JAL-1705 EnsemblGene added, and related refactoring

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

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 2ac4956..e4eb873 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -47,13 +47,18 @@ public class EnsemblCdna extends EnsemblSeqProxy
   /**
    * Answers true unless the feature type is 'exon' (or a sub-type of exon in
    * the Sequence Ontology). Exon features are only retrieved in order to
-   * identify the exon sequence range, and are redundant information on the exon
+   * identify the exon sequence loci, and are redundant information on the exon
    * sequence itself.
    */
   @Override
-  protected boolean retainFeature(String type)
+  protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    return !SequenceOntology.getInstance().isA(type, SequenceOntology.EXON);
+    if (SequenceOntology.getInstance().isA(sf.getType(),
+            SequenceOntology.EXON))
+    {
+      return false;
+    }
+    return super.retainFeature(sf, accessionId);
   }
 
   /**