X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGenome.java;h=458a2336d9f36d5780ecdc9d7788f856e0308541;hb=604cbee405a837565ba1a74aa9bddd62aed685ab;hp=b7db2bc9a0c4cd252ab1fe5dbdedbfce43c1c008;hpb=cb6d2306e75ecea509fb1fde9736ff593e8e5837;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index b7db2bc..458a233 100644
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -1,7 +1,35 @@
+/*
+ * 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;
 
+/**
+ * A client to fetch genomic sequence from Ensembl
+ * 
+ * TODO: not currently used - delete?
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblGenome extends EnsemblSeqProxy
 {
   /*
@@ -12,15 +40,28 @@ public class EnsemblGenome extends EnsemblSeqProxy
       EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
       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 +78,10 @@ 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)