/*
 * Java Genetic Algorithm Library (jenetics-9.1.0).
 * Copyright (c) 2007-2026 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 (franz.wilhelmstoetter@gmail.com)
 */
package io.jenetics;

import static io.jenetics.internal.util.SerialIO.readInt;
import static io.jenetics.internal.util.SerialIO.writeInt;

import java.io.IOException;
import java.io.InvalidObjectException;
import java.io.ObjectInput;
import java.io.ObjectInputStream;
import java.io.ObjectOutput;
import java.io.Serial;
import java.io.Serializable;
import java.util.Objects;

import io.jenetics.util.BaseSeq;
import io.jenetics.util.Factory;
import io.jenetics.util.ISeq;
import io.jenetics.util.MSeq;
import io.jenetics.util.Verifiable;

/**
 * The central class the GA is working with, is the {@code Genotype}. It is the
 * structural representative of an individual. This class is the encoded problem
 * solution with one to many {@link Chromosome}.
 * <p>
 * <img alt="Genotype" src="doc-files/Genotype.svg" width="400" height="252" >
 * </p>
 * The chromosomes of a genotype don't have to have necessarily the same size.
 * It is only required that all genes are from the same type and the genes within
 * a chromosome have the same constraints; e.g., the same min- and max values
 * for the genes value.
 * {@snippet lang="java":
 * final Genotype<DoubleGene> genotype = Genotype.of(
 *     DoubleChromosome.of(0.0, 1.0, 8),
 *     DoubleChromosome.of(1.0, 2.0, 10),
 *     DoubleChromosome.of(0.0, 10.0, 9),
 *     DoubleChromosome.of(0.1, 0.9, 5)
 * );
 * }
 * The code snippet above creates a genotype with the same structure as shown in
 * the figure above. In this example the {@link DoubleGene} has been chosen as
 * a gene type.
 *
 * @see Chromosome
 * @see Phenotype
 *
 * @implNote
 * This class is immutable and thread-safe.
 *
 * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
 * @since 1.0
 * @version 7.2
 */
public final class Genotype<G extends Gene<?, G>>
        implements
                BaseSeq<Chromosome<G>>,
                Factory<Genotype<G>>,
                Verifiable,
                Serializable
{
        @Serial
        private static final long serialVersionUID = 3L;

        private final ISeq<Chromosome<G>> _chromosomes;

        //Caching isValid value.
        private byte _valid = -1;

        /**
         * Create a new Genotype from a given sequence of {@code Chromosomes}.
         *
         * @param chromosomes The {@code Chromosome} array the {@code Genotype}
         *         consists of
         * @throws NullPointerException if {@code chromosomes} is null or one of its
         *         elements
         * @throws IllegalArgumentException if {@code chromosome.length == 0}
         */
        Genotype(final ISeq<? extends Chromosome<G>> chromosomes) {
                if (chromosomes.isEmpty()) {
                        throw new IllegalArgumentException("No chromosomes given.");
                }

                _chromosomes = ISeq.upcast(chromosomes);
        }

        /**
         * Return the chromosome at the given index. It is guaranteed that the
         * returned chromosome is not null.
         *
         * @since 4.0
         *
         * @param index the chromosome index
         * @return the chromosome with the given index
         * @throws IndexOutOfBoundsException if
         *         {@code (index < 0 || index >= _length)}.
         */
        @Override
        public Chromosome<G> get(final int index) {
                return _chromosomes.get(index);
        }

        /**
         * Getting the number of chromosomes of this genotype.
         *
         * @return number of chromosomes.
         */
        @Override
        public int length() {
                return _chromosomes.length();
        }

        /**
         * Return the first chromosome. This is an alias for
         * {@snippet lang="java":
         * final Genotype<DoubleGene> gt = null; // @replace substring='null' replacement="..."
         * final Chromosome<DoubleGene> chromosome = gt.get(0);
         * }
         *
         * @since 5.2
         *
         * @return The first chromosome.
         */
        public Chromosome<G> chromosome() {
                return get(0);
        }

        /**
         * Return the first {@link Gene} of the first {@link Chromosome} of this
         * {@code Genotype}. This is an alias for
         * {@snippet lang="java":
         * final Genotype<DoubleGene> gt = null; // @replace substring='null' replacement="..."
         * final DoubleGene gene = gt.get(0).get(0);
         * }
         *
         * @since 5.2
         *
         * @return the first {@link Gene} of the first {@link Chromosome} of this
         *         {@code Genotype}.
         */
        public G gene() {
                return get(0).get(0);
        }

        /**
         * Return the number of genes this genotype consists of. This is the sum of
         * the number of genes of the genotype chromosomes.
         *
         * @return Return the number of genes this genotype consists of
         */
        public int geneCount() {
                int count = 0;
                for (var chromosome : this) {
                        count += chromosome.length();
                }
                return count;
        }

