diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 48fbf283ba0f00a00a3ff41a4e9d1b361be66e13..d2e6b25c1e786dd4fcd90cde39e6d47062cde5c1 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -110,6 +110,7 @@ import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMException;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMFileReader.ValidationStringency;
@@ -153,6 +154,7 @@ public class BamView extends JPanel
private List<BamViewRecord> readsInView;
private Hashtable<String, SAMFileReader> samFileReaderHash = new Hashtable<String, SAMFileReader>();
+ private List<SAMReadGroupRecord> readGroups = new Vector<SAMReadGroupRecord>();
private HashMap<String, Integer> seqLengths = new HashMap<String, Integer>();
private HashMap<String, Integer> offsetLengths;
@@ -210,6 +212,7 @@ public class BamView extends JPanel
private ButtonGroup buttonGroup = new ButtonGroup();
+ private JCheckBoxMenuItem colourByReadGrp = new JCheckBoxMenuItem("Read Group");
private JCheckBoxMenuItem colourByStrandTag = new JCheckBoxMenuItem("RNASeq Strand Specific Tag (XS)");
private JCheckBoxMenuItem colourByCoverageColour = new JCheckBoxMenuItem("Coverage Plot Colours");
private JCheckBoxMenuItem baseQualityColour = new JCheckBoxMenuItem("Base Quality");
@@ -217,6 +220,7 @@ public class BamView extends JPanel
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
+ private ReadGroupFrame readGrpFrame;
private GroupBamFrame groupsFrame = new GroupBamFrame(this, bamFilesMenu);
private CoveragePanel coverageView = new CoveragePanel();
@@ -398,10 +402,11 @@ public class BamView extends JPanel
String msg =
mouseOverSAMRecord.sam.getReadName() + "\n" +
mouseOverSAMRecord.sam.getAlignmentStart() + ".." +
- mouseOverSAMRecord.sam.getAlignmentEnd() + "\nisize=" +
- mouseOverSAMRecord.sam.getInferredInsertSize() + "\nmapq=" +
- mouseOverSAMRecord.sam.getMappingQuality()+"\nrname="+
- mouseOverSAMRecord.sam.getReferenceName();
+ mouseOverSAMRecord.sam.getAlignmentEnd() +
+ (mouseOverSAMRecord.sam.getReadGroup() != null ? "\nRG="+mouseOverSAMRecord.sam.getReadGroup().getId() : "") +
+ "\nisize=" + mouseOverSAMRecord.sam.getInferredInsertSize() +
+ "\nmapq=" + mouseOverSAMRecord.sam.getMappingQuality()+
+ "\nrname="+ mouseOverSAMRecord.sam.getReferenceName();
if( mouseOverSAMRecord.sam.getReadPairedFlag() &&
mouseOverSAMRecord.sam.getProperPairFlag() &&
@@ -572,7 +577,8 @@ public class BamView extends JPanel
}
samFileReader.setValidationStringency(ValidationStringency.SILENT);
samFileReaderHash.put(bam, samFileReader);
-
+
+ readGroups.addAll(samFileReader.getFileHeader().getReadGroups());
return samFileReader;
}
@@ -716,6 +722,9 @@ public class BamView extends JPanel
cnt++;
SAMRecord samRecord = it.next();
+ if(readGrpFrame != null && !readGrpFrame.isReadGroupVisible(samRecord.getReadGroup()))
+ continue;
+
if( samRecordFlagPredicate == null ||
!samRecordFlagPredicate.testPredicate(samRecord))
{
@@ -1033,6 +1042,11 @@ public class BamView extends JPanel
}
}
+ protected void repaintBamView()
+ {
+ laststart = -1;
+ repaint();
+ }
private float getPixPerBaseByWidth()
{
@@ -1485,7 +1499,9 @@ public class BamView extends JPanel
List<Integer> snps = getSNPs(samRecord);
- if(colourByCoverageColour.isSelected() || colourByStrandTag.isSelected() ||
+ if(colourByCoverageColour.isSelected() ||
+ colourByStrandTag.isSelected() ||
+ colourByReadGrp.isSelected() ||
lstStart != recordStart || lstEnd != recordEnd || snps != null)
{
if(colourByStrandTag.isSelected())
@@ -1501,6 +1517,8 @@ public class BamView extends JPanel
}
else if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(bamViewRecord));
+ else if(colourByReadGrp.isSelected())
+ g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
g2.setColor(Color.black);
@@ -1600,8 +1618,10 @@ public class BamView extends JPanel
final int recordEnd = samRecord.getAlignmentEnd()+offset;
List<Integer> snps = getSNPs(samRecord);
- if(colourByCoverageColour.isSelected() || colourByStrandTag.isSelected() ||
- lstStart != recordStart || lstEnd != recordEnd || snps != null)
+ if(colourByCoverageColour.isSelected() ||
+ colourByStrandTag.isSelected() ||
+ colourByReadGrp.isSelected() ||
+ lstStart != recordStart || lstEnd != recordEnd || snps != null)
{
if(colourByStrandTag.isSelected())
{
@@ -1616,6 +1636,8 @@ public class BamView extends JPanel
}
else if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(bamViewRecord));
+ else if(colourByReadGrp.isSelected())
+ g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
g2.setColor(Color.black);
@@ -1796,6 +1818,8 @@ public class BamView extends JPanel
else
g2.setColor(Color.BLACK);
}
+ else if(colourByReadGrp.isSelected())
+ g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, pr.sam1.sam.getReadGroup()));
else if( pr.sam2 != null &&
