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/* 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.
*
*/
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.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.WindowEvent;
import java.awt.event.WindowFocusListener;
import java.io.FileOutputStream;
import java.io.IOException;
import java.lang.management.ManagementFactory;
import java.lang.management.MemoryMXBean;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JSeparator;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
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import org.apache.log4j.Level;
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.FeatureVector;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SelectionChangeEvent;
import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.FeatureDisplay;
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import uk.ac.sanger.artemis.components.FileViewer;
import uk.ac.sanger.artemis.components.SwingWorker;
import uk.ac.sanger.artemis.components.variant.FeatureContigPredicate;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
public class BamView extends JPanel
implements DisplayAdjustmentListener, SelectionChangeListener
private Hashtable<String, SAMFileReader> samFileReaderHash = new Hashtable<String, SAMFileReader>();
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
private Hashtable<String, Integer> offsetLengths;
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protected List<String> bamList;
private List<Integer> hideBamList = new Vector<Integer>();
private SAMRecordFlagPredicate samRecordFlagPredicate;
private boolean isSingle = false;
private boolean isSNPs = false;
private boolean isPairedStackView = false;
private FeatureDisplay feature_display;
private Selection selection;
private JPanel mainPanel;
private Ruler ruler;
private int startBase = -1;
private int endBase = -1;
private boolean showBaseAlignment = false;
private JMenu bamFilesMenu = new JMenu("BAM files");
private JCheckBoxMenuItem logMenuItem = new JCheckBoxMenuItem("Use Log Scale", logScale);
private JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View", isStackView);
private JCheckBoxMenuItem colourByCoverageColour = new JCheckBoxMenuItem("Coverage Plot Colours");
private JCheckBoxMenuItem baseQualityColour = new JCheckBoxMenuItem("Base Quality");
private JCheckBoxMenuItem markInsertions = new JCheckBoxMenuItem("Mark Insertions", true);
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private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
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private Color lightGrey = new Color(200, 200, 200);
private Color darkGreen = new Color(0, 150, 0);
private Color darkOrange = new Color(255,140,0);
private Color deepPink = new Color(139,10,80);
private Point lastMousePoint = null;
private SAMRecord mouseOverSAMRecord = null;
private SAMRecord highlightSAMRecord = null;
private String mouseOverInsertion;
// record of where a mouse drag starts
private int dragStart = -1;
private int maxHeight = 800;
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private int BASE_HEIGHT;
private PopupMessageFrame popFrame = new PopupMessageFrame();
private PopupMessageFrame waitingFrame = new PopupMessageFrame("waiting...");
public static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(BamView.class);
public BamView(List<String> bamList,
this.bamList = bamList;
// filter out unmapped reads by default
setSamRecordFlagPredicate(
new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
try
{
getEntry(reference,entryGroup);
}
catch (NoSequenceException e)
{
e.printStackTrace();
}
}
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();
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());
ALIGNMENT_PIX_PER_BASE = fm.charWidth('M');
BASE_HEIGHT = fm.getMaxAscent();
MultiLineToolTipUI.initialize();
setToolTipText("");
}
public String getToolTipText()
{
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if(mouseOverSAMRecord == null)
return null;
String msg =
mouseOverSAMRecord.getReadName() + "\n" +
mouseOverSAMRecord.getAlignmentStart() + ".." +
mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
mouseOverSAMRecord.getInferredInsertSize() + "\nmapq=" +
mouseOverSAMRecord.getMappingQuality()+"\nrname="+
mouseOverSAMRecord.getReferenceName();
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if( mouseOverSAMRecord.getReadPairedFlag() &&
mouseOverSAMRecord.getProperPairFlag() &&
!mouseOverSAMRecord.getMateUnmappedFlag())
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{
msg = msg +
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(mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
(mouseOverSAMRecord.getMateNegativeStrandFlag() ? "-" : "+");
}
else
msg = msg +
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(mouseOverSAMRecord.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"))
{
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();
System.out.println("create... " + bamIndexFile.getAbsolutePath());
}
else
bamIndexFile = new File(bam + ".bai");
/**
* Get the SAM file reader.
