From f6fc5e76b8b7695512b2357667a6b9c95a3d4edb Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 21 Jul 2010 15:47:46 +0000
Subject: [PATCH] initial code for identifying synonymous / non-synonymous
change
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14274 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/VCFview.java | 216 ++++++++++++++++--
1 file changed, 193 insertions(+), 23 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index afa338e39..e2eea2444 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -49,6 +49,7 @@ import java.util.List;
import java.util.Vector;
import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
@@ -68,6 +69,11 @@ import org.apache.log4j.Level;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureKeyPredicate;
+import uk.ac.sanger.artemis.FeatureSegment;
+import uk.ac.sanger.artemis.FeatureSegmentVector;
+import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SelectionChangeEvent;
@@ -89,6 +95,7 @@ import uk.ac.sanger.artemis.io.Location;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.io.Range;
+import uk.ac.sanger.artemis.sequence.AminoAcidSequence;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
@@ -109,7 +116,7 @@ public class VCFview extends JPanel
private Selection selection;
private int nbasesInView;
private int seqLength;
- private Bases bases;
+ private EntryGroup entryGroup;
private String chr;
private String mouseOverVCFline;
private int mouseOverIndex = -1;
@@ -117,6 +124,11 @@ public class VCFview extends JPanel
private int dragStart = -1;
private JPopupMenu popup;
private int LINE_HEIGHT = 15;
+
+ private boolean showSynonymous = true;
+ private boolean showNonSynonymous = true;
+ private boolean showDeletions = true;
+ private boolean showInsertions = true;
public VCFview(final JFrame frame,
final JPanel vcfPanel,
@@ -142,11 +154,11 @@ public class VCFview extends JPanel
(vcfFiles.size()+1)*(LINE_HEIGHT+5)));
if(feature_display != null)
- this.bases = feature_display.getBases();
+ this.entryGroup = feature_display.getEntryGroup();
else if(reference != null)
- this.bases = getReference(reference).getSequenceEntry().getBases();
- if(bases != null)
- this.seqLength = bases.getLength();
+ this.entryGroup = getReference(reference);
+ if(entryGroup != null)
+ this.seqLength = entryGroup.getSequenceEntry().getBases().getLength();
try
{
@@ -312,6 +324,53 @@ public class VCFview extends JPanel
}
});
topPanel.add(combo);
+
+ // popup menu
+ popup = new JPopupMenu();
+ final JCheckBoxMenuItem showSyn = new JCheckBoxMenuItem(
+ "Show synonymous", showSynonymous);
+ showSyn.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ showSynonymous = showSyn.isSelected();
+ repaint();
+ }
+ });
+ popup.add(showSyn);
+
+ final JCheckBoxMenuItem showNonSyn = new JCheckBoxMenuItem(
+ "Show non-synonymous", showNonSynonymous);
+ showNonSyn.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonSynonymous = showNonSyn.isSelected();
+ repaint();
+ }
+ });
+ popup.add(showNonSyn);
+
+
+ final JCheckBoxMenuItem showDeletionsMenu = new JCheckBoxMenuItem(
+ "Show deletions", showDeletions);
+ showDeletionsMenu.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ showDeletions = showDeletionsMenu.isSelected();
+ repaint();
+ }
+ });
+ popup.add(showDeletionsMenu);
+
+ final JCheckBoxMenuItem showInsertionsMenu = new JCheckBoxMenuItem(
+ "Show insertions", showInsertions);
+ showInsertionsMenu.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ showInsertions = showInsertionsMenu.isSelected();
+ repaint();
+ }
+ });
+ popup.add(showInsertionsMenu);
}
private static EntryGroup getReference(String reference)
@@ -435,6 +494,9 @@ public class VCFview extends JPanel
String region = chr+":"+start+"-"+end;
drawSelectionRange((Graphics2D)g, pixPerBase, start, end);
+
+ FeatureVector features = getCDSFeaturesInRange(start, end);
+
// a region is specified; random access
for (int i = 0; i < tr.length; i++)
{
@@ -445,7 +507,7 @@ public class VCFview extends JPanel
{
while ((s = iter.next()) != null)
{
- drawVariantCall(g, s, start, i, pixPerBase);
+ drawVariantCall(g, s, start, i, pixPerBase, features);
}
}
catch (IOException e)
@@ -459,6 +521,31 @@ public class VCFview extends JPanel
drawScale((Graphics2D)g, start, end, pixPerBase, getHeight());
}
+ private FeatureVector getCDSFeaturesInRange(int start, int end)
+ {
+ try
+ {
+ Range range = new Range(start, end);
+ FeatureVector features = entryGroup.getFeaturesInRange(range);
+
+ FeatureKeyPredicate predicate = new FeatureKeyPredicate(Key.CDS);
+ final FeatureVector cdsFeatures = new FeatureVector();
+
+ for(int i=0; i<features.size(); i++)
+ {
+ final Feature this_feature = features.elementAt(i);
+ if(predicate.testPredicate(this_feature))
+ cdsFeatures.add(this_feature);
