org.bridgedb.examples.ExHello Maven / Gradle / Ivy
package org.bridgedb.examples;
import java.util.Set;
import org.bridgedb.BridgeDb;
import org.bridgedb.DataSource;
import org.bridgedb.IDMapper;
import org.bridgedb.IDMapperException;
import org.bridgedb.Xref;
import org.bridgedb.bio.DataSourceTxt;
public class ExHello
{
public static void main(String args[]) throws ClassNotFoundException, IDMapperException
{
// This example shows how to map an identifier
// using BridgeWebservice
// first we have to load the driver
// and initialize information about DataSources
Class.forName("org.bridgedb.webservice.bridgerest.BridgeRest");
DataSourceTxt.init();
// now we connect to the driver and create a IDMapper instance.
IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human");
// We create an Xref instance for the identifier that we want to look up.
// In this case we want to look up Entrez gene 3643.
Xref src = new Xref ("3643", DataSource.getExistingBySystemCode("L"));
// let's see if there are cross-references to Ensembl
Set dests = mapper.mapID(src, DataSource.getExistingBySystemCode("En"));
// and print the results.
// with getURN we obtain valid MIRIAM urn's if possible.
System.out.println (src.getMiriamURN() + " maps to:");
for (Xref dest : dests)
System.out.println(" " + dest.getMiriamURN());
}
}