AbstractEAConfiguration.java

1 
package net.bmahe.genetics4j.core.spec;
2
3 
import java.util.Collection;
4 
import java.util.Collections;
5 
import java.util.Comparator;
6 
import java.util.List;
7 
import java.util.Optional;
8 
import java.util.function.Function;
9 
import java.util.function.Supplier;
10
11 
import org.apache.commons.lang3.Validate;
12 
import org.immutables.value.Value;
13
14 
import net.bmahe.genetics4j.core.Genotype;
15 
import net.bmahe.genetics4j.core.Population;
16 
import net.bmahe.genetics4j.core.combination.AllCasesGenotypeCombinator;
17 
import net.bmahe.genetics4j.core.combination.GenotypeCombinator;
18 
import net.bmahe.genetics4j.core.spec.chromosome.ChromosomeSpec;
19 
import net.bmahe.genetics4j.core.spec.combination.CombinationPolicy;
20 
import net.bmahe.genetics4j.core.spec.mutation.MutationPolicy;
21 
import net.bmahe.genetics4j.core.spec.replacement.Elitism;
22 
import net.bmahe.genetics4j.core.spec.replacement.ReplacementStrategy;
23 
import net.bmahe.genetics4j.core.spec.selection.SelectionPolicy;
24 
import net.bmahe.genetics4j.core.spec.selection.Tournament;
25 
import net.bmahe.genetics4j.core.termination.Termination;
26
27 
/**
28 
 * Evolutionary Algorithm Configuration.
29 
 * <p>
30 
 * This describe the set of strategies to use. They describe the genotype, the
31 
 * different policies for selection, combination as well as mutation, and other
32 
 * relevant parameters
33 
 * <p>
34 
 * Fitness computation is delegated to subclasses to better match the various
35 
 * ways in which they can be computed
36 
 *
37 
 * @param <T> Type of the fitness measurement
38 
 */
39 
public abstract class AbstractEAConfiguration<T extends Comparable<T>> {
40 
	/**
41 
	 * Default offspring ratio
42 
	 */
43 
	public static final double DEFAULT_OFFSPRING_RATIO = 1.0;
44
45 
	/**
46 
	 * Default optimization strategy
47 
	 */
48 
	public static final Optimization DEFAULT_OPTIMIZATION = Optimization.MAXIMIZE;
49
50 
	/**
51 
	 * Genotype of the population
52 
	 *
53 
	 * @return
54 
	 */
55 
	public abstract List<ChromosomeSpec> chromosomeSpecs();
56
57 
	/**
58 
	 * Defines the policy to select the parents. The selected parents will be used
59 
	 * for generating the new offsprings
60 
	 *
61 
	 * @return
62 
	 */
63 
	public abstract SelectionPolicy parentSelectionPolicy();
64
65 
	/**
66 
	 * Defines the policy to generate new offsprings from two parents
67 
	 *
68 
	 * @return
69 
	 */
70 
	public abstract CombinationPolicy combinationPolicy();
71
72 
	/**
73 
	 * Defines what mutations to be performed on the offsprings
74 
	 *
75 
	 * @return
76 
	 */
77 
	public abstract List<MutationPolicy> mutationPolicies();
78
79 
	/**
80 
	 * Defines the replacement strategy
81 
	 * <p>
82 
	 * The replacement strategy is what will determine the next population based on
83 
	 * the generated and mutated offsprings along with the current population
84 
	 * <p>
85 
	 * If not specified, the default replacement strategy will be to use Elitism
86 
	 * with tournament selection of 3 individuals for both offsprings and survivors.
87 
	 * The default offspring ratio is {@link Elitism#DEFAULT_OFFSPRING_RATIO}
88 
	 *
89 
	 * @return
90 
	 */
91 
	@Value.Default
92 
	public ReplacementStrategy replacementStrategy() {
93 1 1. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism::builder → KILLED
 
		final var replacementStrategyBuilder = Elitism.builder();
94
95 4 1. replacementStrategy : replaced call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringRatio with receiver → SURVIVED
2. replacementStrategy : Substituted 3 with 4 → SURVIVED
3. replacementStrategy : Substituted 0.99 with 1.0 → SURVIVED
4. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringRatio → KILLED
 
		replacementStrategyBuilder.offspringRatio(Elitism.DEFAULT_OFFSPRING_RATIO)
96 4 1. replacementStrategy : Substituted 3 with 4 → SURVIVED
2. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/selection/Tournament::of → KILLED
3. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringSelectionPolicy → KILLED
4. replacementStrategy : replaced call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringSelectionPolicy with receiver → KILLED
 
				.offspringSelectionPolicy(Tournament.of(3))
97 3 1. replacementStrategy : replaced call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::survivorSelectionPolicy with receiver → KILLED
2. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/selection/Tournament::of → KILLED
3. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::survivorSelectionPolicy → KILLED
 
