxMenuItem cbStrandStackView = new JCheckBoxMenuItem("Strand Stack");
  private JCheckBoxMenuItem cbIsizeStackView = new JCheckBoxMenuItem("Inferred Size", false);
  private JCheckBoxMenuItem cbCoverageView = new JCheckBoxMenuItem("Coverage", false);
  private JCheckBoxMenuItem cbCoverageStrandView = new JCheckBoxMenuItem("Coverage by Strand", false);
  private JCheckBoxMenuItem cbLastSelected;
  
  private ButtonGroup buttonGroup = new ButtonGroup();
  
  private JCheckBoxMenuItem colourByCoverageColour = new JCheckBoxMenuItem("Coverage Plot Colours");
  private JCheckBoxMenuItem baseQualityColour = new JCheckBoxMenuItem("Base Quality");
  private JCheckBoxMenuItem markInsertions = new JCheckBoxMenuItem("Mark Insertions", true);
  private AlphaComposite translucent = 
    AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
  
  private CoveragePanel coverageView = new CoveragePanel();
  
  protected static String BAM_SUFFIX = ".*\\.(bam|cram)$";
  /** Used to colour the frames. */
  private static Color LIGHT_GREY = new Color(200, 200, 200);
  private static Color DARK_GREEN = new Color(0, 150, 0);
  private static Color DARK_ORANGE = new Color(255,140,0);
  private static Color DEEP_PINK   = new Color(139,10,80);
  
  private Point lastMousePoint = null;
  private BamViewRecord mouseOverSAMRecord = null;
  private BamViewRecord highlightSAMRecord = null;
  private String mouseOverInsertion;
  // record of where a mouse drag starts
  protected int dragStart = -1;
  
  private static int MAX_BASES = 26000;
  private int maxHeight = 800;
  
  private boolean concatSequences = false;
  private int ALIGNMENT_PIX_PER_BASE;
  private int BASE_HEIGHT;

  private JPopupMenu popup;
  private PopupMessageFrame popFrame = new PopupMessageFrame();
  private PopupMessageFrame waitingFrame = new PopupMessageFrame("waiting...");
  private ExecutorService bamReadTaskExecutor;
  private int MAX_COVERAGE = Integer.MAX_VALUE;
  
  public static org.apache.log4j.Logger logger4j = 
    org.apache.log4j.Logger.getLogger(BamView.class);
  
  public BamView(List<String> bamList, 
                String reference,
                int nbasesInView,
                final EntryEdit entry_edit,
                final FeatureDisplay feature_display,
                final Bases bases,
                final JPanel containerPanel,
                final JFrame frame)
  {
    this(bamList, reference, nbasesInView, feature_display, bases, containerPanel, frame);
    this.entry_edit = entry_edit;
  }
  
  public BamView(List<String> bamList, 
                 String reference,
                 int nbasesInView,
                 final FeatureDisplay feature_display,
                 final Bases bases,
                 final JPanel containerPanel,
                 final JFrame frame)
  {
    super();
    setBackground(Color.white);
    this.bamList = bamList;
    this.nbasesInView = nbasesInView;
    this.feature_display = feature_display;
    this.bases = bases;

    containerPanel.setLayout(new BoxLayout(containerPanel, BoxLayout.Y_AXIS));
    containerPanel.add(mainPanel);
    
    // filter out unmapped reads by default
    setSamRecordFlagPredicate(
        new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
    
    if(reference != null)
    {
      System.setProperty("reference", reference); // for CRAM
      EntryGroup entryGroup = new SimpleEntryGroup();
      try
      {
        getEntry(reference,entryGroup);
      }
      catch (NoSequenceException e)
      {
        e.printStackTrace();
      }
    }
    
    if(Options.getOptions().getIntegerProperty("bam_read_thread") != null)
    { 
      logger4j.debug("BAM READ THREADS="+Options.getOptions().getIntegerProperty("bam_read_thread"));
      bamReadTaskExecutor = Executors.newFixedThreadPool(
          Options.getOptions().getIntegerProperty("bam_read_thread"));
    }
    else
      bamReadTaskExecutor = Executors.newFixedThreadPool(1);
    
    
    if(Options.getOptions().getIntegerProperty("bam_max_coverage") != null)
    { 
      logger4j.debug("BAM MAX COVERAGE="+Options.getOptions().getIntegerProperty("bam_max_coverage"));
      MAX_COVERAGE = Options.getOptions().getIntegerProperty("bam_max_coverage");
    }  

    try
    {
      readHeaderPicard();
    }
    catch(java.lang.UnsupportedClassVersionError err)
    {
      JOptionPane.showMessageDialog(null, 
          "This requires Java 1.6 or higher.", 
          "Check Java Version", JOptionPane.WARNING_MESSAGE);
    }
    catch (IOException e)
    {
      e.printStackTrace();
    }

    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');
    BASE_HEIGHT = fm.getMaxAscent();
    selection = new Selection(null);
    
    MultiLineToolTipUI.initialize();
    setToolTipText("");
    
    buttonGroup.add(cbStackView);
    buttonGroup.add(cbPairedStackView);
    buttonGroup.add(cbStrandStackView);
    buttonGroup.add(cbIsizeStackView);
    buttonGroup.add(cbCoverageView);
    buttonGroup.add(cbCoverageStrandView);
    addMouseListener(new PopupListener());

    jspView = new JScrollPane(this, 
        JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
        JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    
    jspView.setViewportBorder(BorderFactory.createMatteBorder(0, 0, 1, 0, Color.DARK_GRAY));
    Border empty = new EmptyBorder(0,0,0,0);
    jspView.setBorder(empty);
    jspView.getVerticalScrollBar().setUnitIncrement(8);

    addBamToPanel(frame);
  }
  
  public String getToolTipText()
  {
    if(mouseOverSAMRecord == null)
      return null;
    
    String msg = 
        mouseOverSAMRecord.sam.getReadName() + "\n" + 
        mouseOverSAMRecord.sam.getAlignmentStart() + ".." +
        mouseOverSAMRecord.sam.getAlignmentEnd() + "\nisize=" +
        mouseOverSAMRecord.sam.getInferredInsertSize() + "\nmapq=" +
        mouseOverSAMRecord.sam.getMappingQuality()+"\nrname="+
        mouseOverSAMRecord.sam.getReferenceName();

    if( mouseOverSAMRecord.sam.getReadPairedFlag() && 
        mouseOverSAMRecord.sam.getProperPairFlag() && 
       !mouseOverSAMRecord.sam.getMateUnmappedFlag())
    {
      msg = msg +
        "\nstrand (read/mate): "+
       (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
       (mouseOverSAMRecord.sam.getMateNegativeStrandFlag() ? "-" : "+");
    }
    else
      msg = msg +
        "\nstrand (read/mate): "+
       (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+");
    
    if(msg != null && mouseOverInsertion != null)
      msg = msg + "\nInsertion at:" +mouseOverInsertion;
    
    return msg;
  }
  
  /**
   * Get the BAM index file from the list
   * @param bam
   * @return
   * @throws IOException
   */
  private File getBamIndexFile(String bam) throws IOException
  {
    File bamIndexFile = null;
    if (bam.startsWith("http") || bam.startsWith("ftp"))
    {
      final URL urlBamIndexFile = new URL(bam + ".bai");
      InputStream is = urlBamIndexFile.openStream();

