SmithWatermanGotohTester.java

/*
 * $Id: SmithWatermanGotohTester.java,v 1.1 2006/02/03 05:00:22 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.test;

import jaligner.Alignment;
import jaligner.Sequence;
import jaligner.SmithWatermanGotoh;
import jaligner.formats.Format;
import jaligner.formats.Pair;
import jaligner.matrix.Matrix;
import jaligner.matrix.MatrixLoader;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.Random;

/**
 * Testing the scores of the alignments of {@link jaligner.SmithWatermanGotoh}.
 * 
 * @author Bram Minnaert
 */

public class SmithWatermanGotohTester {

    public static void main(String[] args) {

        int numberOfTests = Integer.parseInt(args[0]);
        int sequencesSize = Integer.parseInt(args[1]);
        Random random = new Random();
        Format format = new Pair();

        try {
            ArrayList matrices = new ArrayList();
            for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) {
                matrices.add(i.next());
            }
            int countOfMatrices = matrices.size();

            int i = 1;
            while (i <= numberOfTests) {

                System.gc();

                String s1 = RandomSequenceGenerator.generate(sequencesSize);
                String s2 = RandomSequenceGenerator.generate(sequencesSize);

                int o = random.nextInt(50);
                int e = random.nextInt(10);

                if (s1.length() > 0 && s2.length() > 0 && o >= e) {

                    Matrix matrix = (Matrix) MatrixLoader
                            .load((String) matrices.get(random
                                    .nextInt(countOfMatrices)));
                    Sequence seq1 = new Sequence(s1);
                    Sequence seq2 = new Sequence(s2);

                    Alignment alignment1 = SmithWatermanGotoh.align(seq1, seq2,
                            matrix, o, e);

                    if (!alignment1.checkScore()) {
                        System.err.println("Invalid alignment found:");
                        System.err.println("Sequence 1 = " + s1);
                        System.err.println("Sequence 2 = " + s2);
                        System.err.println(format.format(alignment1));
                        System.err.println(alignment1.getSummary());
                        System.err
                                .println("The score of the alignment above is: "
                                        + alignment1.calculateScore());
                        System.exit(1);
                    }

                    Alignment alignment2 = SmithWatermanGotoh.align(seq2, seq1,
                            matrix, o, e);
                    if (!alignment1.checkScore()) {
                        System.err.println("Invalid alignment found:");
                        System.err.println("Sequence 1 = " + s2);
                        System.err.println("Sequence 2 = " + s1);
                        System.err.println(format.format(alignment2));
                        System.err.println(alignment2.getSummary());
                        System.err
                                .println("The score of the alignment above is: "
                                        + alignment2.calculateScore());
                        System.exit(1);
                    }

                    if (alignment1.getScore() != alignment2.getScore()) {
                        System.err.println("Not symmetric alignment:");

                        System.err.println("Alignment #1: ");
                        System.err.println("Sequence 1 = " + s1);
                        System.err.println("Sequence 2 = " + s2);
                        System.err.println(format.format(alignment1));
                        System.err.println(alignment1.getSummary());

                        System.err.println();

                        System.err.println("Alignment #2: ");
                        System.err.println("Sequence 1 = " + s2);
                        System.err.println("Sequence 2 = " + s1);
                        System.err.println(format.format(alignment2));
                        System.err.println(alignment2.getSummary());

                        System.exit(1);
                    }
                }
                System.out.println("Processed " + i + "/" + numberOfTests);
                i++;
            }
        } catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }
    }
}