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Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
int offset = getSequenceOffset(samRecord.getReferenceName());
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committed
int recordStart = samRecord.getAlignmentStart()+offset;
int recordEnd = samRecord.getAlignmentEnd()+offset;
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committed
if(lstStart != recordStart || lstEnd != recordEnd)
{
if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
g2.setColor(Color.black);
else
g2.setColor(Color.blue);
if(maxEnd < recordStart)
{
ypos = (getHeight() - scaleHeight)-2;
maxEnd = recordEnd+2;
}
else
ypos = ypos-2;
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committed
g2.setColor(darkGreen);
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lstStart = recordStart;
lstEnd = recordEnd;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
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/**
* Draw the reads as lines in vertical stacks. The reads are colour
* coded as follows:
*
* blue - reads are unique and are paired with a mapped mate
* black - reads are unique and are not paired or have an unmapped mate
* green - reads are duplicates
*
* @param g2
* @param seqLength
* @param pixPerBase
* @param start
* @param end
*/
private void drawStrandStackView(Graphics2D g2,
int seqLength,
float pixPerBase,
int start,
int end)
{
drawSelectionRange(g2, pixPerBase,start, end);
BasicStroke stroke = new BasicStroke(
1.3f,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
int scaleHeight = 15;
drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));
int ymid = (getHeight()/ 2);
// positive strand
drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -2, pixPerBase, stroke);
// negative strand
drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), 2, pixPerBase, stroke);
}
private void drawStrand(Graphics2D g2,
boolean isStrandNegative,
int scaleHeight,
int ymid,
int ystep,
float pixPerBase,
Stroke stroke)
{
int ypos = (getHeight() - scaleHeight);
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
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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(lstStart != recordStart || lstEnd != recordEnd)
{
if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
g2.setColor(Color.black);
else
g2.setColor(Color.blue);
if(maxEnd < recordStart)
{
ypos = ymid + ystep;
maxEnd = recordEnd+2;
}
else
ypos = ypos + ystep;
}
else
g2.setColor(darkGreen);
lstStart = recordStart;
lstEnd = recordEnd;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
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/**
* Draw the reads as lines in vertical stacks. The reads are colour
* coded as follows:
*
* blue - reads are unique and are paired with a mapped mate
* black - reads are unique and are not paired or have an unmapped mate
* green - reads are duplicates
*
* @param g2
* @param seqLength
* @param pixPerBase
* @param start
* @param end
*/
private void drawPairedStackView(Graphics2D g2,
int seqLength,
float pixPerBase,
int start,
int end)
{
drawSelectionRange(g2, pixPerBase,start, end);
if(isShowScale())
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Vector<PairedRead> pairedReads = new Vector<PairedRead>();
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
continue;
SAMRecord samNextRecord = null;
if(i < readsInView.size()-1)
{
samNextRecord = readsInView.get(++i);
PairedRead pr = new PairedRead();
if(samRecord.getReadName().equals(samNextRecord.getReadName()))
{
if(samRecord.getAlignmentStart() < samNextRecord.getAlignmentStart())
{
pr.sam1 = samRecord;
pr.sam2 = samNextRecord;
}
else
{
pr.sam2 = samRecord;
pr.sam1 = samNextRecord;
}
}
else
{
--i;
pr.sam1 = samRecord;
pr.sam2 = null;
}
pairedReads.add(pr);
}
}
Collections.sort(pairedReads, new PairedReadComparator());
Stroke originalStroke = new BasicStroke (1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
Stroke stroke =
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
scaleHeight = 0;
int ypos = getHeight() - scaleHeight - 3;
int lastEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<pairedReads.size(); i++)
{
PairedRead pr = pairedReads.get(i);
if(pr.sam1.getAlignmentStart() > lastEnd)
{
ypos = getHeight() - scaleHeight - 3;
if(pr.sam2 != null)
{
lastEnd = pr.sam2.getAlignmentEnd();
}
else
lastEnd = pr.sam1.getAlignmentEnd();
}
else
ypos = ypos - 3;
if(ypos > r.getMaxY() || ypos < r.getMinY())
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
if(pr.sam2 != null)
{
drawTranslucentJointedLine(g2,
(int)((pr.sam1.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase),
(int)((pr.sam2.getAlignmentStart()-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();
drawTranslucentJointedLine(g2,
(int)( (prStart-getBaseAtStartOfView())*pixPerBase),
(int)( (pr.sam1.getMateAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
}
}
if( pr.sam1.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
( pr.sam2 != null && pr.sam2.getReadNegativeStrandFlag() ) )
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView);
if(pr.sam2 != null)
drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView);
}
}
/**
* Draw a read that apparently has a read mate that is not in view.
