-
tjc authored
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14956 ee4ac58c-ac51-4696-9907-e4b3aa274f04
tjc authoredgit-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14956 ee4ac58c-ac51-4696-9907-e4b3aa274f04
BamView.java 91.04 KiB
/* JamView
*
* created: 2009
*
* This file is part of Artemis
*
* Copyright(C) 2009 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or(at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package uk.ac.sanger.artemis.components.alignment;
import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.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.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.event.WindowEvent;
import java.awt.event.WindowFocusListener;
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.net.URL;
import java.util.Collections;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JButton;import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.JTextField;
import javax.swing.UIManager;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
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.Options;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SelectionChangeEvent;
import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.SimpleEntryGroup;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryFileDialog;
import uk.ac.sanger.artemis.components.FeatureDisplay;
import uk.ac.sanger.artemis.components.FileViewer;
import uk.ac.sanger.artemis.components.MessageDialog;
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.io.EntryInformation;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
public class BamView extends JPanel
implements DisplayAdjustmentListener, SelectionChangeListener
{
private static final long serialVersionUID = 1L;
private List<SAMRecord> readsInView;
private Hashtable<String, SAMFileReader> samFileReaderHash = new Hashtable<String, SAMFileReader>();
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
private Hashtable<String, Integer> offsetLengths;
private Vector<String> seqNames = new Vector<String>();
protected List<String> bamList;
private List<Integer> hideBamList = new Vector<Integer>();
private SAMRecordFlagPredicate samRecordFlagPredicate; private SAMRecordMapQPredicate samRecordMapQPredicate;
private Bases bases;
private JScrollPane jspView;
private JScrollBar scrollBar;
private JComboBox combo;
private boolean isOrientation = false;
private boolean isSingle = false;
private boolean isSNPs = false;
private boolean isStackView = true;
private boolean isPairedStackView = false;
private boolean isStrandStackView = false;
private boolean isCoverage = false;
private boolean isSNPplot = false;
private FeatureDisplay feature_display;
private Selection selection;
private JPanel mainPanel;
private CoveragePanel coveragePanel;
private SnpPanel snpPanel;
private boolean showScale = true;
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 int maxUnitIncrement = 8;
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 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);
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
/** Used to colour the frames. */
private Color lightGrey = new Color(200, 200, 200);
private Color darkGreen = new Color(0, 150, 0);
private Color darkOrange = new Color(255,140,0);
private 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;
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...");
public static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(BamView.class);
public BamView(List<String> bamList,
String reference,
int nbasesInView)
{
super();
setBackground(Color.white);
this.bamList = bamList;
this.nbasesInView = nbasesInView;
// filter out unmapped reads by default
setSamRecordFlagPredicate(
new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
if(reference != null)
{
EntryGroup entryGroup = new SimpleEntryGroup();
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();
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("");
}
public String getToolTipText()
{
if(mouseOverSAMRecord == null)
return null;
String msg = mouseOverSAMRecord.getReadName() + "\n" +
mouseOverSAMRecord.getAlignmentStart() + ".." +
mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
mouseOverSAMRecord.getInferredInsertSize() + "\nmapq=" +
mouseOverSAMRecord.getMappingQuality()+"\nrname="+
mouseOverSAMRecord.getReferenceName();
if( mouseOverSAMRecord.getReadPairedFlag() &&
mouseOverSAMRecord.getProperPairFlag() &&
!mouseOverSAMRecord.getMateUnmappedFlag())
{
msg = msg +
"\nstrand (read/mate): "+
(mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
(mouseOverSAMRecord.getMateNegativeStrandFlag() ? "-" : "+");
}
else
msg = msg +
"\nstrand (read/mate): "+
(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");
return bamIndexFile;
}
/**
* 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;
}
private void readHeaderPicard() throws IOException
{
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());
}
//inputSam.close();
}
/**
* Read a SAM or BAM file.
