X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=9729a8347f2de9bc3a2e8c32ed7c5a2f070e7be7;hb=4d74e766d77156f71533564b32006a06df8f01bd;hp=74cc803d1f4dd910aa8ed181fc37063af26f0629;hpb=7fef0501bb64f11080bdb93ee0824416d84784cc;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 74cc803..9729a83 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -40,7 +40,6 @@ import java.util.Map;
 public class RNAHelicesColour extends ResidueColourScheme
 {
 
-
   /**
    * Maps sequence positions to the RNA helix they belong to. Key: position,
    * Value: helix TODO: Revise or drop in favour of annotation position numbers
@@ -61,12 +60,14 @@ public class RNAHelicesColour extends ResidueColourScheme
   {
     super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
+    ColourSchemeProperty.resetRnaHelicesShading();
     refresh();
   }
 
   public RNAHelicesColour(AnnotatedCollectionI alignment)
   {
     super(ResidueProperties.nucleotideIndex);
+    ColourSchemeProperty.resetRnaHelicesShading();
     alignmentChanged(alignment, null);
   }
 
@@ -90,6 +91,10 @@ public class RNAHelicesColour extends ResidueColourScheme
     // This loop will find the first rna structure annotation by which to colour
     // the sequences.
     AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    if (annotations == null)
+    {
+      return;
+    }
     for (int i = 0; i < annotations.length; i++)
     {