copy only the sequence associated alignment annotation displayed in the current view

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 88a6e37..b68008a 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1479,9 +1479,10 @@ public class AlignViewport
       if (selectionGroup == null)
     {
         sequences = alignment.getSequencesArray();
+        AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); 
         for (int i=0; i<sequences.length; i++)
         {
-          sequences[i] = new Sequence(sequences[i]); // construct new sequence
+          sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
         }
     }
       else