JAL-1705 reworked Ensembl clients now fetching and mapping 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 9c88b7c..b8c9c3f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,11 +1,19 @@
 package jalview.ext.ensembl;
 
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntology;
 
 import com.stevesoft.pat.Regex;
 
 public class EnsemblCdna extends EnsemblSeqProxy
 {
+  /*
+   * fetch exon features on genomic sequence (to identify the cdnaregions)
+   * and cds and variation features (to retain)
+   */
+  private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
+      EnsemblFeatureType.exon, EnsemblFeatureType.cds,
+      EnsemblFeatureType.variation };
 
   public EnsemblCdna()
   {
@@ -31,9 +39,41 @@ public class EnsemblCdna extends EnsemblSeqProxy
   }
 
   @Override
-  public String getTestQuery()
+  protected EnsemblFeatureType[] getFeaturesToFetch()
   {
-    return "ENST00000288602";
+    return FEATURES_TO_FETCH;
+  }
+
+  /**
+   * Answers true unless the feature type is 'exon' (or a sub-type of exon in
+   * the Sequence Ontology). Exon features are only retrieved in order to
+   * identify the exon sequence range, and are redundant information on the exon
+   * sequence itself.
+   */
+  @Override
+  protected boolean retainFeature(String type)
+  {
+    return !SequenceOntology.getInstance().isA(type, SequenceOntology.EXON);
+  }
+
+  /**
+   * 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
+   */
+  @Override
+  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  {
+    if (SequenceOntology.getInstance().isA(sf.getType(),
+            SequenceOntology.EXON))
+    {
+      String parentFeature = (String) sf.getValue("Parent");
+      if (("transcript:" + accId).equals(parentFeature))
+      {
+        return true;
+      }
+    }
+    return false;
   }
 
 }