From 35b4e58bcfe18bae34456b618c6f4ffdf7c7f170 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 10:58:54 +0100
Subject: [PATCH] JAL-674 patch to ensure existing annotation is properly
 wired up when transferred to newly annotated version

---
 src/jalview/analysis/AlignSeq.java |    1 +
 1 file changed, 1 insertion(+)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index dd29d73..e7fed8d 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1116,6 +1116,7 @@ public class AlignSeq
                 AlignmentAnnotation alan = annotations.get(ap);
                 alan.liftOver(sq, sp2sq);
                 alan.setSequenceRef(sq);
+                sq.addAlignmentAnnotation(alan);
               }
             }
             else
-- 
1.7.10.2