NeatChromosomeCombinator.java

package net.bmahe.genetics4j.neat.combination;

import java.util.ArrayList;

import java.util.Comparator;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Objects;

import java.util.Set;

import java.util.random.RandomGenerator;

import org.apache.commons.lang3.Validate;

import org.apache.logging.log4j.LogManager;

import org.apache.logging.log4j.Logger;

import net.bmahe.genetics4j.core.chromosomes.Chromosome;

import net.bmahe.genetics4j.core.combination.ChromosomeCombinator;

import net.bmahe.genetics4j.core.spec.AbstractEAConfiguration;

import net.bmahe.genetics4j.neat.Connection;

import net.bmahe.genetics4j.neat.chromosomes.NeatChromosome;

import net.bmahe.genetics4j.neat.combination.parentcompare.ChosenOtherChromosome;

import net.bmahe.genetics4j.neat.combination.parentcompare.ParentComparisonHandler;

import net.bmahe.genetics4j.neat.spec.combination.NeatCombination;

import net.bmahe.genetics4j.neat.spec.combination.parentcompare.ParentComparisonPolicy;

/**

 * Implements genetic crossover for NEAT (NeuroEvolution of Augmenting Topologies) neural network chromosomes.

 * <p>NeatChromosomeCombinator performs innovation-number-based genetic recombination between two neural network

 * chromosomes, creating offspring that inherit network topology and connection weights from both parents while

 * preserving the historical tracking essential to the NEAT algorithm.

 * <p>NEAT crossover algorithm:

 * <ol>

 * <li><strong>Parent comparison</strong>: Determine which parent is "fitter" using comparison policy</li>

 * <li><strong>Gene alignment</strong>: Match connections by innovation number between parents</li>

 * <li><strong>Matching genes</strong>: Randomly inherit from either parent (biased by inheritance threshold)</li>

 * <li><strong>Disjoint genes</strong>: Inherit from fitter parent when innovation ranges overlap</li>

 * <li><strong>Excess genes</strong>: Inherit from fitter parent beyond other parent's range</li>

 * <li><strong>Gene re-enabling</strong>: Potentially re-enable disabled genes based on threshold</li>

 * </ol>

 * <p>Key genetic operations:

 * <ul>

 * <li><strong>Innovation alignment</strong>: Uses innovation numbers to match corresponding genes</li>

 * <li><strong>Fitness-biased inheritance</strong>: Favors genes from fitter parent based on inheritance threshold</li>

 * <li><strong>Gene state management</strong>: Handles enabled/disabled connection states during crossover</li>

 * <li><strong>Topology preservation</strong>: Ensures offspring have valid network topology</li>

 * </ul>

 * <p>Gene classification:

 * <ul>

 * <li><strong>Matching genes</strong>: Same innovation number in both parents, inherit randomly</li>

 * <li><strong>Disjoint genes</strong>: Innovation number exists in one parent within other's range</li>

 * <li><strong>Excess genes</strong>: Innovation number beyond other parent's highest innovation</li>

 * <li><strong>Disabled genes</strong>: May be re-enabled if other parent has enabled version</li>

 * </ul>

 * <p>Common usage patterns:

 * <pre>{@code

 * // Create NEAT chromosome combinator

 * RandomGenerator randomGen = RandomGenerator.getDefault();

 * NeatCombination policy = NeatCombination.builder()

 *     .inheritanceThresold(0.7)  // 70% bias toward fitter parent

 *     .reenableGeneInheritanceThresold(0.25)  // 25% gene re-enabling chance

 *     .parentComparisonPolicy(FitnessComparison.build())

 *     .build();

 * ParentComparisonHandler comparisonHandler = new FitnessComparisonHandler();

 * NeatChromosomeCombinator<Double> combinator = new NeatChromosomeCombinator<>(

 *     randomGen, policy, comparisonHandler

 * );

 * // Perform crossover

 * NeatChromosome parent1 = // ... first parent

 * NeatChromosome parent2 = // ... second parent

 * Double fitness1 = 0.85;

 * Double fitness2 = 0.72;

 * List<Chromosome> offspring = combinator.combine(

 *     eaConfiguration, parent1, fitness1, parent2, fitness2

 * );

 * NeatChromosome child = (NeatChromosome) offspring.get(0);

 * }</pre>

 * <p>Inheritance threshold effects:

 * <ul>

 * <li><strong>0.5</strong>: Unbiased inheritance, equal probability from both parents</li>

 * <li><strong>&gt; 0.5</strong>: Bias toward fitter parent, promotes convergence</li>

 * <li><strong>&lt; 0.5</strong>: Bias toward less fit parent, increases diversity</li>

 * <li><strong>1.0</strong>: Always inherit from fitter parent (when fitness differs)</li>

 * </ul>

 * <p>Gene re-enabling mechanism:

 * <ul>

 * <li><strong>Preservation</strong>: Disabled genes maintain connection topology information</li>

 * <li><strong>Re-activation</strong>: Chance to re-enable genes that are enabled in other parent</li>

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 * <li><strong>Exploration</strong>: Allows rediscovery of previously disabled connection patterns</li>

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 * <li><strong>Genetic diversity</strong>: Prevents permanent loss of structural information</li>

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 * </ul>

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 * <p>Duplicate connection prevention:

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 * <ul>

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 * <li><strong>Links cache</strong>: Tracks already included connections to prevent duplicates</li>

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 * <li><strong>Topology validation</strong>: Ensures each connection appears at most once</li>

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 * <li><strong>Cache efficiency</strong>: O(1) lookup for connection existence checking</li>

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 * <li><strong>Memory management</strong>: Cache cleared after each crossover operation</li>

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 * </ul>

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 * <p>Performance considerations:

