From b45345a4ee49f07b6f66e80535ca5f140a954e41 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 10 Oct 2006 13:37:23 +0000
Subject: [PATCH] Must repaint whole alignPanel

---
 src/jalview/gui/AlignViewport.java |    6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ddb871e..743c8dd 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -389,7 +389,7 @@ public class AlignViewport
 
         if(ap!=null)
         {
-          ap.annotationPanel.repaint();
+          ap.repaint();
         }
         updatingConservation = false;
       }
@@ -523,7 +523,7 @@ public class AlignViewport
 
         if (ap != null)
         {
-          ap.annotationPanel.repaint();
+          ap.repaint();
         }
 
 
@@ -1439,7 +1439,7 @@ public class AlignViewport
       // be done to remove redundancy.
       CigarArray aligview = getViewAsCigars(selectedOnly);
       if (aligview!=null) {
-        return new AlignmentView(aligview, 
+        return new AlignmentView(aligview,
             (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
       }
       return null;
-- 
1.7.10.2