X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCds.java;h=8f13d99df94f71654fb11655176bc43dd2ddcfed;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=63df7a79bf6aec7a1adb643ef085175e768d4799;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 63df7a7..8f13d99 100644
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
@@ -82,23 +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))
+      if ( accId.equals(parentFeature))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+    return result;
   }
 
   /**
@@ -107,11 +130,10 @@ public class EnsemblCds extends EnsemblSeqProxy
    * and also means we don't need to keep CDS features on CDS sequence (where
    * they are redundant information).
    */
-  @Override
   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;
   }