package org.cipres.kepler.jrun;

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

import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;

import org.cipres.guigen.*;
import org.cipres.helpers.JRun;
import org.cipres.helpers.RegistryGuigenWrapper;

public class JRunTester {

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		// TODO Auto-generated method stub
		
		// GUIGen part
		String xmlLocation = "/Users/zhijieguan/work/ClustalW/clustalw.xml";
		File guiXmlFile = new File(xmlLocation);
		try {
			UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
		} catch (ClassNotFoundException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} catch (InstantiationException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} catch (IllegalAccessException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} catch (UnsupportedLookAndFeelException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
		try {
			new TestGui(guiXmlFile, null, null, new RegistryGuigenWrapper(), false);
		} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}

		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();
		}

		// test1 is to test the general execution of ClustalW
		// with the command generated by GUIGen
		// wait until the execution finishes
		try {
			JRun test1 = new JRun();
			test1.setExecutable("/Users/zhijieguan/work/ClustalW/clustalw");
			// test1.setArguments("  -infile=/Users/zhijieguan/work/ClustalW/globin.pep  -outfile=/Users/zhijieguan/work/ClustalW/aout.txt -output=NEXUS -quicktree=fast -ktuple=1 -topdiags=5 -window=5 -pairgap=3 -score=percent ");
			test1.setArguments((String[]) argsFileLines.toArray(new String[argsFileLines.size()]));
			test1.setOutputFilename("/Users/zhijieguan/work/ClustalW/runout");
			test1.setErrorFilename("/Users/zhijieguan/work/ClustalW/runerror");
			test1.setWorkingDirPath("/Users/zhijieguan/work/ClustalW/");
			test1.setWaitForExecution(true);
			System.out.println(test1.execute());
			System.out.println(test1.getExitCode());
			System.out.println("Standard Output: \n" + test1.getStandardOutput());
			System.out.println("Standard Error: \n" + test1.getStandardError());
		}
		catch (final InterruptedException interruptedErr) {
			interruptedErr.printStackTrace();
		}
		catch (final IOException ioErr) {
			ioErr.printStackTrace();
		}

	}

}