127 lines
5.6 KiB
Java
Executable File
127 lines
5.6 KiB
Java
Executable File
/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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import org.junit.Assert;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.MathUtils;
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import java.io.File;
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import java.util.List;
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import java.util.ArrayList;
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import java.util.Collections;
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/**
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* Basic unit test for MathUtils
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*/
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public class MathUtilsUnitTest extends BaseTest {
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@BeforeClass
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public static void init() { }
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/**
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* Tests that we get the right values from the binomial distribution
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*/
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@Test
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public void testBinomialProbability() {
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logger.warn("Executing testBinomialProbability");
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(2, 3, 0.5), 0.375, 0.0001) == 0);
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(10, 100, 0.5), 1.365543e-17, 1e-18) == 0);
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(73, 217, 0.02), 4.521904e-67, 1e-68) == 0);
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(100, 300, 0.02), 9.27097e-91, 1e-92) == 0);
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(150, 300, 0.98), 6.462892e-168, 1e-169) == 0);
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(120, 300, 0.98), 3.090054e-221, 1e-222) == 0);
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbability(112, 300, 0.98), 2.34763e-236, 1e-237) == 0);
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}
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/**
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* Tests that we get the right values from the multinomial distribution
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*/
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@Test
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public void testMultinomialProbability() {
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logger.warn("Executing testMultinomialProbability");
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int[] counts0 = { 2, 0, 1 };
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double[] probs0 = { 0.33, 0.33, 0.34 };
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.multinomialProbability(counts0, probs0), 0.111078, 1e-6) == 0);
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int[] counts1 = { 10, 20, 30 };
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double[] probs1 = { 0.25, 0.25, 0.50 };
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.multinomialProbability(counts1, probs1), 0.002870301, 1e-9) == 0);
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int[] counts2 = { 38, 82, 50, 36 };
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double[] probs2 = { 0.25, 0.25, 0.25, 0.25 };
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.multinomialProbability(counts2, probs2), 1.88221e-09, 1e-10) == 0);
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int[] counts3 = { 1, 600, 1 };
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double[] probs3 = { 0.33, 0.33, 0.34 };
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Assert.assertTrue(MathUtils.compareDoubles(MathUtils.multinomialProbability(counts3, probs3), 5.20988e-285, 1e-286) == 0);
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}
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/**
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* Tests that the random index selection is working correctly
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*/
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@Test
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public void testRandomIndicesWithReplacement() {
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logger.warn("Executing testRandomIndicesWithReplacement");
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// Check that the size of the list returned is correct
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Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 0).size() == 0);
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Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 1).size() == 1);
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Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 5).size() == 5);
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Assert.assertTrue(MathUtils.sampleIndicesWithReplacement(5, 1000).size() == 1000);
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// Check that the list contains only the k element range that as asked for - no more, no less
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List<Integer> Five = new ArrayList<Integer>();
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Collections.addAll(Five, 0, 1, 2, 3, 4);
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List<Integer> BigFive = MathUtils.sampleIndicesWithReplacement(5, 10000);
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Assert.assertTrue(BigFive.containsAll(Five));
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Assert.assertTrue(Five.containsAll(BigFive));
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}
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/**
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* Tests that we get the right values from the multinomial distribution
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*/
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@Test
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public void testSliceListByIndices() {
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logger.warn("Executing testSliceListByIndices");
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// Check that the list contains only the k element range that as asked for - no more, no less but now
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// use the index list to pull elements from another list using sliceListByIndices
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List<Integer> Five = new ArrayList<Integer>();
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Collections.addAll(Five, 0, 1, 2, 3, 4);
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List<Character> FiveAlpha = new ArrayList<Character>();
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Collections.addAll(FiveAlpha, 'a', 'b', 'c', 'd', 'e');
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List<Integer> BigFive = MathUtils.sampleIndicesWithReplacement(5, 10000);
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List<Character> BigFiveAlpha = MathUtils.sliceListByIndices(BigFive, FiveAlpha);
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Assert.assertTrue(BigFiveAlpha.containsAll(FiveAlpha));
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Assert.assertTrue(FiveAlpha.containsAll(BigFiveAlpha));
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}
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} |