3253-omnibus save

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

diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index ae36749..e9cc9e1 100644 (file)
--- 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.IOException;
@@ -16,6 +18,18 @@ import java.util.Map;
 
 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";
@@ -340,34 +354,9 @@ GeneLociI parseIdMappingResponse(URL url, String accession,
       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