JAL-1705 more lenient test for 'sequence retrieved'

[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 58cf8fa..ec5780f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -1,16 +1,21 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
+import java.util.List;
 
 public class EnsemblCds extends EnsemblSeqProxy
 {
   /*
    * fetch cds features on genomic sequence (to identify the CDS regions)
-   * and variation features (to retain)
+   * and exon and variation features (to retain for display)
    */
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
-      EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+      EnsemblFeatureType.cds, EnsemblFeatureType.exon,
+      EnsemblFeatureType.variation };
 
   /**
    * Constructor
@@ -47,12 +52,12 @@ public class EnsemblCds extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.CDS))
+    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+            SequenceOntologyI.CDS))
     {
       return false;
     }
-    return super.retainFeature(sf, accessionId);
+    return featureMayBelong(sf, accessionId);
   }
 
   /**
@@ -63,8 +68,8 @@ public class EnsemblCds extends EnsemblSeqProxy
   @Override
   protected boolean identifiesSequence(SequenceFeature sf, String accId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.CDS))
+    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+            SequenceOntologyI.CDS))
     {
       String parentFeature = (String) sf.getValue(PARENT);
       if (("transcript:" + accId).equals(parentFeature))
@@ -75,4 +80,18 @@ public class EnsemblCds extends EnsemblSeqProxy
     return false;
   }
 
+  /**
+   * Overrides this method to trivially return a range which is the whole of the
+   * nucleotide sequence. This is both faster than scanning for CDS features,
+   * and also means we don't need to keep CDS features on CDS sequence (where
+   * they are redundant information).
+   */
+  @Override
+  protected int getCdsRanges(SequenceI dnaSeq, List<int[]> ranges)
+  {
+    int len = dnaSeq.getLength();
+    ranges.add(new int[] { 1, len });
+    return len;
+  }
+
 }