From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 10:21:05 +0000 (+0100)
Subject: JAL-674 patch for duplicate row bug
X-Git-Tag: Jalview_2_9~169^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=5a98fbf31c418758a11bbf8f54d5def7e509bb31;hp=d5f22defdce0bf4d162f976027cdbf6c2c43d036;p=jalview.git

JAL-674 patch for duplicate row bug
---

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);