diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 1f09dc1e9b742ed31f67b59c2fbca2da935a5757..7abe2392c55cede07dc78150b89e57bbaa4aae07 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -126,6 +126,7 @@ public class BamView extends JPanel
private String bam;
private SAMRecordFlagPredicate samRecordFlagPredicate;
+ private SAMRecordMapQPredicate samRecordMapQPredicate;
private Bases bases;
private JScrollPane jspView;
@@ -251,18 +252,22 @@ public class BamView extends JPanel
mouseOverSAMRecord.getReadName() + "\n" +
mouseOverSAMRecord.getAlignmentStart() + ".." +
mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
- mouseOverSAMRecord.getInferredInsertSize() + "\nrname=";
+ mouseOverSAMRecord.getInferredInsertSize() + "\nmapq=" +
+ mouseOverSAMRecord.getMappingQuality()+"\nrname="+
+ mouseOverSAMRecord.getReferenceName();
- if(mouseOverSAMRecord.getProperPairFlag() && !mouseOverSAMRecord.getMateUnmappedFlag())
+ if( mouseOverSAMRecord.getReadPairedFlag() &&
+ mouseOverSAMRecord.getProperPairFlag() &&
+ !mouseOverSAMRecord.getMateUnmappedFlag())
{
msg = msg +
- mouseOverSAMRecord.getReferenceName() + "\nstrand (read/mate): "+
+ "\nstrand (read/mate): "+
(mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
(mouseOverSAMRecord.getMateNegativeStrandFlag() ? "-" : "+");
}
else
msg = msg +
- mouseOverSAMRecord.getReferenceName() + "\nstrand (read/mate): "+
+ "\nstrand (read/mate): "+
(mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+");
if(msg != null && mouseOverInsertion != null)
@@ -446,7 +451,9 @@ public class BamView extends JPanel
if( samRecordFlagPredicate == null ||
!samRecordFlagPredicate.testPredicate(samRecord))
{
- readsInView.add(samRecord);
+ if(samRecordMapQPredicate == null ||
+ samRecordMapQPredicate.testPredicate(samRecord))
+ readsInView.add(samRecord);
}
if(cnt > checkMemAfter)
@@ -2058,7 +2065,7 @@ public class BamView extends JPanel
new SAMRecordFilter(BamView.this);
}
});
-
+ menu.add(new JSeparator());
}
public void setVisible(boolean visible)
@@ -2532,6 +2539,7 @@ public class BamView extends JPanel
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);
+ viewDetail.appendString("Mapping Quality "+thisSAMRecord.getMappingQuality()+"\n", Level.DEBUG);
if(thisSAMRecord.getProperPairFlag() && !thisSAMRecord.getMateUnmappedFlag())
{
@@ -2579,6 +2587,19 @@ public class BamView extends JPanel
this.samRecordFlagPredicate = samRecordFlagPredicate;
}
+ protected SAMRecordMapQPredicate getSamRecordMapQPredicate()
+ {
+ return samRecordMapQPredicate;
+ }
+
+ protected void setSamRecordMapQPredicate(
+ SAMRecordMapQPredicate samRecordMapQPredicate)
+ {
+ laststart = -1;
+ lastend = -1;
+ this.samRecordMapQPredicate = samRecordMapQPredicate;
+ }
+
class PairedRead
{
SAMRecord sam1;
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
index db00c329fc06397e403890b8944340ff27697b18..f716302e838635d76ef2a5673d78ad0a4b4feedf 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
@@ -1,30 +1,89 @@
package uk.ac.sanger.artemis.components.alignment;
-import java.awt.GridLayout;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Point;
+import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JFrame;
-import javax.swing.JOptionPane;
+import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JSeparator;
+import javax.swing.JTextField;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import uk.ac.sanger.artemis.components.Utilities;
-
-
+/**
+ * Filter reads bases on their mapping quality (mapq) or the
+ * flags that are set in the BAM file.