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 * <ul>

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 * <li><strong>Linear time complexity</strong>: O(n + m) where n, m are parent connection counts</li>

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 * <li><strong>Innovation sorting</strong>: Leverages pre-sorted connection lists for efficiency</li>

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 * <li><strong>Memory efficiency</strong>: Minimal allocation during crossover</li>

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 * <li><strong>Cache optimization</strong>: Efficient duplicate detection and prevention</li>

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 * </ul>

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 * @param <T> the fitness value type (typically Double)

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 * @see NeatCombination

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 * @see ParentComparisonHandler

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 * @see NeatChromosome

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 * @see ChromosomeCombinator

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*/

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public class NeatChromosomeCombinator<T extends Comparable<T>> implements ChromosomeCombinator<T> {

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	public static final Logger logger = LogManager.getLogger(NeatChromosomeCombinator.class);

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	private final RandomGenerator randomGenerator;

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	private final NeatCombination neatCombination;

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	private final ParentComparisonHandler parentComparisonHandler;

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/**

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	 * Checks whether a connection already exists in the links cache.

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	 * <p>The links cache prevents duplicate connections in the offspring by tracking all connections that have already

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	 * been added. This ensures each connection appears at most once in the resulting chromosome.

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	 * @param linksCache cache mapping from-node indices to sets of to-node indices

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	 * @param connection connection to check for existence

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	 * @return true if connection already exists in cache, false otherwise

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	 * @throws IllegalArgumentException if linksCache or connection is null

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*/

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	private boolean linksCacheContainsConnection(final Map<Integer, Set<Integer>> linksCache,

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			final Connection connection) {

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		Objects.requireNonNull(linksCache);

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		Objects.requireNonNull(connection);

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1 1. linksCacheContainsConnection : removed call to net/bmahe/genetics4j/neat/Connection::fromNodeIndex → SURVIVED

		final int fromNodeIndex = connection.fromNodeIndex();

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1 1. linksCacheContainsConnection : removed call to net/bmahe/genetics4j/neat/Connection::toNodeIndex → SURVIVED

		final int toNodeIndex = connection.toNodeIndex();

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7 1. linksCacheContainsConnection : removed call to java/util/Map::containsKey → SURVIVED
2. linksCacheContainsConnection : removed conditional - replaced equality check with false → SURVIVED
3. linksCacheContainsConnection : removed call to java/lang/Integer::valueOf → SURVIVED
4. linksCacheContainsConnection : removed conditional - replaced equality check with true → KILLED
5. linksCacheContainsConnection : negated conditional → KILLED
6. linksCacheContainsConnection : replaced boolean return with true for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → KILLED
7. linksCacheContainsConnection : Substituted 1 with 0 → KILLED

		return linksCache.containsKey(fromNodeIndex) == true

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11 1. linksCacheContainsConnection : removed call to java/lang/Integer::valueOf → SURVIVED
2. linksCacheContainsConnection : removed conditional - replaced equality check with false → SURVIVED
3. linksCacheContainsConnection : Substituted 1 with 0 → NO_COVERAGE
4. linksCacheContainsConnection : removed call to java/util/Set::contains → SURVIVED
5. linksCacheContainsConnection : negated conditional → KILLED
6. linksCacheContainsConnection : removed call to java/util/Map::get → KILLED
7. linksCacheContainsConnection : Substituted 1 with 0 → KILLED
8. linksCacheContainsConnection : replaced call to java/util/Map::get with argument → KILLED
9. linksCacheContainsConnection : removed call to java/lang/Integer::valueOf → KILLED
10. linksCacheContainsConnection : removed conditional - replaced equality check with true → KILLED
11. linksCacheContainsConnection : Substituted 0 with 1 → KILLED

				&& linksCache.get(fromNodeIndex).contains(toNodeIndex) == true;

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/**

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	 * Adds a connection to the links cache to prevent future duplicates.

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	 * <p>This method records that a connection from the specified source to target node has been added to the offspring,

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	 * preventing the same connection from being added again during the crossover process.

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	 * @param linksCache cache mapping from-node indices to sets of to-node indices

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	 * @param connection connection to add to the cache

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	 * @throws IllegalArgumentException if linksCache or connection is null

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*/

166

	private void insertInlinksCache(final Map<Integer, Set<Integer>> linksCache, final Connection connection) {

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		Objects.requireNonNull(linksCache);

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		Objects.requireNonNull(connection);

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1 1. insertInlinksCache : removed call to net/bmahe/genetics4j/neat/Connection::fromNodeIndex → SURVIVED

		final int fromNodeIndex = connection.fromNodeIndex();

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1 1. insertInlinksCache : removed call to net/bmahe/genetics4j/neat/Connection::toNodeIndex → SURVIVED

		final int toNodeIndex = connection.toNodeIndex();

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7 1. insertInlinksCache : removed call to java/lang/Integer::valueOf → SURVIVED
2. insertInlinksCache : removed call to java/lang/Integer::valueOf → SURVIVED
3. insertInlinksCache : removed call to java/util/Set::add → SURVIVED
4. insertInlinksCache : replaced call to java/util/Map::computeIfAbsent with argument → KILLED
5. insertInlinksCache : removed call to java/util/Map::computeIfAbsent → KILLED
6. lambda$insertInlinksCache$0 : removed call to java/util/HashSet::<init> → KILLED
7. lambda$insertInlinksCache$0 : replaced return value with Collections.emptySet for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::lambda$insertInlinksCache$0 → KILLED

		linksCache.computeIfAbsent(fromNodeIndex, k -> new HashSet<>()).add(toNodeIndex);

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/**

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	 * Determines whether a disabled gene should be re-enabled during crossover.

