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JAL-2154 patch the hack (Jalview2XML tests pass)
author
Jim Procter
<jprocter@issues.jalview.org>
Sat, 23 Jul 2016 10:09:48 +0000
(11:09 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Sat, 23 Jul 2016 10:10:38 +0000
(11:10 +0100)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
3f38082
..
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;
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
- jalview.datamodel.Sequence jseq;
+
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
@@
-2688,14
+2688,14
@@
public class Jalview2XML
}
else
{
}
else
{
- jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+ tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
vamsasSeq[vi].getSequence());
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++;
}
vi++;
}