diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index caaa8085c37acb9cc9cc809fd677657843ca2db2..93664333221d7b21368818af8bf82085412f71dc 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -128,6 +128,7 @@ public class BamView extends JPanel
private boolean isSNPs = false;
private boolean isStackView = false;
private boolean isPairedStackView = false;
+ private boolean isStrandStackView = false;
private boolean isCoverage = false;
private FeatureDisplay feature_display;
@@ -421,6 +422,13 @@ public class BamView extends JPanel
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)
@@ -479,7 +487,7 @@ public class BamView extends JPanel
try
{
readFromBamPicard(start, end);
- if(!isStackView || pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
+ if((!isStackView && !isStrandStackView) || pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
Collections.sort(readsInView, new SAMRecordComparator());
setCursor(cdone);
@@ -501,6 +509,8 @@ public class BamView extends JPanel
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)
@@ -711,8 +721,8 @@ public class BamView extends JPanel
private void drawLineView(Graphics2D g2, int seqLength, float pixPerBase, int start, int end)
{
drawSelectionRange(g2, pixPerBase,start, end);
- if(isShowScale())
- drawScale(g2, start, end, pixPerBase);
+ if(showScale)
+ drawScale(g2, start, end, pixPerBase, getHeight());
Stroke originalStroke =
new BasicStroke (1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
@@ -735,7 +745,7 @@ public class BamView extends JPanel
if(isSingle)
{
int ypos = (getHeight() - scaleHeight) - samRecord.getReadString().length();
- g2.setColor(Color.orange);
+ g2.setColor(Color.black);
drawRead(g2, samRecord, pixPerBase, stroke, ypos);
}
continue;
@@ -806,7 +816,7 @@ public class BamView extends JPanel
{
drawSelectionRange(g2, pixPerBase,start, end);
if(isShowScale())
- drawScale(g2, start, end, pixPerBase);
+ drawScale(g2, start, end, pixPerBase, getHeight());
BasicStroke stroke = new BasicStroke(
1.3f,
@@ -858,6 +868,93 @@ public class BamView extends JPanel
}
}
+ /**
+ * 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;
+
+ g2.setColor(Color.blue);
+
+ 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;
+ drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+ }
+ }
+ }
/**
* Draw the reads as lines in vertical stacks. The reads are colour
@@ -881,7 +978,7 @@ public class BamView extends JPanel
{
drawSelectionRange(g2, pixPerBase,start, end);
if(isShowScale())
- drawScale(g2, start, end, pixPerBase);
+ drawScale(g2, start, end, pixPerBase, getHeight());
Vector<PairedRead> pairedReads = new Vector<PairedRead>();
for(int i=0; i<readsInView.size(); i++)
@@ -1050,28 +1147,28 @@ public class BamView extends JPanel
}
- private void drawScale(Graphics2D g2, int start, int end, float pixPerBase)
+ private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
{
g2.setColor(Color.black);
- g2.drawLine( 0, getHeight()-14,
- (int)((end - getBaseAtStartOfView())*pixPerBase), getHeight()-14);
+ g2.drawLine( 0, ypos-14,
+ (int)((end - getBaseAtStartOfView())*pixPerBase), ypos-14);
int interval = end-start;
if(interval > 256000)
- drawTicks(g2, start, end, pixPerBase, 512000);
+ drawTicks(g2, start, end, pixPerBase, 512000, ypos);
else if(interval > 64000)
- drawTicks(g2, start, end, pixPerBase, 12800);
+ drawTicks(g2, start, end, pixPerBase, 12800, ypos);
else if(interval > 16000)
- drawTicks(g2, start, end, pixPerBase, 3200);
+ drawTicks(g2, start, end, pixPerBase, 3200, ypos);
else if(interval > 4000)
- drawTicks(g2, start, end, pixPerBase, 800);
+ drawTicks(g2, start, end, pixPerBase, 800, ypos);
else if(interval > 1000)
- drawTicks(g2, start, end, pixPerBase, 400);
