From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 3 Oct 2016 08:21:10 +0000 (+0100)
Subject: JAL-2210 need to add both transcript and product, and Ensembl needs to be marked... 
X-Git-Tag: Release_2_10_0~20^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=72f71a390ca98525f99a5dcecc1202696b20e0d7;p=jalview.git

JAL-2210 need to add both transcript and product, and Ensembl needs to be marked as a primary ref on protein, otherwise the ensembl peptide ids on uniprot don’t match up with the ones retrieved from ensembl
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index aef18e9..0ac14e5 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -101,7 +101,7 @@ public class DBRefSource
   public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
   public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
-      EMBLCDSProduct }; // , ENSEMBL }; // Ensembl ENSP* entries are protein
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 
   public static String[] allSources()
   {
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index e26ccda..4c53ef9 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -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">
@@ -249,8 +249,6 @@ public class Uniprot extends DbSourceProxyImpl
                 .get("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);