/* * Copyright (c) 2010 The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import java.util.*; /** * Basic unit test for MathUtils */ public class MathUtilsUnitTest extends BaseTest { @BeforeClass public void init() { } /** * Tests that we get the right values from the binomial distribution */ @Test public void testBinomialProbability() { logger.warn("Executing testBinomialProbability"); Assert.assertEquals(MathUtils.binomialProbability(3, 2, 0.5), 0.375, 0.0001); Assert.assertEquals(MathUtils.binomialProbability(100, 10, 0.5), 1.365543e-17, 1e-18); Assert.assertEquals(MathUtils.binomialProbability(217, 73, 0.02), 4.521904e-67, 1e-68); Assert.assertEquals(MathUtils.binomialProbability(300, 100, 0.02), 9.27097e-91, 1e-92); Assert.assertEquals(MathUtils.binomialProbability(300, 150, 0.98), 6.462892e-168, 1e-169); Assert.assertEquals(MathUtils.binomialProbability(300, 120, 0.98), 3.090054e-221, 1e-222); Assert.assertEquals(MathUtils.binomialProbability(300, 112, 0.98), 2.34763e-236, 1e-237); } /** * Tests that we get the right values from the multinomial distribution */ @Test public void testMultinomialProbability() { logger.warn("Executing testMultinomialProbability"); int[] counts0 = {2, 0, 1}; double[] probs0 = {0.33, 0.33, 0.34}; Assert.assertEquals(MathUtils.multinomialProbability(counts0, probs0), 0.111078, 1e-6); int[] counts1 = {10, 20, 30}; double[] probs1 = {0.25, 0.25, 0.50}; Assert.assertEquals(MathUtils.multinomialProbability(counts1, probs1), 0.002870301, 1e-9); int[] counts2 = {38, 82, 50, 36}; double[] probs2 = {0.25, 0.25, 0.25, 0.25}; Assert.assertEquals(MathUtils.multinomialProbability(counts2, probs2), 1.88221e-09, 1e-10); int[] counts3 = {1, 600, 1}; double[] probs3 = {0.33, 0.33, 0.34}; Assert.assertEquals(MathUtils.multinomialProbability(counts3, probs3), 5.20988e-285, 1e-286); } /** * Tests that the random index selection is working correctly */ @Test public void testRandomIndicesWithReplacement() { logger.warn("Executing testRandomIndicesWithReplacement"); // Check that the size of the list returned is correct Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 0).size() == 0); Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 1).size() == 1); Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 5).size() == 5); Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 1000).size() == 1000); // Check that the list contains only the k element range that as asked for - no more, no less List Five = new ArrayList(); Collections.addAll(Five, 0, 1, 2, 3, 4); List BigFive = MathUtils.sampleIndicesWithReplacement(5, 10000); Assert.assertTrue(BigFive.containsAll(Five)); Assert.assertTrue(Five.containsAll(BigFive)); } /** * Tests that we get the right values from the multinomial distribution */ @Test public void testSliceListByIndices() { logger.warn("Executing testSliceListByIndices"); // Check that the list contains only the k element range that as asked for - no more, no less but now // use the index list to pull elements from another list using sliceListByIndices List Five = new ArrayList(); Collections.addAll(Five, 0, 1, 2, 3, 4); List FiveAlpha = new ArrayList(); Collections.addAll(FiveAlpha, 'a', 'b', 'c', 'd', 'e'); List BigFive = MathUtils.sampleIndicesWithReplacement(5, 10000); List BigFiveAlpha = MathUtils.sliceListByIndices(BigFive, FiveAlpha); Assert.assertTrue(BigFiveAlpha.containsAll(FiveAlpha)); Assert.assertTrue(FiveAlpha.containsAll(BigFiveAlpha)); } /** * Tests