From 663695f530e1cdef9cabdcd75d947219a1dd5c83 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 21 Jun 2016 09:57:36 +0100
Subject: [PATCH] JAL-2113 tidy up canonicalisation of Uniprot xrefs in EMBL
 data

---
 src/jalview/datamodel/xdb/embl/EmblEntry.java |   23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index b750973..ac0d339 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -197,7 +197,10 @@ public class EmblEntry
     // dbref
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
             new int[] { 1, dna.getLength() }, 1, 1));
-    // TODO: transform EMBL Database refs to canonical form
+
+    /*
+     * transform EMBL Database refs to canonical form
+     */
     if (dbRefs != null)
     {
       for (DBRefEntry dbref : dbRefs)
@@ -211,17 +214,6 @@ public class EmblEntry
     {
       for (EmblFeature feature : features)
       {
-        if (feature.dbRefs != null)
-        {
-          for (DBRefEntry dbref : feature.dbRefs)
-          {
-            /*
-             * convert UniProtKB/Swiss-Prot to UNIPROT
-             */
-            dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
-            dna.addDBRef(dbref);
-          }
-        }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
         {
           parseCodingFeature(feature, sourceDb, dna, peptides);
@@ -426,13 +418,17 @@ public class EmblEntry
     }
 
     /*
-     * add mappings for Uniprot xrefs
+     * add dbRefs to sequence, and mappings for Uniprot xrefs
      */
     if (feature.dbRefs != null)
     {
       boolean mappingUsed = false;
       for (DBRefEntry ref : feature.dbRefs)
       {
+        /*
+         * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+         */
+        ref.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
         if (ref.getSource().equals(DBRefSource.UNIPROT))
         {
           String proteinSeqName = DBRefSource.UNIPROT + "|"
@@ -488,6 +484,7 @@ public class EmblEntry
             }
           }
         }
+        dna.addDBRef(ref);
       }
       if (noProteinDbref && product != null)
       {
-- 
1.7.10.2