package org.cipres.kepler.sandbox;

import org.cipres.helpers.GUIRun;

public class TestJar {

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		// TODO Auto-generated method stub
		try {
			GUIRun _grun = new GUIRun("External Program");
	
			_grun.setExecutable("/Users/zhijieguan/C_K_Dist/lib/jar/cipres/bin/mac/clustalw-1.83");
			
			_grun.setUIXMLFile("/Users/zhijieguan/C_K_Dist/configs/ptolemy/configs/kepler/cipres/gui/SequenceAlign_Clustal.xml");
			
			_grun.setOutputFilename("/Users/zhijieguan/.kepler/cipres/tempClustalWOut.log");
			
			_grun.setErrorFilename("/Users/zhijieguan/.kepler/cipres/tempClustalWError.log");
			
			_grun.setWorkingDirPath("/Users/zhijieguan/C_K_Dist/lib/jar/cipres/bin/mac");
			
			// set the input file to the GUIRun object
			_grun.setArgumentValue( "infile", "/Users/zhijieguan/C_K_Dist/sample_data/zfish_nt_12T.fasta" );
			
			// get arguments information with GUIGen interface
			_grun.setArgumentsWithGUIGen();
			
			// Here we assume all the programs executed by GUIRunCIPRes must be finished to get the final results
			// So the GUIRun is set to wait until the execution is finished
			_grun.setWaitForExecution(true);
					
			_grun.execute();    // invoke the external program
		} catch (Exception e) {
			e.printStackTrace();
		}

	}

}