!( pr.sam1.sam.getReadNegativeStrandFlag() ^ pr.sam2.sam.getReadNegativeStrandFlag() ) )
g2.setColor(Color.red);
@@ -2460,7 +2484,7 @@ public class BamView extends JPanel
* @param c
* @return
*/
- private ImageIcon getImageIcon(Color c)
+ ImageIcon getImageIcon(Color c)
{
BufferedImage image = (BufferedImage)this.createImage(10, 10);
Graphics2D g2 = image.createGraphics();
@@ -2503,8 +2527,8 @@ public class BamView extends JPanel
bamFilesMenu.add(groupBams);
bamFilesMenu.addSeparator();
menu.add(bamFilesMenu);
-
-
+
+
final JMenu analyse = new JMenu("Analyse");
menu.add(analyse);
final JMenuItem readCount = new JMenuItem("Read count of selected features ...");
@@ -2608,6 +2632,7 @@ public class BamView extends JPanel
cbCoverageHeatMap.setFont(viewMenu.getFont());
baseQualityColour.setFont(viewMenu.getFont());
+ colourByReadGrp.setFont(viewMenu.getFont());
colourByCoverageColour.setFont(viewMenu.getFont());
colourByStrandTag.setFont(viewMenu.getFont());
markInsertions.setFont(viewMenu.getFont());
@@ -2728,15 +2753,39 @@ public class BamView extends JPanel
final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks", isSNPs);
//
- JMenu colourMenu = new JMenu("Colour By");
+ final JMenu colourMenu = new JMenu("Colour By");
+
+ final JCheckBoxMenuItem colourDefault = new JCheckBoxMenuItem ("Default", true);
+ final ButtonGroup grp = new ButtonGroup();
+ grp.add(colourByReadGrp);
+ grp.add(colourByCoverageColour);
+ grp.add(colourByStrandTag);
+ grp.add(colourDefault);
+
+ colourMenu.add(colourDefault);
+ colourDefault.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ repaintBamView();
+ }
+ });
+
+ colourMenu.add(colourByReadGrp);
+ colourByReadGrp.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ repaintBamView();
+ }
+ });
+
colourMenu.add(colourByCoverageColour);
colourByCoverageColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- if(colourByCoverageColour.isSelected())
- colourByStrandTag.setSelected(false);
- repaint();
+ repaintBamView();
}
});
@@ -2745,10 +2794,7 @@ public class BamView extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- if(colourByStrandTag.isSelected())
- colourByCoverageColour.setSelected(false);
- laststart = -1;
- repaint();
+ repaintBamView();
}
});
@@ -2765,6 +2811,7 @@ public class BamView extends JPanel
repaint();
}
});
+ colourMenu.addSeparator();
colourMenu.add(baseQualityColour);
menu.add(colourMenu);
@@ -2912,6 +2959,16 @@ public class BamView extends JPanel
}
});
+ final JMenuItem readGroupsMenu = new JMenuItem("Read Groups ...");
+ readGroupsMenu.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent arg0)
+ {
+ ReadGroupFrame f = getReadGroupFrame();
+ f.setVisible(true);
+ }
+ });
+ menu.add(readGroupsMenu);
+
JMenuItem filter = new JMenuItem("Filter Reads ...");
menu.add(filter);
filter.addActionListener(new ActionListener()
@@ -2924,7 +2981,7 @@ public class BamView extends JPanel
filterFrame.setVisible(true);
}
});
-
+
JMenuItem maxReadCoverage = new JMenuItem("Read Coverage Threshold ...");
menu.add(maxReadCoverage);
maxReadCoverage.addActionListener(new ActionListener()
@@ -2976,6 +3033,13 @@ public class BamView extends JPanel
viewMenu.add(coverageMenu);
}
+ private ReadGroupFrame getReadGroupFrame()
+ {
+ if(readGrpFrame == null)
+ readGrpFrame = new ReadGroupFrame(readGroups, BamView.this);
+ return readGrpFrame;
+ }
+
private JComponent bamTopPanel(final JFrame frame)
{
final JComponent topPanel;
@@ -3612,12 +3676,13 @@ public class BamView extends JPanel
feature_display.addDisplayAdjustmentListener(bamView);
feature_display.getSelection().addSelectionChangeListener(bamView);
+ if(entry_edit != null)
+ entry_edit.getOneLinePerEntryDisplay().addDisplayAdjustmentListener(bamView);
if(feature_display.getEntryGroup().getSequenceEntry().getEMBLEntry().getSequence()
instanceof uk.ac.sanger.artemis.io.IndexFastaStream)
{
if(entry_edit != null)
{
- entry_edit.getOneLinePerEntryDisplay().addDisplayAdjustmentListener(bamView);
// add reference sequence selection listeners
entry_edit.getEntryGroupDisplay().getIndexFastaCombo().addIndexReferenceListener(bamView.getCombo());
bamView.getCombo().addIndexReferenceListener(entry_edit.getEntryGroupDisplay().getIndexFastaCombo());
@@ -3929,6 +3994,8 @@ public class BamView extends JPanel
viewer.appendString("Read Name "+sam.getReadName()+"\n", Level.INFO);
viewer.appendString("Coordinates "+sam.getAlignmentStart()+".."+
sam.getAlignmentEnd()+"\n", Level.DEBUG);
+ if(sam.getReadGroup() != null)
+ viewer.appendString("Read Group "+sam.getReadGroup().getId()+"\n", Level.DEBUG);
viewer.appendString("Length "+sam.getReadLength()+"\n", Level.DEBUG);
viewer.appendString("Reference Name "+sam.getReferenceName()+"\n", Level.DEBUG);
viewer.appendString("Inferred Size "+sam.getInferredInsertSize()+"\n", Level.DEBUG);