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Commit 4cb2a65d authored by tjc's avatar tjc
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changes for combining reference contigs in a vcf 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14676 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent eca39880
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uk/ac/sanger/artemis/components/variant/VCFview.java
+ 282
− 122
View file @ 4cb2a65d
......@@ -45,12 +45,14 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JComponent;
......@@ -74,6 +76,7 @@ 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.FeaturePredicate;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.Selection;
......@@ -143,6 +146,10 @@ public class VCFview extends JPanel
private boolean showNonOverlappings = true;
private float MIN_QUALITY = -10;
Hashtable<String, Integer> offsetLengths = null;
private boolean concatSequences = false;
private Point lastMousePoint;
private Pattern multiAllelePattern = Pattern.compile("^[AGCT]+,[AGCT,]+$");
private static Pattern tabPattern = Pattern.compile("\t");
......@@ -214,23 +221,10 @@ public class VCFview extends JPanel
//
//
final MouseMotionListener mouseMotionListener = new MouseMotionListener()
{
public void mouseDragged(MouseEvent event)
{
handleCanvasMouseDrag(event);
}
public void mouseMoved(MouseEvent e)
{
findVariantAtPoint(e.getPoint());
}
};
addMouseMotionListener(mouseMotionListener);
addMouseListener(new PopupListener());
//
createMenus(frame);
createMenus(frame, jspView);
setDisplay();
if(feature_display == null)
......@@ -248,16 +242,15 @@ public class VCFview extends JPanel
}
}
private void createMenus(JFrame frame)
private void createMenus(JFrame frame, final JScrollPane jspView)
{
JComponent topPanel;
final JComponent topPanel;
if(feature_display != null)
topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
else
{
topPanel = new JMenuBar();
frame.setJMenuBar((JMenuBar)topPanel);
}
JMenu fileMenu = new JMenu("File");
topPanel.add(fileMenu);
......@@ -323,10 +316,16 @@ public class VCFview extends JPanel
}
});
topPanel.add(zoomOut);
}
final JComboBox combo = new JComboBox(tr[0].getmSeq());
if(tr[0].getmSeq().length > 1)
combo.addItem("Combine All");
if(chr == null)
this.chr = tr[0].getmSeq()[0];
combo.setSelectedItem(this.chr);
combo.setEditable(false);
combo.setMaximumRowCount(20);
......@@ -334,12 +333,53 @@ public class VCFview extends JPanel
combo.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
if(combo.getSelectedItem().equals("Combine All"))
concatSequences = true;
else
{
VCFview.this.chr = (String) combo.getSelectedItem();
concatSequences = false;
}
repaint();
}
});
topPanel.add(combo);
if(topPanel instanceof JPanel)
vcfPanel.add(topPanel, BorderLayout.NORTH);
// auto hide top panel
final JCheckBox buttonAutoHide = new JCheckBox("Hide", true);
buttonAutoHide.setToolTipText("Auto-Hide");
topPanel.add(buttonAutoHide);
final MouseMotionListener mouseMotionListener = new MouseMotionListener()
{
public void mouseDragged(MouseEvent event)
{
handleCanvasMouseDrag(event);
}
public void mouseMoved(MouseEvent e)
{
findVariantAtPoint(e.getPoint());
int thisHgt = HEIGHT;
if (thisHgt < 5)
thisHgt = 15;
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
if (y < thisHgt)
topPanel.setVisible(true);
else
{
if (buttonAutoHide.isSelected())
topPanel.setVisible(false);
}
}
};
addMouseMotionListener(mouseMotionListener);
// popup menu
popup = new JPopupMenu();
......@@ -561,25 +601,96 @@ public class VCFview extends JPanel
return msg;
}
/**
* For VCF files with multiple references sequences, calculate
* the offset from the start of the concatenated sequence for
* a given reference.
