diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index fcee2c9c48fb7d29d45629344a1d32f4fe354aee..caf355ba1b95243c0cd4ca3a2b9511f37558a8d0 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -117,11 +117,26 @@ class VCFRecord
return null;
}
+ protected String getFormatValue(String key)
+ {
+ String fmts[] = getFormat().split(":");
+ for(int i=0; i<fmts.length; i++)
+ {
+ if(fmts[i].equals(key))
+ {
+ String vals[] = getSampleDataString().split(":");
+ if(vals.length == fmts.length)
+ return vals[i];
+ }
+ }
+ return null;
+ }
+
/**
* Return the sample data as a tab-delimited string
* @return
*/
- private String getSampleDataString()
+ protected String getSampleDataString()
{
if(data == null)
return "";
@@ -470,6 +485,14 @@ class VCFRecord
{
if(VCFRecord.MULTI_ALLELE_PATTERN.matcher(alt).matches())
return true;
+
+ // look at probability of each genotype (PL) information as well
+ String pl;
+ if((pl = getFormatValue("PL")) != null &&
+ pl.split(",").length == 3 &&
+ pl.split(",")[1].equals("0")) // middle value is zero, e.g.
+ return true;
+
return false;
}
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index f8b7414f2c7e0c1282928f4b51606a960497181d..86a75f942e696e0dc95b7a18ab1b7821eff16e5a 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -128,7 +128,7 @@ public class VCFview extends JPanel
private int seqLength;
private EntryGroup entryGroup;
private String chr;
- private String mouseOverVCFline;
+ private VCFRecord mouseVCF;
private int mouseOverIndex = -1;
private boolean vcf_v4 = false;
@@ -695,17 +695,18 @@ public class VCFview extends JPanel
public String getToolTipText()
{
- if(mouseOverVCFline == null)
+ if(mouseVCF == null)
return null;
-
- String parts[] = tabPattern.split(mouseOverVCFline, 0);
+
String msg =
- "Seq: "+parts[0]+"\n";
- msg += "Pos: "+parts[1]+"\n";
- msg += "ID: "+parts[2]+"\n";
- msg += "Variant: "+parts[3]+" -> "+parts[4]+"\n";
- msg += "Qual: "+parts[5]+"\n";
-
+ "Seq: "+mouseVCF.getChrom()+"\n";
+ msg += "Pos: "+mouseVCF.getPos()+"\n";
+ msg += "ID: "+mouseVCF.getID()+"\n";
+ msg += "Variant: "+mouseVCF.getRef()+" -> "+mouseVCF.getAlt().toString()+"\n";
+ msg += "Qual: "+mouseVCF.getQuality()+"\n";
+ String pl;
+ if((pl = mouseVCF.getFormatValue("PL")) != null && pl.split(",").length > 1)
+ msg += "PL: "+pl+"\n";
return msg;
}
@@ -755,7 +756,7 @@ public class VCFview extends JPanel
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
- mouseOverVCFline = null;
+ mouseVCF = null;
float pixPerBase = getPixPerBaseByWidth();
int start = getBaseAtStartOfView();
@@ -1013,18 +1014,15 @@ public class VCFview extends JPanel
g.setColor(Color.gray);
else if(record.getAlt().isInsertion(vcf_v4))
g.setColor(Color.yellow);
+ else if(record.getAlt().isMultiAllele())
+ {
+ g.setColor(Color.orange);
+ g.fillArc(pos[0]-3, pos[1]-LINE_HEIGHT-3, 6, 6, 0, 360);
+ }
else if(record.getAlt().length() == 1 && record.getRef().length() == 1)
g.setColor(getColourForSNP(record, features, basePosition));
else
- {
