List of usage examples for org.apache.commons.math3.random RandomGenerator nextLong
long nextLong();
long value from this random number generator's sequence. From source file:com.analog.lyric.math.DimpleRandom.java
/** * Construct using specified underlying random generator and a randomly generated seed. * <p>/*from w w w . j a va2 s . com*/ * The random value used to seed the generator can be obtained via {@link #getSeed()}. * <p> * @since 0.08 */ public DimpleRandom(RandomGenerator randomGenerator) { this(randomGenerator, randomGenerator.nextLong()); }
From source file:com.github.rinde.rinsim.util.StochasticSuppliersTest.java
/** * Tests whether the rescaling of the mean of a truncated normal distribution * is implemented correctly.//from www. j av a 2s . c om */ @Test public void testNormalScaleMean() { final double[] means = new double[] { 1d, 2d, 3d, 10d, 100d }; final double[] sds = new double[] { 1d, 1d, 3d, 5d, 100d }; for (int i = 0; i < means.length; i++) { final StochasticSupplier<Double> ss = StochasticSuppliers.normal().mean(means[i]).std(sds[i]) .lowerBound(0).scaleMean().redrawWhenOutOfBounds().buildDouble(); final RandomGenerator rng = new MersenneTwister(123); final SummaryStatistics stats = new SummaryStatistics(); for (int j = 0; j < 10000; j++) { stats.addValue(ss.get(rng.nextLong())); } // 1 % deviation from mean is acceptable final double allowedDeviation = 0.01 * means[i]; assertEquals(means[i], stats.getMean(), allowedDeviation); } }
From source file:com.github.rinde.rinsim.scenario.generator.PoissonProcessTest.java
/** * Tests whether the Poisson process has a Poisson distribution. *//*w w w .ja v a 2s .c om*/ @Test public void testPoissonDistribution() { final double length = poisson.getLength(); final Frequency f = new Frequency(); final RandomGenerator rng = new MersenneTwister(0); for (int i = 0; i < 1000; i++) { final List<Double> doubles = poisson.generate(rng.nextLong()); final List<Long> list = newArrayList(); for (final double d : doubles) { list.add(DoubleMath.roundToLong(d, RoundingMode.HALF_UP)); } ascendingOrderTest(list); // add the number of announcements f.addValue(list.size()); } final double averageIntensity; if (poisson instanceof NonHomogenous && ((NonHomogenous) poisson).lambd instanceof SineIntensity) { final SineIntensity si = (SineIntensity) ((NonHomogenous) poisson).lambd; final double period = 1d / si.getFrequency(); final double periods = length / period; final double totalEvents = si.area() * periods; averageIntensity = totalEvents / length; } else { averageIntensity = poisson.intensity; } assertTrue(isPoissonProcess(f, averageIntensity, length, 0.001)); assertFalse(isPoissonProcess(f, 2, length, 0.01)); assertFalse(isPoissonProcess(f, 0.1, length, 0.0001)); assertFalse(isPoissonProcess(f, 15, length, 0.001)); assertFalse(isPoissonProcess(f, 1000, length, 0.0001)); }
From source file:com.github.rinde.rinsim.central.SolverSimTest.java
/** * Tests whether the simulator produces the same objective value as the * solver.//from w ww.jav a 2 s .co m * @throws IOException In case file loading fails. */ @Test public void testOffline() throws IOException { final Gendreau06Scenario scenario = Gendreau06Parser.parser().addFile(ScenarioPaths.GENDREAU).offline() .parse().get(0); final RandomGenerator rng = new MersenneTwister(123); for (int i = 0; i < 5; i++) { final long seed = rng.nextLong(); final DebugSolverCreator dsc = new DebugSolverCreator(seed, SI.MILLI(SI.SECOND)); final Gendreau06ObjectiveFunction obj = Gendreau06ObjectiveFunction.instance(); final ExperimentResults results = Experiment.builder() .addConfiguration(Central.solverConfiguration(dsc)).addScenario(scenario) .usePostProcessor(PostProcessors.statisticsPostProcessor(obj)).perform(); assertEquals(1, results.getResults().size()); assertEquals(1, dsc.arraysSolver.getInputs().size()); assertEquals(1, dsc.arraysSolver.getOutputs().size()); final SolutionObject[] sols = dsc.arraysSolver.getOutputs().get(0); int objVal = 0; for (final SolutionObject sol : sols) { objVal += sol.objectiveValue; } // convert the objective values computed by the solver to the unit of the // gendreau benchmark (minutes). final UnitConverter converter = SI.MILLI(SI.SECOND).getConverterTo(NonSI.MINUTE); final double objValInMinutes = converter.convert(objVal); final GlobalStateObject solverInput = dsc.solver.getInputs().get(0); final ImmutableList<ImmutableList<Parcel>> solverOutput = dsc.solver.getOutputs().get(0); assertEquals(obj.computeCost((StatisticsDTO) results.getResults().asList().get(0).getResultObject()), objValInMinutes, 0.2); final StatisticsDTO stats = Solvers.computeStats(solverInput, solverOutput); assertTrue(stats.toString(), obj.isValidResult(stats)); assertEquals(objValInMinutes, obj.computeCost(stats), 0.1); assertEquals(objValInMinutes, decomposedCost(solverInput, solverOutput, obj), 0.01); } }
From source file:com.milaboratory.core.motif.BitapPatternTest.java
@Test public void testRandomMMIndelLast1() throws Exception { RandomGenerator rg = new Well19937c(); long seed = rg.nextLong(); rg = new Well19937c(seed); int its = TestUtil.its(1000, 100000); out: for (int i = 0; i < its; ++i) { NucleotideSequence seq = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 5, 60); NucleotideSequence seqM = seq;// w w w .ja v a 2 s . co m int muts = 1 + rg.nextInt(Math.min(10, seq.size())); for (int j = 0; j < muts; ++j) seqM = UniformMutationsGenerator.createUniformMutationAsObject(seqM, rg).mutate(seqM); NucleotideSequence seqLeft = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence seqRight = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence fullSeq = SequencesUtils.concatenate(seqLeft, seqM, seqRight); Motif<NucleotideSequence> motif = new Motif<>(seq); BitapPattern bitapPattern = motif.toBitapPattern(); BitapMatcher bitapMatcher = bitapPattern.substitutionAndIndelMatcherLast(muts, fullSeq); boolean found = false; int pos; while ((pos = bitapMatcher.findNext()) >= 0) { if (pos == seqLeft.size() + seqM.size() - 1) found = true; } assertTrue("On iteration = " + i + " with seed " + seed, found); } }
From source file:com.milaboratory.core.motif.BitapPatternTest.java
@Test public void testRandomMMIndelFirst1() throws Exception { RandomGenerator rg = new Well19937c(); long seed = rg.nextLong(); rg = new Well19937c(seed); int its = TestUtil.its(1000, 100000); out: for (int i = 0; i < its; ++i) { NucleotideSequence seq = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 5, 60); NucleotideSequence seqM = seq;// w w w . j a va 2s .com int muts = 1 + rg.nextInt(Math.min(10, seq.size())); for (int j = 0; j < muts; ++j) seqM = UniformMutationsGenerator.createUniformMutationAsObject(seqM, rg).mutate(seqM); NucleotideSequence seqLeft = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence seqRight = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence fullSeq = SequencesUtils.concatenate(seqLeft, seqM, seqRight); Motif<NucleotideSequence> motif = new Motif<>(seq); BitapPattern bitapPattern = motif.toBitapPattern(); BitapMatcher bitapMatcher = bitapPattern.mismatchAndIndelMatcherFirst(muts, fullSeq); boolean found = false; int pos; while ((pos = bitapMatcher.findNext()) >= 0) { if (pos == seqLeft.size()) found = true; } assertTrue("On iteration = " + i + " with seed " + seed, found); } }
From source file:com.milaboratory.core.motif.BitapPatternTest.java
