From abdc3727a6f984cee558c65065003e1b6814bf31 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 21 Apr 2014 10:05:05 +0100 Subject: [PATCH] JAL-1427 make sure we are working with dataset sequence when adding cross refs to sequence id matcher --- src/jalview/analysis/SequenceIdMatcher.java | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index cc2b458..e217aa1 100755 --- 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]); + SequenceI dbseq = seqs[i]; + while (dbseq.getDatasetSequence()!=null) + { + dbseq = dbseq.getDatasetSequence(); + } // 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++) { -- 1.7.10.2