				.survivorSelectionPolicy(Tournament.of(3));
98
99 2 1. replacementStrategy : removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::build → KILLED
2. replacementStrategy : replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::replacementStrategy → KILLED
 
		return replacementStrategyBuilder.build();
100 
	}
101
102 
	/**
103 
	 * Post-processing of a population after it got evaluated
104 
	 * <p>
105 
	 * This gives the opportunity to filter out, repair or rescore individuals
106 
	 *
107 
	 * @return Population to be used by the remaining evolution process
108 
	 */
109 
	public abstract Optional<Function<Population<T>, Population<T>>> postEvaluationProcessor();
110
111 
	/**
112 
	 * Defines termination condition
113 
	 *
114 
	 * @return
115 
	 */
116 
	public abstract Termination<T> termination();
117
118 
	/**
119 
	 * Defines how to generate individuals
120 
	 * <p>
121 
	 * If not specified, the system will rely on the chromosome factories
122 
	 *
123 
	 * @return
124 
	 */
125 
	public abstract Optional<Supplier<Genotype>> genotypeGenerator();
126
127 
	/**
128 
	 * Seed the initial population with specific individuals
129 
	 *
130 
	 * @return
131 
	 */
132 
	@Value.Default
133 
	public Collection<Genotype> seedPopulation() {
134 1 1. seedPopulation : removed call to java/util/Collections::emptyList → KILLED
 
		return Collections.emptyList();
135 
	}
136
137 
	/**
138 
	 * Defines how to combine the offspring chromosomes generated
139 
	 * <p>
140 
	 * Combination of individuals is done on a per chromosome basis. This means some
141 
	 * parents may generate a different number of children for each chromosome. This
142 
	 * method will therefore define how to take all these generated chromosomes and
143 
	 * combine them into offspring individuals
144 
	 * <p>
145 
	 * The current default implementation is to generate as many individual as there
146 
	 * are combinations of generated chromosomes
147 
	 *
148 
	 * @return
149 
	 */
150 
	@Value.Default
151 
	public GenotypeCombinator genotypeCombinator() {
152 2 1. genotypeCombinator : removed call to net/bmahe/genetics4j/core/combination/AllCasesGenotypeCombinator::<init> → KILLED
2. genotypeCombinator : replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::genotypeCombinator → KILLED
 
		return new AllCasesGenotypeCombinator();
153 
	}
154
155 
	/**
156 
	 * Defines how many children will be generated at each iteration. Value must be
157 
	 * between 0 and 1 (inclusive) and represents a fraction of the population size
158 
	 *
159 
	 * @return
160 
	 */
161 
	@Value.Default
162 
	public double offspringGeneratedRatio() {
163 2 1. offspringGeneratedRatio : Substituted 1.0 with 2.0 → KILLED
2. offspringGeneratedRatio : replaced double return with 0.0d for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::offspringGeneratedRatio → KILLED
 
		return DEFAULT_OFFSPRING_RATIO;
164 
	}
165
166 
	/**
167 
	 * Defines the optimization goal, whether we want to maximize the fitness or
168 
	 * minimize it
169 
	 *
170 
	 * @return
171 
	 */
172 
	@Value.Default
173 
	public Optimization optimization() {
174 1 1. optimization : replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::optimization → KILLED
 
		return DEFAULT_OPTIMIZATION;
175 
	}
176
177 
	/**
178 
	 * Validates the configuration
179 
	 */
180 
	@Value.Check
181 
	protected void check() {
182 
		Validate.isTrue(chromosomeSpecs().size() > 0, "No chromosomes were specified");
183 
		Validate.inclusiveBetween(0.0d, 1.0d, offspringGeneratedRatio());
184 
	}
185
186 
	/**
187 
	 * Returns a specific chromosome spec from the genotype definition
188 
	 *
189 
	 * @param index
190 
	 * @return
191 
	 */
192 
	public ChromosomeSpec getChromosomeSpec(final int index) {
193 
		Validate.isTrue(index >= 0);
194 
		Validate.isTrue(index < chromosomeSpecs().size());
195
196 3 1. getChromosomeSpec : replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::getChromosomeSpec → KILLED
2. getChromosomeSpec : removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::chromosomeSpecs → KILLED
3. getChromosomeSpec : removed call to java/util/List::get → KILLED
 
		return chromosomeSpecs().get(index);
197 
	}
198
199 
	/**
200 
	 * Returns the currently number of chromosomes defined in the genotype
201 
	 *
202 
	 * @return
203 
	 */
204 
	public int numChromosomes() {
205 3 1. numChromosomes : replaced int return with 0 for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::numChromosomes → KILLED
2. numChromosomes : removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::chromosomeSpecs → KILLED
3. numChromosomes : removed call to java/util/List::size → KILLED
 
