JAL-2189 apply license

[jalview.git] / src / jalview / ext / ensembl / EnsemblFeatures.java

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index 22faba9..b28a37f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -1,3 +1,23 @@
+/*
+ * 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.Alignment;
@@ -27,6 +47,24 @@ class EnsemblFeatures extends EnsemblRestClient
   private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
       EnsemblFeatureType.exon, EnsemblFeatureType.variation };
 
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblFeatures()
+  {
+    super();
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblFeatures(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -61,8 +99,7 @@ class EnsemblFeatures extends EnsemblRestClient
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
     StringBuffer urlstring = new StringBuffer(128);
-    urlstring.append(ENSEMBL_REST).append("/overlap/id/")
-            .append(ids.get(0));
+    urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
 
     // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
     urlstring.append("?content-type=text/x-gff3");