From a32b2c8d6f9d68da9fdcd07e2557c62c90fed630 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 6 Aug 2008 12:16:06 +0000 Subject: [PATCH] extra checks for datasetsequence for when getDbRefs is called --- src/jalview/analysis/CrossRef.java | 3 ++- src/jalview/io/VamsasAppDatastore.java | 4 ++-- src/jalview/ws/DasSequenceFeatureFetcher.java | 1 + 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java index f355d1f..d063eed 100644 --- a/src/jalview/analysis/CrossRef.java +++ b/src/jalview/analysis/CrossRef.java @@ -158,7 +158,8 @@ public class CrossRef { if (cdna[c].getSource().equals(DBRefSource.EMBLCDS)) { - // retrieve CDS dataset sequences + System.err.println("TODO: unimplemented sequence retrieval for coding region sequence."); + // TODO: retrieve CDS dataset sequences // need global dataset sequence retriever/resolver to reuse refs // and construct Mapping entry. // insert gaps in CDS according to peptide gaps. diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index dbd0a63..1964c2f 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -351,9 +351,9 @@ public class VamsasAppDatastore } } } - - if (sq.getDBRef() != null) + if (sq.getDatasetSequence()==null && sq.getDBRef() != null) { + // only sync database references for dataset sequences DBRefEntry[] entries = sq.getDBRef(); jalview.datamodel.DBRefEntry dbentry; for (int db = 0; db < entries.length; db++) diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java index 01bb64d..e3f7478 100644 --- a/src/jalview/ws/DasSequenceFeatureFetcher.java +++ b/src/jalview/ws/DasSequenceFeatureFetcher.java @@ -100,6 +100,7 @@ public class DasSequenceFeatureFetcher DasCoordinateSystem[] coords = source.getCoordinateSystem(); for (int c = 0; c < coords.length; c++) { + // TODO: match UniProt coord system canonically (?) - does UniProt==uniprot==UNIPROT ? if (coords[c].getName().indexOf("UniProt") > -1) { uniprotCount++; -- 1.7.10.2