JAL-1705 EnsemblGene added, and related refactoring

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

diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index 60f8c46..b9fbbdf 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -43,10 +43,14 @@ public class EnsemblGenome extends EnsemblSeqProxy
    * redundant information on the transcript sequence itself.
    */
   @Override
-  protected boolean retainFeature(String type)
+  protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    return !SequenceOntology.getInstance().isA(type,
-            SequenceOntology.TRANSCRIPT);
+    if (SequenceOntology.getInstance().isA(sf.getType(),
+            SequenceOntology.TRANSCRIPT))
+    {
+      return false;
+    }
+    return super.retainFeature(sf, accessionId);
   }
 
   /**