X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=30808fb5f88d4a2cbfb653aa134cf619d8e1c956;hb=32c56f877253fa8917d4f4640ed65d6e63376dac;hp=17f1842af68e78de06c2f132520ea8fb28872df0;hpb=86e1bfc3ed99bee91069b3238eb291c3955338d3;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 17f1842..30808fb 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -165,8 +165,9 @@ public class Uniprot extends DbSourceProxyImpl
       // uniprotxml parameter required since december 2007
       // uniprotkb dbname changed introduced december 2008
       File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
-              null, ".xml");
-      Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
+              "xml");
+      Vector<UniprotEntry> entries = getUniprotEntries(
+              new FileReader(file));
 
       if (entries != null)
       {
@@ -193,10 +194,11 @@ 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());
+    SequenceI sequence = new Sequence(id,
+            entry.getUniprotSequence().getContent());
     sequence.setDescription(getUniprotEntryDescription(entry));
 
     final String dbVersion = getDbVersion();
@@ -205,10 +207,10 @@ public class Uniprot extends DbSourceProxyImpl
     {
       DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
               accessionId);
+
+      // mark dbRef as a primary reference for this sequence
       dbRefs.add(dbRef);
     }
-    sequence.setSourceDBRef((dbRefs != null && dbRefs.size() > 0) ? dbRefs
-            .get(0) : null);
 
     Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
     for (PDBEntry pdb : entry.getDbReference())
@@ -222,6 +224,38 @@ public class Uniprot extends DbSourceProxyImpl
       {
         onlyPdbEntries.addElement(pdb);
       }
+      if ("EMBL".equals(pdb.getType()))
+      {
+        // look for a CDS reference and add it, too.
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
+        if (cdsId != null && cdsId.trim().length() > 0)
+        {
+          // remove version
+          String[] vrs = cdsId.split("\\.");
+          dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
+                  : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
+          dbRefs.add(dbr);
+        }
+      }
+      if ("Ensembl".equals(pdb.getType()))
+      {
+        /*UniprotXML
+         * <dbReference type="Ensembl" id="ENST00000321556">
+        * <molecule id="Q9BXM7-1"/>
+        * <property type="protein sequence ID" value="ENSP00000364204"/>
+        * <property type="gene ID" value="ENSG00000158828"/>
+        * </dbReference> 
+         */
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
+        if (cdsId != null && cdsId.trim().length() > 0)
+        {
+          dbr = new DBRefEntry(DBRefSource.ENSEMBL,
+                  DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
+          dbRefs.add(dbr);
+
+        }
+      }
+
     }
 
     sequence.setPDBId(onlyPdbEntries);
@@ -233,7 +267,10 @@ public class Uniprot extends DbSourceProxyImpl
         sequence.addSequenceFeature(sf);
       }
     }
-    sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
+    for (DBRefEntry dbr : dbRefs)
+    {
+      sequence.addDBRef(dbr);
+    }
     return sequence;
   }