diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 9b2c0184bad0ef5e90d47c2d9ad687e0851d3f49..1f09dc1e9b742ed31f67b59c2fbca2da935a5757 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -27,6 +27,7 @@ import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Composite;
import java.awt.Dimension;
import java.awt.FlowLayout;
@@ -124,6 +125,8 @@ public class BamView extends JPanel
private Vector<String> seqNames = new Vector<String>();
private String bam;
+ private SAMRecordFlagPredicate samRecordFlagPredicate;
+
private Bases bases;
private JScrollPane jspView;
private JScrollBar scrollBar;
@@ -439,7 +442,12 @@ public class BamView extends JPanel
{
cnt++;
SAMRecord samRecord = it.next();
- readsInView.add(samRecord);
+
+ if( samRecordFlagPredicate == null ||
+ !samRecordFlagPredicate.testPredicate(samRecord))
+ {
+ readsInView.add(samRecord);
+ }
if(cnt > checkMemAfter)
{
@@ -1611,6 +1619,42 @@ public class BamView extends JPanel
{
topPanel = new JMenuBar();
frame.setJMenuBar((JMenuBar)topPanel);
+
+ JMenu fileMenu = new JMenu("File");
+ topPanel.add(fileMenu);
+
+ JMenuItem readBam = new JMenuItem("Read BAM...");
+ fileMenu.add(readBam);
+ readBam.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String[] s = new String[0];
+ BamView.main(s);
+ BamView.this.setVisible(false);
+
+ Component comp = BamView.this;
+
+ while( !(comp instanceof JFrame) )
+ comp = comp.getParent();
+ ((JFrame)comp).dispose();
+ }
+ });
+
+ JMenuItem exit = new JMenuItem("Exit");
+ fileMenu.add(exit);
+ exit.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ int status = JOptionPane.showConfirmDialog(BamView.this,
+ "Close BamView?", "Close",
+ JOptionPane.OK_CANCEL_OPTION);
+ if(status != JOptionPane.OK_OPTION)
+ return;
+ System.exit(0);
+ }
+ });
}
if(seqNames.size() > 1)
@@ -2004,6 +2048,17 @@ public class BamView extends JPanel
}
});
}
+
+ JMenuItem filter = new JMenuItem("Filter by Flag...");
+ menu.add(filter);
+ filter.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new SAMRecordFilter(BamView.this);
+ }
+ });
+
}
public void setVisible(boolean visible)
@@ -2510,6 +2565,19 @@ public class BamView extends JPanel
viewDetail.appendString("\nSecond Of Pair "+
(thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
}
+
+ protected SAMRecordFlagPredicate getSamRecordFlagPredicate()
+ {
+ return samRecordFlagPredicate;
+ }
+
+ protected void setSamRecordFlagPredicate(
+ SAMRecordFlagPredicate samRecordFlagPredicate)
+ {
+ laststart = -1;
+ lastend = -1;
+ this.samRecordFlagPredicate = samRecordFlagPredicate;
+ }
class PairedRead
{
@@ -2579,6 +2647,4 @@ public class BamView extends JPanel
view.jspView.getVerticalScrollBar().getMaximum());
frame.setVisible(true);
}
-
-
}
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
new file mode 100644
index 0000000000000000000000000000000000000000..ecca4ee92bbc16fe98765c5fd879dea3936592c3
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFilter.java
@@ -0,0 +1,76 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.GridLayout;
+
+import javax.swing.JCheckBox;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+class SAMRecordFilter extends JPanel
+{
+ private static final long serialVersionUID = 1L;
+
+ public SAMRecordFilter(final BamView bamView)
+ {
+ super();
+ int nflags = SAMRecordFlagPredicate.FLAGS.length;
+ setLayout(new GridLayout(nflags, 2));
+
+ final JCheckBox flagCheck[] = new JCheckBox[nflags];
+ for(int j=0; j<nflags; j++)
+ {
+ flagCheck[j] = new JCheckBox(
+ SAMRecordFlagPredicate.FLAGS_DESCRUIPTION[j], false);