* @throws IOException
*/
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);
}
//inputSam.close();
//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)
{
boolean multipleBAM = false;
if(bamList.size() > 1)
multipleBAM = true;
CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
int checkMemAfter = 8000;
int cnt = 0;
while ( it.hasNext() )
{
try
{
cnt++;
SAMRecord samRecord = it.next();
if( samRecordFlagPredicate == null ||
!samRecordFlagPredicate.testPredicate(samRecord))
{
if(samRecordMapQPredicate == null ||
samRecordMapQPredicate.testPredicate(samRecord))
{
if(multipleBAM)
samRecord.setAttribute("FL", bamIndex);
readsInView.add(samRecord);
}
}
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.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);
}
/**
* Override
*/
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
mouseOverSAMRecord = null;
int seqLength = getSequenceLength();
float pixPerBase = getPixPerBaseByWidth();
int start;
int end;
if(startBase > 0)
start = startBase;
else
start = getBaseAtStartOfView();
if(endBase > 0)
end = endBase;
else
{
end = start + nbasesInView - 1;
if(end > seqLength)
end = seqLength;
}
boolean changeToStackView = false;
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
if(laststart != start ||
lastend != end)
{
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);
laststart = start;
lastend = end;
if(showBaseAlignment)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
{
if(isStackView)
drawStackView(g2, seqLength, pixPerBase, start, end);
else if(isPairedStackView)
drawPairedStackView(g2, seqLength, pixPerBase, start, end);
else 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(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;
ruler.repaint();
int ypos = 0;
String refSeq = null;
int refSeqStart = start;
end = start + ( mainPanel.getWidth() * ALIGNMENT_PIX_PER_BASE );
if(bases != null)
{
// draw the reference sequence
ypos+=11;
try
{
int seqEnd = end+2;
if(seqEnd > bases.getLength())
seqEnd = bases.getLength();
if(refSeqStart < 1)
refSeqStart = 1;
refSeq =
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
g2.setColor(lightGrey);
g2.fillRect(0, ypos-11, mainPanel.getWidth(), 11);
drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
g2.setColor(Color.black);
g2.drawString(refSeq, 0, ypos);
}
catch (OutOfRangeException e)
{
e.printStackTrace();
}
}
else
drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
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;
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++)
{
if (!drawn[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();
}
}
if(ypos > getHeight())
{
Dimension d = getPreferredSize();
d.setSize(getPreferredSize().getWidth(), ypos);
setPreferredSize(d);
revalidate();
}
}
/**
* Draw the query sequence
* @param g2
* @param read
* @param pixPerBase
* @param ypos
*/
private void drawSequence(Graphics2D g2, SAMRecord samRecord,
int ypos, String refSeq, int refSeqStart)
{
if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
g2.setColor(Color.black);
else
g2.setColor(Color.blue);
Color col = g2.getColor();
int xpos;
int len = 0;
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);
}
// 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(deepPink);
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.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 = 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());
Stroke stroke =
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
g2.setStroke(stroke);
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++)
{
SAMRecord samRecord = readsInView.get(i);
SAMRecord samNextRecord = null;
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
{
if(isSingle)
{
int ypos = getYPos(scaleHeight, samRecord.getReadString().length()); // (getHeight() - scaleHeight) - samRecord.getReadString().length();
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
g2.setColor(Color.black);
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
} continue;
}
int ypos = getYPos(scaleHeight, Math.abs(samRecord.getInferredInsertSize()));
if( (ypos > r.getMaxY() || ypos < r.getMinY()) && ypos > 0 )
continue;
if(i < readsInView.size()-1)
{
samNextRecord = readsInView.get(++i);
if(samRecord.getReadName().equals(samNextRecord.getReadName()))
{
// draw connection between paired reads
if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
(samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
g2.setColor(Color.LIGHT_GRAY);
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);
}
else
{
drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
i--;
}
}
else
{
drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
}
}
drawYScale(g2, scaleHeight);
}
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;
}
/**
* Draw the reads as lines in vertical stacks. The reads are colour
* coded as follows:
*
* blue - reads are unique and are paired with a mapped mate * black - reads are unique and are not paired or have an unmapped mate
* green - reads are duplicates
*
* @param g2
* @param seqLength
* @param pixPerBase
* @param start
* @param end
*/
private void drawStackView(Graphics2D g2,
int seqLength,
float pixPerBase,
int start,
int end)
{
drawSelectionRange(g2, pixPerBase,start, end);
if(isShowScale())
drawScale(g2, start, end, pixPerBase, getHeight());
BasicStroke stroke = new BasicStroke(
1.3f,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
g2.setStroke(stroke);
int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
scaleHeight = 0;
int ypos = (getHeight() - scaleHeight);
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
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 ) // mate is unmapped
g2.setColor(Color.black);
else
g2.setColor(Color.blue);
if(maxEnd < recordStart)
{
ypos = (getHeight() - scaleHeight)-2;
maxEnd = recordEnd+2;
}
else
ypos = ypos-2;
}
else
g2.setColor(darkGreen);
lstStart = recordStart; lstEnd = recordEnd;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
}
}
/**
* 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();
g2.setColor(Color.blue);
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);
}
}
}
/**
* Draw the reads as lines in vertical stacks. The reads are colour
* coded as follows:
*
* blue - reads are unique and are paired with a mapped mate
* black - reads are unique and are not paired or have an unmapped mate
* green - reads are duplicates
*
* @param g2
* @param seqLength
* @param pixPerBase
* @param start
* @param end
*/
private void drawPairedStackView(Graphics2D g2,
int seqLength,
float pixPerBase,
int start,
int end)
{
drawSelectionRange(g2, pixPerBase,start, end);
if(isShowScale())
drawScale(g2, start, end, pixPerBase, getHeight());
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);
g2.setStroke(stroke);
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())
continue;
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, int scaleHeight)
{
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(samRecord));
else if(offTheTop)
g2.setColor(darkOrange);
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);
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
*/
private void drawRead(Graphics2D g2, SAMRecord thisRead,
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);
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 = thisRead;
}
}
if (isSNPs)
showSNPsOnReads(g2, thisRead, pixPerBase, ypos, offset);
}
/**
* 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)
{
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());
}
}
}
/**
* Draw a translucent line
* @param g2
* @param start
* @param end
* @param ypos
*/
private void drawTranslucentLine(Graphics2D g2, int start, int end, int ypos)
{
Composite origComposite = g2.getComposite();
g2.setComposite(translucent);
g2.drawLine(start, ypos, end, ypos);
g2.setComposite(origComposite);
}
/** * Draw a translucent line
* @param g2
* @param start
* @param end
* @param ypos
*/
private void drawTranslucentJointedLine(Graphics2D g2, int start, int end, int ypos)
{
Composite origComposite = g2.getComposite();
g2.setComposite(translucent);
int mid = (int) ((end-start)/2.f)+start;
//g2.drawLine(start, ypos, end, ypos);
g2.drawLine(start, ypos, mid, ypos-5);
g2.drawLine(mid, ypos-5, end, ypos);
g2.setComposite(origComposite);
}
/**
* Display the SNPs for the given read.
