JAL-2154 patch the hack (Jalview2XML tests pass)

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1633a5d..1a82a68 100644 (file)
--- 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>();
 
@@ -2678,21 +2678,24 @@ 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
       {
-        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++;
       }
 
@@ -2708,7 +2711,7 @@ public class Jalview2XML
           hiddenSeqs = new ArrayList<SequenceI>();
         }
 
-        hiddenSeqs.add(seqRefIds.get(seqId));
+        hiddenSeqs.add(tmpSeq);
       }
     }