From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 23 Jul 2016 10:09:48 +0000 (+0100)
Subject: JAL-2154 patch the hack (Jalview2XML tests pass)
X-Git-Tag: Release_2_10_0~125^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7c25229cd1f73806388e1d08f3f67f05cd332133;p=jalview.git

JAL-2154 patch the hack (Jalview2XML tests pass)
---

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++;
       }