        /**
         * Test if this genotype is valid. A genotype is valid if all its
         * {@link Chromosome}s are valid.
         *
         * @return true if this genotype is valid, false otherwise.
         */
        @Override
        public boolean isValid() {
                byte valid = _valid;
                if (valid == -1) {
                        valid = (byte)(_chromosomes.forAll(Verifiable::isValid) ? 1 : 0);
                        _valid = valid;
                }

                return _valid == 1;
        }

        /**
         * Create a new Genotype which consists of the chromosomes from the given
         * {@code fromIndex} (inclusively) to the given {@code toIndex} (exclusively).
         * This method creates a <em>view</em> of the underlying chromosomes.
         *
         * @since 7.2
         *
         * @param fromIndex the start chromosome index, inclusively
         * @param toIndex the end chromosome index, exclusively
         * @return a new genotype consisting of the chromosomes within the given
         *         indexes
         * @throws IndexOutOfBoundsException for an illegal end point index value
         *          ({@code fromIndex < 0 || toIndex > length() || fromIndex > toIndex}).
         */
        public Genotype<G> slice(int fromIndex, int toIndex) {
                return new Genotype<>(_chromosomes.subSeq(fromIndex, toIndex));
        }

        /**
         * Return a new, random genotype by creating new, random chromosomes (calling
         * the {@link Chromosome#newInstance()} method) from the chromosomes of this
         * genotype.
         */
        @Override
        public Genotype<G> newInstance() {
                return new Genotype<>(_chromosomes.map(Factory::newInstance));
        }

        @Override
        public int hashCode() {
                return _chromosomes.hashCode();
        }

        @Override
        public boolean equals(final Object obj) {
                return obj instanceof Genotype<?> other &&
                        Objects.equals(_chromosomes, other._chromosomes);
        }

        @Override
        public String toString() {
                return _chromosomes.toString();
        }

        /**
         * Create a new {@code Genotype} from a given array of {@code Chromosomes}.
         *
         * @since 3.0
         *
         * @param <G> the gene type
         * @param first the first {@code Chromosome} of the {@code Genotype}
         * @param rest the rest of the genotype chromosomes.
         * @return a new {@code Genotype} from the given chromosomes
         * @throws NullPointerException if {@code chromosomes} is {@code null} or
         *         one of its elements.
         */
        @SafeVarargs
        public static <G extends Gene<?, G>> Genotype<G> of(
                final Chromosome<G> first,
                final Chromosome<G>... rest
        ) {
                final MSeq<Chromosome<G>> seq = MSeq.ofLength(1 + rest.length);
                seq.set(0, first);
                for (int i = 0; i < rest.length; ++i) {
                        seq.set(i + 1, rest[i]);
                }
                return new Genotype<>(seq.toISeq());
        }

        /**
         * Create a new {@code Genotype} which consists of {@code n} chromosomes,
         * which are created by the given {@code factory}. This method can be used
         * for easily creating a <i>gene matrix</i>. The following example will
         * create a 10x5 {@code DoubleGene} <i>matrix</i>.
         * {@snippet lang="java":
         * final Genotype<DoubleGene> gt = Genotype
         *     .of(DoubleChromosome.of(0.0, 1.0, 10), 5);
         * }
         *
         * @since 3.0
         *
         * @param <G> the gene type
         * @param factory the factory which creates the chromosomes this genotype
         *        consists of
         * @param n the number of chromosomes this genotype consists of
         * @return new {@code Genotype} containing {@code n} chromosomes
         * @throws IllegalArgumentException if {@code n < 1}
         * @throws NullPointerException if the {@code factory} is {@code null}
         */
        public static <G extends Gene<?, G>> Genotype<G>
        of(final Factory<? extends Chromosome<G>> factory, final int n) {
                final ISeq<Chromosome<G>> ch = ISeq.of(factory::newInstance, n);
                return new Genotype<>(ch);
        }

        /**
         * Create a new {@code Genotype} from a given array of {@code chromosomes}.
         *
         * @since 3.0
         *
         * @param <G> the gene type
         * @param chromosomes the {@code Chromosome}s the returned genotype consists
         *        of
         * @return a new {@code Genotype} from the given chromosomes
         * @throws NullPointerException if {@code chromosomes} is {@code null} or
         *         one of its elements.
         * @throws IllegalArgumentException if {@code chromosome.length() < 1}
         */
        public static <G extends Gene<?, G>> Genotype<G>
        of(final Iterable<? extends Chromosome<G>> chromosomes) {
                return new Genotype<>(ISeq.of(chromosomes));
        }


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

        @Serial
        private Object writeReplace() {
                return new SerialProxy(SerialProxy.GENOTYPE, this);
        }

        @Serial
        private void readObject(final ObjectInputStream stream)
                throws InvalidObjectException
        {
                throw new InvalidObjectException("Serialization proxy required.");
        }

        void write(final ObjectOutput out) throws IOException {
                writeInt(_chromosomes.length(), out);
                for (var ch : _chromosomes) {
                        out.writeObject(ch);
                }
        }

        @SuppressWarnings({"unchecked", "rawtypes"})
        static Object read(final ObjectInput in)
                throws IOException, ClassNotFoundException
        {
                final int length = readInt(in);
                final MSeq chromosomes = MSeq.ofLength(length);
                for (int i = 0; i < length; ++i) {
                        chromosomes.set(i, in.readObject());
                }

                return new Genotype(chromosomes.asISeq());
        }

}