/* Copyright (c) 2011 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library 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 Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */
package compbio.runner._impl;

import java.util.Arrays;
import java.util.List;

import compbio.engine.client.CommandBuilder;
import compbio.engine.client.Executable;
import compbio.engine.client.RunConfiguration;
import compbio.metadata.Limit;
import compbio.metadata.LimitsManager;

/*
 @see http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=netNglyc
 */
public class NetNglyc implements Executable<NetNglyc> {

	private static final String command = "/homes/www-refine/bin/Brunak/NOBACK/netNglyc-1.0a/netNglyc";

	List<String> params;

	public NetNglyc() {
	}

	@Override
	public CommandBuilder<NetNglyc> getParameters(ExecProvider provider) {
		return null; // Arrays.asList(new String[] { "-a", "-f" }); // "-g"
		// potentially
	}

	public static List<String> getTestArgs() {
		return Arrays.asList(new String[] { "-a", "-f" });
	}

	@Override
	public NetNglyc addParameters(List<String> parameters) {
		this.params = parameters;
		return this;
	}

	public static String getTestCommand() {
		return command;
	}

	public String getCommandName() {
		return "netNglyc";
	}

	@Override
	public List<String> getCreatedFiles() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String getInput() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public <V> V getResults(String directory) {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String getOutput() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String getError() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public Limit<NetNglyc> getLimit(String presetName) {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public LimitsManager<NetNglyc> getLimits() {
		// TODO Auto-generated method stub
		return null;
	}
	@Override
	public String getClusterJobSettings() {
		// TODO Auto-generated method stub
		return null; 
	}
}