      // Create temp file.
      bamIndexFile = File.createTempFile(urlBamIndexFile.getFile().replaceAll(
          "[\\/\\s]", "_"), ".bai");
      bamIndexFile.deleteOnExit();

      FileOutputStream out = new FileOutputStream(bamIndexFile);
      int c;
      while ((c = is.read()) != -1)
        out.write(c);
      out.flush();
      out.close();
      is.close();

      logger4j.debug("create... " + bamIndexFile.getAbsolutePath());
    }
    else
    {
      bamIndexFile = new File(bam + ".bai");
      if(!bamIndexFile.exists())
      {
        final File cramIndexFile = new File(bam + ".crai");
        if(cramIndexFile.exists())
          return cramIndexFile;
      }
    }

    return bamIndexFile;
  }
    
  /**
   * Get the SAM file reader.
   * @param bam
   * @return
   * @throws IOException
   */
  private SAMFileReader getSAMFileReader(final String bam) throws IOException
  {
    // parsing of the header happens during SAMFileReader construction, 
    // so need to set the default stringency
    SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
    
    if(samFileReaderHash.containsKey(bam))
      return samFileReaderHash.get(bam);

    File bamIndexFile = getBamIndexFile(bam);
    if(!bamIndexFile.exists())
    {
      try
      {
        logger4j.warn("Index file not found so using picard to index the BAM.");
        // Use Picard to index the file
        // requires reads to be sorted by coordinate
        new BuildBamIndex().instanceMain(
          new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000", "VALIDATION_STRINGENCY=SILENT" });
      }
      catch(SAMException e)
      {
        String ls = System.getProperty("line.separator");
        String msg = 
            "BAM index file is missing. The BAM file needs to be sorted and indexed"+ls+
            "This can be done using samtools (http://samtools.sf.net/):"+ls+ls+
            "samtools sort <in.bam> <out.prefix>"+ls+
            "samtools index <sorted.bam>";
        
        throw new SAMException(msg);
      }
    }
    
    final SAMFileReader samFileReader;
    
    if(feature_display != null && bam.endsWith("cram"))
    {
      final CRAMReferenceSequenceFile ref = new CRAMReferenceSequenceFile(
        feature_display.getEntryGroup().getSequenceEntry(), this);
      
      final Map<Object, ReferenceSequenceFile> referenceFactory = 
          new HashMap<Object, ReferenceSequenceFile>();
      referenceFactory.put(bamIndexFile, ref);

      try
      {
        Class<?> cls = getClass().getClassLoader().loadClass("net.sf.samtools.ReferenceDiscovery");
        Field f = cls.getDeclaredField("referenceFactory");
        f.set(null, referenceFactory);
      }
      catch (ClassNotFoundException e)
      {
        System.err.println("Check cramtools.jar is in the CLASSPATH. "+e.getMessage());
      }
      catch (SecurityException e)
      {
        e.printStackTrace();
      }
      catch (NoSuchFieldException e)
      {
        e.printStackTrace();
      }
      catch (IllegalArgumentException e)
      {
        e.printStackTrace();
      }
      catch (IllegalAccessException e)
      {
        e.printStackTrace();
      }

      
      //net.sf.samtools.ReferenceDiscovery.referenceFactory.put(bamIndexFile, ref);
    }
    
    if(bam.startsWith("ftp"))
    {
      FTPSeekableStream fss = new FTPSeekableStream(new URL(bam));
      samFileReader = new SAMFileReader(fss, bamIndexFile, false);
    }
    else if(!bam.startsWith("http"))
    {
      File bamFile = new File(bam);
      samFileReader = new SAMFileReader(bamFile, bamIndexFile);
    }
    else
    {
      final URL urlBamFile = new URL(bam);
      samFileReader = new SAMFileReader(urlBamFile, bamIndexFile, false);
    }
    samFileReader.setValidationStringency(ValidationStringency.SILENT);
    samFileReaderHash.put(bam, samFileReader);
    
    return samFileReader;
  }

  private void readHeaderPicard() throws IOException
  {
    final SAMFileReader inputSam = getSAMFileReader(bamList.get(0));
    final SAMFileHeader header = inputSam.getFileHeader();

    for(SAMSequenceRecord seq: header.getSequenceDictionary().getSequences())
    {
      seqLengths.put(seq.getSequenceName(),
                     seq.getSequenceLength());
      seqNames.add(seq.getSequenceName());
    }
  }
  
  class BamReadTask implements Runnable 
  {
    private int start; 
    private int end; 
    private short bamIndex; 
    private float pixPerBase;
    private CountDownLatch latch;
    BamReadTask(int start, int end, short bamIndex, float pixPerBase, CountDownLatch latch)  
    {
      this.start = start;
      this.end = end;
      this.bamIndex = bamIndex;
      this.pixPerBase = pixPerBase;
      this.latch = latch;
    }

    public void run() 
    {
      try
      {
        readFromBamPicard(start, end, bamIndex, pixPerBase) ;
      }
      catch (OutOfMemoryError ome)
      {
        throw ome;
      }
      catch(IOException me)
      {
        me.printStackTrace();
      }
      finally
      {
        latch.countDown();
      }
    }
  }

  /**
   * Read a SAM or BAM file.
   * @throws IOException 
   */
  private void readFromBamPicard(int start, int end, short bamIndex, float pixPerBase) 
          throws IOException
  {
    // Open the input file.  Automatically detects whether input is SAM or BAM
    // and delegates to a reader implementation for the appropriate format.
    final String bam = bamList.get(bamIndex);
    final SAMFileReader inputSam = getSAMFileReader(bam);
    
    //final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
    if(isConcatSequences())
    {
      for(String seq: seqNames)
      {
        int sLen = seqLengths.get(seq);
        int offset = getSequenceOffset(seq); 
        int sBeg = offset+1;
        int sEnd = sBeg+sLen-1;

        if( (sBeg >= start && sBeg <= end) ||
            (sBeg <= start && sEnd >= start) )
        {
          int thisStart = start - offset;
          if(thisStart < 1)
            thisStart = 1;
          int thisEnd   = end - offset;
          if(thisEnd > sLen)
            thisEnd = sLen;

          iterateOverBam(inputSam, seq, thisStart, thisEnd, bamIndex, pixPerBase, bam);
          //System.out.println("READ "+seq+"  "+thisStart+".."+thisEnd+" "+start+" --- "+offset);
        }
      }
    }
    else
    {
      String refName = (String) combo.getSelectedItem();
      iterateOverBam(inputSam, refName, start, end, bamIndex, pixPerBase, bam);
    }
    //inputSam.close();
  }
  
