+ * Returns the gene id related to the given identifier (which may be for a
+ * gene, transcript or protein), or null if none is found
+ *
+ * @param identifier
+ * @param objectType
+ * @return
+ */
+ public String getGeneId(String identifier, String objectType)
+ {
+ return parseGeneId(getResult(identifier, objectType));
+ }
+
+ /**
+ * Parses the JSON response and returns the gene identifier, or null if not
+ * found. If the returned object_type is Gene, returns the id, if Transcript
+ * returns the Parent. If it is Translation (peptide identifier), then the
+ * Parent is the transcript identifier, so we redo the search with this value.
+ *
+ * @param br
+ * @return
+ */
+ 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))
+ {
+ // got the gene - just returns its id
+ geneId = val.get(JSON_ID).toString();
+ }
+ else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+ {
+ // got the transcript - return its (Gene) Parent
+ geneId = val.get(PARENT).toString();
+ }
+ else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+ {
+ // got the protein - get its Parent, restricted to type Transcript
+ String transcriptId = val.get(PARENT).toString();
+ geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+ }
+
+ return geneId;
+ }
+
+ /**
+ * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the