- if(record.getAlt().isMultiAllele())
- {
- g.setColor(Color.orange);
- g.fillArc(pos[0]-3, pos[1]-LINE_HEIGHT-3, 6, 6, 0, 360);
- }
- else
- g.setColor(Color.pink);
- }
+ g.setColor(Color.pink);
}
if(markAsNewStop)
@@ -1081,7 +1079,7 @@ public class VCFview extends JPanel
else if(variant.equals("T"))
return Color.black;
else
- return Color.magenta;
+ return Color.magenta; // non-variant
}
/**
@@ -1229,7 +1227,7 @@ public class VCFview extends JPanel
mousePoint.getX() > pos[0]-3 &&
mousePoint.getX() < pos[0]+3)
{
- mouseOverVCFline = record.toString();
+ mouseVCF = record;
mouseOverIndex = i;
}
}
@@ -1477,34 +1475,33 @@ public class VCFview extends JPanel
if(showDetails != null)
popup.remove(showDetails);
- if( mouseOverVCFline != null )
+ if( mouseVCF != null )
{
- final String parts[] = tabPattern.split(mouseOverVCFline, 0);
-
- showDetails = new JMenuItem("Show details of : "+parts[0]+":"+parts[1]+" "+parts[2]);
+ showDetails = new JMenuItem("Show details of : "+
+ mouseVCF.getChrom()+":"+mouseVCF.getPos()+" "+mouseVCF.getID());
showDetails.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- FileViewer viewDetail = new FileViewer(parts[0]+":"+parts[1]+" "+parts[2], true, false);
+ FileViewer viewDetail = new FileViewer(
+ mouseVCF.getChrom()+":"+mouseVCF.getPos()+" "+mouseVCF.getID(), true, false);
viewDetail.appendString(header[mouseOverIndex]+"\n", Level.INFO);
- viewDetail.appendString("Seq : "+parts[0]+"\n", Level.DEBUG);
- viewDetail.appendString("Pos : "+parts[1]+"\n", Level.DEBUG);
- viewDetail.appendString("ID : "+parts[2]+"\n", Level.DEBUG);
- viewDetail.appendString("Ref : "+parts[3]+"\n", Level.DEBUG);
- viewDetail.appendString("Alt : "+parts[4]+"\n", Level.DEBUG);
- viewDetail.appendString("Qual : "+parts[5]+"\n", Level.DEBUG);
- viewDetail.appendString("Filter: "+parts[6]+"\n", Level.DEBUG);
- viewDetail.appendString("Info : "+parts[7]+"\n", Level.DEBUG);
+ viewDetail.appendString("Seq : "+mouseVCF.getChrom()+"\n", Level.DEBUG);
+ viewDetail.appendString("Pos : "+mouseVCF.getPos()+"\n", Level.DEBUG);
+ viewDetail.appendString("ID : "+mouseVCF.getID()+"\n", Level.DEBUG);
+ viewDetail.appendString("Ref : "+mouseVCF.getRef()+"\n", Level.DEBUG);
+ viewDetail.appendString("Alt : "+mouseVCF.getAlt().toString()+"\n", Level.DEBUG);
+ viewDetail.appendString("Qual : "+mouseVCF.getQuality()+"\n", Level.DEBUG);
+ viewDetail.appendString("Filter: "+mouseVCF.getFilter()+"\n", Level.DEBUG);
+ viewDetail.appendString("Info : "+mouseVCF.getInfo()+"\n", Level.DEBUG);
- if(parts.length > 8)
+ if(mouseVCF.getFormat() != null)
{
viewDetail.appendString("\nGenotype information:\n", Level.INFO);
- viewDetail.appendString("Format: "+parts[8]+"\n", Level.DEBUG);
- for(int i=9; i<parts.length; i++)
- viewDetail.appendString(parts[i]+"\n", Level.DEBUG);
+ viewDetail.appendString("Format: "+mouseVCF.getFormat()+"\n", Level.DEBUG);
+ viewDetail.appendString(mouseVCF.getSampleDataString()+"\n", Level.DEBUG);
}
viewDetail.getTextPane().setCaretPosition(0);