X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=add71b3b7935ba6cafb84e42c5371bc73ef7c3d0;hb=8e7cf85a7f61f425e808cac53ead7bc27e402242;hp=56657e0578c517e8c02717e1d57060a77a557f70;hpb=353109c11d706b29ae5bc9606f0e12223aa45a98;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index 56657e0..add71b3 100644
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -3,6 +3,7 @@ package jalview.ext.ensembl;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.GeneLociI;
+import jalview.util.JSONUtils;
 import jalview.util.MapList;
 
 import java.io.BufferedReader;
@@ -13,10 +14,8 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 public class EnsemblMap extends EnsemblRestClient
@@ -98,18 +97,6 @@ public class EnsemblMap extends EnsemblRestClient
   }
 
   @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return "application/json";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "application/json";
-  }
-
-  @Override
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
     return null; // not used
@@ -131,30 +118,15 @@ public class EnsemblMap extends EnsemblRestClient
           String fromRef, String toRef, int[] queryRange)
   {
     URL url = null;
-    BufferedReader br = null;
-
     try
     {
       url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
               queryRange[1]);
-      br = getHttpResponse(url, null);
-      return (parseAssemblyMappingResponse(br));
+      return (parseAssemblyMappingResponse(url));
     } catch (Throwable t)
     {
       System.out.println("Error calling " + url + ": " + t.getMessage());
       return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
     }
   }
 
@@ -173,22 +145,21 @@ public class EnsemblMap extends EnsemblRestClient
    * @param br
    * @return
    */
-  protected int[] parseAssemblyMappingResponse(BufferedReader br)
+  @SuppressWarnings("unchecked")
+  protected int[] parseAssemblyMappingResponse(URL url)
   {
     int[] result = null;
-    JSONParser jp = new JSONParser();
 
     try
     {
-      JSONObject parsed = (JSONObject) jp.parse(br);
-      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
-
-      Iterator rvals = mappings.iterator();
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+      if (rvals == null)
+    	  return null;
       while (rvals.hasNext())
       {
         // todo check for "mapped"
-        JSONObject val = (JSONObject) rvals.next();
-        JSONObject mapped = (JSONObject) val.get(MAPPED);
+        Map<String, Object> val = (Map<String, Object>) rvals.next();
+        Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
         int start = Integer.parseInt(mapped.get("start").toString());
         int end = Integer.parseInt(mapped.get("end").toString());
         String strand = mapped.get("strand").toString();
@@ -248,34 +219,19 @@ public class EnsemblMap extends EnsemblRestClient
           int end, String cdsOrCdna)
   {
     URL url = null;
-    BufferedReader br = null;
-
     try
     {
       String domain = new EnsemblInfo().getDomain(division);
       if (domain != null)
       {
         url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
-        br = getHttpResponse(url, null);
-        return (parseIdMappingResponse(br, accession, domain));
+        return (parseIdMappingResponse(url, accession, domain));
       }
       return null;
     } catch (Throwable t)
     {
       System.out.println("Error calling " + url + ": " + t.getMessage());
       return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
     }
   }
 
@@ -321,17 +277,16 @@ public class EnsemblMap extends EnsemblRestClient
    * @param domain
    * @return
    */
-  GeneLociI parseIdMappingResponse(BufferedReader br, String accession,
+  @SuppressWarnings("unchecked")
+GeneLociI parseIdMappingResponse(URL url, String accession,
           String domain)
   {
-    JSONParser jp = new JSONParser();
 
     try
     {
-      JSONObject parsed = (JSONObject) jp.parse(br);
-      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
-
-      Iterator rvals = mappings.iterator();
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+      if (rvals == null)
+    	  return null;
       String assembly = null;
       String chromosome = null;
       int fromEnd = 0;
@@ -339,11 +294,11 @@ public class EnsemblMap extends EnsemblRestClient
 
       while (rvals.hasNext())
       {
-        JSONObject val = (JSONObject) rvals.next();
-        JSONObject original = (JSONObject) val.get("original");
+        Map<String, Object> val = (Map<String, Object>) rvals.next();
+        Map<String, Object> original = (Map<String, Object>) val.get("original");
         fromEnd = Integer.parseInt(original.get("end").toString());
 
-        JSONObject mapped = (JSONObject) val.get(MAPPED);
+        Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
         int start = Integer.parseInt(mapped.get("start").toString());
         int end = Integer.parseInt(mapped.get("end").toString());
         String ass = mapped.get("assembly_name").toString();