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	 * <p>If the chosen parent has a disabled connection but the other parent has the same connection enabled, there is a

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	 * configurable chance to re-enable the connection in the offspring. This mechanism prevents permanent loss of

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	 * potentially useful connections.

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	 * @param chosenParent the connection selected for inheritance

184

	 * @param otherParent  the corresponding connection from the other parent

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	 * @return true if the disabled connection should be re-enabled, false otherwise

186

	 * @throws IllegalArgumentException if either connection is null

187

*/

188

	protected boolean shouldReEnable(final Connection chosenParent, final Connection otherParent) {

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		Objects.requireNonNull(chosenParent);

190

		Objects.requireNonNull(otherParent);

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1 1. shouldReEnable : Substituted 0 with 1 → KILLED

		boolean shouldReEnable = false;

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9 1. shouldReEnable : removed conditional - replaced equality check with true → KILLED
2. shouldReEnable : removed call to net/bmahe/genetics4j/neat/Connection::isEnabled → KILLED
3. shouldReEnable : negated conditional → KILLED
4. shouldReEnable : removed call to net/bmahe/genetics4j/neat/Connection::isEnabled → KILLED
5. shouldReEnable : Substituted 1 with 0 → KILLED
6. shouldReEnable : removed conditional - replaced equality check with false → KILLED
7. shouldReEnable : removed conditional - replaced equality check with true → KILLED
8. shouldReEnable : negated conditional → KILLED
9. shouldReEnable : removed conditional - replaced equality check with false → KILLED

		if (chosenParent.isEnabled() == false && otherParent.isEnabled() == true) {

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6 1. shouldReEnable : changed conditional boundary → SURVIVED
2. shouldReEnable : removed call to java/util/random/RandomGenerator::nextDouble → SURVIVED
3. shouldReEnable : removed conditional - replaced comparison check with false → KILLED
4. shouldReEnable : negated conditional → KILLED
5. shouldReEnable : removed conditional - replaced comparison check with true → KILLED
6. shouldReEnable : removed call to net/bmahe/genetics4j/neat/spec/combination/NeatCombination::reenableGeneInheritanceThresold → KILLED

			if (randomGenerator.nextDouble() < neatCombination.reenableGeneInheritanceThresold()) {

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1 1. shouldReEnable : Substituted 1 with 0 → KILLED

				shouldReEnable = true;

2 1. shouldReEnable : replaced boolean return with true for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::shouldReEnable → KILLED
2. shouldReEnable : replaced boolean return with false for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::shouldReEnable → KILLED

		return shouldReEnable;

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/**

203

	 * Constructs a new NEAT chromosome combinator with the specified components.

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	 * <p>The combinator uses the random generator for stochastic decisions during crossover, the combination policy for

206

	 * inheritance parameters, and the comparison handler for determining parent fitness relationships.

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	 * @param _randomGenerator         random number generator for stochastic crossover decisions

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	 * @param _neatCombination         crossover policy defining inheritance parameters

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	 * @param _parentComparisonHandler handler for comparing parent fitness and determining inheritance bias

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	 * @throws IllegalArgumentException if any parameter is null

212

*/

213

	public NeatChromosomeCombinator(final RandomGenerator _randomGenerator,

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			final NeatCombination _neatCombination,

215

			final ParentComparisonHandler _parentComparisonHandler) {

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		Objects.requireNonNull(_randomGenerator);

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		Objects.requireNonNull(_neatCombination);

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		Objects.requireNonNull(_parentComparisonHandler);

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1 1. <init> : Removed assignment to member variable randomGenerator → KILLED

		this.randomGenerator = _randomGenerator;

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1 1. <init> : Removed assignment to member variable neatCombination → KILLED

		this.neatCombination = _neatCombination;

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1 1. <init> : Removed assignment to member variable parentComparisonHandler → KILLED

		this.parentComparisonHandler = _parentComparisonHandler;

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/**

226

	 * Performs genetic crossover between two NEAT chromosomes to produce offspring.

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	 * <p>This method implements the NEAT crossover algorithm, aligning genes by innovation number and applying

229

	 * inheritance rules based on parent fitness and configuration parameters. The result is a single offspring

230

	 * chromosome that inherits network topology and connection weights from both parents.

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	 * <p>Crossover process:

233

	 * <ol>

234

	 * <li>Compare parent fitness to determine inheritance bias</li>

235

	 * <li>Align genes by innovation number between parents</li>

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	 * <li>Process matching genes with random inheritance (biased)</li>

237

	 * <li>Process disjoint genes based on fitness comparison</li>

238

	 * <li>Process excess genes from fitter parent</li>

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	 * <li>Apply gene re-enabling rules for disabled connections</li>

240

	 * </ol>

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	 * @param eaConfiguration     evolutionary algorithm configuration containing fitness comparator

243

	 * @param firstChromosome     first parent chromosome (must be NeatChromosome)

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	 * @param firstParentFitness  fitness value of first parent

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	 * @param secondChromosome    second parent chromosome (must be NeatChromosome)

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	 * @param secondParentFitness fitness value of second parent

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	 * @return list containing single offspring chromosome

248

	 * @throws IllegalArgumentException if chromosomes are not NeatChromosome instances or any parameter is null

249

*/

250

	@Override

251

	public List<Chromosome> combine(final AbstractEAConfiguration<T> eaConfiguration, final Chromosome firstChromosome,

252

			final T firstParentFitness, final Chromosome secondChromosome, final T secondParentFitness) {

253

		Objects.requireNonNull(eaConfiguration);

254

		Objects.requireNonNull(firstChromosome);

255

		Objects.requireNonNull(firstParentFitness);

256

		Validate.isInstanceOf(NeatChromosome.class, firstChromosome);

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		Objects.requireNonNull(secondChromosome);

258

		Objects.requireNonNull(secondParentFitness);

