X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCds.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCds.java;h=8a71b64662f20d35a7dfbb8f53f49303928dfbfd;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=8b2550d8abc8037fef4ca8a9867473c199da207f;hpb=5610d0f46a76d4269d25148d42f92d867fa1061a;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 8b2550d..8a71b64 100644
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -102,23 +102,26 @@ public class EnsemblCds extends EnsemblSeqProxy
   }
 
   /**
-   * Answers true if the sequence feature type is 'CDS' (or a subtype of CDS in
-   * the Sequence Ontology), and the Parent of the feature is the transcript we
-   * are retrieving
+   * Answers a list of sequence features (if any) whose type is 'CDS' (or a
+   * subtype of CDS in the Sequence Ontology), and whose Parent is the
+   * transcript we are retrieving
    */
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
-            SequenceOntologyI.CDS))
+    List<SequenceFeature> result = new ArrayList<>();
+    List<SequenceFeature> sfs = seq.getFeatures()
+            .getFeaturesByOntology(SequenceOntologyI.CDS);
+    for (SequenceFeature sf : sfs)
     {
       String parentFeature = (String) sf.getValue(PARENT);
       if (("transcript:" + accId).equals(parentFeature))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+    return result;
   }
 
   /**
@@ -130,7 +133,7 @@ public class EnsemblCds extends EnsemblSeqProxy
   protected List<int[]> getCdsRanges(SequenceI dnaSeq)
   {
     int len = dnaSeq.getLength();
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     ranges.add(new int[] { 1, len });
     return ranges;
   }