X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=c6daa662a2ea321f69e19d35b754819c4e4928a8;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=f619d071cfc9128647e96aae4b18f353e74d450c;hpb=50eb1f492f5c64b56594ee49be8183fab8a2f73b;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index f619d07..c6daa66 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -19,6 +19,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceCollectionI;
@@ -125,7 +126,6 @@ public class AnnotationColourGradient extends FollowerColourScheme
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    // TODO Auto-generated method stub
     super.alignmentChanged(alignment, hiddenReps);
 
     if (seqAssociated && annotation.getCalcId() != null)
@@ -138,7 +138,9 @@ public class AnnotationColourGradient extends FollowerColourScheme
       {
         seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
       }
-      for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+      // resolve the context containing all the annotation for the sequence
+      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+      for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
         if (alan.sequenceRef != null