From 96153c4037c295b5a23ebb3196a0df7465732d92 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 30 Sep 2016 17:40:19 +0100
Subject: [PATCH] JAL-2210 add uniprot+mapping between ENST and ENSP seqs

---
 src/jalview/ext/ensembl/EnsemblSeqProxy.java |   40 ++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 1bcfe22..c749b94 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -2,9 +2,11 @@ package jalview.ext.ensembl;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Dna;
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -282,6 +284,44 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         DBRefEntry dbr = new DBRefEntry(getDbSource(),
                 getEnsemblDataVersion(), proteinSeq.getName(), map);
         querySeq.getDatasetSequence().addDBRef(dbr);
+        DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
+                new String[] { DBRefSource.UNIPROT });
+        DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
+                new String[] { DBRefSource.UNIPROT });
+        if (uprots != null)
+        {
+          for (DBRefEntry up : uprots)
+          {
+            // locate local uniprot ref and map
+            List<DBRefEntry> upx = DBRefUtils.searchRefs(upxrefs, up.getAccessionId());
+            DBRefEntry upxref;
+            if (upx.size() != 0)
+            {
+              upxref = upx.get(0);
+
+              if (upx.size() > 1)
+              {
+                Cache.log
+                        .warn("Implementation issue - multiple uniprot acc on product sequence.");
+              }
+            }
+            else
+            {
+              upxref = new DBRefEntry(DBRefSource.UNIPROT,
+                    getEnsemblDataVersion(), up.getAccessionId());
+            }
+
+            Mapping newMap = new Mapping(ds, mapList);
+            upxref.setVersion(getEnsemblDataVersion());
+            upxref.setMap(newMap);
+            if (upx.size() == 0)
+            {
+              // add the new uniprot ref
+              querySeq.getDatasetSequence().addDBRef(upxref);
+            }
+            
+          }
+        }
         
         /*
          * copy exon features to protein, compute peptide variants from dna 
-- 
1.7.10.2