+ drawTicks(g2, start, end, pixPerBase, 400, ypos);
else
- drawTicks(g2, start, end, pixPerBase, 100);
+ drawTicks(g2, start, end, pixPerBase, 100, ypos);
}
- private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division)
+ private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division, int ypos)
{
int markStart = (Math.round(start/division)*division);
@@ -1083,21 +1180,21 @@ public class BamView extends JPanel
if(sm > start)
{
x = (sm-getBaseAtStartOfView())*pixPerBase;
- g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-12);
+ 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, getHeight()-1);
- g2.drawLine((int)x, getHeight()-14,(int)x, getHeight()-11);
+ 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, getHeight()-14,(int)x, getHeight()-12);
+ g2.drawLine((int)x, ypos-14,(int)x, ypos-12);
}
if(m == 1)
@@ -1329,7 +1426,7 @@ public class BamView extends JPanel
{
public void mouseDragged(MouseEvent event)
{
- handleCanvasMouseDragOrClick(event);
+ handleCanvasMouseDrag(event);
}
public void mouseMoved(MouseEvent e)
@@ -1436,8 +1533,6 @@ public class BamView extends JPanel
mainPanel.add(jspView, BorderLayout.CENTER);
JPanel bottomPanel = new JPanel(new BorderLayout());
-
-
coveragePanel = new CoveragePanel(this);
bottomPanel.add(coveragePanel, BorderLayout.CENTER);
@@ -1530,7 +1625,8 @@ public class BamView extends JPanel
final JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
-
+ final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
+
checkBoxStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1542,7 +1638,9 @@ public class BamView extends JPanel
if(isStackView)
{
isPairedStackView = !isStackView;
+ isStrandStackView = !isStackView;
checkBoxPairedStackView.setSelected(!isStackView);
+ checkBoxStrandStackView.setSelected(!isStackView);
}
repaint();
}
@@ -1561,13 +1659,35 @@ public class BamView extends JPanel
if(isPairedStackView)
{
isStackView = !isPairedStackView;
+ isStrandStackView = !isPairedStackView;
checkBoxStackView.setSelected(!isPairedStackView);
+ checkBoxStrandStackView.setSelected(!isPairedStackView);
}
repaint();
}
});
view.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();
+ }
+ repaint();
+ }
+ });
+ view.add(checkBoxStrandStackView);
JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
checkBoxCoverage.addActionListener(new ActionListener()
@@ -1615,6 +1735,13 @@ public class BamView extends JPanel
mainPanel.setVisible(visible);
}
+ private void setViewportMidPoint()
+ {
+ Point p = jspView.getViewport().getLocation();
+ p.y = (getHeight() - jspView.getViewport().getViewRect().height)/2;
+ jspView.getViewport().setViewPosition(p);
+ }
+
private int getBaseAtStartOfView()
{
if(feature_display != null)
@@ -1648,8 +1775,10 @@ public class BamView extends JPanel
else if(jspView != null)
{
jspView.setColumnHeaderView(null);
- jspView.getVerticalScrollBar().setValue(
- jspView.getVerticalScrollBar().getMaximum());
+
+ if(!isStrandStackView)
+ jspView.getVerticalScrollBar().setValue(
+ jspView.getVerticalScrollBar().getMaximum());
showBaseAlignment = false;
}
@@ -1661,7 +1790,6 @@ public class BamView extends JPanel
scrollBar.setBlockIncrement(nbasesInView);
}
}
-
/**
@@ -1794,7 +1922,7 @@ public class BamView extends JPanel
/**
* Handle a mouse drag event on the drawing canvas.
**/
- private void handleCanvasMouseDragOrClick(final MouseEvent event)
+ private void handleCanvasMouseDrag(final MouseEvent event)
{
if(event.getButton() == MouseEvent.BUTTON3 || bases == null)
return;
@@ -1853,7 +1981,7 @@ public class BamView extends JPanel
return selection;
}
- public List<SAMRecord> getReadsInView()
+ protected List<SAMRecord> getReadsInView()
{
return readsInView;
}