From 586bcf511622737d2beaaf2ac83e4ffa5b3e857f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 14 Apr 2011 09:47:10 +0000
Subject: [PATCH] changes to filtering of reads
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15952 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 22 ++--
.../components/alignment/SAMRecordFilter.java | 106 +++++++++++-------
.../SAMRecordFlagConjunctionPredicate.java | 75 +++++--------
.../alignment/SAMRecordFlagPredicate.java | 13 ++-
4 files changed, 115 insertions(+), 101 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index dc79b8faa..6d4a1eea9 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -142,9 +142,11 @@ public class BamView extends JPanel
protected List<String> bamList;
private List<Integer> hideBamList = new Vector<Integer>();
- private SAMRecordFlagPredicate samRecordFlagPredicate;
+ private SAMRecordPredicate samRecordFlagPredicate;
private SAMRecordMapQPredicate samRecordMapQPredicate;
-
+
+ private SAMRecordFilter filterFrame;
+
private Bases bases;
private JScrollPane jspView;
private JScrollBar scrollBar;
@@ -237,6 +239,8 @@ public class BamView extends JPanel
this.feature_display = feature_display;
this.bases = bases;
+ System.out.println(nbasesInView);
+
containerPanel.setLayout(new BoxLayout(containerPanel, BoxLayout.Y_AXIS));
containerPanel.add(mainPanel);
@@ -2310,17 +2314,19 @@ public class BamView extends JPanel
}
});
- JMenuItem filter = new JMenuItem("Filter by Flag...");
+ JMenuItem filter = new JMenuItem("Filter Reads ...");
menu.add(filter);
filter.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- new SAMRecordFilter(BamView.this);
+ if(filterFrame == null)
+ filterFrame = new SAMRecordFilter(BamView.this);
+ else
+ filterFrame.setVisible(true);
}
});
-
-
+
final JMenuItem bamSplitter = new JMenuItem("Clone window");
bamSplitter.addActionListener(new ActionListener()
{
@@ -3159,13 +3165,13 @@ public class BamView extends JPanel
viewDetail.appendString(new String(thisSAMRecord.getReadBases()), Level.DEBUG);
}
- protected SAMRecordFlagPredicate getSamRecordFlagPredicate()
+ protected SAMRecordPredicate getSamRecordFlagPredicate()
{
return samRecordFlagPredicate;
}
protected void setSamRecordFlagPredicate(
- SAMRecordFlagPredicate samRecordFlagPredicate)
+ SAMRecordPredicate samRecordFlagPredicate)
{
laststart = -1;
lastend = -1;
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
index 3291258c0..f769a5bbe 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
@@ -7,13 +7,12 @@ import java.awt.Point;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
+import java.util.Vector;
import javax.swing.JButton;
-import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
@@ -24,13 +23,17 @@ import javax.swing.JTextField;
* Filter reads bases on their mapping quality (mapq) or the
* flags that are set in the BAM file.
*/
-class SAMRecordFilter extends JPanel
+class SAMRecordFilter extends JFrame
{
private static final long serialVersionUID = 1L;
public SAMRecordFilter(final BamView bamView)
{
- super(new GridBagLayout());
+ super("Filter Reads");
+
+ JPanel pane = (JPanel) getContentPane();
+ pane.setLayout(new GridBagLayout());
+
int nflags = SAMRecordFlagPredicate.FLAGS.length;
GridBagConstraints c = new GridBagConstraints();
@@ -43,7 +46,7 @@ class SAMRecordFilter extends JPanel
c.gridy = nrows++;
// MAPQ
- add(new JLabel("Mappying quality (mapq) cut-off:"),c);
+ pane.add(new JLabel(" By Mappying Quality (mapq) cut-off:"),c);
c.gridy = nrows++;
c.gridwidth = 1;
@@ -59,7 +62,7 @@ class SAMRecordFilter extends JPanel
setQualityCutOff(cutOff, bamView);
}
});
- add(cutOff,c);
+ pane.add(cutOff,c);
c.gridx = 1;
final JButton setCutOff = new JButton("SET");
@@ -70,64 +73,63 @@ class SAMRecordFilter extends JPanel
setQualityCutOff(cutOff, bamView);
}
});
- add(setCutOff,c);
