From 5a98fbf31c418758a11bbf8f54d5def7e509bb31 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 11:21:05 +0100
Subject: [PATCH] JAL-674 patch for duplicate row bug

---
 src/jalview/analysis/AlignSeq.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index e7fed8d..d05aa96 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1113,7 +1113,7 @@ public class AlignSeq
               if (removeOldAnnots) {
                 annotations.remove(ap);
               } else {
-                AlignmentAnnotation alan = annotations.get(ap);
+                AlignmentAnnotation alan = annotations.remove(ap);
                 alan.liftOver(sq, sp2sq);
                 alan.setSequenceRef(sq);
                 sq.addAlignmentAnnotation(alan);
-- 
1.7.10.2