259

		Validate.isInstanceOf(NeatChromosome.class, secondChromosome);

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261

		final NeatChromosome firstNeatChromosome = (NeatChromosome) firstChromosome;

262

		final NeatChromosome secondNeatChromosome = (NeatChromosome) secondChromosome;

263

		Validate.isTrue(

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4 1. combine : Substituted 0 with 1 → SURVIVED
2. combine : removed call to net/bmahe/genetics4j/neat/spec/NeatNodeLayout::isCompatibleWith → KILLED
3. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getNodeLayout → KILLED
4. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getNodeLayout → KILLED

				firstNeatChromosome.getNodeLayout().isCompatibleWith(secondNeatChromosome.getNodeLayout()),

265

					"Cannot combine NEAT chromosomes with incompatible node layouts");

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1 1. combine : removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::fitnessComparator → KILLED

		final Comparator<T> fitnessComparator = eaConfiguration.fitnessComparator();

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1 1. combine : removed call to net/bmahe/genetics4j/neat/spec/combination/NeatCombination::inheritanceThresold → KILLED

		final double inheritanceThresold = neatCombination.inheritanceThresold();

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1 1. combine : removed call to net/bmahe/genetics4j/neat/spec/combination/NeatCombination::parentComparisonPolicy → KILLED

		final ParentComparisonPolicy parentComparisonPolicy = neatCombination.parentComparisonPolicy();

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1 1. combine : removed call to java/util/Comparator::compare → KILLED

		final int fitnessComparison = fitnessComparator.compare(firstParentFitness, secondParentFitness);

271

		final ChosenOtherChromosome comparedChromosomes = parentComparisonHandler

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1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/parentcompare/ParentComparisonHandler::compare → KILLED

				.compare(parentComparisonPolicy, firstNeatChromosome, secondNeatChromosome, fitnessComparison);

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1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/parentcompare/ChosenOtherChromosome::chosen → KILLED

		final NeatChromosome bestChromosome = comparedChromosomes.chosen();

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1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/parentcompare/ChosenOtherChromosome::other → KILLED

		final NeatChromosome worstChromosome = comparedChromosomes.other();

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1 1. combine : removed call to java/util/ArrayList::<init> → KILLED

		final List<Connection> combinedConnections = new ArrayList<>();

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1 1. combine : removed call to java/util/HashMap::<init> → KILLED

		final Map<Integer, Set<Integer>> linksCache = new HashMap<>();

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1 1. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getConnections → KILLED

		final var bestConnections = bestChromosome.getConnections();

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1 1. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getConnections → KILLED

		final var worstConnections = worstChromosome.getConnections();

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1 1. combine : Substituted 0 with 1 → KILLED

		int indexBest = 0;

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1 1. combine : Substituted 0 with 1 → KILLED

		int indexWorst = 0;

284

285

10 1. combine : negated conditional → KILLED
2. combine : changed conditional boundary → KILLED
3. combine : removed conditional - replaced comparison check with false → KILLED
4. combine : changed conditional boundary → KILLED
5. combine : removed conditional - replaced comparison check with false → KILLED
6. combine : removed call to java/util/List::size → KILLED
7. combine : removed conditional - replaced comparison check with true → KILLED
8. combine : removed conditional - replaced comparison check with true → KILLED
9. combine : removed call to java/util/List::size → KILLED
10. combine : negated conditional → KILLED

		while (indexBest < bestConnections.size() && indexWorst < worstConnections.size()) {

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1 1. combine : removed call to java/util/List::get → KILLED

			final var bestConnection = bestConnections.get(indexBest);

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1 1. combine : removed call to java/util/List::get → KILLED

			final var worstConnection = worstConnections.get(indexWorst);

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5 1. combine : removed call to net/bmahe/genetics4j/neat/Connection::innovation → KILLED
2. combine : negated conditional → KILLED
3. combine : removed conditional - replaced equality check with false → KILLED
4. combine : removed call to net/bmahe/genetics4j/neat/Connection::innovation → KILLED
5. combine : removed conditional - replaced equality check with true → KILLED

			if (bestConnection.innovation() == worstConnection.innovation()) {

291

/**

292

				 * If innovation is the same, we pick the connection randomly

293

*/

294

				var original = bestConnection;

295

				var other = worstConnection;

296

7 1. combine : removed call to java/util/random/RandomGenerator::nextDouble → SURVIVED
2. combine : changed conditional boundary → SURVIVED
3. combine : removed conditional - replaced comparison check with true → KILLED
4. combine : removed conditional - replaced comparison check with false → KILLED
5. combine : Replaced double subtraction with addition → KILLED
6. combine : negated conditional → KILLED
7. combine : Substituted 1.0 with 2.0 → KILLED

				if (randomGenerator.nextDouble() < 1 - inheritanceThresold) {

297

					original = worstConnection;

298

					other = bestConnection;

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4 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → SURVIVED
2. combine : removed conditional - replaced equality check with true → SURVIVED
3. combine : negated conditional → KILLED
4. combine : removed conditional - replaced equality check with false → KILLED

				if (linksCacheContainsConnection(linksCache, original) == false) {

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/**

303

					 * If the chosen gene is disabled but the other one is enabled, then there is a chance we will re-enable

304

					 * it

305

*/

306

6 1. combine : removed conditional - replaced equality check with true → KILLED
2. combine : removed conditional - replaced equality check with false → KILLED
3. combine : removed call to net/bmahe/genetics4j/neat/Connection::isEnabled → KILLED
4. combine : Substituted 1 with 0 → KILLED
5. combine : negated conditional → KILLED
6. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::shouldReEnable → KILLED

					final boolean isEnabled = shouldReEnable(original, other) ? true : original.isEnabled();

