Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 31552af..e44b610 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -276,8 +276,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       {
         // clunky: ensure Uniprot xref if we have one is on mapped sequence
         SequenceI ds = proteinSeq.getDatasetSequence();
-        ds.setSourceDBRef(proteinSeq.getSourceDBRef());
-
+        // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence()
         Mapping map = new Mapping(ds, mapList);
         DBRefEntry dbr = new DBRefEntry(getDbSource(),
                 getEnsemblDataVersion(), proteinSeq.getName(), map);
@@ -322,7 +321,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     DBRefEntry self = new DBRefEntry(getDbSource(),
             getEnsemblDataVersion(), seq.getName());
     seq.addDBRef(self);
-    seq.setSourceDBRef(self);
   }
 
   /**
@@ -382,7 +380,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         {
           DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(),
                   getEnsemblDataVersion(), name);
-          sq.setSourceDBRef(dbref);
+          sq.addDBRef(dbref);
         }
       }
       if (alignment == null)