From 09441f80c87860cdeae589cd298df907d7d7074a Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 30 Apr 2013 16:21:15 +0100
Subject: [PATCH] adjustable read line height
---
.../artemis/components/alignment/BamView.java | 134 ++++++++++++------
1 file changed, 91 insertions(+), 43 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index e7e32f866..72d10b752 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -96,11 +96,14 @@ import javax.swing.JRadioButton;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
+import javax.swing.JSlider;
import javax.swing.JTextField;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
import org.apache.log4j.Level;
@@ -251,6 +254,8 @@ public class BamView extends JPanel
private ExecutorService bamReadTaskExecutor;
private int MAX_COVERAGE = Integer.MAX_VALUE;
+ private float readLnHgt = 2.0f;
+
public static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(BamView.class);
@@ -1340,8 +1345,9 @@ public class BamView extends JPanel
drawScale(g2, start, end, pixPerBase, getHeight());
final Stroke stroke =
- new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ new BasicStroke (readLnHgt, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
g2.setStroke(stroke);
+ int ydiff = (int) Math.round(1.5*readLnHgt);
final int scaleHeight;
if(isShowScale())
@@ -1371,7 +1377,7 @@ public class BamView extends JPanel
continue;
g2.setColor(Color.black);
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
}
continue;
}
@@ -1413,18 +1419,18 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
- drawRead(g2, bamViewNextRecord, pixPerBase, ypos, baseAtStartOfView, getSNPs(samNextRecord));
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
+ drawRead(g2, bamViewNextRecord, pixPerBase, ypos, baseAtStartOfView, getSNPs(samNextRecord), ydiff);
}
else
{
- drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps);
+ drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps, ydiff);
i--;
}
}
else
{
- drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps);
+ drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps, ydiff);
}
}
@@ -1467,7 +1473,7 @@ public class BamView extends JPanel
drawScale(g2, start, end, pixPerBase, getHeight());
final BasicStroke stroke = new BasicStroke(
- 1.3f,
+ readLnHgt,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
g2.setStroke(stroke);
@@ -1479,9 +1485,10 @@ public class BamView extends JPanel
scaleHeight = 0;
int ypos = (getHeight() - scaleHeight);
- int ydiff = 2;
+ int ydiff = (int) Math.round(1.5*readLnHgt);
+
if(isOrientation)
- ydiff= 4;
+ ydiff= 2*ydiff;
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
@@ -1546,7 +1553,7 @@ public class BamView extends JPanel
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
}
}
@@ -1572,7 +1579,7 @@ public class BamView extends JPanel
{
drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
final BasicStroke stroke = new BasicStroke(
- 1.3f,
+ readLnHgt,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
@@ -1580,14 +1587,16 @@ public class BamView extends JPanel
drawScale(g2, start, end, pixPerBase, ((getHeight()+scaleHeight)/2));
int ymid = (getHeight()/ 2);
- int ydiff = 2;
+ int ydiff = (int) Math.round(1.5*readLnHgt);
if(isOrientation)
- ydiff= 4;
+ ydiff= 2*ydiff;
+
+ g2.setStroke(stroke);
// positive strand
- drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -ydiff, pixPerBase, stroke);
+ drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -ydiff, pixPerBase);
// negative strand
- drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), ydiff, pixPerBase, stroke);
+ drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), ydiff, pixPerBase);
}
@@ -1596,8 +1605,7 @@ public class BamView extends JPanel
int scaleHeight,
int ymid,
int ystep,
- float pixPerBase,
- Stroke stroke)
+ float pixPerBase)
{
int hgt = getHeight();
int ypos = (hgt - scaleHeight);
@@ -1666,7 +1674,7 @@ public class BamView extends JPanel
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ystep);
}
}
}
@@ -1731,10 +1739,9 @@ public class BamView extends JPanel
}
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);
+ Stroke originalStroke = new BasicStroke (readLnHgt, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+
+ g2.setStroke( new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND));
final int scaleHeight;
if(isShowScale())
@@ -1742,9 +1749,9 @@ public class BamView extends JPanel
else
scaleHeight = 0;
- int ydiff = 3;
+ int ydiff = (int) Math.round(2.3*readLnHgt);
if(isOrientation)
- ydiff= 5;
+ ydiff= 2*ydiff;
int ypos = getHeight() - scaleHeight - ydiff;
int lastEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
@@ -1826,9 +1833,9 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
- drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam1.sam));
+ drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam1.sam), ydiff);
if(pr.sam2 != null)
- drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam2.sam));
+ drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam2.sam), ydiff);
}
}
@@ -1946,7 +1953,7 @@ public class BamView extends JPanel
* @param stroke
*/
private void drawLoneRead(Graphics2D g2, BamViewRecord bamViewRecord, int ypos,
- float pixPerBase, int baseAtStartOfView, int scaleHeight, List<Integer> snps)
+ float pixPerBase, int baseAtStartOfView, int scaleHeight, List<Integer> snps, int ydiff)
{
SAMRecord samRecord = bamViewRecord.sam;
boolean offTheTop = false;
@@ -1997,7 +2004,7 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
/*if (isSNPs)
showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);*/
@@ -2108,7 +2115,8 @@ public class BamView extends JPanel
final float pixPerBase,
final int ypos,
final int baseAtStartOfView,
- final List<Integer> snps)
+ final List<Integer> snps,
+ final int ydiff)
{
SAMRecord thisRead = bamViewRecord.sam;
int offset = getSequenceOffset(thisRead.getReferenceName());
@@ -2121,7 +2129,7 @@ public class BamView extends JPanel
{
Stroke originalStroke = g2.getStroke();
Stroke stroke =
- new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ new BasicStroke (readLnHgt*1.6f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
g2.setStroke(stroke);
Color c = g2.getColor();
g2.setColor(Color.black);
@@ -2159,7 +2167,7 @@ public class BamView extends JPanel
}
if(isOrientation)
- drawArrow(g2, thisRead, thisStart, thisEnd, pixPerBase, ypos);
+ drawArrow(g2, thisRead, thisStart, thisEnd, pixPerBase, ypos, ydiff);
// test if the mouse is over this read
if(lastMousePoint != null)
@@ -2185,22 +2193,28 @@ public class BamView extends JPanel
* @param pixPerBase
* @param ypos
*/
- private void drawArrow(Graphics2D g2,
- SAMRecord thisRead,
- int thisStart,
- int thisEnd,
- float pixPerBase,
- int ypos)
+ private void drawArrow(final Graphics2D g2,
+ final SAMRecord thisRead,
+ final int thisStart,
+ final int thisEnd,
+ final float pixPerBase,
+ int ypos,
+ int ydiff)
{
+ if(ydiff < 0)
+ ydiff = -ydiff;
+
if(thisRead.getReadNegativeStrandFlag())
{
- int apos = ypos + 2;
+ ypos-=readLnHgt/2;
+ int apos = ypos + ydiff - 1;
g2.drawLine((int)( (thisStart+5) * pixPerBase), apos,
(int)( thisStart * pixPerBase), ypos);
}
else
{
- int apos = ypos - 2;
+ ypos+=readLnHgt/2;
+ int apos = ypos - ydiff + 1;
g2.drawLine((int)( (thisEnd-5) * pixPerBase), apos,
(int)( thisEnd * pixPerBase), ypos);
}
@@ -2279,12 +2293,20 @@ public class BamView extends JPanel
*/
private void showSNPsOnReads(final List<Integer> snps,
final Graphics2D g2,
- float pixPerBase, int ypos)
+ float pixPerBase, final int ypos)
{
+ final Stroke originalStroke = g2.getStroke();
+ final BasicStroke stroke = new BasicStroke(
+ 1.3f,
+ BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_MITER);
+ g2.setStroke(stroke);
+
g2.setColor(Color.red);
for(int pos: snps)
g2.drawLine((int) (pos * pixPerBase), ypos + 2,
(int) (pos * pixPerBase), ypos - 2);
+ g2.setStroke(originalStroke);
}
@@ -3160,22 +3182,30 @@ public class BamView extends JPanel
{
lastMousePoint = e.getPoint();
- int thisHgt = HEIGHT;
+ int thisHgt = HEIGHT-2;
if (thisHgt < 5)
thisHgt = 15;
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
+ Point p = jspView.getViewport().getViewPosition();
+ boolean isVis = topPanel.isVisible();
+
if (y < thisHgt)
{
topPanel.setVisible(true);
+ if(!isVis)
+ p.y += topPanel.getHeight();
}
else
{
if (buttonAutoHide.isSelected())
- topPanel.setVisible(false);
+ topPanel.setVisible(false);
}
+
+ if(topPanel.isVisible())
+ jspView.getViewport().setViewPosition(p);
mainPanel.repaint();
- mainPanel.revalidate();
+ //mainPanel.revalidate();
}
};
addMouseMotionListener(mouseMotionListener);
@@ -3249,6 +3279,18 @@ public class BamView extends JPanel
topPanel.add(buttonAutoHide);
+
+ final JSlider slider = new JSlider(13, 52, (int) (readLnHgt*10));
+ slider.addChangeListener(new ChangeListener(){
+ public void stateChanged(ChangeEvent arg0)
+ {
+ readLnHgt = (slider.getValue()/10.f);
+ repaintBamView();
+ }
+ });
+ topPanel.add(new JLabel(" Read Line Height:"));
+ topPanel.add(slider);
+
if(feature_display != null)
{
JButton close = new JButton("Close");
@@ -3257,6 +3299,12 @@ public class BamView extends JPanel
{
public void actionPerformed(ActionEvent e)
{
+ int status = JOptionPane.showConfirmDialog(frame,
+ "Close the BAM panel?", "Close",
+ JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+
final JPanel containerPanel = (JPanel) mainPanel.getParent();
feature_display.removeDisplayAdjustmentListener(BamView.this);
feature_display.getSelection().removeSelectionChangeListener(BamView.this);
--
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