+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import java.io.BufferedReader;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+/**
+ * A client for the Ensembl xrefs/symbol REST service;
+ *
+ * @see http://rest.ensembl.org/documentation/info/xref_external
+ * @author gmcarstairs
+ *
+ */
public class EnsemblSymbol extends EnsemblXref
{
/**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param domain
+ * @param dbName
+ * @param dbVersion
+ */
+ public EnsemblSymbol(String domain, String dbName, String dbVersion)
+ {
+ super(domain, dbName, dbVersion);
+ }
+
+ /**
* Returns the first "id" value in gene identifier format from the JSON
* response, or null if none found
*
* @return
* @throws IOException
*/
- protected String parseResponse(BufferedReader br)
+ protected String parseSymbolResponse(BufferedReader br)
throws IOException
{
JSONParser jp = new JSONParser();
protected URL getUrl(String id, Species species)
{
- String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
- + id
- + "?content-type=application/json";
+ String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
+ + id + "?content-type=application/json";
try
{
return new URL(url);
List<String> result = new ArrayList<String>();
List<String> ids = new ArrayList<String>();
ids.add(identifier);
-
+
String[] queries = identifier.split(getAccessionSeparator());
BufferedReader br = null;
try
{
br = getHttpResponse(url, ids);
}
- String geneId = parseResponse(br);
+ String geneId = parseSymbolResponse(br);
if (geneId != null)
{
result.add(geneId);