* @param g2
* @param thisRead
* @param pixPerBase
* @param ypos
*/
private void showSNPsOnReads(Graphics2D g2, SAMRecord thisRead,
float pixPerBase, int ypos, int offset)
{
int thisStart = thisRead.getAlignmentStart();
int thisEnd = thisRead.getAlignmentEnd();
// use alignment blocks of the contiguous alignment of
// subsets of read bases to a reference sequence
List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
try
{
char[] refSeq = bases.getSubSequenceC(
new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
byte[] readSeq = thisRead.getReadBases();
Color col = g2.getColor();
g2.setColor(Color.red);
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 JFrame frame,
final boolean autohide,
final FeatureDisplay feature_display)
{
this.mainPanel = mainPanel;
final JComponent topPanel;
if(feature_display != null)
{
this.feature_display = feature_display;
this.selection = feature_display.getSelection();
topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
}
else
{
topPanel = new JMenuBar();
frame.setJMenuBar((JMenuBar)topPanel);
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(new JSeparator());
fileMenu.add(exit);
exit.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
int status = JOptionPane.showConfirmDialog(BamView.this,
"Exit BamView?", "Exit",
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;
}
// auto hide top panel
final JCheckBox buttonAutoHide = new JCheckBox("Hide", autohide);
buttonAutoHide.setToolTipText("Auto-Hide");
final MouseMotionListener mouseMotionListener = new MouseMotionListener()
{
public void mouseDragged(MouseEvent event)
{
handleCanvasMouseDrag(event);
}
public void mouseMoved(MouseEvent e)
{
lastMousePoint = e.getPoint();
int thisHgt = HEIGHT;
if (thisHgt < 5)
thisHgt = 15;
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
if (y < thisHgt)
{
topPanel.setVisible(true);
}
else
{
if (buttonAutoHide.isSelected())
topPanel.setVisible(false);
}
mainPanel.repaint();
mainPanel.revalidate();
}
};
addMouseMotionListener(mouseMotionListener);
combo = new JComboBox(seqNames);
combo.setEditable(false);
combo.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);
}
});
topPanel.add(combo);
if(feature_display == null)
{
final JTextField baseText = new JTextField(8);
JButton goTo = new JButton("GoTo:"); goTo.setToolTipText("Go to base position");
goTo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
try
{
int basePosition = Integer.parseInt(baseText.getText());
scrollBar.setValue(basePosition);
}
catch (NumberFormatException nfe)
{
JOptionPane.showMessageDialog(BamView.this,
"Expecting a base number!", "Number Format",
JOptionPane.WARNING_MESSAGE);
}
}
});
topPanel.add(goTo);
topPanel.add(baseText);
JButton zoomIn = new JButton("-");
Insets ins = new Insets(1,1,1,1);
zoomIn.setMargin(ins);
zoomIn.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
}
});
topPanel.add(zoomIn);
JButton zoomOut = new JButton("+");
zoomOut.setMargin(ins);
zoomOut.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (showBaseAlignment)
return;
setZoomLevel((int) (BamView.this.nbasesInView * .9));
}
});
topPanel.add(zoomOut);
}
topPanel.add(buttonAutoHide);
mainPanel.setPreferredSize(new Dimension(900, 400));
jspView = new JScrollPane(this,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
setDisplay(1, nbasesInView, null);
mainPanel.setLayout(new BorderLayout());
if(topPanel instanceof JPanel)
mainPanel.add(topPanel, BorderLayout.NORTH);
mainPanel.add(jspView, BorderLayout.CENTER);
JPanel bottomPanel = new JPanel(new BorderLayout());
coveragePanel = new CoveragePanel(this);
bottomPanel.add(coveragePanel, BorderLayout.CENTER);
//
snpPanel = new SnpPanel(this, bases);
bottomPanel.add(snpPanel, BorderLayout.NORTH);
if(feature_display == null)
{
scrollBar = new JScrollBar(JScrollBar.HORIZONTAL, 1, nbasesInView, 1,
getMaxBasesInPanel(getSequenceLength()));
scrollBar.setUnitIncrement(nbasesInView/20);
scrollBar.addAdjustmentListener(new AdjustmentListener()
{
public void adjustmentValueChanged(AdjustmentEvent e)
{
repaint();
if(coveragePanel != null)
coveragePanel.repaint();
if(snpPanel != null)
snpPanel.repaint();
}
});
bottomPanel.add(scrollBar, BorderLayout.SOUTH);
}
mainPanel.add(bottomPanel, BorderLayout.SOUTH);
coveragePanel.setPreferredSize(new Dimension(900, 100));
coveragePanel.setVisible(false);
