JAL-2743 class Javadoc

[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 56657e0..b1c9d86 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -19,6 +19,18 @@ 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 +110,6 @@ 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 +257,10 @@ 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)