Merge branch 'develop' into task/JAL-2196pdbeProperties

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 4c53ef9..caed598 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -225,8 +225,7 @@ public class Uniprot extends DbSourceProxyImpl
       if ("EMBL".equals(pdb.getType()))
       {
         // look for a CDS reference and add it, too.
-        String cdsId = (String) pdb.getProperty()
-                .get("protein sequence ID");
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
         if (cdsId != null && cdsId.trim().length() > 0)
         {
           // remove version
@@ -245,8 +244,7 @@ public class Uniprot extends DbSourceProxyImpl
         * <property type="gene ID" value="ENSG00000158828"/>
         * </dbReference> 
          */
-        String cdsId = (String) pdb.getProperty()
-                .get("protein sequence ID");
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
         if (cdsId != null && cdsId.trim().length() > 0)
         {
           dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
@@ -267,12 +265,10 @@ public class Uniprot extends DbSourceProxyImpl
         sequence.addSequenceFeature(sf);
       }
     }
-    // we use setDBRefs to assign refs quickly.
-    sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
-    // need to use ensurePrimaries to reify any refs that should become primary
-    // refs
-    DBRefUtils.ensurePrimaries(sequence); // promote any direct refs to primary
-                                          // source dbs
+    for (DBRefEntry dbr : dbRefs)
+    {
+      sequence.addDBRef(dbr);
+    }
     return sequence;
   }