X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGenome.java;h=20987e188ab2ffbe47bc9abb9ab466cf37de8791;hb=deb6365c5607804ab43f8bb29e7d1a11f298789b;hp=8238da01cb4bb36cc6c36a5746b66a14892a436e;hpb=0b8abe58b934e03c34575b06d532a99f0ba70196;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index 8238da0..20987e1 100644
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -2,6 +2,14 @@ package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
 
+/**
+ * A client to fetch genomic sequence from Ensembl
+ * 
+ * TODO: not currently used - delete?
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblGenome extends EnsemblSeqProxy
 {
   /*
@@ -10,17 +18,30 @@ public class EnsemblGenome extends EnsemblSeqProxy
    */
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
       EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
-      EnsemblFeatureType.cds /*, EnsemblFeatureType.variation */};
+      EnsemblFeatureType.cds, EnsemblFeatureType.variation };
 
+  /**
+   * 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
@@ -37,9 +58,10 @@ public class EnsemblGenome extends EnsemblSeqProxy
 
   /**
    * Answers true unless the feature type is 'transcript' (or a sub-type of
-   * transcript in the Sequence Ontology). Transcript features are only
-   * retrieved in order to identify the transcript sequence range, and are
-   * redundant information on the transcript sequence itself.
+   * 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)