more fixes for identifying heterozygous sites

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15553 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/VCFRecord.java

@@ -73,7 +73,7 @@ class VCFRecord
     rec.pos   = Integer.parseInt(parts[1]);
     rec.ID    = parts[2];
     rec.ref   = parts[3];
-    rec.var   = rec.new VariantBase(parts[4]);
+    rec.var   = new VariantBase(rec, parts[4]);
     
     try
     {
@@ -232,7 +232,7 @@ class VCFRecord
    */
   protected void setAlt(String alt)
   {
-    this.var = new VariantBase(alt);
+    this.var = new VariantBase(this, alt);
   }
 
   /**
@@ -428,108 +428,4 @@ class VCFRecord
     
     return 3;
   }
-  
-  public class VariantBase
-  {
-    private String alt;
-    public VariantBase(String alt)
-    {
-      this.alt = alt;
-    }
-    
-    public String toString()
-    {
-      return alt;
-    }
-    
-    protected int length()
-    {
-      return alt.length();
-    }
-    
-    /**
-     * Is this a deletion type.
-     * @param variant
-     * @return
-     */
-    protected boolean isDeletion(boolean vcf_v4)
-    {
-      if(vcf_v4)
-      {
-        if( alt.length() < ref.length() && !(alt.indexOf(",") > -1) )
-          return true;
-      }
-      else if(alt.indexOf("D")>-1)
-        return true;
-      return false;
-    }
-    
-    /**
-     * Is this an insertion type.
-     * @param variant
-     * @return
-     */
-    protected boolean isInsertion(boolean vcf_v4)
-    {
-      if(vcf_v4)
-      {
-        if( alt.length() > ref.length() && !(alt.indexOf(",") > -1) )
-          return true;
-      }
-      else if(alt.indexOf("I")>-1)
-        return true;
-      return false;
-    }
-
-    protected boolean isMultiAllele()
-    {
-      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;
-    }
-    
-    protected int getNumAlleles()
-    {
-      if (alt.equals(".")) 
-        return 1;
-
-      return alt.split(",").length+1;
-    }
-
-    protected int getNumberOfDeletions(boolean vcf_v4)
-    {
-      String alt = getAlt().toString();
-      if(vcf_v4)
-      {
-        if(alt.equals("."))
-          return getRef().length();
-        return getRef().length()-alt.length();
-      }
-      
-      int index = alt.indexOf("D");
-      int ndel = 0;
-      try
-      {
-        ndel = Integer.parseInt( alt.substring(index+1) );
-      }
-      catch(NumberFormatException e) { e.printStackTrace(); }
-      return ndel;
-    }
-    
-    protected boolean isNonVariant()
-    {
-      if(alt.equals(".") && ref.length() == 1)
-        return true;
-      return false;
-    }
-  }
-  
 }
\ No newline at end of file

uk/ac/sanger/artemis/components/variant/VCFview.java

@@ -706,7 +706,7 @@ public class VCFview extends JPanel
     msg += "Qual: "+mouseVCF.getQuality()+"\n";
     String pl;
     if((pl = mouseVCF.getFormatValue("PL")) != null && pl.split(",").length > 1)
-      msg += "PL: "+pl+"\n";
+      msg += "Genotype likelihood (PL): "+pl+"\n";
     return msg;
   }
   
@@ -1008,15 +1008,15 @@ public class VCFview extends JPanel
 
     if(colourScheme == QUAL_COLOUR_SCHEME)
       g.setColor(getQualityColour(record));
-    else if(record.getAlt().isDeletion(vcf_v4))
-      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().isDeletion(vcf_v4))
+      g.setColor(Color.gray);
+    else if(record.getAlt().isInsertion(vcf_v4))
+      g.setColor(Color.yellow);
     else if(record.getAlt().length() == 1 && record.getRef().length() == 1)
     {
       g.setColor(getColourForSNP(record, features, basePosition));

uk/ac/sanger/artemis/components/variant/VariantBase.java

+
+package uk.ac.sanger.artemis.components.variant;
+
+public class VariantBase
+{
+  private VCFRecord record;
+  private String alt;
+
+  public VariantBase(VCFRecord record, String alt)
+  {
+    this.record = record;
+    this.alt = alt;
+  }
+
+  public String toString()
+  {
+    return alt;
+  }
+
+  protected int length()
+  {
+    return alt.length();
+  }
+
+  /**
+   * Is this a deletion type.
+   * @param variant
+   * @return
+   */
+  protected boolean isDeletion(boolean vcf_v4)
+  {
+    if (vcf_v4)
+    {
+      if (alt.length() < record.getRef().length() && !(alt.indexOf(",") > -1))
+        return true;
+    }
+    else if (alt.indexOf("D") > -1)
+      return true;
+    return false;
+  }
+
+  /**
+   * Is this an insertion type.
+   * 
+   * @param variant
+   * @return
+   */
+  protected boolean isInsertion(boolean vcf_v4)
+  {
+    if (vcf_v4)
+    {
+      if (alt.length() > record.getRef().length() && !(alt.indexOf(",") > -1))
+        return true;
+    }
+    else if (alt.indexOf("I") > -1)
+      return true;
+    return false;
+  }
+
+  protected boolean isMultiAllele()
+  {
+    if (VCFRecord.MULTI_ALLELE_PATTERN.matcher(alt).matches())
+      return true;
+
+    // look at probability of each genotype (PL) information as well
+    String pl;
+    if ((pl = record.getFormatValue("PL")) != null && pl.split(",").length == 3 &&
+         pl.split(",")[1].equals("0")) // middle value is zero, e.g.
+      return true;
+
+    return false;
+  }
+
+  protected int getNumAlleles()
+  {
+    if (alt.equals("."))
+      return 1;
+
+    return alt.split(",").length + 1;
+  }
+
+  protected int getNumberOfDeletions(boolean vcf_v4)
+  {
+    if (vcf_v4)
+    {
+      if (alt.equals("."))
+        return record.getRef().length();
+      return record.getRef().length() - alt.length();
+    }
+
+    int index = alt.indexOf("D");
+    int ndel = 0;
+    try
+    {
+      ndel = Integer.parseInt(alt.substring(index + 1));
+    }
+    catch (NumberFormatException e)
+    {
+      e.printStackTrace();
+    }
+    return ndel;
+  }
+
+  protected boolean isNonVariant()
+  {
+    if (alt.equals(".") && record.getRef().length() == 1)
+      return true;
+    return false;
+  }
+}
\ No newline at end of file