From 5032b43237bbea731ace206835a3a393708b3f9e Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 12 Nov 2009 12:34:23 +0000
Subject: [PATCH] show strand information in the tooltip and add an option to
show the details of a read
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@12335 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 86 ++++++++++++++++++-
1 file changed, 83 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 205a39d65..9b2c0184b 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -80,6 +80,8 @@ import javax.swing.UIManager;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
+import org.apache.log4j.Level;
+
import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
@@ -99,6 +101,7 @@ import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryFileDialog;
import uk.ac.sanger.artemis.components.FeatureDisplay;
+import uk.ac.sanger.artemis.components.FileViewer;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.SwingWorker;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
@@ -238,12 +241,26 @@ public class BamView extends JPanel
public String getToolTipText()
{
- String msg = (mouseOverSAMRecord != null ?
+ if(mouseOverSAMRecord == null)
+ return null;
+
+ String msg =
mouseOverSAMRecord.getReadName() + "\n" +
mouseOverSAMRecord.getAlignmentStart() + ".." +
mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
- mouseOverSAMRecord.getInferredInsertSize() + "\nrname=" +
- mouseOverSAMRecord.getReferenceName() : null);
+ mouseOverSAMRecord.getInferredInsertSize() + "\nrname=";
+
+ if(mouseOverSAMRecord.getProperPairFlag() && !mouseOverSAMRecord.getMateUnmappedFlag())
+ {
+ msg = msg +
+ mouseOverSAMRecord.getReferenceName() + "\nstrand (read/mate): "+
+ (mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
+ (mouseOverSAMRecord.getMateNegativeStrandFlag() ? "-" : "+");
+ }
+ else
+ msg = msg +
+ mouseOverSAMRecord.getReferenceName() + "\nstrand (read/mate): "+
+ (mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+");
if(msg != null && mouseOverInsertion != null)
msg = msg + "\nInsertion at:" +mouseOverInsertion;
@@ -2356,6 +2373,8 @@ public class BamView extends JPanel
class PopupListener extends MouseAdapter
{
JMenuItem gotoMateMenuItem;
+ JMenuItem showDetails;
+
public void mouseClicked(MouseEvent e)
{
if(e.isPopupTrigger() ||
@@ -2396,6 +2415,9 @@ public class BamView extends JPanel
if(gotoMateMenuItem != null)
popup.remove(gotoMateMenuItem);
+
+ if(showDetails != null)
+ popup.remove(showDetails);
if( mouseOverSAMRecord != null &&
mouseOverSAMRecord.getReadPairedFlag() &&
@@ -2424,6 +2446,22 @@ public class BamView extends JPanel
}
});
popup.add(gotoMateMenuItem);
+ }
+
+ 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());
@@ -2431,6 +2469,48 @@ public class BamView extends JPanel
}
}
+ 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);
+
+ if(thisSAMRecord.getProperPairFlag() && !thisSAMRecord.getMateUnmappedFlag())
+ {
+ 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("\nFirst of Pair "+
+ (thisSAMRecord.getFirstOfPairFlag() ? "yes" : "no"), Level.DEBUG);
+ viewDetail.appendString("\nMate Unmapped "+
+ (thisSAMRecord.getMateUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
+ viewDetail.appendString("\nProper Pair "+
+ (thisSAMRecord.getProperPairFlag() ? "yes" : "no"), Level.DEBUG);
+ viewDetail.appendString("\nRead Fails Vendor\nQuality Check "+
+ (thisSAMRecord.getReadFailsVendorQualityCheckFlag() ? "yes" : "no"), Level.DEBUG);
+ viewDetail.appendString("\nRead Unmapped "+
+ (thisSAMRecord.getReadUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
+ viewDetail.appendString("\nSecond Of Pair "+
+ (thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
+ }
+
class PairedRead
{
SAMRecord sam1;
--
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