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6 1. combine : replaced call to net/bmahe/genetics4j/neat/Connection$Builder::from with receiver → KILLED
2. combine : removed call to net/bmahe/genetics4j/neat/Connection::builder → KILLED
3. combine : replaced call to net/bmahe/genetics4j/neat/Connection$Builder::isEnabled with receiver → KILLED
4. combine : removed call to net/bmahe/genetics4j/neat/Connection$Builder::isEnabled → KILLED
5. combine : removed call to net/bmahe/genetics4j/neat/Connection$Builder::build → KILLED
6. combine : removed call to net/bmahe/genetics4j/neat/Connection$Builder::from → KILLED

					final var childConnection = Connection.builder().from(original).isEnabled(isEnabled).build();

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1 1. combine : removed call to java/util/List::add → KILLED

					combinedConnections.add(childConnection);

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1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → SURVIVED

					insertInlinksCache(linksCache, original);

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2 1. combine : Removed increment 1 → KILLED
2. combine : Changed increment from 1 to -1 → KILLED

				indexBest++;

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2 1. combine : Removed increment 1 → SURVIVED
2. combine : Changed increment from 1 to -1 → KILLED

				indexWorst++;

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6 1. combine : removed call to net/bmahe/genetics4j/neat/Connection::innovation → SURVIVED
2. combine : changed conditional boundary → SURVIVED
3. combine : removed call to net/bmahe/genetics4j/neat/Connection::innovation → KILLED
4. combine : negated conditional → KILLED
5. combine : removed conditional - replaced comparison check with true → KILLED
6. combine : removed conditional - replaced comparison check with false → KILLED

			} else if (bestConnection.innovation() > worstConnection.innovation()) {

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/**

317

				 * If the fitnesses are equal, then we randomly inherit from the parent Otherwise, we do not inherit from

318

				 * the lesser gene

319

*/

320

10 1. combine : removed conditional - replaced equality check with false → SURVIVED
2. combine : removed conditional - replaced comparison check with false → NO_COVERAGE
3. combine : Replaced double subtraction with addition → NO_COVERAGE
4. combine : removed conditional - replaced comparison check with true → NO_COVERAGE
5. combine : Substituted 1.0 with 2.0 → NO_COVERAGE
6. combine : negated conditional → NO_COVERAGE
7. combine : removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE
8. combine : changed conditional boundary → NO_COVERAGE
9. combine : negated conditional → KILLED
10. combine : removed conditional - replaced equality check with true → KILLED

				if (fitnessComparison == 0 && randomGenerator.nextDouble() < 1.0 - inheritanceThresold) {

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					final var original = worstConnection;

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4 1. combine : negated conditional → NO_COVERAGE
2. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → NO_COVERAGE
3. combine : removed conditional - replaced equality check with true → NO_COVERAGE
4. combine : removed conditional - replaced equality check with false → NO_COVERAGE

					if (linksCacheContainsConnection(linksCache, original) == false) {

323

3 1. combine : replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → NO_COVERAGE
2. combine : removed call to java/util/List::add → NO_COVERAGE
3. combine : removed call to net/bmahe/genetics4j/neat/Connection::copyOf → NO_COVERAGE

						combinedConnections.add(Connection.copyOf(original));

324

1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → NO_COVERAGE

						insertInlinksCache(linksCache, original);

2 1. combine : Removed increment 1 → TIMED_OUT
2. combine : Changed increment from 1 to -1 → KILLED

				indexWorst++;

329

			} else {

330

331

/**

332

				 * If the fitnesses are equal, then we randomly inherit from the parent Otherwise, we always inherit from

333

				 * the better gene

334

*/

335

336

8 1. combine : removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE
2. combine : changed conditional boundary → NO_COVERAGE
3. combine : removed conditional - replaced comparison check with false → NO_COVERAGE
4. combine : removed conditional - replaced equality check with false → SURVIVED
5. combine : removed conditional - replaced comparison check with true → NO_COVERAGE
6. combine : negated conditional → NO_COVERAGE
7. combine : negated conditional → KILLED
8. combine : removed conditional - replaced equality check with true → KILLED

				if (fitnessComparison != 0 || randomGenerator.nextDouble() < inheritanceThresold) {

337

					if (linksCacheContainsConnection(linksCache, bestConnection) == false) {

338

3 1. combine : replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → SURVIVED
2. combine : removed call to net/bmahe/genetics4j/neat/Connection::copyOf → KILLED
3. combine : removed call to java/util/List::add → KILLED

						combinedConnections.add(Connection.copyOf(bestConnection));

339

1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → SURVIVED

						insertInlinksCache(linksCache, bestConnection);

340

341

342

2 1. combine : Removed increment 1 → TIMED_OUT
2. combine : Changed increment from 1 to -1 → KILLED

				indexBest++;

/*

347

		 * Case where the best connection has more genes. It's called excess genes

348

*/

349

5 1. combine : negated conditional → KILLED
2. combine : removed conditional - replaced comparison check with false → KILLED
3. combine : changed conditional boundary → KILLED
4. combine : removed conditional - replaced comparison check with true → KILLED
5. combine : removed call to java/util/List::size → KILLED

		while (indexBest < bestConnections.size()) {

350

/**

351

			 * If the fitnesses are equal, then we randomly inherit from the parent Otherwise, we always inherit from the

352

			 * better gene

353

*/

354

8 1. combine : removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE
2. combine : removed conditional - replaced comparison check with true → NO_COVERAGE
3. combine : changed conditional boundary → NO_COVERAGE
4. combine : negated conditional → NO_COVERAGE
5. combine : removed conditional - replaced comparison check with false → NO_COVERAGE
6. combine : removed conditional - replaced equality check with false → SURVIVED
7. combine : negated conditional → KILLED
8. combine : removed conditional - replaced equality check with true → KILLED

			if (fitnessComparison != 0 || randomGenerator.nextDouble() < inheritanceThresold) {

355

1 1. combine : removed call to java/util/List::get → KILLED

				final var bestConnection = bestConnections.get(indexBest);

356

				if (linksCacheContainsConnection(linksCache, bestConnection) == false) {

357

3 1. combine : replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → SURVIVED
2. combine : removed call to java/util/List::add → KILLED
3. combine : removed call to net/bmahe/genetics4j/neat/Connection::copyOf → KILLED

					combinedConnections.add(Connection.copyOf(bestConnection));

358

1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → SURVIVED

					insertInlinksCache(linksCache, bestConnection);

			indexBest++;

363

364

365

/*

366

		 * Case where the worst connection has more genes. It's called excess genes. Since we don't inherit when their

367

		 * fitness aren't equal, it means we can skip the excess genes from the weaker connections. However we will

368

		 * randomly inherit if their fitnesses are equal

369

*/

370

8 1. combine : removed conditional - replaced equality check with false → SURVIVED
2. combine : changed conditional boundary → NO_COVERAGE
3. combine : negated conditional → NO_COVERAGE
4. combine : removed conditional - replaced comparison check with false → NO_COVERAGE
5. combine : removed call to java/util/List::size → NO_COVERAGE
6. combine : removed conditional - replaced comparison check with true → NO_COVERAGE
7. combine : negated conditional → KILLED
8. combine : removed conditional - replaced equality check with true → KILLED

		while (fitnessComparison == 0 && indexWorst < worstConnections.size()) {

371

7 1. combine : removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE
2. combine : Substituted 1.0 with 2.0 → NO_COVERAGE
3. combine : removed conditional - replaced comparison check with false → NO_COVERAGE
4. combine : changed conditional boundary → NO_COVERAGE
5. combine : Replaced double subtraction with addition → NO_COVERAGE
6. combine : removed conditional - replaced comparison check with true → NO_COVERAGE
7. combine : negated conditional → NO_COVERAGE

			if (randomGenerator.nextDouble() < 1.0 - inheritanceThresold) {

372

1 1. combine : removed call to java/util/List::get → NO_COVERAGE

				final var worstConnection = worstConnections.get(indexWorst);

373

4 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → NO_COVERAGE
2. combine : removed conditional - replaced equality check with false → NO_COVERAGE
3. combine : removed conditional - replaced equality check with true → NO_COVERAGE
4. combine : negated conditional → NO_COVERAGE

				if (linksCacheContainsConnection(linksCache, worstConnection) == false) {

374

					combinedConnections.add(Connection.copyOf(worstConnection));

375

1 1. combine : removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → NO_COVERAGE

					insertInlinksCache(linksCache, worstConnection);

2 1. combine : Changed increment from 1 to -1 → NO_COVERAGE
2. combine : Removed increment 1 → NO_COVERAGE

			indexWorst++;

380

381

382

2 1. combine : replaced return value with Collections.emptyList for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::combine → KILLED
2. combine : removed call to java/util/List::of → KILLED

		return List.of(

383

1 1. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getNodeLayout → KILLED

				new NeatChromosome(bestChromosome.getNodeLayout(),

384

1 1. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getMinWeightValue → SURVIVED

						bestChromosome.getMinWeightValue(),

385

2 1. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getMaxWeightValue → SURVIVED
2. combine : removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::<init> → KILLED

						bestChromosome.getMaxWeightValue(),

386

						combinedConnections));

387

388

Mutations

149

1.1
Location : linksCacheContainsConnection
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::fromNodeIndex → SURVIVED Covering tests

150

1.1
Location : linksCacheContainsConnection
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::toNodeIndex → SURVIVED Covering tests

152

1.1
Location : linksCacheContainsConnection
Killed by : none removed call to java/util/Map::containsKey → SURVIVED Covering tests

2.2
Location : linksCacheContainsConnection
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

3.3
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced equality check with true → KILLED

4.4
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] negated conditional → KILLED

5.5
Location : linksCacheContainsConnection
Killed by : none removed call to java/lang/Integer::valueOf → SURVIVED Covering tests

6.6
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced boolean return with true for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → KILLED

7.7
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] Substituted 1 with 0 → KILLED

153

1.1
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] negated conditional → KILLED

2.2
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to java/util/Map::get → KILLED

3.3
Location : linksCacheContainsConnection
Killed by : none removed call to java/lang/Integer::valueOf → SURVIVED Covering tests

5.5
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced call to java/util/Map::get with argument → KILLED

6.6
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to java/lang/Integer::valueOf → KILLED

8.8
Location : linksCacheContainsConnection
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

9.9
Location : linksCacheContainsConnection
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] Substituted 0 with 1 → KILLED

10.10
Location : linksCacheContainsConnection
Killed by : none Substituted 1 with 0 → NO_COVERAGE

11.11
Location : linksCacheContainsConnection
Killed by : none removed call to java/util/Set::contains → SURVIVED Covering tests

170

1.1
Location : insertInlinksCache
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::fromNodeIndex → SURVIVED Covering tests

171

1.1
Location : insertInlinksCache
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::toNodeIndex → SURVIVED Covering tests

173

1.1
Location : insertInlinksCache
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced call to java/util/Map::computeIfAbsent with argument → KILLED

2.2
Location : insertInlinksCache
Killed by : none removed call to java/lang/Integer::valueOf → SURVIVED Covering tests

3.3
Location : insertInlinksCache
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to java/util/Map::computeIfAbsent → KILLED

4.4
Location : insertInlinksCache
Killed by : none removed call to java/lang/Integer::valueOf → SURVIVED Covering tests

5.5
Location : lambda$insertInlinksCache$0
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to java/util/HashSet::<init> → KILLED

