JAL-2110 ensuring mapped dbrefs between protein and cds

[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 c86469f..31552af 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -5,7 +5,6 @@ import jalview.analysis.Dna;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -315,13 +314,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     for (DBRefEntry xref : xrefs)
     {
       seq.addDBRef(xref);
-      /*
-       * Save any Uniprot xref to be the reference for SIFTS mapping
-       */
-      if (DBRefSource.UNIPROT.equals(xref.getSource()))
-      {
-        seq.setSourceDBRef(xref);
-      }
     }
 
     /*
@@ -330,6 +322,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     DBRefEntry self = new DBRefEntry(getDbSource(),
             getEnsemblDataVersion(), seq.getName());
     seq.addDBRef(self);
+    seq.setSourceDBRef(self);
   }
 
   /**
@@ -387,8 +380,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         if (ids.contains(name)
                 || ids.contains(name.replace("ENSP", "ENST")))
         {
-          DBRefUtils.parseToDbRef(sq, getDbSource(),
+          DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(),
                   getEnsemblDataVersion(), name);
+          sq.setSourceDBRef(dbref);
         }
       }
       if (alignment == null)