package org.cipres.kepler.jrun;

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;

import org.cipres.helpers.JRun;

public class JRunTester3 {

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		// TODO Auto-generated method stub
		
		final ArrayList argsFileLines = new ArrayList();

		try {
			final FileReader argsFile = new FileReader("/Users/zhijieguan/work/ClustalW/argum.txt");
			final BufferedReader reader = new BufferedReader(argsFile);
			String line;

			while ((line = reader.readLine()) != null)
				argsFileLines.add(line);
		}
		catch (final IOException ioErr) {
			ioErr.printStackTrace();
		}

		// test3 is to test checkStatus
		JRun test3 = new JRun();
		test3.setExecutable("/Users/zhijieguan/work/ClustalW/clustalw");
		test3.setOutputFilename("/Users/zhijieguan/work/ClustalW/runout");
		test3.setErrorFilename("/Users/zhijieguan/work/ClustalW/error");
		test3.setWorkingDirPath("/Users/zhijieguan/work/ClustalW/");
		test3.setWaitForExecution(false);
		test3.setArguments((String[]) argsFileLines.toArray(new String[argsFileLines.size()]));

		try {
			System.out.println( test3.execute() );
		}
		catch (final InterruptedException interruptedErr) {
			interruptedErr.printStackTrace();
		}
		catch (final IOException ioErr) {
			ioErr.printStackTrace();
		}

		while (test3.checkStatus()!=0) {
			System.out.println("I am waiting!");
		}
		
		System.out.println( test3.checkStatus());
	}

}