* @param refName
* @return
*/
protected int getSequenceOffset(String refName)
{
if(!concatSequences)
return 0;
if(offsetLengths == null)
{
String[] contigs = tr[0].getmSeq();
FeatureVector features = entryGroup.getAllFeatures();
offsetLengths = new Hashtable<String, Integer>(contigs.length);
for(int i=0; i<contigs.length; i++)
{
FeatureContigPredicate predicate = new FeatureContigPredicate(contigs[i]);
for(int j=0; j<features.size(); j++)
{
if(predicate.testPredicate(features.elementAt(j)))
{
offsetLengths.put(contigs[i], features.elementAt(j).getFirstBase()-1);
break;
}
}
}
}
return offsetLengths.get(refName);
}
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
mouseOverVCFline = null;
float pixPerBase = getPixPerBaseByWidth();
String s;
int start = getBaseAtStartOfView();
int end = start+nbasesInView;
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++)
{
if(concatSequences)
{
String[] contigs = tr[0].getmSeq();
for(int j=0; j<contigs.length; j++)
{
int offset = getSequenceOffset(contigs[j]);
int nextOffset;
if(j<contigs.length-1)
nextOffset = getSequenceOffset(contigs[j+1]);
else
nextOffset = seqLength;
if( (offset >= start && offset < end) ||
(offset < start && start < nextOffset) )
{
int thisStart = start - offset;
if(thisStart < 1)
thisStart = 1;
int thisEnd = end - offset;
drawRegion(g, contigs[j]+":"+thisStart+"-"+thisEnd, i, start, pixPerBase, features);
}
}
}
else
drawRegion(g, chr+":"+start+"-"+end, i, start, pixPerBase, features);
}
if(feature_display == null)
drawScale((Graphics2D)g, start, end, pixPerBase, getHeight());
}
private void drawRegion(Graphics g,
String region,
int i,
int start,
float pixPerBase,
FeatureVector features)
{
String s;
TabixReader.Iterator iter = tr[i].query(region); // get the iterator
if (iter == null)
return;
......@@ -595,10 +706,6 @@ public class VCFview extends JPanel
}
}
if(feature_display == null)
drawScale((Graphics2D)g, start, end, pixPerBase, getHeight());
}
private FeatureVector getCDSFeaturesInRange(int start, int end)
{
try
......@@ -780,7 +887,8 @@ public class VCFview extends JPanel
{
//String parts[] = line.split("\\t");
String parts[] = tabPattern.split(line, 0);
int basePosition = Integer.parseInt(parts[1]);
int basePosition = Integer.parseInt(parts[1]) + getSequenceOffset(parts[0]);
if( !showVariant(parts[3], parts[4], features, basePosition, parts[5]) )
return;
......@@ -921,48 +1029,84 @@ public class VCFview extends JPanel
return pos;
}
private void findVariantAtPoint(Point lastMousePoint)
private void findVariantAtPoint(Point mousePoint)
{
float pixPerBase = getPixPerBaseByWidth();
String s;
int start = getBaseAtStartOfView();
int end = start+nbasesInView;
String region = chr+":"+start+"-"+end;
FeatureVector features = getCDSFeaturesInRange(start, end);
for (int i = 0; i < tr.length; i++)
{
if(concatSequences)
{
String[] contigs = tr[0].getmSeq();
for(int j=0; j<contigs.length; j++)
{
int offset = getSequenceOffset(contigs[j]);
int nextOffset;
if(j<contigs.length-1)
nextOffset = getSequenceOffset(contigs[j+1]);
else
nextOffset = seqLength;
if( (offset >= start && offset < end) ||
(offset < start && start < nextOffset) )
{
int thisStart = start - offset;
if(thisStart < 1)
thisStart = 1;
int thisEnd = end - offset;
searchRegion(contigs[j]+":"+thisStart+"-"+thisEnd, i, mousePoint, features, start, pixPerBase);
}
}
}
else
searchRegion(chr+":"+start+"-"+end, i, mousePoint, features, start, pixPerBase);
}
}
private void searchRegion(String region, int i, Point mousePoint, FeatureVector features,
int start, float pixPerBase)
{
TabixReader.Iterator iter = tr[i].query(region); // get the iterator
if (iter == null)
return;
try
{
String s;
while ((s = iter.next()) != null)
isMouseOver(mousePoint, s, features, i, start, pixPerBase);
}
catch (IOException e)
{
e.printStackTrace();
}
}
private void isMouseOver(Point mousePoint,
String s,
FeatureVector features,
int i,
int start, float pixPerBase)
{
String parts[] = tabPattern.split(s, 7);
int basePosition = Integer.parseInt(parts[1]);
int basePosition = Integer.parseInt(parts[1]) + getSequenceOffset(parts[0]);
if( !showVariant(parts[3], parts[4], features, basePosition, parts[5]) )
continue;
return;
int pos[] = getScreenPosition(basePosition, pixPerBase, start, i);
if(lastMousePoint != null &&
lastMousePoint.getY() < pos[1] &&
lastMousePoint.getY() > pos[1]-LINE_HEIGHT &&
lastMousePoint.getX() > pos[0]-3 &&
lastMousePoint.getX() < pos[0]+3)
if(mousePoint != null &&
mousePoint.getY() < pos[1] &&
mousePoint.getY() > pos[1]-LINE_HEIGHT &&
mousePoint.getX() > pos[0]-3 &&
mousePoint.getX() < pos[0]+3)
{
mouseOverVCFline = s;
mouseOverIndex = i;
}
}
}
catch (IOException e)
{
e.printStackTrace();
}
}
}
private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
{
......@@ -1260,6 +1404,22 @@ public class VCFview extends JPanel
repaint();
}
class FeatureContigPredicate implements FeaturePredicate
{
String contigName;
FeatureContigPredicate(String contigName)
{
this.contigName = contigName;
}
public boolean testPredicate(Feature feature)
{
if(feature.getIDString().equals(contigName))
return true;
return false;
}
}
public static void main(String args[])
{
List<String> vcfFileList = new Vector<String>();
......
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