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 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -158,7 +158,8 @@ public class CrossRef
       {\r
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))\r
         {\r
-          // retrieve CDS dataset sequences\r
+          System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");\r
+          // TODO: retrieve CDS dataset sequences\r
           // need global dataset sequence retriever/resolver to reuse refs\r
           // and construct Mapping entry.\r
           // insert gaps in CDS according to peptide gaps.\r

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index dbd0a63..1964c2f 100644 (file)
--- 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 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -100,6 +100,7 @@ public class DasSequenceFeatureFetcher
       DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
       for (int c = 0; c < coords.length; c++)\r
       {\r
+        // TODO: match UniProt coord system canonically (?) - does UniProt==uniprot==UNIPROT ? \r
         if (coords[c].getName().indexOf("UniProt") > -1)\r
         {\r
           uniprotCount++;\r