+ pane.add(setCutOff,c);
// FLAGS
c.gridwidth = 2;
c.gridx = 0;
c.gridy = nrows++;
- add(new JSeparator(),c);
+ pane.add(new JSeparator(),c);
c.gridy = nrows++;
- add(new JLabel("To filter reads using the FLAG column in the BAM file"),c);
+ pane.add(new JLabel(" By SAM FLAG column:"),c);
c.gridy = nrows++;
- add(new JLabel("select any of the options below to hide the reads with"),c);
+ pane.add(new JLabel(" Select below to show or hide only the reads with "),c);
c.gridy = nrows++;
- add(new JLabel("that flag set."),c);
- final JCheckBox flagCheck[] = new JCheckBox[nflags];
- final SAMRecordFlagPredicate predicate = bamView.getSamRecordFlagPredicate();
+ pane.add(new JLabel(" the flag set."),c);
+
+ final JComboBox flagCombo[] = new JComboBox[nflags];
+ final String[] items = {"", "SHOW", "HIDE"};
+ c.gridwidth = 1;
for(int j=0; j<nflags; j++)
{
- flagCheck[j] = new JCheckBox(
- SAMRecordFlagPredicate.FLAGS_DESCRUIPTION[j], false);
-
- if(predicate != null &&
- predicate.isFlagSet(SAMRecordFlagPredicate.FLAGS[j]))
- flagCheck[j].setSelected(true);
+ flagCombo[j] = new JComboBox(items);
+ if(SAMRecordFlagPredicate.FLAGS_DESCRIPTION[j].equalsIgnoreCase("Read Unmapped"))
+ flagCombo[j].setSelectedItem("HIDE");
- flagCheck[j].addItemListener(new ItemListener()
+ flagCombo[j].addActionListener(new ActionListener()
{
- public void itemStateChanged(ItemEvent e)
+ public void actionPerformed(ActionEvent e)
{
- filterChange(bamView, flagCheck);
- }
+ filterChange(bamView, flagCombo);
+ }
});
c.gridy = nrows++;
- add(flagCheck[j], c);
+ c.gridx = 0;
+ pane.add(flagCombo[j], c);
+ c.gridx = 1;
+ pane.add(new JLabel(SAMRecordFlagPredicate.FLAGS_DESCRIPTION[j]), c);
}
-
- final JFrame f = new JFrame("Filter Settings");
JButton closeFrame = new JButton("Close");
closeFrame.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- f.dispose();
+ setVisible(false);
}
});
c.gridx = 1;
c.gridy = nrows++;
c.fill = GridBagConstraints.NONE;
- add(closeFrame, c);
+ pane.add(closeFrame, c);
- f.getContentPane().add(this);
- f.pack();
+ pack();
- rightJustifyFrame(f);
- f.setVisible(true);
+ rightJustifyFrame(this);
+ setVisible(true);
}
private void rightJustifyFrame(JFrame frame)
@@ -162,23 +164,45 @@ class SAMRecordFilter extends JPanel
}
bamView.repaint();
}
-
- private void filterChange(final BamView bamView,
- final JCheckBox flagCheck[])
+
+ private void filterChange(final BamView bamView, final JComboBox flagCheck[])
{
int nflags = SAMRecordFlagPredicate.FLAGS.length;
int flagCombined = 0;
- for(int j=0; j<nflags; j++)
+ Vector <SAMRecordPredicate> predicates = new Vector<SAMRecordPredicate>();
+
+ for (int j = 0; j < nflags; j++)
{
- if(flagCheck[j].isSelected())
+ String opt = (String) flagCheck[j].getSelectedItem();
+ if (opt.equals("HIDE"))
flagCombined = flagCombined | SAMRecordFlagPredicate.FLAGS[j];
+ else if(opt.equals("SHOW"))
+ predicates.add(new SAMRecordFlagPredicate( SAMRecordFlagPredicate.FLAGS[j], false ));
}
- if(flagCombined == 0)
+ if (flagCombined == 0 && predicates.size() == 0)
bamView.setSamRecordFlagPredicate(null);
else
- bamView.setSamRecordFlagPredicate(new SAMRecordFlagPredicate(flagCombined));
+ {
+ final SAMRecordPredicate predicate;
+ if(predicates.size() == 0)
+ predicate = new SAMRecordFlagPredicate(flagCombined);
+ else if(flagCombined == 0)
+ {
+ predicate =
+ new SAMRecordFlagConjunctionPredicate(predicates, SAMRecordFlagConjunctionPredicate.OR);
+ }
+ else
+ {
+ SAMRecordFlagPredicate p1 = new SAMRecordFlagPredicate(flagCombined);
+ SAMRecordFlagConjunctionPredicate p2 =
+ new SAMRecordFlagConjunctionPredicate(predicates, SAMRecordFlagConjunctionPredicate.OR);
+
+ predicate = new SAMRecordFlagConjunctionPredicate(p1, p2,
+ SAMRecordFlagConjunctionPredicate.OR);
+ }
+ bamView.setSamRecordFlagPredicate(predicate);
+ }
bamView.repaint();