+ */
class SAMRecordFilter extends JPanel
{
private static final long serialVersionUID = 1L;
public SAMRecordFilter(final BamView bamView)
{
- super();
+ super(new GridBagLayout());
int nflags = SAMRecordFlagPredicate.FLAGS.length;
- setLayout(new GridLayout(nflags+1, 2));
-
+ GridBagConstraints c = new GridBagConstraints();
+
+ int nrows = 0;
+ c.ipadx = 5;
+ c.ipady = 2;
+ c.gridx = 0;
+ c.gridwidth = 2;
+ c.anchor = GridBagConstraints.WEST;
+ c.gridy = nrows++;
+
+ // MAPQ
+ add(new JLabel("Mappying quality (mapq) cut-off:"),c);
+
+ c.gridy = nrows++;
+ c.gridwidth = 1;
+ final JTextField cutOff = new JTextField(12);
+ if(bamView.getSamRecordMapQPredicate() != null)
+ cutOff.setText(Integer.toString(bamView.getSamRecordMapQPredicate().cutOff));
+
+ cutOff.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ setQualityCutOff(cutOff, bamView);
+ }
+ });
+ add(cutOff,c);
+
+ c.gridx = 1;
+ final JButton setCutOff = new JButton("SET");
+ setCutOff.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setQualityCutOff(cutOff, bamView);
+ }
+ });
+ add(setCutOff,c);
+
+ // FLAGS
+ c.gridwidth = 2;
+ c.gridx = 0;
+ c.gridy = nrows++;
+ add(new JSeparator(),c);
+
+ c.gridy = nrows++;
+ add(new JLabel("Reads can be filtered using the FLAG column in the BAM file."),c);
+ c.gridy = nrows++;
+ add(new JLabel("Selecting any of the options below hides the reads with that"),c);
+ c.gridy = nrows++;
+ add(new JLabel("flag set."),c);
final JCheckBox flagCheck[] = new JCheckBox[nflags];
final SAMRecordFlagPredicate predicate = bamView.getSamRecordFlagPredicate();
@@ -44,10 +103,12 @@ class SAMRecordFilter extends JPanel
filterChange(bamView, flagCheck);
}
});
- add(flagCheck[j]);
+
+ c.gridy = nrows++;
+ add(flagCheck[j], c);
}
- final JFrame f = new JFrame("Filter Out Reads Based on Flag");
+ final JFrame f = new JFrame("Filter Settings");
JButton closeFrame = new JButton("Close");
closeFrame.addActionListener(new ActionListener()
{
@@ -56,14 +117,51 @@ class SAMRecordFilter extends JPanel
f.dispose();
}
});
- add(closeFrame);
+ c.gridx = 1;
+ c.gridy = nrows++;
+ c.fill = GridBagConstraints.NONE;
+ add(closeFrame, c);
f.getContentPane().add(this);
f.pack();
- Utilities.centreFrame(f);
+
+ rightJustifyFrame(f);
f.setVisible(true);
}
+ private void rightJustifyFrame(JFrame frame)
+ {
+ final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ int yPos = (screen.height - frame.getSize().height) / 2;
+ int xPos = screen.width - frame.getSize().width;
+ if(yPos < 10)
+ yPos = 10;
+
+ frame.setLocation(new Point(xPos, yPos));
+ }
+
+ private void setQualityCutOff(final JTextField cutOff,
+ final BamView bamView)
+ {
+ String cutOffStr = cutOff.getText().trim();
+ if(cutOffStr.equals(""))
+ bamView.setSamRecordMapQPredicate(null);
+ else
+ {
+ try
+ {
+ SAMRecordMapQPredicate predicate =
+ new SAMRecordMapQPredicate(Integer.parseInt(cutOffStr));
+ bamView.setSamRecordMapQPredicate(predicate);
+ }
+ catch(NumberFormatException nfe)
+ {
+ bamView.setSamRecordMapQPredicate(null);
+ }
+ }
+ bamView.repaint();
+ }
+
private void filterChange(final BamView bamView,
final JCheckBox flagCheck[])
{
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java
new file mode 100644
index 0000000000000000000000000000000000000000..60136aecfaad7147627e6cdc84888b826bd60c86
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java
@@ -0,0 +1,52 @@
+/* SAMRecordMapQPredicate
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2009 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ **/
+
+package uk.ac.sanger.artemis.components.alignment;
+
+import net.sf.samtools.SAMRecord;
+
+/**
+ * Test the SAMRecord mapping quality - mapq flag.
+ **/
+public class SAMRecordMapQPredicate implements SAMRecordPredicate
+{
+ protected int cutOff;
+
+ public SAMRecordMapQPredicate(int cutOff)
+ {
+ this.cutOff = cutOff;
+ }
+
+ /**
+ * Test the given SAMRecord against this predicate.
+ * @param feature The SAMRecord to test the predicate against.
+ * @return Return true if and only if this predicate is true for the given
+ * SAMRecord.
+ **/
+ public boolean testPredicate (final SAMRecord samRecord)
+ {
+ if(samRecord.getMappingQuality() > cutOff)
+ return true;
+ return false;
+ }
+}
+
+