JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 e26ccda..b6f53cd 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -193,7 +193,8 @@ public class Uniprot extends DbSourceProxyImpl
    *          UniprotEntry
    * @return SequenceI instance created from the UniprotEntry instance
    */
-  public SequenceI uniprotEntryToSequenceI(UniprotEntry entry){
+  public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+  {
     String id = getUniprotEntryId(entry);
     SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
             .getContent());
@@ -225,8 +226,7 @@ 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
@@ -236,7 +236,7 @@ public class Uniprot extends DbSourceProxyImpl
           dbRefs.add(dbr);
         }
       }
-      if (false) // "Ensembl".equals(pdb.getType()))
+      if ("Ensembl".equals(pdb.getType()))
       {
         /*UniprotXML
          * <dbReference type="Ensembl" id="ENST00000321556">
@@ -245,12 +245,9 @@ 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)
         {
-          // Only add the product ID
-          dbRefs.remove(dbr);
           dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
                   + ":" + dbVersion, cdsId.trim());
           dbRefs.add(dbr);
@@ -269,12 +266,10 @@ 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;
   }