		return chromosomeSpecs().size();
206 
	}
207
208 
	/**
209 
	 * Return a comparator based on the optimization method and natural order
210 
	 *
211 
	 * @return
212 
	 */
213 
	public Comparator<T> fitnessComparator() {
214
215 7 1. fitnessComparator : removed call to java/lang/MatchException::<init> → NO_COVERAGE
2. fitnessComparator : replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::fitnessComparator → KILLED
3. fitnessComparator : removed call to net/bmahe/genetics4j/core/spec/Optimization::ordinal → KILLED
4. fitnessComparator : removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::optimization → KILLED
5. fitnessComparator : Changed switch default to be first case → KILLED
6. fitnessComparator : RemoveSwitch 0 (case value 1) → KILLED
7. fitnessComparator : RemoveSwitch 1 (case value 2) → KILLED
 
		return switch (optimization()) {
216 1 1. fitnessComparator : removed call to java/util/Comparator::naturalOrder → KILLED
 
			case MAXIMIZE -> Comparator.naturalOrder();
217 1 1. fitnessComparator : removed call to java/util/Comparator::reverseOrder → KILLED
 
			case MINIMIZE -> Comparator.reverseOrder();
218 
		};
219 
	}
220 
}

Mutations

93

1.1
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism::builder → KILLED

95

1.1
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringRatio → KILLED

2.2
Location : replacementStrategy
Killed by : none replaced call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringRatio with receiver → SURVIVED Covering tests

3.3
Location : replacementStrategy
Killed by : none Substituted 3 with 4 → SURVIVED Covering tests

4.4
Location : replacementStrategy
Killed by : none Substituted 0.99 with 1.0 → SURVIVED Covering tests

96

1.1
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/selection/Tournament::of → KILLED

2.2
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringSelectionPolicy → KILLED

3.3
Location : replacementStrategy
Killed by : none Substituted 3 with 4 → SURVIVED Covering tests

4.4
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] replaced call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::offspringSelectionPolicy with receiver → KILLED

97

1.1
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] replaced call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::survivorSelectionPolicy with receiver → KILLED

2.2
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/selection/Tournament::of → KILLED

3.3
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::survivorSelectionPolicy → KILLED

99

1.1
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/spec/replacement/Elitism$Builder::build → KILLED

2.2
Location : replacementStrategy
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::replacementStrategy → KILLED

134

1.1
Location : seedPopulation
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to java/util/Collections::emptyList → KILLED

152

1.1
Location : genotypeCombinator
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] removed call to net/bmahe/genetics4j/core/combination/AllCasesGenotypeCombinator::<init> → KILLED

2.2
Location : genotypeCombinator
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::genotypeCombinator → KILLED

163

1.1
Location : offspringGeneratedRatio
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] Substituted 1.0 with 2.0 → KILLED

2.2
Location : offspringGeneratedRatio
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testEvolveWithPostEvaluationProcessor()] replaced double return with 0.0d for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::offspringGeneratedRatio → KILLED

174

1.1
Location : optimization
Killed by : net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.selection.TournamentSelectionPolicyHandlerTest]/[method:randomIsRequired()] replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::optimization → KILLED

196

1.1
Location : getChromosomeSpec
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testEvolveWithPostEvaluationProcessor()] replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::getChromosomeSpec → KILLED

2.2
Location : getChromosomeSpec
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testEvolveWithPostEvaluationProcessor()] removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::chromosomeSpecs → KILLED

3.3
Location : getChromosomeSpec
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testEvolveWithPostEvaluationProcessor()] removed call to java/util/List::get → KILLED

205

1.1
Location : numChromosomes
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testGetterMethods()] replaced int return with 0 for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::numChromosomes → KILLED

2.2
Location : numChromosomes
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testGetterMethods()] removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::chromosomeSpecs → KILLED

3.3
Location : numChromosomes
Killed by : net.bmahe.genetics4j.core.EASystemTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.EASystemTest]/[method:testGetterMethods()] removed call to java/util/List::size → KILLED

215

1.1
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] replaced return value with null for net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::fitnessComparator → KILLED

2.2
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessWithImprovement()] removed call to net/bmahe/genetics4j/core/spec/Optimization::ordinal → KILLED

3.3
Location : fitnessComparator
Killed by : none removed call to java/lang/MatchException::<init> → NO_COVERAGE

4.4
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::optimization → KILLED

5.5
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] Changed switch default to be first case → KILLED

6.6
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] RemoveSwitch 0 (case value 1) → KILLED

7.7
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] RemoveSwitch 1 (case value 2) → KILLED

216

1.1
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] removed call to java/util/Comparator::naturalOrder → KILLED

217

1.1
Location : fitnessComparator
Killed by : net.bmahe.genetics4j.core.termination.TerminationsTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.termination.TerminationsTest]/[method:ofStableFitnessNoImprovement()] removed call to java/util/Comparator::reverseOrder → KILLED

Active mutators

Tests examined


Report generated by PIT 1.19.6