X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=c688a6f4a486d9b07ee99aa8d782702f28e2a7d2;hb=d37b5f923a24c0708066744ffebeeae4678bf9c8;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..c688a6f 100644
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -3,6 +3,8 @@ package jalview.ext.ensembl;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
 import jalview.util.MapList;
 
 import java.io.BufferedReader;
@@ -19,6 +21,18 @@ import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
+/**
+ * A client for the Ensembl REST service /map endpoint, to convert from
+ * coordinates of one genome assembly to another.
+ * <p>
+ * Note that species and assembly identifiers passed to this class must be valid
+ * in Ensembl. They are not case sensitive.
+ * 
+ * @author gmcarstairs
+ * @see https://rest.ensembl.org/documentation/info/assembly_map
+ * @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
+ * @see https://rest.ensembl.org/info/species?content-type=text/xml
+ */
 public class EnsemblMap extends EnsemblRestClient
 {
   private static final String MAPPED = "mapped";
@@ -98,18 +112,6 @@ 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
@@ -257,7 +259,10 @@ public class EnsemblMap extends EnsemblRestClient
       {
         url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
         br = getHttpResponse(url, null);
-        return (parseIdMappingResponse(br, accession, domain));
+        if (br != null)
+        {
+          return (parseIdMappingResponse(br, accession, domain));
+        }
       }
       return null;
     } catch (Throwable t)
@@ -383,34 +388,9 @@ public class EnsemblMap extends EnsemblRestClient
       final String chr = chromosome;
       List<int[]> fromRange = Collections.singletonList(new int[] { 1,
           fromEnd });
-      final MapList map = new MapList(fromRange, regions, 1, 1);
-      return new GeneLociI()
-      {
-
-        @Override
-        public String getSpeciesId()
-        {
-          return species == null ? "" : species;
-        }
-
-        @Override
-        public String getAssemblyId()
-        {
-          return as;
-        }
-
-        @Override
-        public String getChromosomeId()
-        {
-          return chr;
-        }
-
-        @Override
-        public MapList getMap()
-        {
-          return map;
-        }
-      };
+      Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
+      return new GeneLocus(species == null ? "" : species, as, chr,
+              mapping);
     } catch (IOException | ParseException | NumberFormatException e)
     {
       // ignore