snpPanel.setPreferredSize(new Dimension(900, 100));
snpPanel.setVisible(false);
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
jspView.getVerticalScrollBar().setUnitIncrement(maxUnitIncrement);
if(feature_display == null)
{
addKeyListener(new KeyAdapter()
{
public void keyPressed(final KeyEvent event)
{
switch (event.getKeyCode())
{
case KeyEvent.VK_UP:
setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
break;
case KeyEvent.VK_DOWN:
if (showBaseAlignment)
break;
setZoomLevel((int) (BamView.this.nbasesInView * .9));
break;
default:
break;
}
}
});
}
addMouseListener(new PopupListener());
setFocusable(true);
requestFocusInWindow();
}
private void addToViewMenu(final int thisBamIndex)
{
File f = new File(bamList.get(thisBamIndex));
final JCheckBoxMenuItem cbBam = new JCheckBoxMenuItem(
f.getName(), true);
bamFilesMenu.add(cbBam);
cbBam.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if(cbBam.isSelected())
hideBamList.remove(new Integer(thisBamIndex));
else hideBamList.add(new Integer(thisBamIndex));
laststart = -1;
lastend = -1;
repaint();
}
});
}
private void createMenus(JComponent menu)
{
final JMenuItem addBam = new JMenuItem("Add Bam ...");
menu.add(addBam);
addBam.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
FileSelectionDialog bamFileSelection = new FileSelectionDialog(
null, false, "BamView", "BAM");
List<String> bamFiles = bamFileSelection.getFiles(".*\\.bam$");
int count = bamList.size();
bamList.addAll(bamFileSelection.getFiles(".*\\.bam$"));
for(int i=0; i<bamFiles.size(); i++)
addToViewMenu(i+count);
laststart = -1;
lastend = -1;
repaint();
}
});
bamFilesMenu.setFont(addBam.getFont());
menu.add(bamFilesMenu);
for(int i=0; i<bamList.size(); i++)
addToViewMenu(i);
menu.add(new JSeparator());
JMenu viewMenu = new JMenu("Views");
ButtonGroup group = new ButtonGroup();
final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
final JCheckBoxMenuItem checkIsizeStackView = new JCheckBoxMenuItem("Inferred Size View", false);
checkBoxStackView.setFont(checkIsizeStackView.getFont());
baseQualityColour.setFont(checkIsizeStackView.getFont());
colourByCoverageColour.setFont(checkIsizeStackView.getFont());
markInsertions.setFont(checkIsizeStackView.getFont());
group.add(checkBoxStackView);
group.add(checkBoxPairedStackView);
group.add(checkBoxStrandStackView);
group.add(checkIsizeStackView);
checkIsizeStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
if(checkIsizeStackView.isSelected())
{
isStackView = false;
isPairedStackView = false;
isStrandStackView = false;
logMenuItem.setEnabled(true);
}
repaint(); }
});
viewMenu.add(checkIsizeStackView);
checkBoxStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
isStackView = !isStackView;
if(isStackView)
{
isPairedStackView = !isStackView;
isStrandStackView = !isStackView;
checkBoxPairedStackView.setSelected(!isStackView);
checkBoxStrandStackView.setSelected(!isStackView);
logMenuItem.setEnabled(false);
}
repaint();
}
});
viewMenu.add(checkBoxStackView);
checkBoxPairedStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
isPairedStackView = !isPairedStackView;
if(isPairedStackView)
{
isStackView = !isPairedStackView;
isStrandStackView = !isPairedStackView;
checkBoxStackView.setSelected(!isPairedStackView);
checkBoxStrandStackView.setSelected(!isPairedStackView);
logMenuItem.setEnabled(false);
}
repaint();
}
});
viewMenu.add(checkBoxPairedStackView);
checkBoxStrandStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
isStrandStackView = !isStrandStackView;
if(isStrandStackView)
{
isStackView = !isStrandStackView;
isPairedStackView = !isStrandStackView;
checkBoxStackView.setSelected(!isStrandStackView);
checkBoxPairedStackView.setSelected(!isStrandStackView);
setViewportMidPoint();
logMenuItem.setEnabled(false);
}
repaint();
}
});
viewMenu.add(checkBoxStrandStackView);
menu.add(viewMenu);
final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks");
//
JMenu colourMenu = new JMenu("Colour By");
colourMenu.add(colourByCoverageColour);
baseQualityColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if(baseQualityColour.isSelected())
{
checkBoxSNPs.setSelected(false);
isSNPs = false;
}
repaint();
}
});
colourMenu.add(baseQualityColour);
menu.add(colourMenu);
//
JMenu showMenu = new JMenu("Show");
JCheckBoxMenuItem checkBoxOrientation = new JCheckBoxMenuItem("Orientation");