* @param bam
* @return
* @throws IOException
*/
private SAMFileReader getSAMFileReader(final String bam) throws IOException
{
if(samFileReaderHash.containsKey(bam))
return samFileReaderHash.get(bam);
File bamIndexFile = getBamIndexFile(bam);
final SAMFileReader samFileReader;
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;
String bam = bamList.get(0);
final SAMFileReader inputSam = getSAMFileReader(bam);
//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());
}
private void readFromBamPicard(int start, int end, int bamIndex)
throws IOException
{
// Open the input file. Automatically detects whether input is SAM or BAM
// and delegates to a reader implementation for the appropriate format.
String bam = bamList.get(bamIndex);
final SAMFileReader inputSam = getSAMFileReader(bam);
//final SAMFileReader inputSam = new SAMFileReader(bamFile, indexFile);
if(concatSequences)
{
int len = 0;
int lastLen = 1;
for(int i=0; i<seqNames.size(); i++)
{
int thisLength = seqLengths.get(seqNames.get(i));
len += thisLength;
if( (lastLen >= start && lastLen < end) ||
(len >= start && len < end) ||
(start >= lastLen && start < len) ||
(end >= lastLen && end < len) )
{
int offset = getSequenceOffset(seqNames.get(i));
int thisStart = start - offset;
if(thisStart < 1)
thisStart = 1;
int thisEnd = end - offset;
if(thisEnd > thisLength)
thisEnd = thisLength;
//System.out.println("READ "+seqNames.get(i)+" "+thisStart+".."+thisEnd);
iterateOverBam(inputSam, seqNames.get(i), thisStart, thisEnd, bamIndex);
}
lastLen = len;
}
}
else
{
String refName = (String) combo.getSelectedItem();
iterateOverBam(inputSam, refName, start, end, bamIndex);
//System.out.println("readFromBamPicard "+start+".."+end);
//System.out.println("Reads in view ... "+readsInView.size());
}
/**
* Iterate over BAM file and load into the <code>List</code> of
* <code>SAMRecord</code>.
* @param inputSam
* @param refName
* @param start
* @param end
*/
private void iterateOverBam(final SAMFileReader inputSam,
String refName, int start, int end,
int bamIndex)
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boolean multipleBAM = false;
if(bamList.size() > 1)
multipleBAM = true;
CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
if( samRecordFlagPredicate == null ||
!samRecordFlagPredicate.testPredicate(samRecord))
{
if(samRecordMapQPredicate == null ||
samRecordMapQPredicate.testPredicate(samRecord))
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if(multipleBAM)
samRecord.setAttribute("FL", bamIndex);
}
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)
"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.",
}
catch(Exception e)
{
System.out.println(e.getMessage());
}
}
it.close();
}
private int getSequenceLength()
{
if(concatSequences)
{
int len = 0;
for(int i=0; i<seqNames.size(); i++)
len += seqLengths.get(seqNames.get(i));
return len;
}
else
return seqLengths.get((String) combo.getSelectedItem());
}
/**
* 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(!concatSequences)
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));
}*/
FeatureVector features = feature_display.getEntryGroup().getAllFeatures();
offsetLengths = new Hashtable<String, Integer>(seqNames.size());
for(int i=0; i<seqNames.size(); i++)
{
FeatureContigPredicate predicate = new FeatureContigPredicate(seqNames.get(i));
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())
JOptionPane.showMessageDialog(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);
return offsetLengths.get(refName);
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
if(startBase > 0)
start = startBase;
else
if(endBase > 0)
end = endBase;
else
end = start + nbasesInView - 1;
if(end > seqLength)
end = seqLength;
boolean changeToStackView = false;
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
synchronized (this)
try
{
float heapFractionUsedBefore = (float) ((float) memory.getHeapMemoryUsage().getUsed() /
(float) memory.getHeapMemoryUsage().getMax());
if(readsInView == null)
readsInView = new Vector<SAMRecord>();
else
readsInView.clear();
for(int i=0; i<bamList.size(); i++)
{
if(!hideBamList.contains(i))
readFromBamPicard(start, end, i);
}
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)
{
checkBoxStackView.setSelected(true);
isStackView = true;
changeToStackView = true;
}
if ((!isStackView && !isStrandStackView)
|| pixPerBase * 1.08f >= ALIGNMENT_PIX_PER_BASE)
{
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(IOException me)
{
me.printStackTrace();
}
catch(net.sf.samtools.util.RuntimeIOException re)
{
JOptionPane.showMessageDialog(this, re.getMessage());
}
//System.out.println(start+".."+end+" " +
// "sequence length = "+getSequenceLength()+
// " pixPerBase="+pixPerBase);
if(showBaseAlignment)
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.setStartAndEnd(start, end);
coveragePanel.setPixPerBase(pixPerBase);
coveragePanel.repaint();
}
if(isSNPplot)
{
snpPanel.setStartAndEnd(start, end);
snpPanel.setPixPerBase(pixPerBase);
snpPanel.repaint();
}
if(changeToStackView)
{
"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.",
return (float)mainPanel.getWidth() / (float)nbasesInView;
