From 7c25229cd1f73806388e1d08f3f67f05cd332133 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 23 Jul 2016 11:09:48 +0100
Subject: [PATCH] JAL-2154 patch the hack (Jalview2XML tests pass)

---
 src/jalview/gui/Jalview2XML.java |   16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3f38082..1a82a68 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2666,7 +2666,7 @@ public class Jalview2XML
     // LOAD SEQUENCES
 
     List<SequenceI> hiddenSeqs = null;
-    jalview.datamodel.Sequence jseq;
+
 
     List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
 
@@ -2688,14 +2688,14 @@ public class Jalview2XML
       }
       else
       {
-        jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+        tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
                 vamsasSeq[vi].getSequence());
-        jseq.setDescription(vamsasSeq[vi].getDescription());
-        jseq.setStart(jseqs[i].getStart());
-        jseq.setEnd(jseqs[i].getEnd());
-        jseq.setVamsasId(uniqueSetSuffix + seqId);
-        seqRefIds.put(vamsasSeq[vi].getId(), jseq);
-        tmpseqs.add(jseq);
+        tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+        tmpSeq.setStart(jseqs[i].getStart());
+        tmpSeq.setEnd(jseqs[i].getEnd());
+        tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+        seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
+        tmpseqs.add(tmpSeq);
         vi++;
       }
 
-- 
1.7.10.2