checkBoxOrientation.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
isOrientation = !isOrientation;
repaint();
}
});
showMenu.add(checkBoxOrientation);
JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
checkBoxSingle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
repaint();
isSingle = !isSingle;
}
});
showMenu.add(checkBoxSingle);
checkBoxSNPs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (isSNPs && bases == null)
{
JOptionPane.showMessageDialog(null,
"No reference sequence supplied to identify SNPs.", "SNPs",
JOptionPane.INFORMATION_MESSAGE);
}
isSNPs = !isSNPs;
if(isSNPs)
baseQualityColour.setSelected(false);
repaint();
}
});
showMenu.add(checkBoxSNPs);
markInsertions.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
repaint();
} });
showMenu.add(markInsertions);
menu.add(showMenu);
//
JMenu graphMenu = new JMenu("Graph");
JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
checkBoxCoverage.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
isCoverage = !isCoverage;
coveragePanel.setVisible(isCoverage);
repaint();
}
});
graphMenu.add(checkBoxCoverage);
JCheckBoxMenuItem checkBoxSNP = new JCheckBoxMenuItem("SNP");
checkBoxSNP.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
isSNPplot = !isSNPplot;
snpPanel.setVisible(isSNPplot);
repaint();
}
});
graphMenu.add(checkBoxSNP);
menu.add(graphMenu);
if(feature_display != null)
{
final JCheckBoxMenuItem checkBoxSync =
new JCheckBoxMenuItem("Asynchronous", asynchronous);
checkBoxSync.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
asynchronous = checkBoxSync.isSelected();
}
});
menu.add(checkBoxSync);
}
menu.add(new JSeparator());
JMenu maxHeightMenu = new JMenu("BamView Height");
menu.add(maxHeightMenu);
final String hgts[] =
{"500", "800", "1000", "1500", "2500", "5000", "50000"};
ButtonGroup bgroup = new ButtonGroup();
for(int i=0; i<hgts.length; i++)
{
final String hgt = hgts[i];
final JCheckBoxMenuItem maxHeightMenuItem = new JCheckBoxMenuItem(hgt);
bgroup.add(maxHeightMenuItem);
maxHeightMenuItem.setSelected(hgts[i].equals(Integer.toString(maxHeight)));
maxHeightMenu.add(maxHeightMenuItem);
maxHeightMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if(maxHeightMenuItem.isSelected())
maxHeight = Integer.parseInt(hgt);
int start = getBaseAtStartOfView();
setDisplay(start, nbasesInView+start, null); }
});
}
menu.add(new JSeparator());
logMenuItem.setFont(checkIsizeStackView.getFont());
menu.add(logMenuItem);
logMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
logScale = logMenuItem.isSelected();
repaint();
}
});
JMenuItem filter = new JMenuItem("Filter by Flag...");
menu.add(filter);
filter.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new SAMRecordFilter(BamView.this);
}
});
menu.add(new JSeparator());
}
public void setVisible(boolean visible)
{
super.setVisible(visible);
mainPanel.setVisible(visible);
}
private void setViewportMidPoint()
{
Point p = jspView.getViewport().getLocation();
p.y = (getHeight() - jspView.getViewport().getViewRect().height)/2;
jspView.getViewport().setViewPosition(p);
}
protected int getBaseAtStartOfView()
{
if(feature_display != null)
return feature_display.getForwardBaseAtLeftEdge();
else
return scrollBar.getValue();
}
/**
* Set the panel size based on the number of bases visible
* and repaint.
* @param nbasesInView
*/
private void setZoomLevel(final int nbasesInView)
{
int startValue = getBaseAtStartOfView();
this.nbasesInView = nbasesInView;
float pixPerBase = getPixPerBaseByWidth();
if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
this.nbasesInView = (int)(mainPanel.getWidth()/pixPerBase);
jspView.getVerticalScrollBar().setValue(0);
if(ruler == null)
ruler = new Ruler();
jspView.setColumnHeaderView(ruler);
showBaseAlignment = true; baseQualityColour.setEnabled(true);
markInsertions.setEnabled(true);
}
else if(jspView != null)
{
jspView.setColumnHeaderView(null);
if(!isStrandStackView)
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
showBaseAlignment = false;
baseQualityColour.setEnabled(false);
markInsertions.setEnabled(false);
}
if(scrollBar != null)
{
scrollBar.setValues(startValue, nbasesInView, 1,
getMaxBasesInPanel(getSequenceLength()));
scrollBar.setUnitIncrement(nbasesInView/20);
scrollBar.setBlockIncrement(nbasesInView);
}
}
/**
* Set the start and end base positions to display.