6.6
Location : insertInlinksCache
Killed by : none removed call to java/util/Set::add → SURVIVED Covering tests

7.7
Location : lambda$insertInlinksCache$0
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced return value with Collections.emptySet for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::lambda$insertInlinksCache$0 → KILLED

192

1.1
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldNeverReEnable()] Substituted 0 with 1 → KILLED

193

2.2
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] removed call to net/bmahe/genetics4j/neat/Connection::isEnabled → KILLED

3.3
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] negated conditional → KILLED

4.4
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] removed call to net/bmahe/genetics4j/neat/Connection::isEnabled → KILLED

5.5
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] Substituted 1 with 0 → KILLED

6.6
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] removed conditional - replaced equality check with false → KILLED

7.7
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] removed conditional - replaced equality check with true → KILLED

8.8
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] negated conditional → KILLED

9.9
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] removed conditional - replaced equality check with false → KILLED

194

2.2
Location : shouldReEnable
Killed by : none changed conditional boundary → SURVIVED Covering tests

4.4
Location : shouldReEnable
Killed by : none removed call to java/util/random/RandomGenerator::nextDouble → SURVIVED Covering tests

6.6
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] removed call to net/bmahe/genetics4j/neat/spec/combination/NeatCombination::reenableGeneInheritanceThresold → KILLED

195

199

2.2
Location : shouldReEnable
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldAlwaysReEnable()] replaced boolean return with false for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::shouldReEnable → KILLED

220

1.1
Location : <init>
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:shouldNeverReEnable()] Removed assignment to member variable randomGenerator → KILLED

221

222

1.1
Location : <init>
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] Removed assignment to member variable parentComparisonHandler → KILLED

264

1.1
Location : combine
Killed by : none Substituted 0 with 1 → SURVIVED Covering tests

2.2
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/spec/NeatNodeLayout::isCompatibleWith → KILLED

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getNodeLayout → KILLED

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:rejectsIncompatibleNodeLayouts()] removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getNodeLayout → KILLED

266

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/core/spec/AbstractEAConfiguration::fitnessComparator → KILLED

267

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/spec/combination/NeatCombination::inheritanceThresold → KILLED

268

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/spec/combination/NeatCombination::parentComparisonPolicy → KILLED

270

272

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/combination/parentcompare/ParentComparisonHandler::compare → KILLED

273

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/combination/parentcompare/ChosenOtherChromosome::chosen → KILLED

274

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/combination/parentcompare/ChosenOtherChromosome::other → KILLED

276

277

279

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getConnections → KILLED

280

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getConnections → KILLED

282

283

285

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with false → KILLED

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] changed conditional boundary → KILLED

5.5
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with false → KILLED

6.6
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to java/util/List::size → KILLED

7.7
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with true → KILLED

8.8
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with true → KILLED

9.9
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to java/util/List::size → KILLED

10.10
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] negated conditional → KILLED

287

288

290

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced equality check with false → KILLED

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/Connection::innovation → KILLED

296

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with true → KILLED

2.2
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced comparison check with false → KILLED

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] Replaced double subtraction with addition → KILLED

4.4
Location : combine
Killed by : none removed call to java/util/random/RandomGenerator::nextDouble → SURVIVED Covering tests

7.7
Location : combine
Killed by : none changed conditional boundary → SURVIVED Covering tests

300

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → SURVIVED Covering tests

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced equality check with false → KILLED

4.4
Location : combine
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

306

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced equality check with true → KILLED

2.2
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced equality check with false → KILLED

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] Substituted 1 with 0 → KILLED

308

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced call to net/bmahe/genetics4j/neat/Connection$Builder::from with receiver → KILLED

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced call to net/bmahe/genetics4j/neat/Connection$Builder::isEnabled with receiver → KILLED

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/Connection$Builder::isEnabled → KILLED

5.5
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/Connection$Builder::build → KILLED

309

310

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → SURVIVED Covering tests

312

313

1.1
Location : combine
Killed by : none Removed increment 1 → SURVIVED Covering tests

314

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::innovation → SURVIVED Covering tests

2.2
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed call to net/bmahe/genetics4j/neat/Connection::innovation → KILLED

3.3
Location : combine
Killed by : none changed conditional boundary → SURVIVED Covering tests

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] negated conditional → KILLED

6.6
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced comparison check with false → KILLED

320

2.2
Location : combine
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

3.3
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced equality check with true → KILLED

4.4
Location : combine
Killed by : none removed conditional - replaced comparison check with false → NO_COVERAGE

5.5
Location : combine
Killed by : none Replaced double subtraction with addition → NO_COVERAGE

6.6
Location : combine
Killed by : none removed conditional - replaced comparison check with true → NO_COVERAGE

7.7
Location : combine
Killed by : none Substituted 1.0 with 2.0 → NO_COVERAGE

8.8
Location : combine
Killed by : none negated conditional → NO_COVERAGE

9.9
Location : combine
Killed by : none removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE

10.10
Location : combine
Killed by : none changed conditional boundary → NO_COVERAGE

322

1.1
Location : combine
Killed by : none negated conditional → NO_COVERAGE

2.2
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → NO_COVERAGE

3.3
Location : combine
Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE

4.4
Location : combine
Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE

323

1.1
Location : combine
Killed by : none replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → NO_COVERAGE

2.2
Location : combine
Killed by : none removed call to java/util/List::add → NO_COVERAGE

3.3
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::copyOf → NO_COVERAGE

324

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → NO_COVERAGE

328

1.1
Location : combine
Killed by : none Removed increment 1 → TIMED_OUT

336

1.1
Location : combine
Killed by : none removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE

2.2
Location : combine
Killed by : none changed conditional boundary → NO_COVERAGE

3.3
Location : combine
Killed by : none removed conditional - replaced comparison check with false → NO_COVERAGE

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] negated conditional → KILLED