}
-
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
index 251fc5c74..57d829444 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
@@ -21,6 +21,8 @@
package uk.ac.sanger.artemis.components.alignment;
+import java.util.Vector;
+
import net.sf.samtools.SAMRecord;
/**
@@ -28,71 +30,44 @@ import net.sf.samtools.SAMRecord;
**/
public class SAMRecordFlagConjunctionPredicate implements SAMRecordPredicate
{
- private SAMRecordPredicate p1;
- private SAMRecordPredicate p2;
+ private Vector<SAMRecordPredicate> predicates;
private int type; // AND or OR
- private boolean is1 = true;
- private boolean is2 = true;
- private static int AND = 0;
+ protected static int AND = 0;
+ protected static int OR = 1;
- public SAMRecordFlagConjunctionPredicate(SAMRecordPredicate p1, SAMRecordPredicate p2, int type, boolean is1, boolean is2)
+ public SAMRecordFlagConjunctionPredicate(SAMRecordPredicate p1, SAMRecordPredicate p2, int type)
{
- this.p1 = p1;
- this.p2 = p2;
+ predicates = new Vector<SAMRecordPredicate>();
+ predicates.add(p1);
+ predicates.add(p2);
this.type = type;
- this.is1 = is1;
- this.is2 = is2;
}
+ public SAMRecordFlagConjunctionPredicate(Vector<SAMRecordPredicate> predicates, int type)
+ {
+ this.predicates = predicates;
+ this.type = type;
+ }
+
public boolean testPredicate(SAMRecord samRecord)
{
- if(type == AND)
+ for(SAMRecordPredicate predicate: predicates)
{
- if(!is1 && !is2)
- {
- if(!p1.testPredicate(samRecord) && !p2.testPredicate(samRecord))
- return true;
- }
- else if(!is1)
- {
- if(!p1.testPredicate(samRecord) && p2.testPredicate(samRecord))
- return true;
- }
- else if(!is2)
+ if(predicate.testPredicate(samRecord))
{
- if(p1.testPredicate(samRecord) && !p2.testPredicate(samRecord))
+ if(type == OR)
return true;
}
- else if(is1 && is2)
+ else
{
- if(p1.testPredicate(samRecord) && p2.testPredicate(samRecord))
- return true;
- }
- }
- else
- {
- if(!is1 && !is2)
- {
- if(!p1.testPredicate(samRecord) || !p2.testPredicate(samRecord))
- return true;
- }
- else if(!is1)
- {
- if(!p1.testPredicate(samRecord) || p2.testPredicate(samRecord))
- return true;
- }
- else if(!is2)
- {
- if(p1.testPredicate(samRecord) || !p2.testPredicate(samRecord))
- return true;
- }
- else if(is1 && is2)
- {
- if(p1.testPredicate(samRecord) || p2.testPredicate(samRecord))
- return true;
+ if(type == AND)
+ return false;
}
}
+
+ if(type == AND)
+ return true;
return false;
}
-
+
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
index 4ae02c6f3..d3b8ea9cf 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
@@ -29,6 +29,7 @@ import net.sf.samtools.SAMRecord;
public class SAMRecordFlagPredicate implements SAMRecordPredicate
{
private int flag;
+ private boolean isSet;
protected static final int READ_PAIRED_FLAG = 0x1;
protected static final int PROPER_PAIR_FLAG = 0x2;
@@ -42,7 +43,7 @@ public class SAMRecordFlagPredicate implements SAMRecordPredicate
protected static final int READ_FAILS_VENDOR_QUALITY_CHECK_FLAG = 0x200;
protected static final int DUPLICATE_READ_FLAG = 0x400;
- protected static final String[] FLAGS_DESCRUIPTION =
+ protected static final String[] FLAGS_DESCRIPTION =
{
"Read Paired",
"Proper Pair",
@@ -74,8 +75,14 @@ public class SAMRecordFlagPredicate implements SAMRecordPredicate
public SAMRecordFlagPredicate(int flag)
+ {
+ this(flag, true);
+ }
+
+ public SAMRecordFlagPredicate(int flag, boolean isSet)
{
this.flag = flag;
+ this.isSet = isSet;
}
/**
@@ -86,10 +93,12 @@ public class SAMRecordFlagPredicate implements SAMRecordPredicate
**/
public boolean testPredicate (final SAMRecord samRecord)
{
+ if(!isSet)
+ return !isFlagSet(samRecord.getFlags());
return isFlagSet(samRecord.getFlags());
}
- protected boolean isFlagSet(int thisFlag)
+ private boolean isFlagSet(int thisFlag)
{
for(int i=0; i<FLAGS.length; i++)
{
--
GitLab