/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.ensembl;
import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
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
*
* @param br
* @return
* @throws IOException
*/
protected String parseSymbolResponse(BufferedReader br) throws IOException
{
JSONParser jp = new JSONParser();
String result = null;
try
{
JSONArray responses = (JSONArray) jp.parse(br);
Iterator rvals = responses.iterator();
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
String id = val.get("id").toString();
if (id != null && isGeneIdentifier(id))
{
result = id;
break;
}
}
} catch (ParseException e)
{
// ignore
}
return result;
}
protected URL getUrl(String id, Species species)
{
String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
+ id + "?content-type=application/json";
try
{
return new URL(url);
} catch (MalformedURLException e)
{
return null;
}
}
/**
* Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
* for the given identifier, for any known model organisms
*
* @param identifier
* @return
*/
public List getIds(String identifier)
{
List result = new ArrayList();
List ids = new ArrayList();
ids.add(identifier);
String[] queries = identifier.split(getAccessionSeparator());
BufferedReader br = null;
try
{
for (String query : queries)
{
for (Species taxon : Species.getModelOrganisms())
{
URL url = getUrl(query, taxon);
if (url != null)
{
br = getHttpResponse(url, ids);
if (br != null)
{
String geneId = parseSymbolResponse(br);
if (geneId != null)
{
result.add(geneId);
}
}
}
}
}
} catch (IOException e)
{
// ignore
} finally
{
if (br != null)
{
try
{
br.close();
} catch (IOException e)
{
// ignore
}
}
}
return result;
}
}