X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=b412849f408a86f65bb639e64778d5f755ed873b;hb=ef3fcd7746645316925b66c36cd56dd68b4a38b7;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..b412849 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -23,6 +23,8 @@ 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;
@@ -117,21 +119,9 @@ 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 +133,7 @@ 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
@@ -165,6 +155,10 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   protected String parseGeneId(JSONObject val)
   {
+    if (val == null)
+    {
+      return null;
+    }
     String geneId = null;
     String type = val.get(OBJECT_TYPE).toString();
     if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
@@ -295,34 +289,10 @@ 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());