{
if(feature_display == null)
return seqLength+nbasesInView/3;
/**
* 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,
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end = start + ( mainPanel.getWidth() * ALIGNMENT_PIX_PER_BASE );
if(bases != null)
{
// draw the reference sequence
ypos+=11;
if(seqEnd > bases.getLength())
seqEnd = bases.getLength();
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
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g2.setColor(lightGrey);
g2.fillRect(0, ypos-11, mainPanel.getWidth(), 11);
drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
}
catch (OutOfRangeException e)
{
e.printStackTrace();
}
}
drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
g2.setStroke(new BasicStroke (2.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND));
Rectangle r = jspView.getViewport().getViewRect();
int nreads = readsInView.size();
ypos += 11;
SAMRecord thisRead = readsInView.get(i);
if (ypos < r.getMaxY() || ypos > r.getMinY())
drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
drawn[i] = true;
int thisEnd = thisRead.getAlignmentEnd();
if (thisEnd == 0)
thisEnd = thisRead.getAlignmentStart() + thisRead.getReadLength();
for (int j = i + 1; j < nreads; j++)
SAMRecord nextRead = readsInView.get(j);
int nextStart = nextRead.getAlignmentStart();
if (nextStart > thisEnd + 1)
{
if (ypos < r.getMaxY() || ypos > r.getMinY())
drawSequence(g2, nextRead, ypos, refSeq, refSeqStart);
drawn[j] = true;
thisEnd = nextRead.getAlignmentEnd();
if (thisEnd == 0)
thisEnd = nextStart + nextRead.getReadLength();
}
else if (ypos > r.getMaxY() || ypos < r.getMinY())
break;
catch (ArrayIndexOutOfBoundsException ae)
{
System.err.println(readsInView.size()+" "+nreads);
ae.printStackTrace();
}
Dimension d = getPreferredSize();
d.setSize(getPreferredSize().getWidth(), ypos);
setPreferredSize(d);
/**
* Draw the query sequence
* @param g2
* @param read
* @param pixPerBase
* @param ypos
*/
private void drawSequence(Graphics2D g2, SAMRecord samRecord,
int ypos, String refSeq, int refSeqStart)
if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
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();
for(int j=0; j<block.getLength(); j++)
int readPos = blockStart-1+j;
xpos = block.getReferenceStart() - 1 + j + offset;
refPos = xpos - refSeqStart + 1;
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);
// 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>();
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(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);
}
}
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// highlight
if(highlightSAMRecord != null &&
highlightSAMRecord.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;
refPos = blocks.get(blocks.size()-1).getReferenceStart()+
blocks.get(blocks.size()-1).getLength()+offset-refSeqStart;
if(lastMousePoint.getY() > ypos-11 && lastMousePoint.getY() < ypos)
if(lastMousePoint.getX() > xstart &&
lastMousePoint.getX() < xend)
{
mouseOverSAMRecord = samRecord;
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(darkGreen);
else if (baseQuality < 30)
g2.setColor(darkOrange);
else
g2.setColor(Color.black);
}
/**
* 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(showScale)
drawScale(g2, start, end, pixPerBase, getHeight());
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
scaleHeight = 0;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
SAMRecord samRecord = readsInView.get(i);
SAMRecord samNextRecord = null;
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
int ypos = getYPos(scaleHeight, samRecord.getReadString().length()); // (getHeight() - scaleHeight) - samRecord.getReadString().length();
if(ypos > r.getMaxY() || ypos < r.getMinY())
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
int ypos = getYPos(scaleHeight, Math.abs(samRecord.getInferredInsertSize()));
if( (ypos > r.getMaxY() || ypos < r.getMinY()) && ypos > 0 )
if(samRecord.getReadName().equals(samNextRecord.getReadName()))
if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
(samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
drawTranslucentLine(g2,
(int)((samRecord.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase),
(int)((samNextRecord.getAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(samRecord));
else 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, ypos, baseAtStartOfView);
drawRead(g2, samNextRecord, pixPerBase, ypos, baseAtStartOfView);
drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView);
drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView);
private int getYPos(int scaleHeight, int size)
{
int ypos;
if(!logScale)
ypos = (getHeight() - scaleHeight) - size;
else
{
int logInfSize = (int)( Math.log(size) * 100);
ypos = (getHeight() - scaleHeight) - logInfSize;
}
return ypos;
}
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/**
* 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
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*
* @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())
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);
