From 0e26aa45a7fbe0f21aa41ef452de1f3a5d3f7e8c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Jul 2016 17:14:45 +0100
Subject: [PATCH] JAL-2154 poke JSeq start/end into Vamsas sequence

---
 src/jalview/gui/Jalview2XML.java |    9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1633a5d..3f38082 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2678,9 +2678,12 @@ public class Jalview2XML
     {
       String seqId = jseqs[i].getId();
 
-      if (seqRefIds.get(seqId) != null)
+      SequenceI tmpSeq = seqRefIds.get(seqId);
+      if (tmpSeq != null)
       {
-        tmpseqs.add(seqRefIds.get(seqId));
+        tmpSeq.setStart(jseqs[i].getStart());
+        tmpSeq.setEnd(jseqs[i].getEnd());
+        tmpseqs.add(tmpSeq);
         multipleView = true;
       }
       else
@@ -2708,7 +2711,7 @@ public class Jalview2XML
           hiddenSeqs = new ArrayList<SequenceI>();
         }
 
-        hiddenSeqs.add(seqRefIds.get(seqId));
+        hiddenSeqs.add(tmpSeq);
       }
     }
 
-- 
1.7.10.2