From: jprocter <Jim Procter>
Date: Wed, 6 Aug 2008 12:16:06 +0000 (+0000)
Subject: extra checks for datasetsequence for when getDbRefs is called
X-Git-Tag: Release_2_4~55
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a32b2c8d6f9d68da9fdcd07e2557c62c90fed630;p=jalview.git

extra checks for datasetsequence for when getDbRefs is called
---

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++;