JAL-2582 recognise ENS…P peptide IDs and make two getParent requests to get gene ID.

[jalview.git] / src / jalview / ext / ensembl / EnsemblGene.java

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 24e3e95..47b473a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -190,7 +190,20 @@ public class EnsemblGene extends EnsemblSeqProxy
           geneIds.add(geneId);
         }
       }
+      else if (isProteinIdentifier(acc))
+      {
+        String tscriptId = new EnsemblLookup(getDomain()).getParent(acc);
+        if (tscriptId != null)
+        {
+          String geneId = new EnsemblLookup(getDomain())
+                  .getParent(tscriptId);
 
+          if (geneId != null && !geneIds.contains(geneId))
+          {
+            geneIds.add(geneId);
+          }
+        }
+      }
       /*
        * if given a gene or other external name, lookup and fetch 
        * the corresponding gene for all model organisms