From a8d30fa38a5d3e9cccf08aa446ca8ab00469bfd4 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 15 Aug 2008 10:00:51 +0000
Subject: [PATCH] xrefs retrieved from Uniprot

---
 src/jalview/ws/dbsources/Uniprot.java |   13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 42f8d72..65141f8 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -196,11 +196,17 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
       Enumeration e = entry.getDbReference().elements();
       Vector onlyPdbEntries = new Vector();
+      Vector dbxrefs = new Vector();
       while (e.hasMoreElements())
       {
         PDBEntry pdb = (PDBEntry) e.nextElement();
         if (!pdb.getType().equals("PDB"))
         {
+          DBRefEntry dbr = new DBRefEntry();
+          dbr.setSource(pdb.getType());
+          dbr.setAccessionId(pdb.getId());
+          dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());
+          dbxrefs.addElement(dbr);
           continue;
         }
 
@@ -220,6 +226,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
                 new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
                         .toString()));
       }
+      en2 = dbxrefs.elements();
+      while (en2.hasMoreElements())
+      {
+     // we always add as uniprot if we retrieved from uniprot or uniprot name
+        sq.addDBRef((DBRefEntry) en2.nextElement());
+                    
+      }
       sq.setPDBId(onlyPdbEntries);
       if (entry.getFeature() != null)
       {
-- 
1.7.10.2