X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGenome.java;h=20987e188ab2ffbe47bc9abb9ab466cf37de8791;hb=d547268f85f377f14dbeb169072caebad45f9e2b;hp=37e8e2b7bbcd32d4ac1aec37e372ffc2b53fb4c3;hpb=9eec40eae88ae4330adc4d6ae38c513742b9e853;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index 37e8e2b..20987e1 100644
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -1,19 +1,47 @@
 package jalview.ext.ensembl;
 
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.SequenceFeature;
 
+/**
+ * A client to fetch genomic sequence from Ensembl
+ * 
+ * TODO: not currently used - delete?
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblGenome extends EnsemblSeqProxy
 {
+  /*
+   * fetch transcript features on genomic sequence (to identify the transcript 
+   * regions) and cds, exon and variation features (to retain)
+   */
+  private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
+      EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
+      EnsemblFeatureType.cds, EnsemblFeatureType.variation };
 
-  public EnsemblGenome() throws Exception
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblGenome()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblGenome(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (Genome)";
+    return "ENSEMBL (Genomic)";
   }
 
   @Override
@@ -22,4 +50,46 @@ public class EnsemblGenome extends EnsemblSeqProxy
     return EnsemblSeqType.GENOMIC;
   }
 
+  @Override
+  protected EnsemblFeatureType[] getFeaturesToFetch()
+  {
+    return FEATURES_TO_FETCH;
+  }
+
+  /**
+   * Answers true unless the feature type is 'transcript' (or a sub-type of
+   * transcript in the Sequence Ontology), or has a parent other than the given
+   * accession id. Transcript features are only retrieved in order to identify
+   * the transcript sequence range, and are redundant information on the
+   * transcript sequence itself.
+   */
+  @Override
+  protected boolean retainFeature(SequenceFeature sf, String accessionId)
+  {
+    if (isTranscript(sf.getType()))
+    {
+      return false;
+    }
+    return featureMayBelong(sf, accessionId);
+  }
+
+  /**
+   * Answers true if the sequence feature type is 'transcript' (or a subtype of
+   * transcript in the Sequence Ontology), and the ID of the feature is the
+   * transcript we are retrieving
+   */
+  @Override
+  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  {
+    if (isTranscript(sf.getType()))
+    {
+      String id = (String) sf.getValue(ID);
+      if (("transcript:" + accId).equals(id))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
 }