JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS

[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 b9fbbdf..8238da0 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -1,7 +1,6 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
 
 public class EnsemblGenome extends EnsemblSeqProxy
 {
@@ -11,7 +10,7 @@ public class EnsemblGenome extends EnsemblSeqProxy
    */
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
       EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
-      EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+      EnsemblFeatureType.cds /*, EnsemblFeatureType.variation */};
 
   public EnsemblGenome()
   {
@@ -45,12 +44,11 @@ public class EnsemblGenome extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.TRANSCRIPT))
+    if (isTranscript(sf.getType()))
     {
       return false;
     }
-    return super.retainFeature(sf, accessionId);
+    return featureMayBelong(sf, accessionId);
   }
 
   /**
@@ -61,8 +59,7 @@ public class EnsemblGenome extends EnsemblSeqProxy
   @Override
   protected boolean identifiesSequence(SequenceFeature sf, String accId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.TRANSCRIPT))
+    if (isTranscript(sf.getType()))
     {
       String id = (String) sf.getValue(ID);
       if (("transcript:" + accId).equals(id))