X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=b1b3c5ae261a8d34820f5335cbc0359fa80f6279;hb=76caf07872d92bdc21faaa9278d9cccd7609d9b8;hp=05cffc2d1259bbf27d64ca80e9d96838ea0dae86;hpb=648ab7d29d683f065f1f11c3f8d373c7ca8d1cbf;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 05cffc2..b1b3c5a 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 
 import java.awt.event.ActionEvent;
@@ -77,16 +78,20 @@ public class RNAHelicesColourChooser
     adjusting = true;
     Vector list = new Vector();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns != null)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
+      for (int i = 0; i < anns.length; i++)
       {
-        list.addElement(label);
-      }
-      else
-      {
-        list.addElement(label + "_" + (index++));
+        String label = anns[i].label;
+        if (!list.contains(label))
+        {
+          list.addElement(label);
+        }
+        else
+        {
+          list.addElement(label + "_" + (index++));
+        }
       }
     }
 
@@ -109,21 +114,7 @@ public class RNAHelicesColourChooser
 
     av.setGlobalColourScheme(rhc);
 
-    if (av.getAlignment().getGroups() != null)
-    {
-      for (SequenceGroup sg : ap.getAlignment().getGroups())
-      {
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        sg.cs = new RNAHelicesColour(sg);
-
-      }
-    }
-
-    ap.paintAlignment(false);
+    ap.paintAlignment(true);
   }
 
   void reset()