diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 7a00004fe5e51c1e571f16db6380fa39705c39fa..2ebc0617c6a312d3b34e9593a1294e7061220ae2 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -67,9 +67,10 @@ class IOUtils
writer.write(line+'\n');
continue;
}
- String parts[] = VCFview.tabPattern.split(line, 0);
- int basePosition = Integer.parseInt(parts[1]) + vcfView.getSequenceOffset(parts[0]);
- if( !vcfView.showVariant(parts[3], parts[4], features, basePosition, parts[5]) )
+
+ VCFRecord record = VCFRecord.parse(line);
+ int basePosition = record.pos + vcfView.getSequenceOffset(record.chrom);
+ if( !vcfView.showVariant(record.ref, record.alt, features, basePosition, record.quality) )
continue;
writer.write(line+'\n');
}
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 7d679d1624e14f8e916bb6e210a727ee1a9bb287..864f7f4ce64a6c84e2d6d4f026615d6f5d395a7f 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -26,6 +26,7 @@ package uk.ac.sanger.artemis.components.variant;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
+import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Graphics;
@@ -543,7 +544,9 @@ public class VCFview extends JPanel
exportVCF.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
+ VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
IOUtils.export(entryGroup, vcfFiles, VCFview.this);
+ VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
}
});
popup.add(exportVCF);
@@ -747,7 +750,7 @@ public class VCFview extends JPanel
thisStart = 1;
int thisEnd = end - offset;
- drawRegion(g, contigs[j]+":"+thisStart+"-"+thisEnd, i, start, pixPerBase, features);
+ drawRegion(g, contigs[j], thisStart+"-"+thisEnd, i, start, pixPerBase, features);
}
}
@@ -757,7 +760,7 @@ public class VCFview extends JPanel
int thisStart = start;
if(thisStart < 1)
thisStart = 1;
- drawRegion(g, chr+":"+thisStart+"-"+end, i, start, pixPerBase, features);
+ drawRegion(g, chr, thisStart+"-"+end, i, start, pixPerBase, features);
}
}
@@ -765,7 +768,8 @@ public class VCFview extends JPanel
drawScale((Graphics2D)g, start, end, pixPerBase, getHeight());
}
- private void drawRegion(Graphics g,
+ private void drawRegion(Graphics g,
+ String chr,
String region,
int i,
int start,
@@ -773,13 +777,16 @@ public class VCFview extends JPanel
FeatureVector features)
{
String s;
- TabixReader.Iterator iter = tr[i].query(region); // get the iterator
+ TabixReader.Iterator iter = tr[i].query(chr+":"+region); // get the iterator
if (iter == null)
return;
try
{
while ((s = iter.next()) != null)
- drawVariantCall(g, s, start, i, pixPerBase, features);
+ {
+ VCFRecord vcfRecord = VCFRecord.parse(s);
+ drawVariantCall(g, vcfRecord, start, i, pixPerBase, features);
+ }
}
catch (IOException e)
{
@@ -892,7 +899,7 @@ public class VCFview extends JPanel
return false;
}
- protected boolean showVariant(String ref, String variant, FeatureVector features, int basePosition, String quality)
+ protected boolean showVariant(String ref, String variant, FeatureVector features, int basePosition, float quality)
{
if(!showDeletions && isDeletion(ref, variant))
return false;
@@ -902,7 +909,7 @@ public class VCFview extends JPanel
try
{
- if(Float.parseFloat(quality) < MIN_QUALITY)
+ if(quality < MIN_QUALITY)
return false;
}
catch(NumberFormatException e)
@@ -967,33 +974,33 @@ public class VCFview extends JPanel
}
- private void drawVariantCall(Graphics g, String line, int start, int index, float pixPerBase, FeatureVector features)
+ private void drawVariantCall(Graphics g, VCFRecord record, int start, int index, float pixPerBase, FeatureVector features)
{
//String parts[] = line.split("\\t");
- String parts[] = tabPattern.split(line, 0);
+ //String parts[] = tabPattern.split(line, 0);
- int basePosition = Integer.parseInt(parts[1]) + getSequenceOffset(parts[0]);
+ int basePosition = record.pos + getSequenceOffset(record.chrom);
- if( !showVariant(parts[3], parts[4], features, basePosition, parts[5]) )
+ if( !showVariant(record.ref, record.alt, features, basePosition, record.quality) )
return;
int pos[] = getScreenPosition(basePosition, pixPerBase, start, index);
- if(isDeletion(parts[3], parts[4]))
+ if(isDeletion(record.ref, record.alt))
g.setColor(Color.gray);
- else if(isInsertion(parts[3], parts[4]))
+ else if(isInsertion(record.ref, record.alt))
g.setColor(Color.yellow);
- else if(parts[4].equals("C") && parts[3].length() == 1)
+ else if(record.alt.equals("C") && record.ref.length() == 1)
g.setColor(Color.red);
- else if(parts[4].equals("A") && parts[3].length() == 1)
+ else if(record.alt.equals("A") && record.ref.length() == 1)
g.setColor(Color.green);
- else if(parts[4].equals("G") && parts[3].length() == 1)
+ else if(record.alt.equals("G") && record.ref.length() == 1)
g.setColor(Color.blue);
- else if(parts[4].equals("T") && parts[3].length() == 1)
+ else if(record.alt.equals("T") && record.ref.length() == 1)
g.setColor(Color.black);
else
{
- Matcher m = multiAllelePattern.matcher(parts[4]);
+ Matcher m = multiAllelePattern.matcher(record.alt);
if(m.matches())
{
g.setColor(Color.orange);
@@ -1165,7 +1172,10 @@ public class VCFview extends JPanel
{
String s;
while ((s = iter.next()) != null)
- isMouseOver(mousePoint, s, features, i, start, pixPerBase);
+ {
+ VCFRecord vcfRecord = VCFRecord.parse(s);
+ isMouseOver(mousePoint, vcfRecord, features, i, start, pixPerBase);
+ }
}
catch (IOException e)
{
@@ -1174,15 +1184,14 @@ public class VCFview extends JPanel
}
private void isMouseOver(Point mousePoint,
- String s,
+ VCFRecord record,
FeatureVector features,
int i,
int start, float pixPerBase)
{
- String parts[] = tabPattern.split(s, 7);
- int basePosition = Integer.parseInt(parts[1]) + getSequenceOffset(parts[0]);
+ int basePosition = record.pos + getSequenceOffset(record.chrom);
- if( !showVariant(parts[3], parts[4], features, basePosition, parts[5]) )
+ if( !showVariant(record.ref, record.alt, features, basePosition, record.quality) )
return;
int pos[] = getScreenPosition(basePosition, pixPerBase, start, i);
@@ -1192,7 +1201,7 @@ public class VCFview extends JPanel
mousePoint.getX() > pos[0]-3 &&
mousePoint.getX() < pos[0]+3)
{
- mouseOverVCFline = s;
+ mouseOverVCFline = record.toString();
mouseOverIndex = i;
}
}