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int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
int offset = getSequenceOffset(samRecord.getReferenceName());
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int recordStart = samRecord.getAlignmentStart()+offset;
int recordEnd = samRecord.getAlignmentEnd()+offset;
if(colourByCoverageColour.isSelected() ||
lstStart != recordStart || lstEnd != recordEnd)
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{
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(samRecord));
else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
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g2.setColor(Color.black);
else
g2.setColor(Color.blue);
if(maxEnd < recordStart)
{
ypos = (getHeight() - scaleHeight)-2;
maxEnd = recordEnd+2;
}
else
ypos = ypos-2;
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g2.setColor(darkGreen);
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lstStart = recordStart;
lstEnd = recordEnd;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
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/**
* 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);
BasicStroke stroke = new BasicStroke(
1.3f,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
int scaleHeight = 15;
drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));
int ymid = (getHeight()/ 2);
// positive strand
drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -2, pixPerBase, stroke);
// negative strand
drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), 2, pixPerBase, stroke);
}
private void drawStrand(Graphics2D g2,
boolean isStrandNegative,
int scaleHeight,
int ymid,
int ystep,
float pixPerBase,
Stroke stroke)
{
int ypos = (getHeight() - scaleHeight);
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
if( samRecord.getReadNegativeStrandFlag() == isStrandNegative )
{
int offset = getSequenceOffset(samRecord.getReferenceName());
int recordStart = samRecord.getAlignmentStart()+offset;
int recordEnd = samRecord.getAlignmentEnd()+offset;
if(colourByCoverageColour.isSelected() ||
lstStart != recordStart || lstEnd != recordEnd)
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(samRecord));
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 = ymid + ystep;
maxEnd = recordEnd+2;
}
else
ypos = ypos + ystep;
}
else
g2.setColor(darkGreen);
lstStart = recordStart;
lstEnd = recordEnd;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
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/**
* 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())
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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;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
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;
if(ypos > r.getMaxY() || ypos < r.getMinY())
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
if(pr.sam2 != null)
{
int offset1 = getSequenceOffset(pr.sam1.getReferenceName());
int offset2 = getSequenceOffset(pr.sam2.getReferenceName());
drawTranslucentJointedLine(g2,
(int)((pr.sam1.getAlignmentEnd()+offset1-getBaseAtStartOfView())*pixPerBase),
(int)((pr.sam2.getAlignmentStart()+offset2-getBaseAtStartOfView())*pixPerBase), ypos);
}
else
{
if(!pr.sam1.getMateUnmappedFlag() &&
pr.sam1.getMateReferenceName().equals(pr.sam1.getReferenceName()))
{
int prStart;
if(pr.sam1.getAlignmentStart() > pr.sam1.getMateAlignmentStart())
prStart = pr.sam1.getAlignmentEnd();
else
prStart = pr.sam1.getAlignmentStart();
int offset = getSequenceOffset(pr.sam1.getReferenceName());
drawTranslucentJointedLine(g2,
(int)( (prStart+offset-getBaseAtStartOfView())*pixPerBase),
(int)( (pr.sam1.getMateAlignmentStart()+offset-getBaseAtStartOfView())*pixPerBase), ypos);
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(pr.sam1));
else 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, ypos, baseAtStartOfView);
if(pr.sam2 != null)
drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView);
}
}
/**
* 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, int baseAtStartOfView)
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(Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
g2.setColor(Color.LIGHT_GRAY);
if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
{
(int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
(int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
int nextStart =
(int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
(int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(samRecord));
else if(offTheTop)
g2.setColor(darkOrange);
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else if(samRecord.getReadNegativeStrandFlag() &&
samRecord.getMateNegativeStrandFlag()) // strand of the query (1 for reverse)
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
g2.drawLine( 0, ypos-14,
(int)((end - getBaseAtStartOfView())*pixPerBase), ypos-14);
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;
g2.drawString(Integer.toString(m), x, ypos-1);
g2.drawLine((int)x, ypos-14,(int)x, ypos-11);
/**
* Draw a y-scale for inferred size (isize) of reads.
