formatting

[jalview.git] / src / jalview / schemes / RNAHelicesColour.java

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 16f822f..4416bfd 100644 (file)
--- 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();
   }
@@ -64,7 +66,8 @@ public class RNAHelicesColour extends ResidueColourScheme
 
   public void refresh()
   {
-    if (lastrefresh != annotation._rnasecstr.hashCode() && annotation.isValidStruc())
+    if (lastrefresh != annotation._rnasecstr.hashCode()
+            && annotation.isValidStruc())
     {
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
@@ -118,6 +121,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return color in RGB
    */
+  @Override
   public Color findColour(char c)
   {
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
@@ -135,7 +139,8 @@ 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;