X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=0a3705282cf7417be4482e31b79392e3302b30b9;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=7cbca667404d9b80ed4a88fcad9791ccfe49e12f;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 7cbca66..0a37052 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,8 +20,11 @@ package jalview.schemes;
 
 import java.awt.*;
 import java.util.Hashtable;
+import java.util.Map;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 /**
@@ -62,14 +65,40 @@ public class RNAHelicesColour extends ResidueColourScheme
     this.annotation = annotation;
     refresh();
   }
+  public RNAHelicesColour(AnnotatedCollectionI alignment)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    alignmentChanged(alignment, null);
+  }
+
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
 
+    // This loop will find the first rna structure annotation by which to colour
+    //  the sequences.
+    AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    for (int i = 0; i < annotations.length; i++) {
+        
+        // is this a sensible way of determining type of annotation?
+        if (annotations[i].getRNAStruc() != null) { 
+                annotation = annotations[i];
+                break;
+        }
+    }
+
+    refresh();
+
+  }
   private long lastrefresh = -1;
 
   public void refresh()
   {
-    if ((annotation._rnasecstr == null
+    
+    if (annotation!=null && ((annotation._rnasecstr == null
     		|| lastrefresh != annotation._rnasecstr.hashCode())
-            && annotation.isValidStruc())
+            && annotation.isValidStruc()))
     {
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();