that we correctly compute mean and standard deviation from a stream of numbers */ @Test public void testRunningAverage() { logger.warn("Executing testRunningAverage"); int[] numbers = {1, 2, 4, 5, 3, 128, 25678, -24}; MathUtils.RunningAverage r = new MathUtils.RunningAverage(); for (int i = 0; i < numbers.length; i++) r.add((double) numbers[i]); Assert.assertEquals((long) numbers.length, r.observationCount()); Assert.assertTrue(r.mean() - 3224.625 < 2e-10); Assert.assertTrue(r.stddev() - 9072.6515881128 < 2e-10); } @Test public void testLog10Gamma() { logger.warn("Executing testLog10Gamma"); Assert.assertEquals(MathUtils.log10Gamma(4.0), 0.7781513, 1e-6); Assert.assertEquals(MathUtils.log10Gamma(10), 5.559763, 1e-6); Assert.assertEquals(MathUtils.log10Gamma(10654), 38280.53, 1e-2); } @Test public void testLog10BinomialCoefficient() { logger.warn("Executing testLog10BinomialCoefficient"); Assert.assertEquals(MathUtils.log10BinomialCoefficient(4, 2), 0.7781513, 1e-6); Assert.assertEquals(MathUtils.log10BinomialCoefficient(10, 3), 2.079181, 1e-6); Assert.assertEquals(MathUtils.log10BinomialCoefficient(103928, 119), 400.2156, 1e-4); } @Test public void testFactorial() { logger.warn("Executing testFactorial"); Assert.assertEquals((int) MathUtils.factorial(4), 24); Assert.assertEquals((int) MathUtils.factorial(10), 3628800); Assert.assertEquals((int) MathUtils.factorial(12), 479001600); } @Test public void testLog10Factorial() { logger.warn("Executing testLog10Factorial"); Assert.assertEquals(MathUtils.log10Factorial(4), 1.380211, 1e-6); Assert.assertEquals(MathUtils.log10Factorial(10), 6.559763, 1e-6); Assert.assertEquals(MathUtils.log10Factorial(12), 8.680337, 1e-6); Assert.assertEquals(MathUtils.log10Factorial(200), 374.8969, 1e-3); Assert.assertEquals(MathUtils.log10Factorial(12342), 45138.26, 1e-1); } @Test(enabled = true) public void testRandomSubset() { Integer[] x = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10}; Assert.assertEquals(MathUtils.randomSubset(x, 0).length, 0); Assert.assertEquals(MathUtils.randomSubset(x, 1).length, 1); Assert.assertEquals(MathUtils.randomSubset(x, 2).length, 2); Assert.assertEquals(MathUtils.randomSubset(x, 3).length, 3); Assert.assertEquals(MathUtils.randomSubset(x, 4).length, 4); Assert.assertEquals(MathUtils.randomSubset(x, 5).length, 5); Assert.assertEquals(MathUtils.randomSubset(x, 6).length, 6); Assert.assertEquals(MathUtils.randomSubset(x, 7).length, 7); Assert.assertEquals(MathUtils.randomSubset(x, 8).length, 8); Assert.assertEquals(MathUtils.randomSubset(x, 9).length, 9); Assert.assertEquals(MathUtils.randomSubset(x, 10).length, 10); Assert.assertEquals(MathUtils.randomSubset(x, 11).length, 10); for (int i = 0; i < 25; i++) Assert.assertTrue(hasUniqueElements(MathUtils.randomSubset(x, 5))); } @Test(enabled = true) public void testArrayShuffle() { Integer[] x = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10}; for (int i = 0; i < 25; i++) { Object[] t = MathUtils.arrayShuffle(x); Assert.assertTrue(hasUniqueElements(t)); Assert.assertTrue(hasAllElements(x, t)); } } /** * Private functions used by testArrayShuffle() */ private boolean hasUniqueElements(Object[] x) { for (int i = 0; i < x.length; i++) for (int j = i + 1; j < x.length; j++) if (x[i].equals(x[j]) || x[i] == x[j]) return false; return true; } private boolean hasAllElements(final Object[] expected, final Object[] actual) { HashSet