JAL-1705 include stop codons in derived CDS; support ensemblgenomes

[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..0547433 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -27,6 +27,24 @@ 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()
   {
@@ -61,7 +79,7 @@ class EnsemblFeatures extends EnsemblRestClient
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
     StringBuffer urlstring = new StringBuffer(128);
-    urlstring.append(ENSEMBL_REST).append("/overlap/id/")
+    urlstring.append(getDomain()).append("/overlap/id/")
             .append(ids.get(0));
 
     // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats