AlignCommandLine.java

/*
 * $Id: AlignCommandLine.java,v 1.2 2009/03/10 15:10:46 ahmed Exp $
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program 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
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */

package jaligner.ui;

import jaligner.Alignment;
import jaligner.Sequence;
import jaligner.SmithWatermanGotoh;
import jaligner.formats.Pair;
import jaligner.matrix.Matrix;
import jaligner.matrix.MatrixLoader;
import jaligner.util.Commons;
import jaligner.util.SequenceParser;

import java.io.File;
import java.util.logging.Level;
import java.util.logging.Logger;

/**
 * Command line interface for JAligner.
 * 
 * @author Ahmed Moustafa (ahmed@users.sf.net)
 */
public class AlignCommandLine {
	
	private static final Logger logger = Logger.getLogger(AlignCommandLine.class.getName());
	
	/**
	 * @param args The command line arguments 
	 */
	public static void main(String[] args) {
	    logger.info( Commons.getJAlignerInfo() ); 
				
        if (args.length == 0) {
        	new AlignWindow().setVisible(true);
        } else {
			if (args.length == 5) {
				try {
					
					String f1 = args[0];					// file name of sequence #1
					String f2 = args[1];					// file name of sequence #2
					String m = args[2];						// scoring matrix id or file name user-defined scoring matrix
					float o = Float.parseFloat(args[3]);	// open gap penalty
					float e = Float.parseFloat(args[4]);	// extend gap penalty
				
					Sequence s1 = SequenceParser.parse(new File(f1));
					Sequence s2 = SequenceParser.parse(new File(f2));
					Matrix matrix = MatrixLoader.load(m);
					Alignment alignment = SmithWatermanGotoh.align (s1, s2, matrix, o, e);
					System.out.println (alignment.getSummary());
					System.out.println (new Pair().format(alignment));
				} catch (Exception e) {
					logger.log(Level.SEVERE, "Failed processing the command line: " + e.getMessage(), e); 
					System.exit(1);
				}
			} else {
				logger.severe( "Invalid number of arguments: " + args.length );
				printUsage();
				System.exit(1);
			}
        }
	
	}
	
	/**
	 * Prints the syntax for using JAligner 
	 */
	private static void printUsage( ) {
		StringBuffer buffer = new StringBuffer();
		buffer.append ( "\n" );
		buffer.append ( "Usage:\n" );
		buffer.append ( "------\n" );
		buffer.append ( "[1] java -jar jaligner.jar <s1> <s2> <matrix> <open> <extend>\n" );
		buffer.append ( "[2] java -jar jaligner.jar\n" );
		buffer.append ( "\n" ) ;
		logger.info(buffer.toString());
	}
}