JAL-3076 refactor for more efficient scan of 'gene' features

[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 8b2550d..8a71b64 100644 (file)
--- 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;
   }