From 2d2ea2257e84a0bd9909bf32ebd22c6fbe5d2336 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 5 Oct 2009 15:13:02 +0000
Subject: [PATCH] all BamView reads to be clickable and provide an option to go
to a read pair mate
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11959 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/FeatureDisplay.java | 2 +-
.../artemis/components/alignment/BamView.java | 66 +++++++++++++++++--
2 files changed, 63 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index ab7dfccd2..14e9d8e81 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.java
@@ -1212,7 +1212,7 @@ public class FeatureDisplay extends EntryGroupPanel
* Scroll the display so that the given base is in the middle of the screen.
* @param base The base to scroll to.
**/
- protected void makeBaseVisible(final int base)
+ public void makeBaseVisible(final int base)
{
makeBaseVisibleInternal(base, true, true);
}
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index e2ec62704..fab7732e8 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -68,6 +68,7 @@ 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;
@@ -157,6 +158,7 @@ public class BamView extends JPanel
private Point lastMousePoint = null;
private SAMRecord mouseOverSAMRecord = null;
+ private SAMRecord highlightSAMRecord = null;
// record of where a mouse drag starts
private int dragStart = -1;
@@ -811,9 +813,10 @@ public class BamView extends JPanel
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
+ int offset = getSequenceOffset(samRecord.getReferenceName());
- int recordStart = samRecord.getAlignmentStart();
- int recordEnd = samRecord.getAlignmentEnd();
+ int recordStart = samRecord.getAlignmentStart()+offset;
+ int recordEnd = samRecord.getAlignmentEnd()+offset;
if(lstStart != recordStart || lstEnd != recordEnd)
{
@@ -1120,9 +1123,25 @@ public class BamView extends JPanel
int thisStart = thisRead.getAlignmentStart()+offset-getBaseAtStartOfView();
int thisEnd = thisRead.getAlignmentEnd()+offset-getBaseAtStartOfView();
+
+ if(highlightSAMRecord != null &&
+ highlightSAMRecord.getReadName().equals(thisRead.getReadName()))
+ {
+ Stroke stroke2 =
+ new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ g2.setStroke(stroke2);
+ Color c = g2.getColor();
+ g2.setColor(Color.black);
+ g2.drawLine((int)( thisStart * pixPerBase), ypos,
+ (int)( thisEnd * pixPerBase), ypos);
+ g2.setColor(c);
+ }
+
g2.setStroke(stroke);
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
+
+
// test if the mouse is over this read
if(lastMousePoint != null)
@@ -1762,6 +1781,7 @@ public class BamView extends JPanel
|| bases == null)
return;
+ highlightSAMRecord = null;
if(event.getClickCount() > 1)
{
getSelection().clear();
@@ -1880,10 +1900,16 @@ public class BamView extends JPanel
*/
class PopupListener extends MouseAdapter
{
+ JMenuItem gotoMateMenuItem;
public void mouseClicked(MouseEvent e)
{
BamView.this.requestFocus();
- handleCanvasMouseDragOrClick(e);
+
+ if(e.getClickCount() > 1)
+ getSelection().clear();
+ else if(e.getButton() == MouseEvent.BUTTON1)
+ highlightSAMRecord = mouseOverSAMRecord;
+ repaint();
}
public void mousePressed(MouseEvent e)
@@ -1906,6 +1932,38 @@ public class BamView extends JPanel
popup = new JPopupMenu();
createViewMenu(popup);
}
+
+ if(gotoMateMenuItem != null)
+ popup.remove(gotoMateMenuItem);
+
+ 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);
+ }
popup.show(e.getComponent(),
e.getX(), e.getY());
}
@@ -1948,7 +2006,7 @@ public class BamView extends JPanel
}
final BamView view = new BamView(bam, reference, nbasesInView);
- JFrame frame = new JFrame("JAM");
+ JFrame frame = new JFrame("BamView");
// translucent
//frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f));
--
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