JAL-2154 ENA specific Ensembl canonical db prefixes

[jalview.git] / src / jalview / util / DBRefUtils.java

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index ed6d860..1965c20 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -59,6 +59,11 @@ public class DBRefUtils
 
     canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
     canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+    // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+    // from ENA.
+    canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+    canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+
 
     dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
     dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
@@ -546,7 +551,7 @@ public class DBRefUtils
 
   /**
    * Returns the (possibly empty) list of those supplied dbrefs which have the
-   * specified source databse
+   * specified source database, with a case-insensitive match of source name
    * 
    * @param dbRefs
    * @param source
@@ -560,7 +565,7 @@ public class DBRefUtils
     {
       for (DBRefEntry dbref : dbRefs)
       {
-        if (source.equals(dbref.getSource()))
+        if (source.equalsIgnoreCase(dbref.getSource()))
         {
           matches.add(dbref);
         }