/*
 * Java Genetic Algorithm Library (jenetics-8.2.0).
 * Copyright (c) 2007-2025 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 java.util.Objects.requireNonNull;
import static io.jenetics.CharacterGene.DEFAULT_CHARACTERS;
import static io.jenetics.internal.util.Hashes.hash;
import static io.jenetics.internal.util.SerialIO.readInt;
import static io.jenetics.internal.util.SerialIO.readString;
import static io.jenetics.internal.util.SerialIO.writeInt;
import static io.jenetics.internal.util.SerialIO.writeString;

import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.io.InvalidObjectException;
import java.io.ObjectInputStream;
import java.io.Serial;
import java.io.Serializable;
import java.util.Objects;
import java.util.function.Function;
import java.util.stream.IntStream;

import io.jenetics.util.CharSeq;
import io.jenetics.util.ISeq;
import io.jenetics.util.IntRange;
import io.jenetics.util.MSeq;

/**
 * Character chromosome which represents character sequences.
 *
 * @see CharacterGene
 *
 * @implNote
 * This class is immutable and thread-safe.
 *
 * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
 * @since 1.0
 * @version 6.1
 */
public class CharacterChromosome
        extends VariableChromosome<CharacterGene>
        implements
                CharSequence,
                Serializable
{
        @Serial
        private static final long serialVersionUID = 3L;

        private transient final CharSeq _validCharacters;

        /**
         * Create a new chromosome from the given {@code genes} array. The genes
         * array is copied, so changes to the given genes array don't affect the
         * genes of this chromosome.
         *
         * @since 4.0
         *
         * @param genes the genes that form the chromosome.
         * @param lengthRange the allowed length range of the chromosome.
         * @throws NullPointerException if the given gene array is {@code null}.
         * @throws IllegalArgumentException if the length of the gene array is
         *         smaller than one.
         */
        protected CharacterChromosome(
                final ISeq<CharacterGene> genes,
                final IntRange lengthRange
        ) {
                super(genes, lengthRange);
                _validCharacters = genes.get(0).validChars();
        }

        @Override
        public char charAt(final int index) {
                return get(index).charValue();
        }

        @Override
        public boolean isEmpty() {
                return super.isEmpty();
        }

        @Override
        public CharacterChromosome subSequence(final int start, final int end) {
                return new CharacterChromosome(_genes.subSeq(start, end), lengthRange());
        }

        /**
         * @throws NullPointerException if the given gene array is {@code null}.
         */
        @Override
        public CharacterChromosome newInstance(final ISeq<CharacterGene> genes) {
                return new CharacterChromosome(genes, lengthRange());
        }

        /**
         * Create a new, <em>random</em> chromosome.
         */
        @Override
        public CharacterChromosome newInstance() {
                return of(_validCharacters, lengthRange());
        }

        /**
         * Maps the gene alleles of this chromosome, given as {@code char[]} array,
         * by applying the given mapper function {@code f}. The mapped gene values
         * are then wrapped into a newly created chromosome.
         * {@snippet lang="java":
         * final CharacterChromosome chromosome = null; // @replace substring='null' replacement="..."
         * final CharacterChromosome uppercase = chromosome.map(Main::uppercase);
         *
         * static int[] uppercase(final int[] values) {
         *     for (int i = 0; i < values.length; ++i) {
         *         values[i] = Character.toUpperCase(values[i]);
         *     }
         *     return values;
         * }
         * }
         *
         * @since 6.1
         *
         * @param f the mapper function
         * @return a newly created chromosome with the mapped gene values
         * @throws NullPointerException if the mapper function is {@code null}.
         * @throws IllegalArgumentException if the length of the mapped
         *         {@code char[]} array is empty or doesn't match with the allowed
         *         length range
         */
        public CharacterChromosome map(final Function<? super char[], char[]> f) {
                requireNonNull(f);

                final char[] chars = f.apply(toArray());
                final var genes = IntStream.range(0, chars.length)
                        .mapToObj(i -> CharacterGene.of(chars[i], _validCharacters))
                        .collect(ISeq.toISeq());

                return newInstance(genes);
        }

        @Override
        public int hashCode() {
                return hash(super.hashCode(), hash(_validCharacters));
        }