  /**
   * 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, 
                             final String refName, final int start, final int end,
                             final short bamIndex, final float pixPerBase,
                             final String bam)
  {
    final MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
    final int checkMemAfter = 8000;
    final int seqOffset = getSequenceOffset(refName);
    final int offset = seqOffset- getBaseAtStartOfView();
    final boolean isCoverageView = isCoverageView(pixPerBase);

    int cnt = 0;

    int nbins = 800;
    int binSize = ((end-start)/nbins)+1;
    if(binSize < 1)
    {
      binSize = 1;
      nbins = end-start+1;
    }
    int max = MAX_COVERAGE*binSize;
    if(max < 1)
      max = Integer.MAX_VALUE;
    final int cov[] = new int[nbins];
    for(int i=0; i<nbins; i++)
      cov[i] = 0;
    
    final CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
    try
    {
      while ( it.hasNext() )
      {
        try
        {
          cnt++;
          SAMRecord samRecord = it.next();

          if( samRecordFlagPredicate == null ||
             !samRecordFlagPredicate.testPredicate(samRecord))
          {
            if(samRecordMapQPredicate == null ||
               samRecordMapQPredicate.testPredicate(samRecord))
            {
              int abeg = samRecord.getAlignmentStart();
              int aend = samRecord.getAlignmentEnd();
              boolean over = false;
              
              for(int i=abeg; i<aend; i++)
              {
                
                int bin = ((i-start)/binSize)-1;
                if(bin < 0)
                  bin = 0;
                else if(bin > nbins-1)
                  bin = nbins-1;
                cov[bin]++;
                if(cov[bin] > max)
                {
                  over = true;
                  break;
                }
              }
             
              if(over)
                continue;

              if(isCoverageView)
                coverageView.addRecord(samRecord, offset, bam);
              if(isCoverage)
                coveragePanel.addRecord(samRecord, offset, bam);
              if(isSNPplot)
                snpPanel.addRecord(samRecord, seqOffset);
              if(!isCoverageView)
                readsInView.add(new BamViewRecord(samRecord, bamIndex));
            }
          }
        
          if(cnt > checkMemAfter)
          {
            cnt = 0;
            float heapFraction =
              (float)((float)memory.getHeapMemoryUsage().getUsed()/
                      (float)memory.getHeapMemoryUsage().getMax());
            logger4j.debug("Heap memory usage (used/max): "+heapFraction);
          
            if(readsInView.size() > checkMemAfter*2 && !waitingFrame.isVisible())
              waitingFrame.showWaiting("loading...", mainPanel);

            if(heapFraction > 0.90) 
            {
              popFrame.show(
                "Using > 90 % of the maximum memory limit:"+
                (memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb.\n"+
                "Not all reads in this range have been read in. Zoom in or\n"+
                "consider increasing the memory for this application.",
                mainPanel,
                15000);
              break;
            }
          }
        }
        catch(Exception e)
        {
          System.err.println(e.getMessage());
        }
      }
    }
    finally
    {
      it.close();
    }
  }

  private int getSequenceLength()
  {
    if(isConcatSequences())
    {
      int len = 0;
      for(String seq: seqNames)
        len += seqLengths.get(seq);
      return len;
    }
    else
      return seqLengths.get((String) combo.getSelectedItem());
  }
  
  /**
   * For BAM files with multiple references sequences, calculate
   * the offset from the start of the concatenated sequence for 
   * a given reference.
   * @param refName
   * @return
   */
  protected int getSequenceOffset(String refName)
  {
    if(!isConcatSequences())
      return 0;
    
    if(offsetLengths == null)
    {   
/*    offsetLengths = new Hashtable<String, Integer>(combo.getItemCount());
      int offset = 0;
      for(int i=0; i<combo.getItemCount(); i++)
      {
        String thisSeqName = (String) combo.getItemAt(i);
        offsetLengths.put(thisSeqName, offset);
        offset += seqLengths.get(combo.getItemAt(i));
      }*/

      final FeatureVector features = feature_display.getEntryGroup().getAllFeatures();
      final HashMap<String, Integer> lookup = new HashMap<String, Integer>();
      for(int i=0; i<features.size(); i++)
        lookup.put(features.elementAt(i).getIDString(), features.elementAt(i).getFirstBase());
        
      offsetLengths = new HashMap<String, Integer>(seqNames.size());
      for(int i=0; i<seqNames.size(); i++)
      {
        final Integer pos = lookup.get(seqNames.get(i));
        if(pos != null)
          offsetLengths.put(seqNames.get(i), pos-1);
       /*final FeatureContigPredicate predicate = new FeatureContigPredicate(seqNames.get(i).trim());
        for(int j=0; j<features.size(); j++)
        {
          if(predicate.testPredicate(features.elementAt(j)))
          {
            offsetLengths.put(seqNames.get(i), features.elementAt(j).getFirstBase()-1);
            break;
          }
        }*/
      }
      
      if(offsetLengths.size() != seqNames.size())
      {
        System.err.println("Found: "+offsetLengths.size() +" of "+ seqNames.size());
        SwingUtilities.invokeLater(new Runnable() 
        {
          public void run() 
          {
            JOptionPane.showMessageDialog(BamView.this, 
                "There is a problem matching the reference sequences\n"+
                "to the names in the BAM file. This may mean the labels\n"+
                "on the reference features do not match those in the in\n"+
                "the BAM file.", 
                "Problem Found", JOptionPane.WARNING_MESSAGE);
          }
        });
        
        //concatSequences = false;
        int offset = 0;
        for(int i=0; i<combo.getItemCount(); i++)
        {
          String thisSeqName = (String) combo.getItemAt(i);
          offsetLengths.put(thisSeqName, offset);
          offset += seqLengths.get(combo.getItemAt(i));
        }
        //return 0;
      }
    }
    return offsetLengths.get(refName);
  }

  /**
   * Override
   */
  protected void paintComponent(Graphics g)
  {
	super.paintComponent(g);
	Graphics2D g2 = (Graphics2D)g;

	mouseOverSAMRecord = null;
    final int seqLength = getSequenceLength();
    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;
      
      if(feature_display != null && nbasesInView < feature_display.getMaxVisibleBases())
        nbasesInView = feature_display.getMaxVisibleBases();
    }

    final float pixPerBase = getPixPerBaseByWidth();
    boolean changeToStackView = false;
    MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
    if(laststart != start ||
       lastend   != end ||
       CoveragePanel.isRedraw())
    {
      if(isCoverageView(pixPerBase))
        coverageView.init(this, pixPerBase, start, end);
      if(isCoverage)
        coveragePanel.init(this, pixPerBase, start, end);
      if(isSNPplot)
        snpPanel.init(this, pixPerBase, start, end);

      synchronized (this)
      {
        try
        {
          float heapFractionUsedBefore = (float) ((float) memory.getHeapMemoryUsage().getUsed() / 
                                                  (float) memory.getHeapMemoryUsage().getMax());
          if(readsInView == null)
            readsInView = new Vector<BamViewRecord>();
          else
            readsInView.clear();

          final CountDownLatch latch = new CountDownLatch(bamList.size()-hideBamList.size());
          //long ms = System.currentTimeMillis();
          for(short i=0; i<bamList.size(); i++)
          {
            if(!hideBamList.contains(i))
              bamReadTaskExecutor.execute(
                  new BamReadTask(start, end, i, pixPerBase, latch));
          }

          try 
          {
            latch.await();
          }
          catch (InterruptedException e) {} // TODO 

