X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSymbol.java;h=ef79d72df4b7a33f1c8863d4d1ca7b42e9e59118;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f731e9412129b31571d8afc5a72b199d93ee5c44;hpb=8e7cf85a7f61f425e808cac53ead7bc27e402242;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index f731e94..ef79d72 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -40,7 +40,9 @@ import org.json.simple.parser.ParseException;
 public class EnsemblSymbol extends EnsemblXref
 {
   private static final String GENE = "gene";
+
   private static final String TYPE = "type";
+
   /**
    * Constructor given the target domain to fetch data from
    * 
@@ -53,18 +55,18 @@ public class EnsemblSymbol extends EnsemblXref
     super(domain, dbName, dbVersion);
   }
 
-//  /**
-//   * Returns the first "id" value in gene identifier format from the JSON
-//   * response, or null if none found
-//   * 
-//   * @param br
-//   * @return
-//   * @throws IOException
-//   */
-//  @SuppressWarnings("unchecked")
-//protected String parseSymbolResponse(BufferedReader br) throws IOException
-//  {
-//  }
+  // /**
+  // * Returns the first "id" value in gene identifier format from the JSON
+  // * response, or null if none found
+  // *
+  // * @param br
+  // * @return
+  // * @throws IOException
+  // */
+  // @SuppressWarnings("unchecked")
+  // protected String parseSymbolResponse(BufferedReader br) throws IOException
+  // {
+  // }
 
   /**
    * Constructs the URL for the REST symbol endpoint
@@ -119,12 +121,14 @@ public class EnsemblSymbol extends EnsemblXref
       {
         for (Species taxon : Species.getModelOrganisms())
         {
-          String geneId = null;///parseSymbolResponse(br);          
+          String geneId = null;/// parseSymbolResponse(br);
           try
           {
-			Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR, null);
+            Iterator<Object> rvals = (Iterator<Object>) getJSON(
+                    getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR,
+                    null);
             if (rvals == null)
-            	continue;
+              continue;
             while (rvals.hasNext())
             {
               Map<String, Object> val = (Map<String, Object>) rvals.next();
@@ -140,7 +144,7 @@ public class EnsemblSymbol extends EnsemblXref
           {
             // ignore
           }
-          
+
           if (geneId != null && !result.contains(geneId))
           {
             result.add(geneId);