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 6b4a1f6..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);
   }
 
   /**
@@ -60,8 +64,8 @@ public class EnsemblGenome extends EnsemblSeqProxy
     if (SequenceOntology.getInstance().isA(sf.getType(),
             SequenceOntology.TRANSCRIPT))
     {
-      String parentFeature = (String) sf.getValue("ID");
-      if (("transcript:" + accId).equals(parentFeature))
+      String id = (String) sf.getValue(ID);
+      if (("transcript:" + accId).equals(id))
       {
         return true;
       }