+ }
+ return cdsFeatures;
+ }
+ catch (OutOfRangeException e1)
+ {
+ e1.printStackTrace();
+ }
+ return null;
+ }
+
/**
* Highlight a selected range
* @param g2
@@ -502,10 +589,27 @@ public class VCFview extends JPanel
return scrollBar.getValue();
}
- private void drawVariantCall(Graphics g, String line, int start, int index, float pixPerBase)
+ private void drawVariantCall(Graphics g, String line, int start, int index, float pixPerBase, FeatureVector features)
{
String parts[] = line.split("\\t");
- int pos[] = getScreenPosition(line, pixPerBase, start, index);
+
+ if(!showDeletions && parts[4].indexOf("D")>-1)
+ return;
+
+ if(!showInsertions && parts[4].indexOf("I")>-1)
+ return;
+
+ if(!showSynonymous || !showNonSynonymous)
+ {
+ boolean isSyn = isSynonymous(features,
+ Integer.parseInt(parts[1]),parts[4].toLowerCase().charAt(0));
+
+ if( (!showSynonymous && isSyn) ||
+ (!showNonSynonymous && !isSyn) )
+ return;
+ }
+
+ int pos[] = getScreenPosition(parts[1], pixPerBase, start, index);
if(parts[4].equals("C"))
g.setColor(Color.red);
@@ -516,16 +620,87 @@ public class VCFview extends JPanel
else if(parts[4].equals("T"))
g.setColor(Color.black);
else
- g.setColor(Color.yellow);
-
+ {
+ if(parts[4].startsWith("D"))
+ g.setColor(Color.gray);
+ else
+ g.setColor(Color.yellow);
+ }
+
g.drawLine(pos[0], pos[1], pos[0], pos[1]-LINE_HEIGHT);
}
- private int[] getScreenPosition(String line, float pixPerBase, int start, int vcfFileIndex)
+ private boolean isSynonymous(FeatureVector features, int basePosition, char variant)
+ {
+ int intronlength = 0;
+ Range lastRange = null;
+
+ for(int i = 0; i<features.size(); i++)
+ {
+ Feature feature = features.elementAt(i);
+
+ if(feature.getRawFirstBase() < basePosition && feature.getRawLastBase() > basePosition)
+ {
+ FeatureSegmentVector segments = feature.getSegments();
+ for(int j=0; j< segments.size(); j++)
+ {
+ FeatureSegment segment = segments.elementAt(j);
+ Range range = segment.getRawRange();
+
+ if(j > 0)
+ {
+ if(feature.isForwardFeature())
+ intronlength+=range.getStart()-lastRange.getEnd()-1;
+ else
+ intronlength+=lastRange.getStart()-range.getEnd()-1;
+
+ if(intronlength < 0)
+ intronlength = 0;
+ }
+
+ if(range.getStart() < basePosition && range.getEnd() > basePosition)
+ {
+ int mod;
+ int codonStart;
+
+ if(feature.isForwardFeature())
+ {
+ mod = (basePosition-feature.getRawFirstBase())%3;
+ codonStart = basePosition-feature.getRawFirstBase()-mod;
+ }
+ else
+ {
+ mod = (feature.getRawLastBase()-basePosition)%3;
+ codonStart = feature.getRawLastBase()-basePosition-mod;
+ }
+
+ codonStart-=intronlength;
+ char codon[] = feature.getBases().substring(codonStart, codonStart+3).toLowerCase().toCharArray();
+
+ //String oldBase = new String(codon);
+ char aaRef = AminoAcidSequence.getCodonTranslation(codon[0], codon[1], codon[2]);
+
+ codon[mod] = variant;
+ char aaNew = AminoAcidSequence.getCodonTranslation(codon[0], codon[1], codon[2]);
+
+ if(aaNew == aaRef)
+ return true;
+ else
+ return false;
+ }
+
+ lastRange = range;
+ }
+ }
+ }
+
+ return true;
+ }
+
+ private int[] getScreenPosition(String base, float pixPerBase, int start, int vcfFileIndex)
{
- String parts[] = line.split("\\t");
int pos[] = new int[2];
- pos[0] = Math.round((Integer.parseInt(parts[1]) - start)*pixPerBase);
+ pos[0] = Math.round((Integer.parseInt(base) - start)*pixPerBase);
pos[1] = getHeight() - 15 - (vcfFileIndex*(LINE_HEIGHT+5));
return pos;
}
@@ -547,7 +722,7 @@ public class VCFview extends JPanel
{
while ((s = iter.next()) != null)
{
- int pos[] = getScreenPosition(s, pixPerBase, start, i);
+ int pos[] = getScreenPosition(s.split("\\t")[1], pixPerBase, start, i);
if(lastMousePoint != null &&
lastMousePoint.getY() < pos[1] &&
lastMousePoint.getY() > pos[1]-LINE_HEIGHT &&
@@ -636,9 +811,9 @@ public class VCFview extends JPanel
try
{
if(dragStart < 0)
- drag_range = new MarkerRange (bases.getForwardStrand(), start, start);
+ drag_range = new MarkerRange (entryGroup.getSequenceEntry().getBases().getForwardStrand(), start, start);
else
- drag_range = new MarkerRange (bases.getForwardStrand(), dragStart, start);
+ drag_range = new MarkerRange (entryGroup.getSequenceEntry().getBases().getForwardStrand(), dragStart, start);
getSelection().setMarkerRange(drag_range);
repaint();
}
@@ -799,9 +974,6 @@ public class VCFview extends JPanel
{
if(e.isPopupTrigger())
{
- if(popup == null)
- popup = new JPopupMenu();
-
if(showDetails != null)
popup.remove(showDetails);
@@ -839,11 +1011,9 @@ public class VCFview extends JPanel
}
});
popup.add(showDetails);
-
- popup.show(e.getComponent(),
- e.getX(), e.getY());
}
-
+ popup.show(e.getComponent(),
+ e.getX(), e.getY());
}
}
}
--
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