From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 6 Oct 2014 11:26:22 +0000 (+0100)
Subject: JAL-654 JAL-1264 sequence associated annotation is duplicated before transfer to... 
X-Git-Tag: Jalview_2_9~174^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=bdd843c2e0bc3a9dac00f8db67601d388e800879;p=jalview.git

JAL-654 JAL-1264 sequence associated annotation is duplicated before transfer to dataset sequence rather than simply relocated to preserve alignment references
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9cc7d54..945a9d4 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1007,14 +1007,13 @@ public class Sequence implements SequenceI
       datasetSequence.updatePDBIds();
       if (annotation != null)
       {
-        Vector<AlignmentAnnotation> _annot = annotation;
-        annotation = null;
-        for (AlignmentAnnotation aa : _annot)
+        for (AlignmentAnnotation aa : annotation)
         {
-          aa.sequenceRef = datasetSequence;
-          aa.adjustForAlignment(); // uses annotation's own record of
+          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+          _aa.sequenceRef = datasetSequence;
+          _aa.adjustForAlignment(); // uses annotation's own record of
                                    // sequence-column mapping
-          datasetSequence.addAlignmentAnnotation(aa);
+          datasetSequence.addAlignmentAnnotation(_aa);
         }
       }
     }