From 98db6c30a9d5539276236a7885bf22a161aa9df9 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 2 May 2007 12:23:17 +0000
Subject: [PATCH] copy only the sequence associated alignment annotation
 displayed in the current view

---
 src/jalview/gui/AlignViewport.java |    3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 88a6e37..b68008a 100755
--- 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
-- 
1.7.10.2