X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSymbol.java;h=1c47f11ff81a0b9b5361384ad3b3fcf9ed4234af;hb=77a7aa4d0c1be9ac6d0e6195a3b0ac3cd73f2875;hp=5b3baa112f6c2b18b159daf8f9c0351c88f1706e;hpb=550c391f0c113658e540783dc89034a34280ef18;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 5b3baa1..1c47f11 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -13,9 +13,26 @@ import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
+/**
+ * A client for the Ensembl xrefs/symbol REST service;
+ * 
+ * @see http://rest.ensembl.org/documentation/info/xref_external
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblSymbol extends EnsemblXref
 {
   /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblSymbol(String d)
+  {
+    super(d);
+  }
+
+  /**
    * Returns the first "id" value in gene identifier format from the JSON
    * response, or null if none found
    * 
@@ -23,7 +40,7 @@ public class EnsemblSymbol extends EnsemblXref
    * @return
    * @throws IOException
    */
-  protected String parseResponse(BufferedReader br)
+  protected String parseSymbolResponse(BufferedReader br)
           throws IOException
   {
     JSONParser jp = new JSONParser();
@@ -51,7 +68,7 @@ public class EnsemblSymbol extends EnsemblXref
 
   protected URL getUrl(String id, Species species)
   {
-    String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
+    String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
             + id
             + "?content-type=application/json";
     try
@@ -91,7 +108,7 @@ public class EnsemblSymbol extends EnsemblXref
             {
               br = getHttpResponse(url, ids);
             }
-            String geneId = parseResponse(br);
+            String geneId = parseSymbolResponse(br);
             if (geneId != null)
             {
               result.add(geneId);