76 lines
3.2 KiB
Java
76 lines
3.2 KiB
Java
package org.broadinstitute.sting.utils;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.Test;
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import java.util.Random;
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/**
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* @author Mauricio Carneiro
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* @since 3/5/12
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*/
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public class BitSetUtilsUnitTest {
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private static int RANDOM_NUMBERS_TO_TRY = 87380;
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private static Random random;
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@BeforeClass
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public void init() {
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random = GenomeAnalysisEngine.getRandomGenerator();
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}
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@Test(enabled = true)
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public void testLongBitSet() {
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long[] numbers = {0L, 1L, 428L, 65536L, 239847L, 4611686018427387903L, Long.MAX_VALUE, Long.MIN_VALUE, -1L, -2L, -7L, -128L, -65536L, -100000L};
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for (long n : numbers)
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Assert.assertEquals(BitSetUtils.longFrom(BitSetUtils.bitSetFrom(n)), n);
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for (int i = 0; i < RANDOM_NUMBERS_TO_TRY; i++) {
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long n = random.nextLong();
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Assert.assertEquals(BitSetUtils.longFrom(BitSetUtils.bitSetFrom(n)), n); // Because class Random uses a seed with only 48 bits, this algorithm will not return all possible long values.
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}
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}
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@Test(enabled = true)
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public void testShortBitSet() {
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short[] numbers = {0, 1, 428, 25934, 23847, 16168, Short.MAX_VALUE, Short.MIN_VALUE, -1, -2, -7, -128, -12312, -31432};
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for (long n : numbers)
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Assert.assertEquals(BitSetUtils.shortFrom(BitSetUtils.bitSetFrom(n)), n);
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for (int i = 0; i < RANDOM_NUMBERS_TO_TRY; i++) {
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short n = (short) random.nextInt();
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Assert.assertEquals(BitSetUtils.shortFrom(BitSetUtils.bitSetFrom(n)), n);
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}
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}
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@Test(enabled = true)
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public void testDNAAndBitSetConversion() {
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String[] dna = {"AGGTGTTGT", "CCCCCCCCCCCCCC", "GGGGGGGGGGGGGG", "TTTTTTTTTTTTTT", "GTAGACCGATCTCAGCTAGT", "AACGTCAATGCAGTCAAGTCAGACGTGGGTT", "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"};
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// Test all contexts of size 1-8.
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for (long n = 0; n < RANDOM_NUMBERS_TO_TRY; n++)
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Assert.assertEquals(BitSetUtils.longFrom(BitSetUtils.bitSetFrom(BitSetUtils.dnaFrom(BitSetUtils.bitSetFrom(n)))), n);
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// Test the special cases listed in the dna array
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for (String d : dna)
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Assert.assertEquals(BitSetUtils.dnaFrom(BitSetUtils.bitSetFrom(d)), d);
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}
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@Test(enabled = true)
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public void testNumberOfBitsToRepresent() {
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Assert.assertEquals(BitSetUtils.numberOfBitsToRepresent(0), 0); // Make sure 0 elements need 0 bits to be represented
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Assert.assertEquals(BitSetUtils.numberOfBitsToRepresent(1), 1); // Make sure 1 element needs 1 bit to be represented
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Assert.assertEquals(BitSetUtils.numberOfBitsToRepresent(3), 2); // Make sure 3 elements need 2 bit to be represented
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for (int i = 1; i < 63; i++) { // Can't test i == 63 because n1 is a negative number
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long n1 = 1L << i;
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long n2 = Math.abs(random.nextLong()) % n1;
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long n3 = n1 | n2;
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Assert.assertEquals(BitSetUtils.numberOfBitsToRepresent(n3), (n3 == n1) ? i : i + 1);
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Assert.assertEquals(BitSetUtils.numberOfBitsToRepresent(n1), i);
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}
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}
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}
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