          //System.out.println("===== NO. THREADS="+
          //     ((java.util.concurrent.ThreadPoolExecutor)bamReadTaskExecutor).getPoolSize()+" TIME="+(System.currentTimeMillis()-ms));

          float heapFractionUsedAfter = (float) ((float) memory.getHeapMemoryUsage().getUsed() / 
                                                 (float) memory.getHeapMemoryUsage().getMax());

          // System.out.println("Heap Max  : "+memory.getHeapMemoryUsage().getMax());
          // System.out.println("Heap Used : "+memory.getHeapMemoryUsage().getUsed());
          // System.out.println("Heap memory used "+heapFractionUsedAfter);

          if ((heapFractionUsedAfter - heapFractionUsedBefore) > 0.06
              && !isStackView() && heapFractionUsedAfter > 0.8)
          {
            cbStackView.setSelected(true);
            changeToStackView = true;
          }

          if((!isStackView() && !isStrandStackView()) || isBaseAlignmentView(pixPerBase))
          {
            Collections.sort(readsInView, new SAMRecordComparator());
          }
          else if( (isStackView() || isStrandStackView()) &&
              bamList.size() > 1)
          {
            // merge multiple BAM files
            Collections.sort(readsInView, new SAMRecordPositionComparator(BamView.this));
          }
        }
        catch (OutOfMemoryError ome)
        {
          JOptionPane.showMessageDialog(this, "Out of Memory");
          readsInView.clear();
          return;
        }
        catch(net.sf.samtools.util.RuntimeIOException re)
        {
          JOptionPane.showMessageDialog(this, re.getMessage());
        }
      }
    }

    laststart = start;
    lastend   = end;
    
    if(showBaseAlignment)
	  drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
	else
	{
	  if(isCoverageView(pixPerBase))
	    drawCoverage(g2,start, end, pixPerBase);
	  else if(isStackView())  
	    drawStackView(g2, seqLength, pixPerBase, start, end);
	  else if(isPairedStackView())
	    drawPairedStackView(g2, seqLength, pixPerBase, start, end);
	  else if(isStrandStackView())
	    drawStrandStackView(g2, seqLength, pixPerBase, start, end);
	  else
	    drawLineView(g2, seqLength, pixPerBase, start, end);
	}
    
    if(isCoverage)
      coveragePanel.repaint();
    if(isSNPplot)
      snpPanel.repaint();

	if(waitingFrame.isVisible())
      waitingFrame.hideFrame();
	if(changeToStackView)
	{
	  popFrame.show(
          "Note :: Changed to the stack view to save memory.\n"+
          "Currently this is using "+ 
          (memory.getHeapMemoryUsage().getUsed()/1000000.f)+" Mb "+
          "and the maximum\nmemory limit is "+
          (memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb.",
          mainPanel,
          15000);
	}
  }
  
  
  private float getPixPerBaseByWidth()
  {
    return (float)mainPanel.getWidth() / (float)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, 
                                 int end)
  {
    ruler.start = start;
    ruler.end = end;

    int ypos = 0;
    String refSeq = null;
    int refSeqStart = start;
    
    end = start + ( mainPanel.getWidth() * ALIGNMENT_PIX_PER_BASE );
    if(bases != null)
    {
      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();
        
        ruler.refSeq = refSeq;
      }
      catch (OutOfRangeException e)
      {
        e.printStackTrace();
      }
    }
    ruler.repaint();
    drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end, Color.PINK);

    g2.setStroke(new BasicStroke (2.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND));
    
    boolean drawn[] = new boolean[readsInView.size()];
    for(int i=0; i<readsInView.size(); i++)
      drawn[i] = false;
    
    Rectangle r = jspView.getViewport().getViewRect();
    int nreads = readsInView.size();
    
    for (int i = 0; i < nreads; i++)
    {
      try
      {
        if (!drawn[i])
        {
          ypos += 11;

          BamViewRecord thisRead = readsInView.get(i);
          if (ypos < r.getMaxY() || ypos > r.getMinY())
            drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
          drawn[i] = true;

          int thisEnd = thisRead.sam.getAlignmentEnd();
          if (thisEnd == 0)
            thisEnd = thisRead.sam.getAlignmentStart() + thisRead.sam.getReadLength();

          for (int j = i + 1; j < nreads; j++)
          {
            if (!drawn[j])
            {
              BamViewRecord nextRead = readsInView.get(j);
              int nextStart = nextRead.sam.getAlignmentStart();
              if (nextStart > thisEnd + 1)
              {
                if (ypos < r.getMaxY() || ypos > r.getMinY())
                  drawSequence(g2, nextRead, ypos, refSeq, refSeqStart);

                drawn[j] = true;
                thisEnd = nextRead.sam.getAlignmentEnd();
                if (thisEnd == 0)
                  thisEnd = nextStart + nextRead.sam.getReadLength();
              }
              else if (ypos > r.getMaxY() || ypos < r.getMinY())
                break;
            }
          }
        }
      }
      catch (ArrayIndexOutOfBoundsException ae)
      {
        System.err.println(readsInView.size()+"  "+nreads);
        ae.printStackTrace();
      }
    }
    
    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, BamViewRecord bamViewRecord, 
                            int ypos, String refSeq, int refSeqStart)
  {
    SAMRecord samRecord = bamViewRecord.sam;
    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);
    
    final Color col = g2.getColor();
    int xpos;
    int len    = 0;
    int refPos = 0;
    String readSeq = samRecord.getReadString();
    int offset = getSequenceOffset(samRecord.getReferenceName());

    byte[] phredQuality = null;
    if(baseQualityColour.isSelected())
      phredQuality = samRecord.getBaseQualities();

    Hashtable<Integer, String> insertions = null;
    List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
    for(int i=0; i<blocks.size(); i++)
    {
      AlignmentBlock block = blocks.get(i);
      int blockStart = block.getReadStart();
      len += block.getLength();
      for(int j=0; j<block.getLength(); j++)
      {
        int readPos = blockStart-1+j;
        xpos = block.getReferenceStart() - 1 + j + offset;
        refPos = xpos - refSeqStart + 1;

        if(phredQuality != null)
          setColourByBaseQuality(g2, phredQuality[readPos]);

        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(isSNPs)
          g2.setColor(col);
      }
          
