From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 09:58:54 +0000 (+0100)
Subject: JAL-674 patch to ensure existing annotation is properly wired up when
X-Git-Tag: Jalview_2_9~169^2~16
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=35b4e58bcfe18bae34456b618c6f4ffdf7c7f170;p=jalview.git

JAL-674 patch to ensure existing annotation is properly wired up when
transferred to newly annotated version
---

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