/* 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.runner._SkeletalCommandBuilder;

/**
 * TODO this needs fixing! Executable does not work
 * 
 * @author pvtroshin
 * 
 */
public class OB extends _SkeletalCommandBuilder {

	// $obdir/OB.pl -i $fa -p $obdir/databases/GES_hydrophobicity.dat -m
	// $obdir/databases/GES_zmat2.dat -n -o $outdir/OB.dat"
	// where $obdir= /homes/www-refine/SSPF_TO1/TarO_newclus/
	private static final String commandName = "OB";
	private static final String command = "/homes/www-refine/SSPF_TO1/TarO_newclus/OB_runner.sh";

	String workDirectory;

	public OB() {
		// TODO Auto-generated constructor stub
	}

	public OB(String workDirectory) {
		this.workDirectory = workDirectory;
	}

	public static String getTestCommand() {
		return command;
	}

	// input -i $fa
	// output -o
	public List<String> getTestArgs() {
		return Arrays.asList(new String[] { "" });
	}

	public static void main(String[] args) {
		new OB();
	}

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

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