* @param start
* @param end
* @param event
*/
public void setDisplay(int start,
int end,
DisplayAdjustmentEvent event)
{
this.startBase = start;
this.endBase = end;
this.nbasesInView = end-start+1;
lastMousePoint = null;
float pixPerBase;
if(jspView.getViewport().getViewRect().width > 0)
pixPerBase = getPixPerBaseByWidth();
else
{
if(feature_display == null)
pixPerBase = 1000.f/(float)(end-start+1);
else
pixPerBase = feature_display.getWidth()/(float)(end-start+1);
}
Dimension d = new Dimension();
d.setSize(nbasesInView*pixPerBase, maxHeight);
setPreferredSize(d);
if(event == null)
{
this.startBase = -1;
this.endBase = -1;
}
}
/**
* Return an Artemis entry from a file
* @param entryFileName
* @param entryGroup
* @return
* @throws NoSequenceException
*/
private Entry getEntry(final String entryFileName, final EntryGroup entryGroup) throws NoSequenceException
{
final Document entry_document = DocumentFactory.makeDocument(entryFileName);
final EntryInformation artemis_entry_information =
Options.getArtemisEntryInformation();
//System.out.println(entryFileName);
final uk.ac.sanger.artemis.io.Entry new_embl_entry =
EntryFileDialog.getEntryFromFile(null, entry_document,
artemis_entry_information,
false);
if(new_embl_entry == null) // the read failed
return null;
Entry entry = null;
try
{
if(entryGroup.getSequenceEntry() != null)
bases = entryGroup.getSequenceEntry().getBases();
if(bases == null)
{
entry = new Entry(new_embl_entry);
bases = entry.getBases();
}
else
entry = new Entry(bases,new_embl_entry);
entryGroup.add(entry);
}
catch(OutOfRangeException e)
{
new MessageDialog(null, "read failed: one of the features in " +
entryFileName + " has an out of range " +
"location: " + e.getMessage());
}
return entry;
}
private boolean isShowScale()
{
return showScale;
}
public void setShowScale(boolean showScale)
{
this.showScale = showScale;
}
public JScrollPane getJspView()
{
return jspView;
}
public void setBases(Bases bases)
{
this.bases = bases;
}
/**
* Remove JScrollPane border
*/
public void removeBorder()
{
Border empty = new EmptyBorder(0,0,0,0);
jspView.setBorder(empty);
}
/** * Handle a mouse drag event on the drawing canvas.
**/
private void handleCanvasMouseDrag(final MouseEvent event)
{
if(event.getButton() == MouseEvent.BUTTON3 || bases == null)
return;
highlightSAMRecord = null;
if(event.getClickCount() > 1)
{
getSelection().clear();
repaint();
return;
}
highlightRange(event,
MouseEvent.BUTTON1_DOWN_MASK & MouseEvent.BUTTON2_DOWN_MASK);
}
/**
*
* @param event
* @param onmask
*/
private void highlightRange(MouseEvent event, int onmask)
{
int seqLength = getSequenceLength();
float pixPerBase = getPixPerBaseByWidth();
int start = (int) ( ( (event.getPoint().getX())/pixPerBase) + getBaseAtStartOfView() );
if(start < 1)
start = 1;
if(start > seqLength)
start = seqLength;
if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
dragStart = start;
else if((event.getModifiersEx() & onmask) != onmask)
dragStart = -1;
MarkerRange drag_range;
try
{
if(dragStart < 0)
drag_range = new MarkerRange (bases.getForwardStrand(), start, start);
else
drag_range = new MarkerRange (bases.getForwardStrand(), dragStart, start);
getSelection().setMarkerRange(drag_range);
repaint();
}
catch (OutOfRangeException e)
{
e.printStackTrace();
}
}
/**
* Get the colour for the given read given to it by the coverage plot.
* @param samRecord
* @return
*/
private Color getColourByCoverageColour(SAMRecord samRecord)
{
LineAttributes lines[] = CoveragePanel.getLineAttributes(bamList.size());
int fileIndex = 0;
if(bamList.size()>1)
fileIndex = (Integer) samRecord.getAttribute("FL");
return lines[fileIndex].getLineColour();
}
private Selection getSelection()
{
return selection;
}
protected List<SAMRecord> getReadsInView()
{
return readsInView;
}
protected int getBasesInView()
{
return nbasesInView;
}
private String getVersion()
{
final ClassLoader cl = this.getClass().getClassLoader();
try
{
String line;
InputStream in = cl.getResourceAsStream("etc/versions");
BufferedReader reader = new BufferedReader(new InputStreamReader(in));
while((line = reader.readLine()) != null)
{
if(line.startsWith("BamView"))
return line.substring( "BamView".length() ).trim();
}
reader.close();
in.close();
}
catch (Exception ex)
{
}
return null;
}
/**
* Artemis event notification
*/
public void displayAdjustmentValueChanged(final DisplayAdjustmentEvent event)
{
if(event.getType() == DisplayAdjustmentEvent.REV_COMP_EVENT &&
event.isRevCompDisplay())
JOptionPane.showMessageDialog(this,
"Flipping the display is not supported by BamView.", "Warning",
JOptionPane.WARNING_MESSAGE);
if(!asynchronous)
{
// if not asynchronous
displayAdjustmentWork(event);
return;
}
SwingWorker worker = new SwingWorker()
{
public Object construct()
{
try
{
Thread.sleep(500);
}
catch (InterruptedException e)
{
e.printStackTrace();
}
if(event.getStart() != ((FeatureDisplay)event.getSource()).getForwardBaseAtLeftEdge())
{ waitingFrame.showWaiting("waiting...", mainPanel);
return null;
}
displayAdjustmentWork(event);
waitingFrame.setVisible(false);
return null;
}
};
worker.start();
}
/**
* Carry out the display agjustment event action.