      // look for insertions
      if(markInsertions.isSelected() && i < blocks.size()-1)
      {
        int blockEnd = blockStart+block.getLength();
        int nextBlockStart = blocks.get(i+1).getReadStart();
        int insertSize = nextBlockStart - blockEnd;
        if(insertSize > 0)
        {
          if(insertions == null)
            insertions = new Hashtable<Integer, String>();

          g2.setColor(DEEP_PINK);

          int xscreen = (refPos+1)*ALIGNMENT_PIX_PER_BASE;
          insertions.put(xscreen, 
              (refPos+refSeqStart+1)+" "+
              readSeq.substring(blockEnd-1, nextBlockStart-1));
          g2.drawLine(xscreen, ypos, xscreen, ypos-BASE_HEIGHT);
          
          // mark on reference sequence as well
          if(bases != null)
            g2.drawLine(xscreen, 11, xscreen, 11-BASE_HEIGHT);
          g2.setColor(col);
        }
      }
      
      // highlight
      if(highlightSAMRecord != null &&
         highlightSAMRecord.sam.getReadName().equals(samRecord.getReadName()))
      {
        refPos =  block.getReferenceStart() + offset - refSeqStart;
        int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
        int width  = block.getLength()*ALIGNMENT_PIX_PER_BASE;
        Color col1 = g2.getColor();
        g2.setColor(Color.red);
        g2.drawRect(xstart, ypos-BASE_HEIGHT, width, BASE_HEIGHT);        
        if(i < blocks.size()-1)
        {
          int nextStart = 
            (blocks.get(i+1).getReferenceStart() + offset - refSeqStart)*ALIGNMENT_PIX_PER_BASE;
          g2.drawLine(xstart+width, ypos-(BASE_HEIGHT/2), nextStart, ypos-(BASE_HEIGHT/2));
        }
        
        g2.setColor(col1);
      }
      else if(i < blocks.size()-1)
      {
        refPos =  block.getReferenceStart() + offset - refSeqStart;
        int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
        int width  = block.getLength()*ALIGNMENT_PIX_PER_BASE;
        int nextStart = 
          (blocks.get(i+1).getReferenceStart() + offset - refSeqStart)*ALIGNMENT_PIX_PER_BASE;
        g2.drawLine(xstart+width, ypos-(BASE_HEIGHT/2), nextStart, ypos-(BASE_HEIGHT/2));
      }
    }

    if(lastMousePoint != null && blocks.size() > 0)
    {
      refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
      int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
      
      refPos = blocks.get(blocks.size()-1).getReferenceStart()+
               blocks.get(blocks.size()-1).getLength()+offset-refSeqStart;
      int xend   = (refPos+len)*ALIGNMENT_PIX_PER_BASE;

      if(lastMousePoint.getY() > ypos-11 && lastMousePoint.getY() < ypos)
      if(lastMousePoint.getX() > xstart &&
         lastMousePoint.getX() < xend)
      {
        mouseOverSAMRecord = bamViewRecord;

        if(insertions != null)
          mouseOverInsertion = insertions.get((int)lastMousePoint.getX());
      }
    }
  }
  
  /**
   * Colour bases on their mapping quality.
   * @param g2
   * @param baseQuality
   */
  private void setColourByBaseQuality(Graphics2D g2, byte baseQuality)
  {
    if (baseQuality < 10)
      g2.setColor(Color.blue);
    else if (baseQuality < 20)
      g2.setColor(DARK_GREEN);
    else if (baseQuality < 30)
      g2.setColor(DARK_ORANGE);
    else
      g2.setColor(Color.black);
  }
  
  /**
   * Draw inferred size 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, Color.PINK);
    if(isShowScale())
      drawScale(g2, start, end, pixPerBase, getHeight());
    
    final Stroke stroke =
      new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
    g2.setStroke(stroke);
    
    final int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    int baseAtStartOfView = getBaseAtStartOfView();
    Rectangle r = jspView.getViewport().getViewRect();
    
    for(int i=0; i<readsInView.size(); i++)
    {
      BamViewRecord bamViewRecord = readsInView.get(i);
      SAMRecord samRecord = bamViewRecord.sam;
      BamViewRecord bamViewNextRecord = null;
      SAMRecord samNextRecord = null;      

      List<Integer> snps = getSNPs(samRecord);
      
      if( !samRecord.getReadPairedFlag() ||  // read is not paired in sequencing
          samRecord.getMateUnmappedFlag() )  // mate is unmapped
      {
        if(isSingle)
        {
          int ypos = getYPos(scaleHeight, samRecord.getReadString().length()); // (getHeight() - scaleHeight) - samRecord.getReadString().length();
          if(ypos > r.getMaxY() || ypos < r.getMinY())
            continue;
          
          g2.setColor(Color.black);
          drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
        }
        continue;
      }

      int ypos = getYPos(scaleHeight, Math.abs(samRecord.getInferredInsertSize()));
      if( (ypos > r.getMaxY() || ypos < r.getMinY()) && ypos > 0 )
        continue;
      
      if(i < readsInView.size()-1)
      {
        bamViewNextRecord = readsInView.get(++i);
        samNextRecord = bamViewNextRecord.sam;

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

            int offset1 = getSequenceOffset(samRecord.getReferenceName());
            int end1   = samRecord.getAlignmentEnd()+offset1-baseAtStartOfView;
            
            int offset2 = getSequenceOffset(samNextRecord.getReferenceName());
            int start2  = samNextRecord.getAlignmentStart()+offset2-baseAtStartOfView;
            
            drawTranslucentLine(g2, 
                   (int)(end1*pixPerBase), (int)(start2*pixPerBase), ypos);
          }
          
          if(colourByCoverageColour.isSelected())
            g2.setColor(getColourByCoverageColour(bamViewRecord));
          else if( (samRecord.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
                    samNextRecord.getReadNegativeStrandFlag()) ||
                   (!samRecord.getReadNegativeStrandFlag() && 
                    !samNextRecord.getReadNegativeStrandFlag()))
            g2.setColor(Color.red);
          else
            g2.setColor(Color.blue);

          drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
          drawRead(g2, bamViewNextRecord, pixPerBase, ypos, baseAtStartOfView, getSNPs(samNextRecord));
        }
        else
        {
          drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps);
          i--;
        }
      }
      else
      {
        drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps);
      }
    }
    
    drawYScale(g2, scaleHeight);
  }
  
  private int getYPos(int scaleHeight, int size)
  {
    if(!logScale)
      return (getHeight() - scaleHeight) - size;
    else
    {
      int logInfSize = (int)( Math.log(size) * 100);
      return (getHeight() - scaleHeight) - logInfSize;
    }
  }
 
