JAL-1705 EnsemblGene added, and related refactoring

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

diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 897371d..58cf8fa 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -45,9 +45,14 @@ public class EnsemblCds extends EnsemblSeqProxy
    * itself.
    */
   @Override
-  protected boolean retainFeature(String type)
+  protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    return !SequenceOntology.getInstance().isA(type, SequenceOntology.CDS);
+    if (SequenceOntology.getInstance().isA(sf.getType(),
+            SequenceOntology.CDS))
+    {
+      return false;
+    }
+    return super.retainFeature(sf, accessionId);
   }
 
   /**
@@ -61,7 +66,7 @@ public class EnsemblCds extends EnsemblSeqProxy
     if (SequenceOntology.getInstance().isA(sf.getType(),
             SequenceOntology.CDS))
     {
-      String parentFeature = (String) sf.getValue("Parent");
+      String parentFeature = (String) sf.getValue(PARENT);
       if (("transcript:" + accId).equals(parentFeature))
       {
         return true;