* @param event
*/
private void displayAdjustmentWork(final DisplayAdjustmentEvent event)
{
if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
{
laststart = -1;
lastend = -1;
BamView.this.startBase = event.getStart();
BamView.this.endBase = event.getEnd();
int width = feature_display.getMaxVisibleBases();
setZoomLevel(width);
repaint();
if(coveragePanel != null && coveragePanel.isVisible())
{
coveragePanel.setStartAndEnd(BamView.this.startBase, BamView.this.endBase);
coveragePanel.setPixPerBase(getPixPerBaseByWidth());
coveragePanel.repaint();
}
if(snpPanel != null && snpPanel.isVisible())
{
snpPanel.setStartAndEnd(BamView.this.startBase, BamView.this.endBase);
snpPanel.setPixPerBase(getPixPerBaseByWidth());
snpPanel.repaint();
}
}
else
{
setDisplay(event.getStart(),
event.getStart()+feature_display.getMaxVisibleBases(), event);
repaint();
if(coveragePanel != null && coveragePanel.isVisible())
coveragePanel.repaint();
if(snpPanel != null && snpPanel.isVisible())
snpPanel.repaint();
}
}
public void selectionChanged(SelectionChangeEvent event)
{
repaint();
}
private class Ruler extends JPanel
{
private static final long serialVersionUID = 1L;
int start;
int end;
public Ruler()
{
super();
setPreferredSize(new Dimension(mainPanel.getWidth(), 15));
setBackground(Color.white);
setFont(getFont().deriveFont(11.f)); }
public void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
drawBaseScale(g2, start, end, 12);
}
private void drawBaseScale(Graphics2D g2, int start, int end, int ypos)
{
int startMark = (((int)(start/10))*10)+1;
if(end > getSequenceLength())
end = getSequenceLength();
for(int i=startMark; i<end; i+=10)
{
int xpos = (i-start)*ALIGNMENT_PIX_PER_BASE;
g2.drawString(Integer.toString(i), xpos, ypos);
xpos+=(ALIGNMENT_PIX_PER_BASE/2);
g2.drawLine(xpos, ypos+1, xpos, ypos+5);
}
}
}
/**
* Popup menu listener
*/
class PopupListener extends MouseAdapter
{
JMenuItem gotoMateMenuItem;
JMenuItem showDetails;
public void mouseClicked(MouseEvent e)
{
if(e.isPopupTrigger() ||
e.getButton() == MouseEvent.BUTTON3)
return;
BamView.this.requestFocus();
if(e.getClickCount() > 1)
getSelection().clear();
else if(e.getButton() == MouseEvent.BUTTON1)
highlightSAMRecord = mouseOverSAMRecord;
else
highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
repaint();
}
public void mousePressed(MouseEvent e)
{
maybeShowPopup(e);
}
public void mouseReleased(MouseEvent e)
{
dragStart = -1;
maybeShowPopup(e);
}
private void maybeShowPopup(MouseEvent e)
{
if(e.isPopupTrigger())
{
if(popup == null)
{
popup = new JPopupMenu(); createMenus(popup);
}
if(gotoMateMenuItem != null)
popup.remove(gotoMateMenuItem);
if(showDetails != null)
popup.remove(showDetails);
if( mouseOverSAMRecord != null &&
mouseOverSAMRecord.getReadPairedFlag() &&
!mouseOverSAMRecord.getMateUnmappedFlag() )
{
final SAMRecord thisSAMRecord = mouseOverSAMRecord;
gotoMateMenuItem = new JMenuItem("Go to mate of : "+
thisSAMRecord.getReadName());
gotoMateMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
String name = thisSAMRecord.getMateReferenceName();
if(name.equals("="))
name = thisSAMRecord.getReferenceName();
int offset = getSequenceOffset(name);
if(feature_display != null)
feature_display.makeBaseVisible(
thisSAMRecord.getMateAlignmentStart()+offset);
else
scrollBar.setValue(
thisSAMRecord.getMateAlignmentStart()+offset-
(nbasesInView/2));
highlightSAMRecord = thisSAMRecord;
}
});
popup.add(gotoMateMenuItem);
}
if( mouseOverSAMRecord != null)
{
final SAMRecord thisSAMRecord = mouseOverSAMRecord;
showDetails = new JMenuItem("Show details of : "+
thisSAMRecord.getReadName());
showDetails.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
FileViewer viewDetail = new FileViewer(thisSAMRecord.getReadName(), true, false);
appendToDetailView(thisSAMRecord, viewDetail);
}
});
popup.add(showDetails);
}
popup.show(e.getComponent(),
e.getX(), e.getY());
}
}
}
private void appendToDetailView(SAMRecord thisSAMRecord, FileViewer viewDetail)
{
viewDetail.appendString("Read Name "+thisSAMRecord.getReadName()+"\n", Level.INFO);
viewDetail.appendString("Coordinates "+thisSAMRecord.getAlignmentStart()+".."+
thisSAMRecord.getAlignmentEnd()+"\n", Level.DEBUG);
viewDetail.appendString("Length "+thisSAMRecord.getReadLength()+"\n", Level.DEBUG);
viewDetail.appendString("Reference Name "+thisSAMRecord.getReferenceName()+"\n", Level.DEBUG);
viewDetail.appendString("Inferred Size "+thisSAMRecord.getInferredInsertSize()+"\n", Level.DEBUG);
viewDetail.appendString("Mapping Quality "+thisSAMRecord.getMappingQuality()+"\n", Level.DEBUG);
if(thisSAMRecord.getReadPairedFlag() && thisSAMRecord.getProperPairFlag() && !thisSAMRecord.getMateUnmappedFlag()) {