* @param g2
* @param thisRead
* @param ypos
* @param pixPerBase
* @param originalStroke
* @param stroke
*/
private void drawLoneRead(Graphics2D g2, SAMRecord samRecord, int ypos,
float pixPerBase, int baseAtStartOfView)
boolean offTheTop = false;
int offset = getSequenceOffset(samRecord.getReferenceName());
int thisStart = samRecord.getAlignmentStart()+offset;
int thisEnd = thisStart + samRecord.getReadString().length() -1;
if(ypos <= 0)
{
offTheTop = true;
ypos = samRecord.getReadString().length();
}
if(Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
g2.setColor(Color.LIGHT_GRAY);
if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
{
(int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
(int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
int nextStart =
(int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
(int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
if(offTheTop)
g2.setColor(darkOrange);
else if(samRecord.getReadNegativeStrandFlag()) // strand of the query (1 for reverse)
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
g2.drawLine( 0, ypos-14,
(int)((end - getBaseAtStartOfView())*pixPerBase), ypos-14);
private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division, int ypos)
int markStart = (Math.round(start/division)*division);
if(markStart < 1)
markStart = 1;
g2.drawString(Integer.toString(m), x, ypos-1);
g2.drawLine((int)x, ypos-14,(int)x, ypos-11);
/**
* Draw a y-scale for inferred size (isize) of reads.
* @param g2
* @param xScaleHeight
*/
private void drawYScale(Graphics2D g2, int xScaleHeight)
int maxY = getPreferredSize().height-xScaleHeight;
if(logScale)
{
int start = 10;
int count = 0;
int ypos = getYPos(xScaleHeight, start);
while(ypos > 0 && count < 15 && start > 1)
{
g2.drawLine(0, ypos, 2, ypos);
g2.drawString(Integer.toString(start), 3, ypos);
start = start*5;
ypos = getYPos(xScaleHeight, start);
count++;
}
return;
}
for(int i=100; i<maxY; i+=100)
{
int ypos = getHeight()-i-xScaleHeight;
g2.drawLine(0, ypos, 2, ypos);
g2.drawString(Integer.toString(i), 3, ypos);
/**
* Draw a given read.
* @param g2
* @param thisRead
* @param pixPerBase
* @param ypos
float pixPerBase,
int ypos,
int baseAtStartOfView)
int offset = getSequenceOffset(thisRead.getReferenceName());
int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
int thisEnd = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
if(highlightSAMRecord != null &&
highlightSAMRecord.getReadName().equals(thisRead.getReadName()))
{
Stroke originalStroke = g2.getStroke();
Stroke stroke =
new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
Color c = g2.getColor();
g2.setColor(Color.black);
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
g2.setColor(c);
}
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
// test if the mouse is over this read
if(lastMousePoint != null)
{
if(lastMousePoint.getY()+2 > ypos && lastMousePoint.getY()-2 < ypos)
if(lastMousePoint.getX() > thisStart * pixPerBase &&
lastMousePoint.getX() < thisEnd * pixPerBase)
{
mouseOverSAMRecord = thisRead;
}
}
showSNPsOnReads(g2, thisRead, pixPerBase, ypos, offset);
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/**
* Highlight a selected range
* @param g2
* @param pixPerBase
* @param start
* @param end
*/
private void drawSelectionRange(Graphics2D g2, float pixPerBase, int start, int end)
{
if(getSelection() != null)
{
Range selectedRange = getSelection().getSelectionRange();
if(selectedRange != null)
{
int rangeStart = selectedRange.getStart();
int rangeEnd = selectedRange.getEnd();
if(end < rangeStart || start > rangeEnd)
return;
int x = (int) (pixPerBase*(rangeStart-getBaseAtStartOfView()));
int width = (int) (pixPerBase*(rangeEnd-rangeStart+1));
g2.setColor(Color.pink);
g2.fillRect(x, 0, width, getHeight());
}
}
}
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/**
* Draw a translucent line
* @param g2
* @param start
* @param end
* @param ypos
*/
private void drawTranslucentLine(Graphics2D g2, int start, int end, int ypos)
{
Composite origComposite = g2.getComposite();
g2.setComposite(translucent);
g2.drawLine(start, ypos, end, ypos);
g2.setComposite(origComposite);
}
/**
* Draw a translucent line
* @param g2
* @param start
* @param end
* @param ypos
*/
private void drawTranslucentJointedLine(Graphics2D g2, int start, int end, int ypos)
{
Composite origComposite = g2.getComposite();
g2.setComposite(translucent);
int mid = (int) ((end-start)/2.f)+start;
//g2.drawLine(start, ypos, end, ypos);
g2.drawLine(start, ypos, mid, ypos-5);
g2.drawLine(mid, ypos-5, end, ypos);
g2.setComposite(origComposite);
}
/**
* Display the SNPs for the given read.
