Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

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

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index 36bd7c5..f19b4d4 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -17,9 +17,26 @@ import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
-public class EnsemblXref extends EnsemblRestClient
+/**
+ * A class to fetch cross-references from Ensembl by calling the /xrefs REST
+ * service
+ * 
+ * @author gmcarstairs
+ * @see http://rest.ensembl.org/documentation/info/xref_id
+ */
+class EnsemblXref extends EnsemblRestClient
 {
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblXref(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -35,8 +52,7 @@ public class EnsemblXref extends EnsemblRestClient
   @Override
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getUrl(ids.get(0));
   }
 
   @Override
@@ -158,7 +174,7 @@ public class EnsemblXref extends EnsemblRestClient
    */
   protected URL getUrl(String identifier)
   {
-    String url = ENSEMBL_REST + "/xrefs/id/" + identifier
+    String url = getDomain() + "/xrefs/id/" + identifier
             + "?content-type=application/json&all_levels=1";
     try
     {