org.jenetics.PermutationChromosome Maven / Gradle / Ivy

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/*
 * Java Genetic Algorithm Library (jenetics-3.2.0).
 * Copyright (c) 2007-2015 Franz Wilhelmstötter
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 * Author:
 *    Franz Wilhelmstötter ([email protected])
 */
package org.jenetics;

import static java.lang.String.format;
import static org.jenetics.internal.util.bit.getAndSet;
import static org.jenetics.util.MSeq.toMSeq;

import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.List;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.IntStream;

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.adapters.XmlAdapter;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import org.jenetics.internal.util.Equality;
import org.jenetics.internal.util.Hash;
import org.jenetics.internal.util.IntRef;
import org.jenetics.internal.util.bit;
import org.jenetics.internal.util.jaxb;
import org.jenetics.internal.util.reflect;
import org.jenetics.internal.util.require;

import org.jenetics.util.ISeq;
import org.jenetics.util.MSeq;
import org.jenetics.util.RandomRegistry;
import org.jenetics.util.Seq;

/**
 * The mutable methods of the {@link AbstractChromosome} has been overridden so
 * that no invalid permutation will be created.
 *
 * @author Franz Wilhelmstötter
 * @since 1.0
 * @version 2.0
 */
@XmlJavaTypeAdapter(PermutationChromosome.Model.Adapter.class)
public final class PermutationChromosome
	extends AbstractChromosome>
	implements Serializable
{
	private static final long serialVersionUID = 2L;

	private ISeq _validAlleles;

	public PermutationChromosome(final ISeq> genes) {
		super(genes);
		_validAlleles = genes.get(0).getValidAlleles();
	}

	public ISeq getValidAlleles() {
		return _validAlleles;
	}

	/**
	 * Check if this chromosome represents still a valid permutation.
	 */
	@Override
	public boolean isValid() {
		if (_valid == null) {
			final byte[] check = bit.newArray(length());
			_valid = _genes.forAll(g -> !getAndSet(check, g.getAlleleIndex()));
		}

		return _valid;
	}

	/**
	 * Create a new, random chromosome.
	 */
	@Override
	public PermutationChromosome newInstance() {
		return of(_validAlleles);
	}

	@Override
	public PermutationChromosome newInstance(final ISeq> genes) {
		return new PermutationChromosome<>(genes);
	}

	@Override
	public int hashCode() {
		return Hash.of(getClass())
				.and(super.hashCode())
				.value();
	}

	@Override
	public boolean equals(final Object obj) {
		return Equality.of(this, obj).test(super::equals);
	}

	@Override
	public String toString() {
		return _genes.asList().stream()
			.map(g -> g.getAllele().toString())
			.collect(Collectors.joining("|"));
	}

	/**
	 * Create a new, random chromosome with the given valid alleles.
	 *
	 * @param  the gene type of the chromosome
	 * @param alleles the valid alleles used for this permutation arrays.
	 * @return a new chromosome with the given alleles
	 */
	public static  PermutationChromosome of(final ISeq alleles) {
		final ISeq> genes = IntStream.range(0, alleles.length())
			.mapToObj(index -> new EnumGene<>(index, alleles))
			.collect(toMSeq())
			.shuffle(RandomRegistry.getRandom())
			.toISeq();

		final PermutationChromosome chromosome =
			new PermutationChromosome<>(genes);
		chromosome._validAlleles = reflect.cast(alleles);
		chromosome._valid = true;

		return chromosome;
	}

	/**
	 * Create a new, random chromosome with the given valid alleles.
	 *
	 * @since 2.0
	 * @param  the gene type of the chromosome
	 * @param alleles the valid alleles used for this permutation arrays.
	 * @return a new chromosome with the given alleles
	 * @throws IllegalArgumentException if the given allele array is empty
	 * @throws NullPointerException if one of the alleles is {@code null}
	 */
	@SafeVarargs
	public static  PermutationChromosome of(final T... alleles) {
		return of(ISeq.of(alleles));
	}

	/**
	 * Create a integer permutation chromosome with the given length.
	 *
	 * @param length the chromosome length.
	 * @return a integer permutation chromosome with the given length.
	 * @throws IllegalArgumentException if the given length is smaller than one.
	 */
	public static PermutationChromosome ofInteger(final int length) {
		return ofInteger(0, require.positive(length));
	}

	/**
	 * Create a integer permutation chromosome with the given length.
	 *
	 * @since 2.0
	 * @param start the start of the integer range (inclusively) of the returned
	 *        chromosome.
	 * @param end the end of the integer range (exclusively) of the returned
	 *        chromosome.
	 * @return a integer permutation chromosome with the given integer range
	 *         values.
	 * @throws java.lang.IllegalArgumentException if {@code end <= start}
	 */
	public static PermutationChromosome
	ofInteger(final int start, final int end) {
		if (end <= start) {
			throw new IllegalArgumentException(format(
				"end <= start: %d <= %d", end, start
			));
		}

		final IntRef index = new IntRef(start);
		final ISeq alleles = MSeq.ofLength(end - start)
			.fill(() -> index.value++)
			.toISeq();

		return of(alleles);
	}

	/* *************************************************************************
	 *  Java object serialization
	 * ************************************************************************/

	private void writeObject(final ObjectOutputStream out)
		throws IOException
	{
		out.defaultWriteObject();

		out.writeObject(_validAlleles);
		for (EnumGene gene : _genes) {
			out.writeInt(gene.getAlleleIndex());
		}
	}

	@SuppressWarnings("unchecked")
	private void readObject(final ObjectInputStream in)
		throws IOException, ClassNotFoundException
	{
		in.defaultReadObject();

		_validAlleles = (ISeq)in.readObject();

		final MSeq> genes = MSeq.ofLength(_validAlleles.length());
		for (int i = 0; i < _validAlleles.length(); ++i) {
			genes.set(i, new EnumGene<>(in.readInt(), _validAlleles));
		}

		_genes = genes.toISeq();
	}

	/* *************************************************************************
	 *  JAXB object serialization
	 * ************************************************************************/

	@XmlRootElement(name = "permutation-chromosome")
	@XmlType(name = "org.jenetics.PermutationChromosome")
	@XmlAccessorType(XmlAccessType.FIELD)
	@SuppressWarnings({"unchecked", "rawtypes"})
	static final class Model {

		@XmlAttribute
		public int length;

		@XmlElementWrapper(name = "valid-alleles")
		@XmlElement(name = "allele")
		public List