* @param g2
* @param thisRead
* @param pixPerBase
* @param ypos
*/
private void showSNPsOnReads(Graphics2D g2, SAMRecord thisRead,
{
int thisStart = thisRead.getAlignmentStart();
int thisEnd = thisRead.getAlignmentEnd();
// use alignment blocks of the contiguous alignment of
// subsets of read bases to a reference sequence
List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
offset = offset - getBaseAtStartOfView();
for(int i=0; i<blocks.size(); i++)
AlignmentBlock block = blocks.get(i);
for(int j=0; j<block.getLength(); j++)
int readPos = block.getReadStart()-1+j;
int refPos = block.getReferenceStart()+j;
if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
{
g2.drawLine((int) ((refPos+offset) * pixPerBase), ypos + 2,
(int) ((refPos+offset) * pixPerBase), ypos - 2);
g2.setColor(col);
}
catch (OutOfRangeException e)
{
e.printStackTrace();
/**
* Add the alignment view to the supplied <code>JPanel</code> in
* a <code>JScrollPane</code>.
* @param mainPanel panel to add the alignment to
* @param autohide automatically hide the top panel containing the buttons
*/
public void addJamToPanel(final JPanel mainPanel,
final boolean autohide,
final FeatureDisplay feature_display)
if(feature_display != null)
{
this.feature_display = feature_display;
this.selection = feature_display.getSelection();
topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
}
else
{
topPanel = new JMenuBar();
frame.setJMenuBar((JMenuBar)topPanel);
JMenu fileMenu = new JMenu("File");
topPanel.add(fileMenu);
JMenuItem readBam = new JMenuItem("Open new BamView ...");
fileMenu.add(readBam);
readBam.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
String[] s = new String[0];
BamView.main(s);
}
});
JMenuItem close = new JMenuItem("Close");
fileMenu.add(close);
close.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
BamView.this.setVisible(false);
Component comp = BamView.this;
while( !(comp instanceof JFrame) )
comp = comp.getParent();
((JFrame)comp).dispose();
}
});
JMenuItem exit = new JMenuItem("Exit");
fileMenu.add(exit);
exit.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
int status = JOptionPane.showConfirmDialog(BamView.this,
JOptionPane.OK_CANCEL_OPTION);
if(status != JOptionPane.OK_OPTION)
return;
System.exit(0);
}
});
if(seqNames.size() > 1)
{
int len = 0;
for(int i=0; i<seqNames.size(); i++)
len += seqLengths.get(seqNames.get(i));
if(feature_display != null &&
len == feature_display.getSequenceLength())
concatSequences = true;
else if(bases != null &&
len == bases.getLength() )
concatSequences = true;
}
final JCheckBox buttonAutoHide = new JCheckBox("Hide", autohide);
buttonAutoHide.setToolTipText("Auto-Hide");
final MouseMotionListener mouseMotionListener = new MouseMotionListener()
}
public void mouseMoved(MouseEvent e)
{
int thisHgt = HEIGHT;
if (thisHgt < 5)
thisHgt = 15;
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
if (y < thisHgt)
}
mainPanel.repaint();
mainPanel.revalidate();
}
};
addMouseMotionListener(mouseMotionListener);
combo = new JComboBox(seqNames);
combo.setEditable(false);
combo.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
laststart = -1;
lastend = -1;
setZoomLevel(BamView.this.nbasesInView);
goTo.addActionListener(new ActionListener()
public void actionPerformed(ActionEvent e)
try
{
int basePosition = Integer.parseInt(baseText.getText());
}
catch (NumberFormatException nfe)
{
JOptionPane.showMessageDialog(BamView.this,
"Expecting a base number!", "Number Format",
JOptionPane.WARNING_MESSAGE);
}
JButton zoomIn = new JButton("-");
Insets ins = new Insets(1,1,1,1);
zoomIn.addActionListener(new ActionListener()
public void actionPerformed(ActionEvent e)
{
setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
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));
jspView = new JScrollPane(this,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
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);
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();
}
});
bottomPanel.add(scrollBar, BorderLayout.SOUTH);
}
mainPanel.add(bottomPanel, BorderLayout.SOUTH);
coveragePanel.setPreferredSize(new Dimension(900, 100));
coveragePanel.setVisible(false);
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
jspView.getVerticalScrollBar().setUnitIncrement(maxUnitIncrement);
public void keyPressed(final KeyEvent event)
setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
setZoomLevel((int) (BamView.this.nbasesInView * .9));
addMouseListener(new PopupListener());
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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();
}
});
}
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{
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);
List<String> bamFiles = bamFileSelection.getBamFiles();
int count = bamList.size();
bamList.addAll(bamFileSelection.getBamFiles());
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", true);
checkBoxStackView.setFont(checkIsizeStackView.getFont());
baseQualityColour.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);
JMenu showMenu = new JMenu("Show");
JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
checkBoxSingle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
repaint();
isSingle = !isSingle;
}