+ flagCheck[j].addChangeListener(new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent e)
+ {
+ filterChange(bamView, flagCheck);
+ }
+ });
+ add(flagCheck[j]);
+ }
+
+ int status = JOptionPane.showConfirmDialog(bamView,
+ this, "Filter Out Reads Based on Flag",
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if(status != JOptionPane.OK_OPTION)
+ return;
+ }
+
+ private void filterChange(final BamView bamView,
+ final JCheckBox flagCheck[])
+ {
+ int nflags = SAMRecordFlagPredicate.FLAGS.length;
+ int flagsChecked = 0;
+ for(int j=0; j<nflags; j++)
+ {
+ if(flagCheck[j].isSelected())
+ flagsChecked++;
+ }
+
+ bamView.setSamRecordFlagPredicate(null);
+
+ if(flagsChecked == 0)
+ {
+ bamView.repaint();
+ return;
+ }
+
+ int flagsOn[] = new int[flagsChecked];
+ int num = 0;
+ for(int j=0; j<nflags; j++)
+ {
+ if(flagCheck[j].isSelected())
+ flagsOn[num++] = SAMRecordFlagPredicate.FLAGS[j];
+ }
+
+ bamView.setSamRecordFlagPredicate(new SAMRecordFlagPredicate(flagsOn));
+ bamView.repaint();
+ }
+
+}
\ 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
new file mode 100644
index 0000000000000000000000000000000000000000..dfd71f73e895f7ec02c7372fed887b19a35b94b3
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
@@ -0,0 +1,98 @@
+/* SAMRecordPredicate
+ *
+ * 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 flag.
+ **/
+public class SAMRecordFlagPredicate implements SAMRecordPredicate
+{
+ private int flag[];
+
+ private static final int READ_PAIRED_FLAG = 0x1;
+ private static final int PROPER_PAIR_FLAG = 0x2;
+ private static final int READ_UNMAPPED_FLAG = 0x4;
+ private static final int MATE_UNMAPPED_FLAG = 0x8;
+ private static final int READ_STRAND_FLAG = 0x10;
+ private static final int MATE_STRAND_FLAG = 0x20;
+ private static final int FIRST_OF_PAIR_FLAG = 0x40;
+ private static final int SECOND_OF_PAIR_FLAG = 0x80;
+ private static final int NOT_PRIMARY_ALIGNMENT_FLAG = 0x100;
+ private static final int READ_FAILS_VENDOR_QUALITY_CHECK_FLAG = 0x200;
+ private static final int DUPLICATE_READ_FLAG = 0x400;
+
+ protected static final String[] FLAGS_DESCRUIPTION =
+ {
+ "Read Paired",
+ "Proper Pair",
+ "Read Unmapped",
+ "Mate Unmapped",
+ "Read on Negative Strand",
+ "Mate on Negative Strand",
+ "First of Pair",
+ "Second of Pair",
+ "Not Primary Alignment",
+ "Read Fails Vendor Quality Check",
+ "Duplicate Read"
+ };
+
+ protected static int[] FLAGS =
+ {
+ READ_PAIRED_FLAG,
+ PROPER_PAIR_FLAG,
+ READ_UNMAPPED_FLAG,
+ MATE_UNMAPPED_FLAG,
+ READ_STRAND_FLAG,
+ MATE_STRAND_FLAG,
+ FIRST_OF_PAIR_FLAG,
+ SECOND_OF_PAIR_FLAG,
+ NOT_PRIMARY_ALIGNMENT_FLAG,
+ READ_FAILS_VENDOR_QUALITY_CHECK_FLAG,
+ DUPLICATE_READ_FLAG
+ };
+
+
+ public SAMRecordFlagPredicate(int flag[])
+ {
+ this.flag = flag;
+ }
+
+ /**
+ * 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)
+ {
+ for(int i=0; i<flag.length; i++)
+ {
+ if((samRecord.getFlags() & flag[i]) == flag[i])
+ return true;
+ }
+ return false;
+ }
+}
+
+
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java
new file mode 100644
index 0000000000000000000000000000000000000000..4b9fe5ed10c99013a74c2d848393904260c80e40
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java
@@ -0,0 +1,41 @@
+/* SAMRecordPredicate
+ *
+ * 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;
+
+/**
+ * Each object that implements this interface represents a predicate that can
+ * be tested with a SAMRecord reference.
+ **/
+
+public interface SAMRecordPredicate {
+ /**
+ * 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.
+ **/
+ boolean testPredicate (final SAMRecord samRecord);
+}
+
+