X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=9b56d6bfe91560cacb1cbb8e9997cfe8a79de196;hb=9d80cca5113c0411aa06559d4bd3f86454459ce7;hp=5f353f85014b792babe5e41ef8cda74e3308ccd4;hpb=7ef3d2f322e86a39a4cf8df7793b434a4d028488;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 5f353f8..9b56d6b 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -23,18 +23,18 @@ package jalview.ext.ensembl;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
 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;
 
 /**
@@ -117,21 +117,9 @@ public class EnsemblLookup extends EnsemblRestClient
     return true;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return "application/json";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "application/json";
-  }
-
   /**
    * Returns the gene id related to the given identifier (which may be for a
-   * gene, transcript or protein)
+   * gene, transcript or protein), or null if none is found
    * 
    * @param identifier
    * @return
@@ -143,7 +131,7 @@ public class EnsemblLookup extends EnsemblRestClient
 
   /**
    * Returns the gene id related to the given identifier (which may be for a
-   * gene, transcript or protein)
+   * gene, transcript or protein), or null if none is found
    * 
    * @param identifier
    * @param objectType
@@ -163,8 +151,12 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param br
    * @return
    */
-  protected String parseGeneId(JSONObject val)
+  protected String parseGeneId(Map<String, Object> val)
   {
+    if (val == null)
+    {
+      return null;
+    }
     String geneId = null;
     String type = val.get(OBJECT_TYPE).toString();
     if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
@@ -197,7 +189,7 @@ 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);
@@ -210,7 +202,7 @@ 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
@@ -218,37 +210,20 @@ 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
-        }
-      }
     }
   }
 
@@ -272,7 +247,7 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param json
    * @return
    */
-  GeneLociI parseGeneLoci(JSONObject json)
+  GeneLociI parseGeneLoci(Map<String, Object> json)
   {
     if (json == null)
     {
@@ -295,34 +270,10 @@ public class EnsemblLookup extends EnsemblRestClient
           fromEnd });
       List<int[]> toRange = Collections.singletonList(new int[] { toStart,
           toEnd });
-      final MapList map = new MapList(fromRange, toRange, 1, 1);
-      return new GeneLociI()
-      {
-
-        @Override
-        public String getSpeciesId()
-        {
-          return species == null ? "" : species;
-        }
-
-        @Override
-        public String getAssemblyId()
-        {
-          return assembly;
-        }
-
-        @Override
-        public String getChromosomeId()
-        {
-          return chromosome;
-        }
-
-        @Override
-        public MapList getMap()
-        {
-          return map;
-        }
-      };
+      final Mapping map = new Mapping(
+              new MapList(fromRange, toRange, 1, 1));
+      return new GeneLocus(species == null ? "" : species, assembly,
+              chromosome, map);
     } catch (NullPointerException | NumberFormatException e)
     {
       Cache.log.error("Error looking up gene loci: " + e.getMessage());