Java tutorial
/** * Copyright 2015 George Belden * * This file is part of ZodiacGenetics. * * ZodiacGenetics is free software: you can redistribute it and/or modify it * under the terms of the GNU General Public License as published by the Free * Software Foundation, either version 3 of the License, or (at your option) any * later version. * * ZodiacGenetics 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. See the GNU General Public License for more * details. * * You should have received a copy of the GNU General Public License along with * ZodiacGenetics. If not, see <http://www.gnu.org/licenses/>. */ package com.ciphertool.genetics.algorithms.crossover; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertSame; import static org.mockito.Matchers.any; import static org.mockito.Matchers.eq; import static org.mockito.Matchers.same; import static org.mockito.Mockito.mock; import static org.mockito.Mockito.times; import static org.mockito.Mockito.verify; import static org.mockito.Mockito.when; import java.lang.reflect.Field; import java.util.List; import org.junit.Test; import org.springframework.util.ReflectionUtils; import com.ciphertool.genetics.algorithms.mutation.MutationAlgorithm; import com.ciphertool.genetics.entities.Chromosome; import com.ciphertool.genetics.entities.KeylessChromosome; import com.ciphertool.genetics.fitness.FitnessEvaluator; import com.ciphertool.genetics.mocks.MockGene; import com.ciphertool.genetics.mocks.MockKeylessChromosome; import com.ciphertool.genetics.mocks.MockSequence; public class LowestCommonGroupCrossoverAlgorithmTest extends CrossoverAlgorithmTestBase { @Test public void testSetFitnessEvaluator() { FitnessEvaluator fitnessEvaluatorToSet = mock(FitnessEvaluator.class); LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorToSet); Field fitnessEvaluatorField = ReflectionUtils.findField(LowestCommonGroupCrossoverAlgorithm.class, "fitnessEvaluator"); ReflectionUtils.makeAccessible(fitnessEvaluatorField); FitnessEvaluator fitnessEvaluatorFromObject = (FitnessEvaluator) ReflectionUtils .getField(fitnessEvaluatorField, lowestCommonGroupCrossoverAlgorithm); assertSame(fitnessEvaluatorToSet, fitnessEvaluatorFromObject); } @SuppressWarnings({ "rawtypes", "unchecked" }) @Test public void testSetMutationAlgorithm() { MutationAlgorithm mutationAlgorithmToSet = mock(MutationAlgorithm.class); LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(mutationAlgorithmToSet); Field mutationAlgorithmField = ReflectionUtils.findField(LowestCommonGroupCrossoverAlgorithm.class, "mutationAlgorithm"); ReflectionUtils.makeAccessible(mutationAlgorithmField); MutationAlgorithm mutationAlgorithmFromObject = (MutationAlgorithm) ReflectionUtils .getField(mutationAlgorithmField, lowestCommonGroupCrossoverAlgorithm); assertSame(mutationAlgorithmToSet, mutationAlgorithmFromObject); } @Test public void testSetMutateDuringCrossover() { boolean mutateDuringCrossoverToSet = true; LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(mutateDuringCrossoverToSet); Field mutateDuringCrossoverField = ReflectionUtils.findField(LowestCommonGroupCrossoverAlgorithm.class, "mutateDuringCrossover"); ReflectionUtils.makeAccessible(mutateDuringCrossoverField); boolean mutateDuringCrossoverFromObject = (boolean) ReflectionUtils.getField(mutateDuringCrossoverField, lowestCommonGroupCrossoverAlgorithm); assertEquals(mutateDuringCrossoverToSet, mutateDuringCrossoverFromObject); } @Test(expected = IllegalStateException.class) public void testCrossoverWithIllegalState() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(null); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(true); KeylessChromosome mom = getMom(); KeylessChromosome dad = getDad(); lowestCommonGroupCrossoverAlgorithm.crossover(mom, dad); } @Test public void testCrossover() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(999.0).thenReturn(-999.0) .thenReturn(999.0).thenReturn(-999.0); /* * We do not need to stub out the evaluate() method because the fitness * value defaults to zero, and this algorithm allows replacements where * the fitness is equal */ lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(null); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(false); KeylessChromosome mom = getMom(); KeylessChromosome dad = getDad(); KeylessChromosome momClone = (KeylessChromosome) mom.clone(); KeylessChromosome dadClone = (KeylessChromosome) dad.clone(); assertEquals(0, mom.getNumberOfChildren()); assertEquals(0, dad.getNumberOfChildren()); List<KeylessChromosome> children = lowestCommonGroupCrossoverAlgorithm.crossover(mom, dad); assertNotNull(children); assertEquals(1, children.size()); assertFalse(children.get(0).equals(mom)); assertFalse(children.get(0).equals(dad)); assertEquals(1, mom.getNumberOfChildren()); assertEquals(1, dad.getNumberOfChildren()); assertEquals(6, children.get(0).getGenes().size()); assertEquals(dad.getGenes().get(0), children.get(0).getGenes().get(0)); assertEquals(mom.getGenes().get(1), children.get(0).getGenes().get(1)); assertEquals(mom.getGenes().get(2), children.get(0).getGenes().get(2)); assertEquals(dad.getGenes().get(3), children.get(0).getGenes().get(3)); assertEquals(mom.getGenes().get(4), children.get(0).getGenes().get(4)); assertEquals(mom.getGenes().get(5), children.get(0).getGenes().get(5)); // The "mom" Chromosome should remain unmodified assertEquals(momClone.getGenes(), mom.getGenes()); // The "dad" Chromosome should remain unmodified assertEquals(dadClone.getGenes(), dad.getGenes()); verify(fitnessEvaluatorMock, times(5)).evaluate(any(Chromosome.class)); } @Test public void testCrossoverNullChild() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(-999.0); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(null); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(false); MockKeylessChromosome mom = new MockKeylessChromosome(); mom.setTargetSize(1); MockGene momGene = new MockGene(); MockSequence momSequence = new MockSequence("m"); momGene.addSequence(momSequence); mom.addGene(momGene); MockKeylessChromosome dad = new MockKeylessChromosome(); dad.setTargetSize(1); MockGene dadGene = new MockGene(); MockSequence dadSequence = new MockSequence("d"); dadGene.addSequence(dadSequence); dad.addGene(dadGene); KeylessChromosome momClone = mom.clone(); KeylessChromosome dadClone = dad.clone(); assertEquals(0, mom.getNumberOfChildren()); assertEquals(0, dad.getNumberOfChildren()); List<KeylessChromosome> children = lowestCommonGroupCrossoverAlgorithm.crossover(mom, dad); assertNotNull(children); assertEquals(0, children.size()); assertEquals(0, mom.getNumberOfChildren()); assertEquals(0, dad.getNumberOfChildren()); // The "mom" Chromosome should remain unmodified assertEquals(momClone.getGenes(), mom.getGenes()); // The "dad" Chromosome should remain unmodified assertEquals(dadClone.getGenes(), dad.getGenes()); verify(fitnessEvaluatorMock, times(1)).evaluate(any(Chromosome.class)); } @Test public void testPerformCrossover_NoMutation() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(999.0).thenReturn(-999.0) .thenReturn(999.0).thenReturn(-999.0); /* * We do not need to stub out the evaluate() method because the fitness * value defaults to zero, and this algorithm allows replacements where * the fitness is equal */ lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(null); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(false); KeylessChromosome mom = getMom(); KeylessChromosome dad = getDad(); KeylessChromosome child = lowestCommonGroupCrossoverAlgorithm.performCrossover(mom, dad); assertNotNull(child); assertFalse(child.equals(mom)); assertFalse(child.equals(dad)); assertEquals(6, child.getGenes().size()); assertEquals(dad.getGenes().get(0), child.getGenes().get(0)); assertEquals(mom.getGenes().get(1), child.getGenes().get(1)); assertEquals(mom.getGenes().get(2), child.getGenes().get(2)); assertEquals(dad.getGenes().get(3), child.getGenes().get(3)); assertEquals(mom.getGenes().get(4), child.getGenes().get(4)); assertEquals(mom.getGenes().get(5), child.getGenes().get(5)); verify(fitnessEvaluatorMock, times(5)).evaluate(any(Chromosome.class)); } @SuppressWarnings({ "rawtypes", "unchecked" }) @Test public void testPerformCrossover_WithMutation() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(999.0).thenReturn(-999.0) .thenReturn(999.0).thenReturn(-999.0); /* * We do not need to stub out the evaluate() method because the fitness * value defaults to zero, and this algorithm allows replacements where * the fitness is equal */ lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); MutationAlgorithm mockMutationAlgorithm = mock(MutationAlgorithm.class); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(mockMutationAlgorithm); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(true); KeylessChromosome mom = getMom(); KeylessChromosome dad = getDad(); KeylessChromosome child = lowestCommonGroupCrossoverAlgorithm.performCrossover(mom, dad); assertNotNull(child); assertFalse(child.equals(mom)); assertFalse(child.equals(dad)); assertEquals(6, child.getGenes().size()); assertEquals(dad.getGenes().get(0), child.getGenes().get(0)); assertEquals(mom.getGenes().get(1), child.getGenes().get(1)); assertEquals(mom.getGenes().get(2), child.getGenes().get(2)); assertEquals(dad.getGenes().get(3), child.getGenes().get(3)); assertEquals(mom.getGenes().get(4), child.getGenes().get(4)); assertEquals(mom.getGenes().get(5), child.getGenes().get(5)); verify(mockMutationAlgorithm, times(1)).mutateChromosome(eq(child)); verify(fitnessEvaluatorMock, times(5)).evaluate(any(Chromosome.class)); } @Test public void testPerformCrossover_ChildEqualsFirstParent() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(-999.0); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(null); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(false); MockKeylessChromosome mom = new MockKeylessChromosome(); mom.setTargetSize(1); MockGene momGene = new MockGene(); MockSequence momSequence = new MockSequence("m"); momGene.addSequence(momSequence); mom.addGene(momGene); MockKeylessChromosome dad = new MockKeylessChromosome(); dad.setTargetSize(1); MockGene dadGene = new MockGene(); MockSequence dadSequence = new MockSequence("d"); dadGene.addSequence(dadSequence); dad.addGene(dadGene); KeylessChromosome momClone = mom.clone(); KeylessChromosome dadClone = dad.clone(); KeylessChromosome child = lowestCommonGroupCrossoverAlgorithm.performCrossover(mom, dad); assertNull(child); // The "mom" Chromosome should remain unmodified assertEquals(momClone.getGenes(), mom.getGenes()); // The "dad" Chromosome should remain unmodified assertEquals(dadClone.getGenes(), dad.getGenes()); verify(fitnessEvaluatorMock, times(1)).evaluate(any(Chromosome.class)); } @Test public void testPerformCrossover_ChildEqualsSecondParent() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(999.0); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); lowestCommonGroupCrossoverAlgorithm.setMutationAlgorithm(null); lowestCommonGroupCrossoverAlgorithm.setMutateDuringCrossover(false); MockKeylessChromosome mom = new MockKeylessChromosome(); mom.setTargetSize(1); MockGene momGene = new MockGene(); MockSequence momSequence = new MockSequence("m"); momGene.addSequence(momSequence); mom.addGene(momGene); MockKeylessChromosome dad = new MockKeylessChromosome(); dad.setTargetSize(1); MockGene dadGene = new MockGene(); MockSequence dadSequence = new MockSequence("d"); dadGene.addSequence(dadSequence); dad.addGene(dadGene); KeylessChromosome momClone = mom.clone(); KeylessChromosome dadClone = dad.clone(); KeylessChromosome child = lowestCommonGroupCrossoverAlgorithm.performCrossover(mom, dad); assertNull(child); // The "mom" Chromosome should remain unmodified assertEquals(momClone.getGenes(), mom.getGenes()); // The "dad" Chromosome should remain unmodified assertEquals(dadClone.getGenes(), dad.getGenes()); verify(fitnessEvaluatorMock, times(1)).evaluate(any(Chromosome.class)); } @Test public void testAttemptToReplaceGeneGroupInChildEqualFitness() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); /* * We do not need to stub out the evaluate() method because the fitness * value defaults to zero, and this algorithm allows replacements where * the fitness is equal */ lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); LowestCommonGroupCrossoverProgressDto crossoverProgressDto = new LowestCommonGroupCrossoverProgressDto(); KeylessChromosome mom = getMom(); KeylessChromosome momClone = (KeylessChromosome) mom.clone(); KeylessChromosome dad = getDad(); KeylessChromosome dadClone = (KeylessChromosome) dad.clone(); crossoverProgressDto.advanceFirstChromosomeEndGeneIndexBy(2); crossoverProgressDto.advanceSecondChromosomeEndGeneIndexBy(2); crossoverProgressDto.setFirstChromosomeSequencePosition(11); crossoverProgressDto.setSecondChromosomeSequencePosition(11); lowestCommonGroupCrossoverAlgorithm.attemptToReplaceGeneGroupInChild(crossoverProgressDto, mom, dad); // The "mom" Chromosome should have the first three Genes replaced assertEquals(6, mom.getGenes().size()); assertEquals(dad.getGenes().get(0), mom.getGenes().get(0)); assertEquals(dad.getGenes().get(1), mom.getGenes().get(1)); assertEquals(dad.getGenes().get(2), mom.getGenes().get(2)); assertEquals(momClone.getGenes().get(3), mom.getGenes().get(3)); assertEquals(momClone.getGenes().get(4), mom.getGenes().get(4)); assertEquals(momClone.getGenes().get(5), mom.getGenes().get(5)); // The "dad" Chromosome should remain unmodified assertEquals(6, dad.getGenes().size()); assertEquals(dadClone.getGenes().get(0), dad.getGenes().get(0)); assertEquals(dadClone.getGenes().get(1), dad.getGenes().get(1)); assertEquals(dadClone.getGenes().get(2), dad.getGenes().get(2)); assertEquals(dadClone.getGenes().get(3), dad.getGenes().get(3)); assertEquals(dadClone.getGenes().get(4), dad.getGenes().get(4)); assertEquals(dadClone.getGenes().get(5), dad.getGenes().get(5)); verify(fitnessEvaluatorMock, times(1)).evaluate(same(mom)); } @Test public void testAttemptToReplaceGeneGroupInChildHigherFitness() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(999.0); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); LowestCommonGroupCrossoverProgressDto crossoverProgressDto = new LowestCommonGroupCrossoverProgressDto(); KeylessChromosome mom = getMom(); KeylessChromosome momClone = (KeylessChromosome) mom.clone(); KeylessChromosome dad = getDad(); KeylessChromosome dadClone = (KeylessChromosome) dad.clone(); crossoverProgressDto.advanceFirstChromosomeEndGeneIndexBy(2); crossoverProgressDto.advanceSecondChromosomeEndGeneIndexBy(2); crossoverProgressDto.setFirstChromosomeSequencePosition(11); crossoverProgressDto.setSecondChromosomeSequencePosition(11); lowestCommonGroupCrossoverAlgorithm.attemptToReplaceGeneGroupInChild(crossoverProgressDto, mom, dad); // The "mom" Chromosome should have the first three Genes replaced assertEquals(6, mom.getGenes().size()); assertEquals(dad.getGenes().get(0), mom.getGenes().get(0)); assertEquals(dad.getGenes().get(1), mom.getGenes().get(1)); assertEquals(dad.getGenes().get(2), mom.getGenes().get(2)); assertEquals(momClone.getGenes().get(3), mom.getGenes().get(3)); assertEquals(momClone.getGenes().get(4), mom.getGenes().get(4)); assertEquals(momClone.getGenes().get(5), mom.getGenes().get(5)); // The "dad" Chromosome should remain unmodified assertEquals(6, dad.getGenes().size()); assertEquals(dadClone.getGenes().get(0), dad.getGenes().get(0)); assertEquals(dadClone.getGenes().get(1), dad.getGenes().get(1)); assertEquals(dadClone.getGenes().get(2), dad.getGenes().get(2)); assertEquals(dadClone.getGenes().get(3), dad.getGenes().get(3)); assertEquals(dadClone.getGenes().get(4), dad.getGenes().get(4)); assertEquals(dadClone.getGenes().get(5), dad.getGenes().get(5)); verify(fitnessEvaluatorMock, times(1)).evaluate(same(mom)); } @Test public void testAttemptToReplaceGeneGroupInChildLowerFitness() { LowestCommonGroupCrossoverAlgorithm lowestCommonGroupCrossoverAlgorithm = new LowestCommonGroupCrossoverAlgorithm(); FitnessEvaluator fitnessEvaluatorMock = mock(FitnessEvaluator.class); when(fitnessEvaluatorMock.evaluate(any(Chromosome.class))).thenReturn(-999.0); lowestCommonGroupCrossoverAlgorithm.setFitnessEvaluator(fitnessEvaluatorMock); LowestCommonGroupCrossoverProgressDto crossoverProgressDto = new LowestCommonGroupCrossoverProgressDto(); KeylessChromosome mom = getMom(); KeylessChromosome momClone = (KeylessChromosome) mom.clone(); KeylessChromosome dad = getDad(); KeylessChromosome dadClone = (KeylessChromosome) dad.clone(); crossoverProgressDto.advanceFirstChromosomeEndGeneIndexBy(2); crossoverProgressDto.advanceSecondChromosomeEndGeneIndexBy(2); crossoverProgressDto.setFirstChromosomeSequencePosition(11); crossoverProgressDto.setSecondChromosomeSequencePosition(11); lowestCommonGroupCrossoverAlgorithm.attemptToReplaceGeneGroupInChild(crossoverProgressDto, mom, dad); // The "mom" Chromosome should remain unmodified assertEquals(6, mom.getGenes().size()); assertEquals(momClone.getGenes().get(0), mom.getGenes().get(0)); assertEquals(momClone.getGenes().get(1), mom.getGenes().get(1)); assertEquals(momClone.getGenes().get(2), mom.getGenes().get(2)); assertEquals(momClone.getGenes().get(3), mom.getGenes().get(3)); assertEquals(momClone.getGenes().get(4), mom.getGenes().get(4)); assertEquals(momClone.getGenes().get(5), mom.getGenes().get(5)); // The "dad" Chromosome should remain unmodified assertEquals(6, dad.getGenes().size()); assertEquals(dadClone.getGenes().get(0), dad.getGenes().get(0)); assertEquals(dadClone.getGenes().get(1), dad.getGenes().get(1)); assertEquals(dadClone.getGenes().get(2), dad.getGenes().get(2)); assertEquals(dadClone.getGenes().get(3), dad.getGenes().get(3)); assertEquals(dadClone.getGenes().get(4), dad.getGenes().get(4)); assertEquals(dadClone.getGenes().get(5), dad.getGenes().get(5)); verify(fitnessEvaluatorMock, times(1)).evaluate(same(mom)); } }