JAL-3567 report mapped location for virtual features in tooltip etc

[jalview.git] / src / jalview / ext / ensembl / EnsemblLookup.java

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 82690a3..b412849 100644 (file)
--- 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;
@@ -117,18 +119,6 @@ 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), or null if none is found
@@ -299,34 +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());