* @param g2
* @param xScaleHeight
*/
private void drawYScale(Graphics2D g2, int xScaleHeight)
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
float pixPerBase,
int ypos,
int baseAtStartOfView)
int offset = getSequenceOffset(thisRead.getReferenceName());
int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
int thisEnd = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
if(highlightSAMRecord != null &&
highlightSAMRecord.getReadName().equals(thisRead.getReadName()))
Stroke originalStroke = g2.getStroke();
Stroke stroke =
new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
Color c = g2.getColor();
g2.setColor(Color.black);
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
g2.setColor(c);
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;
}
}
// 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;
}
}
showSNPsOnReads(g2, thisRead, pixPerBase, ypos, offset);
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/**
* 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-getBaseAtStartOfView()));
int width = (int) (pixPerBase*(rangeEnd-rangeStart+1));
g2.setColor(Color.pink);
g2.fillRect(x, 0, width, getHeight());
}
}
}
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/**
* 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,
{
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();
new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
offset = offset - getBaseAtStartOfView();
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+offset) * pixPerBase), ypos + 2,
(int) ((refPos+offset) * 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 boolean autohide,
final FeatureDisplay feature_display)
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);
JMenu fileMenu = new JMenu("File");
topPanel.add(fileMenu);
JMenuItem readBam = new JMenuItem("Open new BamView ...");
fileMenu.add(readBam);
readBam.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
String[] s = new String[0];
BamView.main(s);
}
});
JMenuItem close = new JMenuItem("Close");
fileMenu.add(close);
close.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
BamView.this.setVisible(false);
Component comp = BamView.this;
while( !(comp instanceof JFrame) )
comp = comp.getParent();
((JFrame)comp).dispose();
}
});
JMenuItem exit = new JMenuItem("Exit");
fileMenu.add(exit);
exit.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
int status = JOptionPane.showConfirmDialog(BamView.this,
JOptionPane.OK_CANCEL_OPTION);
if(status != JOptionPane.OK_OPTION)
return;
System.exit(0);
}
});
if(seqNames.size() > 1)
{
int len = 0;
for(int i=0; i<seqNames.size(); i++)
len += seqLengths.get(seqNames.get(i));
if(feature_display != null &&
len == feature_display.getSequenceLength())
concatSequences = true;
else if(bases != null &&
len == bases.getLength() )
concatSequences = true;
}
final JCheckBox buttonAutoHide = new JCheckBox("Hide", autohide);
buttonAutoHide.setToolTipText("Auto-Hide");
final MouseMotionListener mouseMotionListener = new MouseMotionListener()
}
public void mouseMoved(MouseEvent e)
{
int thisHgt = HEIGHT;
if (thisHgt < 5)
thisHgt = 15;
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
if (y < thisHgt)
}
mainPanel.repaint();
mainPanel.revalidate();
}
};
addMouseMotionListener(mouseMotionListener);
combo = new JComboBox(seqNames);
combo.setEditable(false);
combo.setMaximumRowCount(20);
combo.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
laststart = -1;
lastend = -1;
if(feature_display != null)
setZoomLevel(feature_display.getMaxVisibleBases());
else
setZoomLevel(BamView.this.nbasesInView);
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