Merge branch 'develop' into task/JAL-2196pdbeProperties

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 81b4caf..caed598 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -222,6 +222,38 @@ 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 +265,10 @@ public class Uniprot extends DbSourceProxyImpl
         sequence.addSequenceFeature(sf);
       }
     }
-    sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
+    for (DBRefEntry dbr : dbRefs)
+    {
+      sequence.addDBRef(dbr);
+    }
     return sequence;
   }