  /**
   * 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, 
                             final int seqLength, 
                             final float pixPerBase, 
                             final int start, 
                             final int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
    if(isShowScale())
      drawScale(g2, start, end, pixPerBase, getHeight());

    final BasicStroke stroke = new BasicStroke(
        1.3f,
        BasicStroke.CAP_BUTT, 
        BasicStroke.JOIN_MITER);
    g2.setStroke(stroke);
    
    final int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    int ypos = (getHeight() - scaleHeight);
    int ydiff = 2;
    if(isOrientation)
      ydiff= 4;
    int maxEnd = 0;
    int lstStart = 0;
    int lstEnd = 0;
    final int baseAtStartOfView = getBaseAtStartOfView();
    g2.setColor(Color.blue);
    final Rectangle r = jspView.getViewport().getViewRect();
    
    for(BamViewRecord bamViewRecord: readsInView)
    {
      SAMRecord samRecord = bamViewRecord.sam;
      int offset = getSequenceOffset(samRecord.getReferenceName());

      int recordStart = samRecord.getAlignmentStart()+offset;
      int recordEnd = samRecord.getAlignmentEnd()+offset;
      
      List<Integer> snps = getSNPs(samRecord);
      
      if(colourByCoverageColour.isSelected() ||
         lstStart != recordStart || lstEnd != recordEnd || snps != null)
      { 
        if(colourByCoverageColour.isSelected())
          g2.setColor(getColourByCoverageColour(bamViewRecord));
        else 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 < 0)
        {
          ypos = (getHeight() - scaleHeight)-ydiff;
          maxEnd = recordEnd+2;
        }
        else
          ypos = ypos-ydiff;
      }
      else
        g2.setColor(DARK_GREEN);

      if(snps != null)
        lstStart = -1;
      else
      {
        lstStart = recordStart;
        lstEnd   = recordEnd;
      }
      
      if(ypos > r.getMaxY() || ypos < r.getMinY())
        continue;
      drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
    }
  }
  
  /**
   * 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 drawStrandStackView(Graphics2D g2, 
                                   int seqLength, 
                                   float pixPerBase, 
                                   int start, 
                                   int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);   
    final BasicStroke stroke = new BasicStroke(
        1.3f,
        BasicStroke.CAP_BUTT, 
        BasicStroke.JOIN_MITER);
    
    final int scaleHeight = 15;
    drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));

    int ymid = (getHeight()/ 2);
    int ydiff = 2;
    if(isOrientation)
      ydiff= 4;
    // positive strand    
    drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -ydiff, pixPerBase, stroke);
    
    // negative strand
    drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), ydiff, pixPerBase, stroke);
  }
  
  private void drawStrand(Graphics2D g2, 
                          boolean isStrandNegative, 
                          int scaleHeight,
                          int ymid,
                          int ystep,
                          float pixPerBase,
                          Stroke stroke)
  {
    int hgt = getHeight();
    int ypos = (hgt - scaleHeight);
    int maxEnd = 0;
    int lstStart = 0;
    int lstEnd = 0;
    int baseAtStartOfView = getBaseAtStartOfView();
    g2.setColor(Color.blue);
    Rectangle r = jspView.getViewport().getViewRect();
    
    for(BamViewRecord bamViewRecord: readsInView)
    {
      SAMRecord samRecord = bamViewRecord.sam;
      if( samRecord.getReadNegativeStrandFlag() == isStrandNegative )
      {
        final int offset = getSequenceOffset(samRecord.getReferenceName());
        final int recordStart = samRecord.getAlignmentStart()+offset;
        final int recordEnd   = samRecord.getAlignmentEnd()+offset;
        List<Integer> snps = getSNPs(samRecord);
        
        if(colourByCoverageColour.isSelected() ||
            lstStart != recordStart || lstEnd != recordEnd || snps != null)
        { 
          if(colourByCoverageColour.isSelected())
            g2.setColor(getColourByCoverageColour(bamViewRecord));
          else if (!samRecord.getReadPairedFlag() ||   // read is not paired in sequencing
                    samRecord.getMateUnmappedFlag() )  // mate is unmapped 
            g2.setColor(Color.black);
          else
            g2.setColor(Color.blue);
        
          if(maxEnd < recordStart || ypos < 0 || ypos > hgt)
          {
            ypos = ymid + ystep;
            maxEnd = recordEnd+2;
          }
          else
            ypos = ypos + ystep;
        }
        else
          g2.setColor(DARK_GREEN);

        if(snps != null)
          lstStart = -1;
        else
        {
          lstStart = recordStart;
          lstEnd   = recordEnd;
        }
        
        if(ypos > r.getMaxY() || ypos < r.getMinY())
          continue;

        drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
      }
    }
  }
  
  /**
   * Draw paired reads as lines in a vertical stacks. 
   * @param g2
   * @param seqLength
   * @param pixPerBase
   * @param start
   * @param end
   */
  private void drawPairedStackView(Graphics2D g2, 
                                   final int seqLength, 
                                   final float pixPerBase, 
                                   final int start, 
                                   final int end)
  {
    drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
    if(isShowScale())
      drawScale(g2, start, end, pixPerBase, getHeight());

    final Vector<PairedRead> pairedReads = new Vector<PairedRead>();   
    for(int i=0; i<readsInView.size(); i++)
    {
      BamViewRecord bamViewRecord = readsInView.get(i);
      SAMRecord samRecord = bamViewRecord.sam;
      if( !samRecord.getReadPairedFlag() ||  // read is not paired in sequencing
          samRecord.getMateUnmappedFlag() )  // mate is unmapped
        continue;

      BamViewRecord bamViewNextRecord = null;      
      if(i < readsInView.size()-1)
      {
        bamViewNextRecord = readsInView.get(++i);
        SAMRecord samNextRecord = bamViewNextRecord.sam;
        
        final PairedRead pr = new PairedRead();
        if(samRecord.getReadName().equals(samNextRecord.getReadName()) && 
           isFromSameBamFile(bamViewRecord, bamViewNextRecord, bamList))
        { 
          if(samRecord.getAlignmentStart() < samNextRecord.getAlignmentStart())
          {
            pr.sam1 = bamViewRecord;
            pr.sam2 = bamViewNextRecord;
          }
          else
          {
            pr.sam2 = bamViewRecord;
            pr.sam1 = bamViewNextRecord;
          }
        }
        else
        {
          --i;
          pr.sam1 = bamViewRecord;
          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);
    g2.setStroke(stroke);
    
    final int scaleHeight;
    if(isShowScale())
      scaleHeight = 15;
    else
      scaleHeight = 0;
    
    int ydiff = 3;
    if(isOrientation)
      ydiff= 5;
    int ypos = getHeight() - scaleHeight - ydiff;
    int lastEnd = 0;
    int baseAtStartOfView = getBaseAtStartOfView();
    Rectangle r = jspView.getViewport().getViewRect();

    for(PairedRead pr: pairedReads)
    {
      if(pr.sam1.sam.getAlignmentStart() > lastEnd)
      {
        ypos = getHeight() - scaleHeight - ydiff;
        if(pr.sam2 != null)
          lastEnd = pr.sam2.sam.getAlignmentEnd();
        else
          lastEnd = pr.sam1.sam.getAlignmentEnd();
      }
      else
        ypos = ypos - ydiff;
      