@Test public void testRandomMM1() throws Exception { RandomGenerator rg = new Well19937c(); long seed = rg.nextLong(); rg = new Well19937c(seed); int its = TestUtil.its(1000, 100000); out: for (int i = 0; i < its; ++i) { NucleotideSequence seq = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 5, 60); NucleotideSequence seqM = seq;//w w w .ja v a2 s . co m int mms = 1 + rg.nextInt(Math.min(10, seq.size())); for (int j = 0; j < mms; ++j) seqM = UniformMutationsGenerator.createUniformMutationAsObject(seqM, rg, MutationType.Substitution) .mutate(seqM); int realMMs = SequencesUtils.mismatchCount(seq, 0, seqM, 0, seqM.size()); NucleotideSequence seqLeft = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence seqRight = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence fullSeq = SequencesUtils.concatenate(seqLeft, seqM, seqRight); Motif<NucleotideSequence> motif = new Motif<>(seq); BitapPattern bitapPattern = motif.toBitapPattern(); // Not filtered BitapMatcher bitapMatcher = bitapPattern.substitutionOnlyMatcherFirst(mms, fullSeq); boolean found = false; int pos; while ((pos = bitapMatcher.findNext()) >= 0) { if (pos == seqLeft.size()) { found = true; assertEquals(realMMs, bitapMatcher.getNumberOfErrors()); } assertTrue("On iteration = " + i + " with seed " + seed, SequencesUtils.mismatchCount(fullSeq, pos, seq, 0, seq.size()) <= mms); } assertTrue("On iteration = " + i + " with seed " + seed, found); } }
From source file:com.milaboratory.core.motif.BitapPatternTest.java
@Test public void testRandomMM2() throws Exception { RandomGenerator rg = new Well19937c(); long seed = rg.nextLong(); rg = new Well19937c(seed); int its = TestUtil.its(1000, 100000); int e = 0;//from w w w .j a va 2 s .c o m out: for (int i = 0; i < its; ++i) { NucleotideSequence seq = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 10, 60); NucleotideSequence seqM = seq; int mms = 1 + rg.nextInt(3); for (int j = 0; j < mms; ++j) seqM = UniformMutationsGenerator.createUniformMutationAsObject(seqM, rg, MutationType.Substitution) .mutate(seqM); int realMMs = SequencesUtils.mismatchCount(seq, 0, seqM, 0, seqM.size()); NucleotideSequence seqLeft = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence seqRight = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 0, 40); NucleotideSequence fullSeq = SequencesUtils.concatenate(seqLeft, seqM, seqRight); Motif<NucleotideSequence> motif = new Motif<>(seq); BitapPattern bitapPattern = motif.toBitapPattern(); // Filtered BitapMatcherFilter bitapMatcher = new BitapMatcherFilter( bitapPattern.substitutionOnlyMatcherFirst(mms, fullSeq)); boolean found = false; int pos; while ((pos = bitapMatcher.findNext()) >= 0) { if (pos == seqLeft.size()) { found = true; assertEquals(realMMs, bitapMatcher.getNumberOfErrors()); } assertTrue("On iteration = " + i + " with seed " + seed, SequencesUtils.mismatchCount(fullSeq, pos, seq, 0, seq.size()) <= mms); } if (!found) ++e; } assertTrue(e <= Math.max(5E-5 * its, 1.0)); }
From source file:com.cloudera.oryx.kmeans.computation.cluster.KMeansParallel.java
/** * Main constructor that includes the option to uses a fixed {@code Random} instance * for running the k-means algorithm for testing purposes. */// w w w . j av a 2 s. c o m public KMeansParallel(RandomGenerator random, int projectionBits, int projectionSamples) { this.projectionBits = projectionBits; this.projectionSamples = projectionSamples; if (random == null) { this.seed = System.currentTimeMillis(); } else { this.seed = random.nextLong(); } }
From source file:com.github.rinde.rinsim.scenario.generator.TimeWindowsTest.java
/** * Test whether calling generate with the same seed yields equal results. *//*w w w . jav a2 s . c o m*/ @Test public void determinismTest() { final RandomGenerator rng = new MersenneTwister(123L); for (final TravelTimes tt : DistanceTT.values()) { for (final Parcel.Builder parcelBuilder : parcelBuilders()) { for (int i = 0; i < 10; i++) { final long seed = rng.nextLong(); timeWindowGenerator.generate(seed, parcelBuilder, tt, END_TIME); final TimeWindow p1 = parcelBuilder.getPickupTimeWindow(); final TimeWindow d1 = parcelBuilder.getDeliveryTimeWindow(); timeWindowGenerator.generate(seed, parcelBuilder, tt, END_TIME); final TimeWindow p2 = parcelBuilder.getPickupTimeWindow(); final TimeWindow d2 = parcelBuilder.getDeliveryTimeWindow(); assertNotSame(p1, p2); assertNotSame(d1, d2); assertEquals(p1, p2); assertEquals(d1, d2); } } } }