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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();
}
});
}
{
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());
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;
checkBoxStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
isStackView = !isStackView;
if(isStackView)
{
isPairedStackView = !isStackView;
checkBoxPairedStackView.setSelected(!isStackView);
checkBoxPairedStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
isPairedStackView = !isPairedStackView;
if(isPairedStackView)
{
isStackView = !isPairedStackView;
checkBoxStackView.setSelected(!isPairedStackView);
}
repaint();
}
});
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();
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 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);
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);
final JCheckBoxMenuItem checkBoxSync =
new JCheckBoxMenuItem("Asynchronous", asynchronous);
checkBoxSync.addActionListener(new ActionListener()
public void actionPerformed(ActionEvent e)
{
asynchronous = checkBoxSync.isSelected();
}
});
JMenu maxHeightMenu = new JMenu("BamView Height");
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);
}
});
}
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);
}
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
*/
if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
this.nbasesInView = (int)(mainPanel.getWidth()/pixPerBase);
if(ruler == null)
ruler = new Ruler();
jspView.setColumnHeaderView(ruler);
showBaseAlignment = true;
markInsertions.setEnabled(true);
}
else if(jspView != null)
{
jspView.setColumnHeaderView(null);
if(!isStrandStackView)
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
markInsertions.setEnabled(false);
{
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;
else
{
if(feature_display == null)
pixPerBase = 1000.f/(float)(end-start+1);
else
pixPerBase = feature_display.getWidth()/(float)(end-start+1);
}
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();
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;
}
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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.
**/
if(event.getButton() == MouseEvent.BUTTON3 || bases == null)
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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 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;
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();
/**
* 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 int getBasesInView()
{
return nbasesInView;
}
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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;
}
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;
}
public Object construct()
{
try
{
Thread.sleep(500);
}
catch (InterruptedException e)
{
e.printStackTrace();
}
if(event.getStart() != ((FeatureDisplay)event.getSource()).getForwardBaseAtLeftEdge())
{
waitingFrame.showWaiting("waiting...", mainPanel);
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.repaint();
if(snpPanel != null && snpPanel.isVisible())
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();
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();
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;
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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)
{
maybeShowPopup(e);
}
private void maybeShowPopup(MouseEvent e)
{
if(e.isPopupTrigger())
if(gotoMateMenuItem != null)
popup.remove(gotoMateMenuItem);
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if(showDetails != null)
popup.remove(showDetails);
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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);
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}
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());
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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);
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if(thisSAMRecord.getReadPairedFlag() && thisSAMRecord.getProperPairFlag() && !thisSAMRecord.getMateUnmappedFlag())
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{
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 "+
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(thisSAMRecord.getFirstOfPairFlag() ? "yes" : "no"), Level.DEBUG);
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(thisSAMRecord.getMateUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
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(thisSAMRecord.getProperPairFlag() ? "yes" : "no"), Level.DEBUG);
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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 "+
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(thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\n\nRead Bases:\n", Level.INFO);
viewDetail.appendString(new String(thisSAMRecord.getReadBases()), Level.DEBUG);
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}
protected SAMRecordFlagPredicate getSamRecordFlagPredicate()
{
return samRecordFlagPredicate;
}
protected void setSamRecordFlagPredicate(
SAMRecordFlagPredicate samRecordFlagPredicate)
{
laststart = -1;
lastend = -1;
this.samRecordFlagPredicate = samRecordFlagPredicate;
}
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protected SAMRecordMapQPredicate getSamRecordMapQPredicate()
{
return samRecordMapQPredicate;
}
protected void setSamRecordMapQPredicate(
SAMRecordMapQPredicate samRecordMapQPredicate)
{
laststart = -1;
lastend = -1;
this.samRecordMapQPredicate = samRecordMapQPredicate;
}
class PairedRead
{
SAMRecord sam1;
SAMRecord sam2;
if(args.length == 0 && BamFrame.isMac())
{
try
{
Thread.sleep(1000);
}
catch (InterruptedException e1) {}
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;
{
System.err.println("No files found.");
else if(!args[0].startsWith("-"))
{
for(int i=0; i< args.length; i++)
bam.add(args[i]);
}
int nbasesInView = 1000;
{
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);
}
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");*/
final BamView view = new BamView(bam, reference, nbasesInView);
// 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);
view.jspView.getVerticalScrollBar().setValue(
view.jspView.getVerticalScrollBar().getMaximum());