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JAL-1427 make sure we are working with dataset sequence when adding cross refs to...
author
Jim Procter
<jprocter@dundee.ac.uk>
Mon, 21 Apr 2014 09:05:05 +0000
(10:05 +0100)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Mon, 21 Apr 2014 13:11:39 +0000
(14:11 +0100)
src/jalview/analysis/SequenceIdMatcher.java
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diff --git
a/src/jalview/analysis/SequenceIdMatcher.java
b/src/jalview/analysis/SequenceIdMatcher.java
index
cc2b458
..
e217aa1
100755
(executable)
--- a/
src/jalview/analysis/SequenceIdMatcher.java
+++ b/
src/jalview/analysis/SequenceIdMatcher.java
@@
-40,10
+40,15
@@
public class SequenceIdMatcher
// TODO: deal with ID collisions - SequenceI should be appended to list
// associated with this key.
names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
// TODO: deal with ID collisions - SequenceI should be appended to list
// associated with this key.
names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
+ SequenceI dbseq = seqs[i];
+ while (dbseq.getDatasetSequence()!=null)
+ {
+ dbseq = dbseq.getDatasetSequence();
+ }
// add in any interesting identifiers
// add in any interesting identifiers
- if (seqs[i].getDBRef() != null)
+ if (dbseq.getDBRef() != null)
{
{
- DBRefEntry dbr[] = seqs[i].getDBRef();
+ DBRefEntry dbr[] = dbseq.getDBRef();
SeqIdName sid = null;
for (int r = 0; r < dbr.length; r++)
{
SeqIdName sid = null;
for (int r = 0; r < dbr.length; r++)
{