From 91416b3038a6f3fc655791512770da07cb6cb251 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 8 Jun 2006 18:17:35 +0000 Subject: [PATCH] Introduced DbRefEntry to DasSourceCoordinateSystem check to only call sources for sequences with a particular DBRefEntry id (PDB or Uniprot currently) --- src/jalview/gui/SequenceFetcher.java | 2 +- src/jalview/io/DasSequenceFeatureFetcher.java | 25 +++++++++++++---- src/jalview/io/ModellerDescription.java | 2 +- src/jalview/io/SequenceFeatureFetcher.java | 3 +- src/jalview/io/WSWUBlastClient.java | 2 +- src/jalview/util/DBRefUtils.java | 37 +++++++++++++++++++++++-- 6 files changed, 59 insertions(+), 12 deletions(-) diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 6bdba4a..e2b5730 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -437,7 +437,7 @@ public class SequenceFetcher // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source // JBPNote - PDB DBRefEntry should also carry the chain and mapping information - DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid); + DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid); sequences[i].getDatasetSequence().addDBRef(dbentry); } else diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java index 99a2b70..8f104c5 100755 --- a/src/jalview/io/DasSequenceFeatureFetcher.java +++ b/src/jalview/io/DasSequenceFeatureFetcher.java @@ -251,7 +251,10 @@ public class DasSequenceFeatureFetcher implements Runnable while (seqIndex < sequences.size()) { Sequence sequence = (Sequence) sequences.get(seqIndex); - Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {"DBREF"}); + Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), + new String[] { + jalview.datamodel.DBRefSource.PDB, + jalview.datamodel.DBRefSource.UNIPROT}); for(int sourceIndex=0; sourceIndex