From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 29 Jun 2012 15:19:19 +0000 (+0100)
Subject: JAL-1065 JAL-1066 ensure non-residue based schemes actually override the new findColo... 
X-Git-Tag: Jalview_2_9~442
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9e16113678909f36fa3212c0fa7db1a61107ee5c;p=jalview.git

JAL-1065 JAL-1066 ensure non-residue based schemes actually override the new findColor methods
---

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 16f822f..bfb760e 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -21,6 +21,7 @@ import java.awt.*;
 import java.util.Hashtable;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
 
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
@@ -56,6 +57,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    */
   public RNAHelicesColour(AlignmentAnnotation annotation)
   {
+    super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
     refresh();
   }
@@ -118,6 +120,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return color in RGB
    */
+  @Override
   public Color findColour(char c)
   {
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
@@ -135,7 +138,8 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return Color in RGB
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     refresh();
     Color currentColour = Color.white;