X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblXref.java;h=714a5c011120801f85cd571dab9af79be73fff13;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=9b58e58cd341d3154e47959862ce38fc807043ab;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index 9b58e58..714a5c0 100644
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -105,14 +105,14 @@ class EnsemblXref extends EnsemblRestClient
 
     try
     {
-      Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(identifier), ids, -1, MODE_ITERATOR, null);
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(
+              getUrl(identifier), ids, -1, MODE_ITERATOR, null);
       while (rvals.hasNext())
       {
         Map<String, Object> val = (Map<String, Object>) rvals.next();
         String db = val.get("dbname").toString();
         String id = val.get("primary_id").toString();
-        if (db != null && id != null
-                && !GO_GENE_ONTOLOGY.equals(db))
+        if (db != null && id != null && !GO_GENE_ONTOLOGY.equals(db))
         {
           db = DBRefUtils.getCanonicalName(db);
           DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
@@ -126,23 +126,24 @@ class EnsemblXref extends EnsemblRestClient
     return result;
   }
 
-//  /**
-//   * Parses "primary_id" and "dbname" values from the JSON response and
-//   * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
-//   * don't parse "synonyms" as they appear to be either redirected or obsolete
-//   * in Uniprot.
-//   * 
-//   * @param br
-//   * @return
-//   * @throws IOException
-//   */
-//  @SuppressWarnings("unchecked")
-//protected List<DBRefEntry> parseResponse(BufferedReader br)
-//          throws IOException
-//  {
-//    return result;
-//  }
-//
+  // /**
+  // * Parses "primary_id" and "dbname" values from the JSON response and
+  // * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note
+  // we
+  // * don't parse "synonyms" as they appear to be either redirected or obsolete
+  // * in Uniprot.
+  // *
+  // * @param br
+  // * @return
+  // * @throws IOException
+  // */
+  // @SuppressWarnings("unchecked")
+  // protected List<DBRefEntry> parseResponse(BufferedReader br)
+  // throws IOException
+  // {
+  // return result;
+  // }
+  //
   private String xrefVersion = "ENSEMBL:0";
 
   /**
@@ -165,8 +166,8 @@ class EnsemblXref extends EnsemblRestClient
    */
   protected URL getUrl(String identifier)
   {
-    String url = getDomain() + "/xrefs/id/" + identifier
-            + CONTENT_TYPE_JSON + "&all_levels=1";
+    String url = getDomain() + "/xrefs/id/" + identifier + CONTENT_TYPE_JSON
+            + "&all_levels=1";
     try
     {
       return new URL(url);