JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index f619d07..c6daa66 100755 (executable)
--- 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