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 JRunTester4 {
	

	/**
	 * @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();
		}

		// test4 is to test destroying the execution
		JRun test4 = new JRun();
		test4.setExecutable("/Users/zhijieguan/work/ClustalW/clustalw");
		// test4.setOutputFileName("/Users/zhijieguan/work/ClustalW/runout");
		// test4.setErrorFileName("/Users/zhijieguan/work/ClustalW/error");
		test4.setWorkingDirPath("/Users/zhijieguan/work/ClustalW/");
		test4.setWaitForExecution(false);
		test4.setArguments((String[]) argsFileLines.toArray(new String[argsFileLines.size()]));

		try {
			System.out.println( test4.execute() );
		}
		catch (final InterruptedException interruptedErr) {
			interruptedErr.printStackTrace();
		}
		catch (final IOException ioErr) {
			ioErr.printStackTrace();
		}

		if (test4.checkStatus()!=0) {
			test4.stopExecution();
			System.out.println("I tried to stop the execution");
		} else {
			System.out.println("Unfortunately the programs finished!");
		}
		try {
			System.out.println( test4.checkStatus());
		} catch (Exception ex) {
			System.out.println("Seems the execution is killed!");
			ex.printStackTrace();
		}
	}

}