5.5
Location : combine
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

6.6
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced equality check with true → KILLED

7.7
Location : combine
Killed by : none removed conditional - replaced comparison check with true → NO_COVERAGE

8.8
Location : combine
Killed by : none negated conditional → NO_COVERAGE

337

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → SURVIVED Covering tests

3.3
Location : combine
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced equality check with false → KILLED

338

3.3
Location : combine
Killed by : none replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → SURVIVED Covering tests

339

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → SURVIVED Covering tests

342

2.2
Location : combine
Killed by : none Removed increment 1 → TIMED_OUT

349

2.2
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with false → KILLED

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced comparison check with true → KILLED

354

1.1
Location : combine
Killed by : none removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE

2.2
Location : combine
Killed by : none removed conditional - replaced comparison check with true → NO_COVERAGE

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced equality check with true → KILLED

5.5
Location : combine
Killed by : none changed conditional boundary → NO_COVERAGE

6.6
Location : combine
Killed by : none negated conditional → NO_COVERAGE

7.7
Location : combine
Killed by : none removed conditional - replaced comparison check with false → NO_COVERAGE

8.8
Location : combine
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

355

356

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → SURVIVED Covering tests

2.2
Location : combine
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed conditional - replaced equality check with false → KILLED

357

1.1
Location : combine
Killed by : none replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → SURVIVED Covering tests

358

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → SURVIVED Covering tests

370

2.2
Location : combine
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

3.3
Location : combine
Killed by : none changed conditional boundary → NO_COVERAGE

4.4
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickWorstNoReEnable()] removed conditional - replaced equality check with true → KILLED

5.5
Location : combine
Killed by : none negated conditional → NO_COVERAGE

6.6
Location : combine
Killed by : none removed conditional - replaced comparison check with false → NO_COVERAGE

7.7
Location : combine
Killed by : none removed call to java/util/List::size → NO_COVERAGE

8.8
Location : combine
Killed by : none removed conditional - replaced comparison check with true → NO_COVERAGE

371

1.1
Location : combine
Killed by : none removed call to java/util/random/RandomGenerator::nextDouble → NO_COVERAGE

2.2
Location : combine
Killed by : none Substituted 1.0 with 2.0 → NO_COVERAGE

3.3
Location : combine
Killed by : none removed conditional - replaced comparison check with false → NO_COVERAGE

4.4
Location : combine
Killed by : none changed conditional boundary → NO_COVERAGE

5.5
Location : combine
Killed by : none Replaced double subtraction with addition → NO_COVERAGE

6.6
Location : combine
Killed by : none removed conditional - replaced comparison check with true → NO_COVERAGE

7.7
Location : combine
Killed by : none negated conditional → NO_COVERAGE

372

1.1
Location : combine
Killed by : none removed call to java/util/List::get → NO_COVERAGE

373

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::linksCacheContainsConnection → NO_COVERAGE

2.2
Location : combine
Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE

3.3
Location : combine
Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE

4.4
Location : combine
Killed by : none negated conditional → NO_COVERAGE

374

1.1
Location : combine
Killed by : none replaced call to net/bmahe/genetics4j/neat/Connection::copyOf with argument → NO_COVERAGE

2.2
Location : combine
Killed by : none removed call to java/util/List::add → NO_COVERAGE

3.3
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/Connection::copyOf → NO_COVERAGE

375

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::insertInlinksCache → NO_COVERAGE

379

1.1
Location : combine
Killed by : none Changed increment from 1 to -1 → NO_COVERAGE

2.2
Location : combine
Killed by : none Removed increment 1 → NO_COVERAGE

382

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] replaced return value with Collections.emptyList for net/bmahe/genetics4j/neat/combination/NeatChromosomeCombinator::combine → KILLED

383

1.1
Location : combine
Killed by : net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getNodeLayout → KILLED

384

1.1
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getMinWeightValue → SURVIVED Covering tests

385

2.2
Location : combine
Killed by : none removed call to net/bmahe/genetics4j/neat/chromosomes/NeatChromosome::getMaxWeightValue → SURVIVED Covering tests

Active mutators

CONDITIONALS_BOUNDARY

CONSTRUCTOR_CALLS

EMPTY_RETURNS

EXPERIMENTAL_ARGUMENT_PROPAGATION

EXPERIMENTAL_BIG_DECIMAL

EXPERIMENTAL_BIG_INTEGER

EXPERIMENTAL_MEMBER_VARIABLE

EXPERIMENTAL_NAKED_RECEIVER

EXPERIMENTAL_REMOVE_SWITCH_MUTATOR_[0-99]

EXPERIMENTAL_SWITCH

FALSE_RETURNS

INCREMENTS

INLINE_CONSTS

INVERT_NEGS

MATH

NEGATE_CONDITIONALS

NON_VOID_METHOD_CALLS

NULL_RETURNS

PRIMITIVE_RETURNS

REMOVE_CONDITIONALS_EQUAL_ELSE

REMOVE_CONDITIONALS_EQUAL_IF

REMOVE_CONDITIONALS_ORDER_ELSE

REMOVE_CONDITIONALS_ORDER_IF

REMOVE_INCREMENTS

TRUE_RETURNS

VOID_METHOD_CALLS

Tests examined

net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatChromosomeCombinatorTest]/[method:combinePickBestReEnable()] (4 ms)

net.bmahe.genetics4j.neat.combination.NeatCombinationHandlerTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.combination.NeatCombinationHandlerTest]/[method:resolve()] (9 ms)

PIT

support