fr.ens.transcriptome.corsen.util.StatTest.java Source code

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Here is the source code for fr.ens.transcriptome.corsen.util.StatTest.java

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/*
 *                  Corsen development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU General Public Licence version 2 or later. This
 * should be distributed with the code. If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/licenses/gpl-2.0.txt
 *
 * Copyright for this code is held jointly by the microarray platform
 * of the cole Normale Suprieure and the individual authors.
 * These should be listed in @author doc comments.
 *
 * For more information on the Corsen project and its aims,
 * or to join the Corsen google group, visit the home page
 * at:
 *
 *      http://transcriptome.ens.fr/corsen
 *
 */

package fr.ens.transcriptome.corsen.util;

import java.util.ArrayList;
import java.util.List;
import java.util.Random;

import junit.framework.TestCase;

import org.apache.commons.math.stat.descriptive.moment.Mean;
import org.apache.commons.math.stat.descriptive.rank.Max;
import org.apache.commons.math.stat.descriptive.rank.Median;
import org.apache.commons.math.stat.descriptive.rank.Min;
import org.apache.commons.math.stat.descriptive.rank.Percentile;

import fr.ens.transcriptome.corsen.util.Stats;
import fr.ens.transcriptome.corsen.util.Stats.DataDouble;

public class StatTest extends TestCase {

    private static final Random random = new Random(System.currentTimeMillis());

    public void testToDoube() {

        List<DataDouble> list = new ArrayList<DataDouble>();
        DataDouble dd1 = new DataDouble(2f, 5);
        DataDouble dd2 = new DataDouble(-3f, 3);
        DataDouble dd3 = new DataDouble(6f, 2);

        list.add(dd1);
        list.add(dd2);
        list.add(dd3);

        double[] result = Stats.toDouble(list);
        double sum = 0;

        for (double d : result)
            sum += d;

        assertEquals((double) (2 * 5 + (-3 * 3) + 6 * 2), sum);
    }

    private static final List<DataDouble> generate() {

        List<DataDouble> list = new ArrayList<DataDouble>();

        for (int i = 0; i < 100; i++) {

            DataDouble dd = new DataDouble(random.nextDouble() * 1000, random.nextInt(20));
            list.add(dd);

        }

        return list;
    }

    public void testPercentile() {

        Percentile percentile = new Percentile();

        for (int j = 0; j < 10; j++) {
            for (int i = 0; i < 98; i++) {

                List<DataDouble> list = generate();
                double p = random.nextInt(99) + 1;

                assertEquals(percentile.evaluate(Stats.toDouble(list), p), Stats.percentile(list, p));

            }
        }

    }

    public void testMin() {

        Min min = new Min();

        for (int i = 0; i < 10000; i++) {

            List<DataDouble> list = generate();
            assertEquals(min.evaluate(Stats.toDouble(list)), Stats.min(list));
        }
    }

    public void testFirstQuartile() {

        Percentile percentile = new Percentile();

        for (int i = 0; i < 1000; i++) {

            List<DataDouble> list = generate();
            assertEquals(percentile.evaluate(Stats.toDouble(list), 25.0), Stats.firstQuartile(list));
        }
    }

    public void testMedian() {

        Median median = new Median();

        for (int i = 0; i < 1000; i++) {

            List<DataDouble> list = generate();
            assertEquals(median.evaluate(Stats.toDouble(list)), Stats.median(list));
        }
    }

    public void testMean() {

        Mean mean = new Mean();

        for (int i = 0; i < 1000; i++) {

            List<DataDouble> list = generate();
            assertEquals(mean.evaluate(Stats.toDouble(list)), Stats.mean(list));
        }
    }

    public void testThirdQuartile() {

        Percentile percentile = new Percentile();

        for (int i = 0; i < 1000; i++) {

            List<DataDouble> list = generate();
            assertEquals(percentile.evaluate(Stats.toDouble(list), 75.0), Stats.thirdQuartile(list));
        }
    }

    public void testMax() {

        Max max = new Max();

        for (int i = 0; i < 1000; i++) {

            List<DataDouble> list = generate();
            assertEquals(max.evaluate(Stats.toDouble(list)), Stats.max(list));
        }
    }

}