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

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

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 952f01e..7384327 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -21,9 +21,13 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import com.stevesoft.pat.Regex;
 
 /**
@@ -109,23 +113,27 @@ public class EnsemblCdna extends EnsemblSeqProxy
   }
 
   /**
-   * Answers true if the sequence feature type is 'exon' (or a subtype of exon
-   * 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 'exon' (or a
+   * subtype of exon 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.EXON))
+    List<SequenceFeature> result = new ArrayList<>();
+    List<SequenceFeature> sfs = seq.getFeatures()
+            .getFeaturesByOntology(SequenceOntologyI.EXON);
+    for (SequenceFeature sf : sfs)
     {
       String parentFeature = (String) sf.getValue(PARENT);
       if (("transcript:" + accId).equals(parentFeature))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+
+    return result;
   }
 
   /**