X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=fc37b8ae40f78212d6f76fb33250770812b30023;hp=c6b794aebdec283445a70c63127bcd663039fd7d;hb=8e7cf85a7f61f425e808cac53ead7bc27e402242;hpb=6f1a50917d60504ae3eb46377d3020271accacaf

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index c6b794a..fc37b8a 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -25,16 +25,14 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GeneLociI;
 import jalview.util.MapList;
 
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 /**
@@ -151,7 +149,7 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param br
    * @return
    */
-  protected String parseGeneId(JSONObject val)
+  protected String parseGeneId(Map<String, Object> val)
   {
     if (val == null)
     {
@@ -189,7 +187,7 @@ public class EnsemblLookup extends EnsemblRestClient
   public String getSpecies(String identifier)
   {
     String species = null;
-    JSONObject json = getResult(identifier, null);
+    Map<String, Object> json = getResult(identifier, null);
     if (json != null)
     {
       Object o = json.get(SPECIES);
@@ -202,7 +200,7 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Calls the /lookup/id rest service and returns the response as a JSONObject,
+   * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
    * or null if any error
    * 
    * @param identifier
@@ -210,37 +208,20 @@ public class EnsemblLookup extends EnsemblRestClient
    *          (optional)
    * @return
    */
-  protected JSONObject getResult(String identifier, String objectType)
+  @SuppressWarnings("unchecked")
+  protected Map<String, Object> getResult(String identifier, String objectType)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
-    BufferedReader br = null;
     try
     {
-      URL url = getUrl(identifier, objectType);
-
-      if (url != null)
-      {
-        br = getHttpResponse(url, ids);
-      }
-      return br == null ? null : (JSONObject) (new JSONParser().parse(br));
-    } catch (IOException | ParseException e)
+      return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
+    } 
+    catch (IOException | ParseException e)
     {
       System.err.println("Error parsing " + identifier + " lookup response "
               + e.getMessage());
       return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
     }
   }
 
@@ -264,7 +245,7 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param json
    * @return
    */
-  GeneLociI parseGeneLoci(JSONObject json)
+  GeneLociI parseGeneLoci(Map<String, Object> json)
   {
     if (json == null)
     {