      if(ypos > r.getMaxY() || ypos < r.getMinY())
        continue;
      
      g2.setStroke(originalStroke);
      
      if(highlightSAMRecord != null && 
          highlightSAMRecord.sam.getReadName().equals(pr.sam1.sam.getReadName()))
        g2.setColor(Color.black);
      else
        g2.setColor(Color.gray);
      
      if(pr.sam2 != null)
      {
        if(!readsOverlap(pr.sam1.sam, pr.sam2.sam))
        {
          int offset1 = getSequenceOffset(pr.sam1.sam.getReferenceName());
          int offset2 = getSequenceOffset(pr.sam2.sam.getReferenceName());
          drawTranslucentJointedLine(g2, 
              (int)((pr.sam1.sam.getAlignmentEnd()+offset1-getBaseAtStartOfView())*pixPerBase),
              (int)((pr.sam2.sam.getAlignmentStart()+offset2-getBaseAtStartOfView())*pixPerBase), ypos);
        }
      }
      else if(!pr.sam1.sam.getMateUnmappedFlag() &&
               pr.sam1.sam.getProperPairFlag() &&
               pr.sam1.sam.getMateReferenceName().equals(pr.sam1.sam.getReferenceName()))
      {
        final int prStart, prEnd;
        if(pr.sam1.sam.getAlignmentStart() > pr.sam1.sam.getMateAlignmentStart())
        {
          prStart = pr.sam1.sam.getMateAlignmentStart();
          prEnd = pr.sam1.sam.getAlignmentStart();
        }
        else
        {
          prStart = pr.sam1.sam.getAlignmentEnd();
          prEnd = pr.sam1.sam.getMateAlignmentStart();
        }

        int offset = getSequenceOffset(pr.sam1.sam.getReferenceName());
        drawTranslucentJointedLine(g2, 
              (int)( (prStart+offset-getBaseAtStartOfView())*pixPerBase),
              (int)( (prEnd  +offset-getBaseAtStartOfView())*pixPerBase), ypos);
      }
      
      if(colourByCoverageColour.isSelected())
        g2.setColor(getColourByCoverageColour(pr.sam1));
      else if(   pr.sam2 != null && 
              !( pr.sam1.sam.getReadNegativeStrandFlag() ^ pr.sam2.sam.getReadNegativeStrandFlag() ) )
        g2.setColor(Color.red);
      else
        g2.setColor(Color.blue);

      drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam1.sam));
      if(pr.sam2 != null)
        drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam2.sam));
    }
  }
  
  /**
   * Check if two records are from the same BAM file
   * @param sam1
   * @param sam2
   * @param bamList
   * @return
   */
  private boolean isFromSameBamFile(final BamViewRecord sam1, 
                                    final BamViewRecord sam2, 
                                    final List<String> bamList)
  {
    if(bamList == null || bamList.size()<2)
      return true;

    final short o1 = sam1.bamIndex;
    final short o2 = sam2.bamIndex;
    if(o1 != -1 && o2 != -1)
      if( o1 != o2 )
        return false;
    
    return true;
  }
  
  
  /**
   * Check if two records overlap
   * @param s1
   * @param s2
   * @return true id the two reads overlap
   */
  private boolean readsOverlap(final SAMRecord s1, 
                               final SAMRecord s2)
  {
    if( (s2.getAlignmentStart() >= s1.getAlignmentStart() &&
         s2.getAlignmentStart() <= s1.getAlignmentEnd()) ||
        (s2.getAlignmentEnd()   >= s1.getAlignmentStart() &&
         s2.getAlignmentEnd()   <= s1.getAlignmentEnd()) )
      return true;
    
    if( (s1.getAlignmentStart() >= s2.getAlignmentStart() &&
         s1.getAlignmentStart() <= s2.getAlignmentEnd()) ||
        (s1.getAlignmentEnd()   >= s2.getAlignmentStart() &&
         s1.getAlignmentEnd()   <= s2.getAlignmentEnd()) )
     return true;
    return false;
  }
  
  /**
   * Draw the read coverage.
   * @param g2
   * @param start
   * @param end
   * @param pixPerBase
   */
  private void drawCoverage(Graphics2D g2, int start, int end, float pixPerBase)
  {
    int scaleHeight = 0;
    if(isShowScale())
    {
      drawScale(g2, start, end, pixPerBase, getHeight());
      scaleHeight = 15;
    }

    int hgt = jspView.getVisibleRect().height-scaleHeight;
    if(!cbCoverageStrandView.isSelected())
    {
      try
      {
        int y = getHeight()-6-( (hgt* MAX_COVERAGE)/(coverageView.max/coverageView.windowSize) );
        g2.setColor(Color.YELLOW);
        // draw the threshold for the coverage max read cut-off
        g2.fillRect(0, y, getWidth(), 8);
      }
      catch(Exception e){}
    }

    g2.translate(0, getHeight()-hgt-scaleHeight);
    coverageView.drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
    coverageView.draw(g2, getWidth(), hgt);
    coverageView.drawMax(g2);  
  }
  
  /**
   * 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, BamViewRecord bamViewRecord, int ypos, 
      float pixPerBase, int baseAtStartOfView, int scaleHeight, List<Integer> snps)
  {
    SAMRecord samRecord = bamViewRecord.sam;
    boolean offTheTop = false;
    int offset = getSequenceOffset(samRecord.getReferenceName());
    int thisStart = samRecord.getAlignmentStart()+offset;
    int thisEnd   = thisStart + samRecord.getReadString().length() -1;
    
    if(ypos <= 0)
    {
      offTheTop = true;
      ypos = samRecord.getReadString().length();
    }
    
    if(samRecord.getInferredInsertSize() == 0)
    {
      offTheTop = true;
      ypos = getHeight() - scaleHeight - 5;
    }
      
    if(samRecord.getInferredInsertSize() != 0 &&
      Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
    {
      g2.setColor(Color.LIGHT_GRAY);
      
      if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
      {
        int nextStart = 
          (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
        drawTranslucentLine(g2, 
          (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
      }
      else
      {
        int nextStart = 
            (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
        drawTranslucentLine(g2, 
            (int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
      }
    }
    
    if(colourByCoverageColour.isSelected())
      g2.setColor(getColourByCoverageColour(bamViewRecord));
    else if(offTheTop)
      g2.setColor(DARK_ORANGE); 
    else if(samRecord.getReadNegativeStrandFlag() &&
            samRecord.getMateNegativeStrandFlag()) // strand of the query (1 for reverse)
      g2.setColor(Color.red);
    else
      g2.setColor(Color.blue);
 
    drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
    
    /*if (isSNPs)
      showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);*/
  }

  
  private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
  {
    g2.setColor(Color.black);
    g2.drawLine( 0, ypos-14,
                 (int)((end - getBaseAtStartOfView())*pixPerBase),   ypos-14);
    int interval = end-start;
    
