public class EnsemblLookup extends EnsemblRestClient
{
+ private static final String OBJECT_TYPE_TRANSLATION = "Translation";
+ private static final String PARENT = "Parent";
+ private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+ private static final String ID = "id";
+ private static final String OBJECT_TYPE_GENE = "Gene";
+ private static final String OBJECT_TYPE = "object_type";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
* @param identifier
* @return
*/
- public String getParent(String identifier)
+ public String getGeneId(String identifier)
{
List<String> ids = Arrays.asList(new String[] { identifier });
{
br = getHttpResponse(url, ids);
}
- return (parseResponse(br));
+ return br == null ? null : parseResponse(br);
} catch (IOException e)
{
// ignore
}
/**
- * Parses "Parent" from the JSON response and returns the value, or null if
- * not found
+ * 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 parseResponse(BufferedReader br) throws IOException
{
- String parent = null;
+ String geneId = null;
JSONParser jp = new JSONParser();
try
{
JSONObject val = (JSONObject) jp.parse(br);
- parent = val.get("Parent").toString();
+ String type = val.get(OBJECT_TYPE).toString();
+ if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+ {
+ geneId = val.get(ID).toString();
+ }
+ else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+ {
+ geneId = val.get(PARENT).toString();
+ }
+ else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+ {
+ String transcriptId = val.get(PARENT).toString();
+ try
+ {
+ geneId = getGeneId(transcriptId);
+ } catch (StackOverflowError e)
+ {
+ /*
+ * unlikely data condition error!
+ */
+ System.err
+ .println("** Ensembl lookup "
+ + getUrl(transcriptId).toString()
+ + " looping on Parent!");
+ }
+ }
} catch (ParseException e)
{
// ignore
}
- return parent;
+ return geneId;
}
}