viewDetail.appendString("Mate Reference Name "+thisSAMRecord.getMateReferenceName()+"\n", Level.DEBUG);
viewDetail.appendString("Mate Start Coordinate "+thisSAMRecord.getMateAlignmentStart()+"\n", Level.DEBUG);
viewDetail.appendString("Strand (read/mate) "+
(thisSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
(thisSAMRecord.getMateNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
}
else
{
viewDetail.appendString("Strand (read) "+
(thisSAMRecord.getReadNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
}
viewDetail.appendString("\n\nCigar String "+thisSAMRecord.getCigarString(), Level.DEBUG);
viewDetail.appendString("\n\nFlags:", Level.INFO);
viewDetail.appendString("\nDuplicate Read "+
(thisSAMRecord.getDuplicateReadFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\nRead Paired "+
(thisSAMRecord.getReadPairedFlag() ? "yes" : "no"), Level.DEBUG);
if(thisSAMRecord.getReadPairedFlag())
{
viewDetail.appendString("\nFirst of Pair "+
(thisSAMRecord.getFirstOfPairFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\nMate Unmapped "+
(thisSAMRecord.getMateUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\nProper Pair "+
(thisSAMRecord.getProperPairFlag() ? "yes" : "no"), Level.DEBUG);
}
viewDetail.appendString("\nRead Fails Vendor\nQuality Check "+
(thisSAMRecord.getReadFailsVendorQualityCheckFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\nRead Unmapped "+
(thisSAMRecord.getReadUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
if(thisSAMRecord.getReadPairedFlag())
viewDetail.appendString("\nSecond Of Pair "+
(thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\n\nRead Bases:\n", Level.INFO);
viewDetail.appendString(new String(thisSAMRecord.getReadBases()), Level.DEBUG);
}
protected SAMRecordFlagPredicate getSamRecordFlagPredicate()
{
return samRecordFlagPredicate;
}
protected void setSamRecordFlagPredicate(
SAMRecordFlagPredicate samRecordFlagPredicate)
{
laststart = -1;
lastend = -1;
this.samRecordFlagPredicate = samRecordFlagPredicate;
}
protected SAMRecordMapQPredicate getSamRecordMapQPredicate()
{
return samRecordMapQPredicate;
}
protected void setSamRecordMapQPredicate(
SAMRecordMapQPredicate samRecordMapQPredicate)
{
laststart = -1;
lastend = -1;
this.samRecordMapQPredicate = samRecordMapQPredicate;
}
class PairedRead {
SAMRecord sam1;
SAMRecord sam2;
}
public static void main(String[] args)
{
BamFrame frame = new BamFrame();
if(args.length == 0 && BamFrame.isMac())
{
try
{
Thread.sleep(1000);
}
catch (InterruptedException e1) {}
if(frame.getBamFile() != null)
args = new String[]{ frame.getBamFile() };
}
List<String> bam = new Vector<String>();
String reference = null;
if(args.length == 0)
{
System.setProperty("default_directory", System.getProperty("user.dir"));
FileSelectionDialog fileSelection = new FileSelectionDialog(
null, true, "BamView", "BAM");
bam = fileSelection.getFiles(".*\\.bam$");
reference = fileSelection.getReferenceFile();
if(reference == null || reference.equals(""))
reference = null;
if(bam == null || bam.size() < 1)
{
System.err.println("No files found.");
System.exit(0);
}
}
else if(!args[0].startsWith("-"))
{
for(int i=0; i< args.length; i++)
bam.add(args[i]);
}
int nbasesInView = 1000;
for(int i=0;i<args.length; i++)
{
if(args[i].equals("-a"))
{
while(i < args.length-1 && !args[++i].startsWith("-"))
{
String filename = args[i];
if(FileSelectionDialog.isListOfFiles(filename))
bam.addAll(FileSelectionDialog.getListOfFiles(filename));
else
bam.add(filename);
}
--i;
}
else if(args[i].equals("-r"))
reference = args[++i];
else if(args[i].equals("-v"))
nbasesInView = Integer.parseInt(args[++i]);
else if(args[i].equals("-s"))
System.setProperty("samtoolDir", args[++i]);
else if(args[i].startsWith("-h"))
{
System.out.println("-h\t show help");
System.out.println("-a\t BAM/SAM file to display"); System.out.println("-r\t reference file (optional)");
System.out.println("-v\t number of bases to display in the view (optional)");
/*System.out.println("-s\t samtool directory");*/
System.exit(0);
}
}
final BamView view = new BamView(bam, reference, nbasesInView);
frame.setTitle("BamView v"+view.getVersion());
// translucent
//frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f));
frame.addWindowFocusListener(new WindowFocusListener()
{
public void windowGainedFocus(WindowEvent e)
{
view.requestFocus();
}
public void windowLostFocus(WindowEvent e){}
});
view.addJamToPanel((JPanel)frame.getContentPane(), frame, false, null);
frame.pack();
view.jspView.getVerticalScrollBar().setValue(
view.jspView.getVerticalScrollBar().getMaximum());
frame.setVisible(true);
}
}