    if(interval > 256000)
      drawTicks(g2, start, end, pixPerBase, 512000, ypos);
    else if(interval > 64000)
      drawTicks(g2, start, end, pixPerBase, 12800, ypos);
    else if(interval > 16000)
      drawTicks(g2, start, end, pixPerBase, 3200, ypos);
    else if(interval > 4000)
      drawTicks(g2, start, end, pixPerBase, 800, ypos);
    else if(interval > 1000)
      drawTicks(g2, start, end, pixPerBase, 400, ypos);
    else
      drawTicks(g2, start, end, pixPerBase, 100, ypos);
  }
  
  private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division, int ypos)
  {
    int markStart = (Math.round(start/division)*division);
    
    if(markStart < 1)
      markStart = 1;
    
    int sm = markStart-(division/2);
    float x;
    if(sm > start)
    {
      x = (sm-getBaseAtStartOfView())*pixPerBase;
      g2.drawLine((int)x, ypos-14,(int)x, ypos-12);
    }
    
    for(int m=markStart; m<end; m+=division)
    {
      x = (m-getBaseAtStartOfView())*pixPerBase;
      g2.drawString(Integer.toString(m), x, ypos-1);
      g2.drawLine((int)x, ypos-14,(int)x, ypos-11);
      
      sm = m+(division/2);
      
      if(sm < end)
      {
        x = (sm-getBaseAtStartOfView())*pixPerBase;
        g2.drawLine((int)x, ypos-14,(int)x, ypos-12);
      }
      
      if(m == 1)
        m = 0;
    }
  }
  
  /**
   * Draw a y-scale for inferred size (isize) of reads.
   * @param g2
   * @param xScaleHeight
   */
  private void drawYScale(Graphics2D g2, int xScaleHeight)
  {
    g2.setColor(Color.black);
    int maxY = getPreferredSize().height-xScaleHeight;
    
    if(logScale)
    {
      int start = 10;
      int count = 0;
      int ypos = getYPos(xScaleHeight, start);
      
      while(ypos > 0 && count < 15 && start > 1)
      {
        g2.drawLine(0, ypos, 2, ypos);
        g2.drawString(Integer.toString(start), 3, ypos);
        start = start*5;
        ypos = getYPos(xScaleHeight, start);
        count++;
      }
      return;
    }
    
    for(int i=100; i<maxY; i+=100)
    {
      int ypos = getHeight()-i-xScaleHeight;
      g2.drawLine(0, ypos, 2, ypos);
      g2.drawString(Integer.toString(i), 3, ypos);
    }
  }
  
  /**
   * Draw a given read.
   * @param g2
   * @param thisRead
   * @param pixPerBase
   * @param ypos
   * @param baseAtStartOfView
   * @param snps
   */
  private void drawRead(Graphics2D g2, 
      final BamViewRecord bamViewRecord,
      final float pixPerBase,
      final int ypos,
      final int baseAtStartOfView,
      final List<Integer> snps)
  {
    SAMRecord thisRead = bamViewRecord.sam;
    int offset = getSequenceOffset(thisRead.getReferenceName());

    int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
    int thisEnd   = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
    
    if(highlightSAMRecord != null && 
       highlightSAMRecord.sam.getReadName().equals(thisRead.getReadName()))
    {
       Stroke originalStroke = g2.getStroke();
       Stroke stroke =
         new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
       g2.setStroke(stroke);
       Color c = g2.getColor();
       g2.setColor(Color.black);
       g2.drawLine((int)( thisStart * pixPerBase), ypos,
                   (int)( thisEnd * pixPerBase), ypos);
       g2.setColor(c);
       g2.setStroke(originalStroke);
    }

    if(thisRead.getCigar().getCigarElements().size() == 1)
      g2.drawLine((int)( thisStart * pixPerBase), ypos,
                  (int)( thisEnd * pixPerBase), ypos);
    else
    {
      List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
      Color c = g2.getColor();
      int lastEnd = 0;
      for(int i=0; i<blocks.size(); i++)
      {
        AlignmentBlock block = blocks.get(i);
        int blockStart = block.getReferenceStart()+offset-baseAtStartOfView;
        int blockEnd = blockStart + block.getLength() - 1;

        g2.drawLine((int)( blockStart * pixPerBase), ypos,
                    (int)( blockEnd * pixPerBase), ypos);
        if(i > 0 && blockStart != lastEnd)
        {
          g2.setColor(Color.gray);
          g2.drawLine((int)( blockStart * pixPerBase), ypos,
                      (int)( lastEnd * pixPerBase), ypos);
          g2.setColor(c);
        }
        lastEnd = blockEnd;
      }
    }
    
    if(isOrientation)
      drawArrow(g2, thisRead, thisStart, 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 = bamViewRecord;
      }
    }
    
    if (isSNPs && snps != null)
      showSNPsOnReads(snps, g2, pixPerBase, ypos);
  }
  
  /**
   * Draw arrow on the read to indicate orientation.
   * @param g2
   * @param thisRead
   * @param thisStart
   * @param thisEnd
   * @param pixPerBase
   * @param ypos
   */
  private void drawArrow(Graphics2D g2,
                         SAMRecord thisRead, 
                         int thisStart, 
                         int thisEnd, 
                         float pixPerBase, 
                         int ypos)
  {
    if(thisRead.getReadNegativeStrandFlag())
    {
      int apos = ypos + 2;
      g2.drawLine((int)( (thisStart+5) * pixPerBase), apos,
                  (int)( thisStart * pixPerBase), ypos);
    }
    else
    {
      int apos = ypos - 2;
      g2.drawLine((int)( (thisEnd-5) * pixPerBase), apos,
                  (int)( thisEnd * 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, Color c)
  {
    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-getBaseAtStartOfView()));
        int width = (int) (pixPerBase*(rangeEnd-rangeStart+1));
        
        g2.setColor(c);
        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 snps
   * @param g2
   * @param pixPerBase
   * @param ypos
   */
  private void showSNPsOnReads(final List<Integer> snps,
                               final Graphics2D g2,
                               float pixPerBase, int ypos)
  {
    g2.setColor(Color.red);
    for(int pos: snps)
      g2.drawLine((int) (pos * pixPerBase), ypos + 2,
                  (int) (pos * pixPerBase), ypos - 2);
  }
  
  
  /**
   * Get the SNP positions
   * @param samRecord
   */
  private List<Integer> getSNPs(final SAMRecord samRecord)
  {
    if(!isSNPs)  // return null if not displaying SNPs
      return null;
    int rbeg = samRecord.getAlignmentStart();
    int rend = samRecord.getAlignmentEnd();
    int offset = getSequenceOffset(samRecord.getReferenceName());
    ArrayList<Integer> snps = null;
    
    // use alignment blocks of the contiguous alignment of
    // subsets of read bases to a reference sequence
    try
    {
      final char[] refSeq = bases.getSubSequenceC(
          new Range(rbeg+offset, rend+offset), Bases.FORWARD);
      final byte[] readSeq = samRecord.getReadBases();