HypergeometricTest.java

/*
 *                       EnrichmentMap Cytoscape Plugin
 *
 * Copyright (c) 2008-2009 Bader Lab, Donnelly Centre for Cellular and Biomolecular 
 * Research, University of Toronto
 *
 * Contact: http://www.baderlab.org
 *
 * Code written by: Ruth Isserlin
 * Authors: Daniele Merico, Ruth Isserlin, Oliver Stueker, Gary D. Bader
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published
 * by the Free Software Foundation; either version 2.1 of the License, or
 * (at your option) any later version.
 *
 * This library 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.  The software and
 * documentation provided hereunder is on an "as is" basis, and
 * University of Toronto
 * has no obligations to provide maintenance, support, updates, 
 * enhancements or modifications.  In no event shall the
 * University of Toronto
 * be liable to any party for direct, indirect, special,
 * incidental or consequential damages, including lost profits, arising
 * out of the use of this software and its documentation, even if
 * University of Toronto
 * has been advised of the possibility of such damage.  
 * See the GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, write to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
 *
 */

// $Id$
// $LastChangedDate$
// $LastChangedRevision$
// $LastChangedBy$
// $HeadURL$

package org.baderlab.csplugins.enrichmentmap;

import static org.junit.Assert.*;

import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.util.Scanner;

import org.baderlab.csplugins.enrichmentmap.task.Hypergeometric;
import org.junit.Test;

/**
 * @author revilo
 * <p>
 * Date   Jul 24, 2009<br>
 * Time   11:50:07 AM<br>
 *
 */
public class HypergeometricTest {
    int N, n, m, k;
    double pValue, expected_pVal;
    Reader testData = null;
 
    private StreamUtil streamUtil = new StreamUtil();
    
    @Test
    public void testHyperGeomPvalueSmall() {
        N = 50;
        n = 10;
        m = 5;
        k = 4;
        
        pValue = Hypergeometric.hyperGeomPvalue(N, n, m, k);
        assertEquals(0.003964583, pValue, 0.0005);

        k = 5;
        pValue = Hypergeometric.hyperGeomPvalue(N, n, m, k);
        assertEquals(0.0001189375, pValue, 0.0005);
        
    }
    
    @Test
    public void testHyperGeomPvalueBig() throws IOException{
        String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/HypergeometricTest_pvalues.csv";
        InputStream reader = streamUtil.getInputStream(testDataFileName);
        
        try(Scanner scanner = new Scanner(reader,"UTF-8")) {
        	String fullText = scanner.useDelimiter("\\A").next();
	        String[] lines = fullText.split("\r\n?|\n");         
	        
	        for (int i=0; i < lines.length ; i++ ) {
	            if (i==0) {
	                // Skip headerline
	            } else {
	                String[] tokens = lines[i].split(",");
	                N = Integer.parseInt(tokens[0]);
	                n = Integer.parseInt(tokens[1]);
	                m = Integer.parseInt(tokens[2]);
	                k = Integer.parseInt(tokens[3]);
	                expected_pVal = Double.parseDouble(tokens[4]);
	                pValue = Hypergeometric.hyperGeomPvalueSum(N, n, m, k, 1);
	                
	                assertEquals(expected_pVal, pValue, 0.00000005);
	            }
	        }
        }
    }
    
    @Test(expected=ArithmeticException.class)
    public void testHyperGeomPvalueBad() {
    	Hypergeometric.hyperGeomPvalueSum(128, 63, 105, 2, 0);
    }
    
}