        @Override
        public boolean equals(final Object obj) {
                return obj != null &&
                        getClass() == obj.getClass() &&
                        Objects.equals(_validCharacters, ((CharacterChromosome)obj)._validCharacters) &&
                        super.equals(obj);
        }

        @Override
        public String toString() {
                return new String(toArray());
        }

        /**
         * Returns a char array containing all the elements in this chromosome
         * in a proper sequence.  If the chromosome fits in the specified array, it is
         * returned therein. Otherwise, a new array is allocated with the length of
         * this chromosome.
         *
         * @since 3.0
         *
         * @param array the array into which the elements of this chromosome are to
         *        be stored, if it is big enough; otherwise, a new array is
         *        allocated for this purpose.
         * @return an array containing the elements of this chromosome
         * @throws NullPointerException if the given {@code array} is {@code null}
         */
        public char[] toArray(final char[] array) {
                final char[] a = array.length >= length()
                        ? array
                        : new char[length()];

                for (int i = length(); --i >= 0;) {
                        a[i] = charAt(i);
                }

                return a;
        }

        /**
         * Returns a char array containing all the elements in this chromosome
         * in a proper sequence.
         *
         * @since 3.0
         *
         * @return an array containing the elements of this chromosome
         */
        public char[] toArray() {
                return toArray(new char[length()]);
        }


        /* *************************************************************************
         * Static factory methods.
         * ************************************************************************/

        /**
         * Create a new chromosome with the {@code validCharacters} char set as
         * valid characters.
         *
         * @since 4.3
         *
         * @param validCharacters the valid characters for this chromosome.
         * @param lengthRange the allowed length range of the chromosome.
         * @return a new {@code CharacterChromosome} with the given parameter
         * @throws NullPointerException if the {@code validCharacters} is
         *         {@code null}.
         * @throws IllegalArgumentException if the length of the gene sequence is
         *         empty, doesn't match with the allowed length range, the minimum
         *         or maximum of the range is smaller or equal zero, or the given
         *         range size is zero.
         */
        public static CharacterChromosome of(
                final CharSeq validCharacters,
                final IntRange lengthRange
        ) {
                return new CharacterChromosome(
                        CharacterGene.seq(validCharacters, lengthRange),
                        lengthRange
                );
        }

        /**
         * Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
         * char set as valid characters.
         *
         * @param lengthRange the allowed length range of the chromosome.
         * @return a new {@code CharacterChromosome} with the given parameter
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static CharacterChromosome of(final IntRange lengthRange) {
                return of(DEFAULT_CHARACTERS, lengthRange);
        }

        /**
         * Create a new chromosome with the {@code validCharacters} char set as
         * valid characters.
         *
         * @since 4.3
         *
         * @param validCharacters the valid characters for this chromosome.
         * @param length the {@code length} of the new chromosome.
         * @return a new {@code CharacterChromosome} with the given parameter
         * @throws NullPointerException if the {@code validCharacters} is
         *         {@code null}.
         * @throws IllegalArgumentException if the length of the gene sequence is
         *         empty, doesn't match with the allowed length range, the minimum
         *         or maximum of the range is smaller or equal zero, or the given
         *         range size is zero.
         */
        public static CharacterChromosome of(
                final CharSeq validCharacters,
                final int length
        ) {
                return of(validCharacters, IntRange.of(length));
        }

        /**
         * Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
         * char set as valid characters.
         *
         * @param length the {@code length} of the new chromosome.
         * @return a new {@code CharacterChromosome} with the given parameter
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static CharacterChromosome of(final int length) {
                return of(DEFAULT_CHARACTERS, length);
        }

        /**
         * Create a new chromosome from the given genes (given as string).
         *
         * @param alleles the character genes.
         * @param validChars the valid characters.
         * @return a new {@code CharacterChromosome} with the given parameter
         * @throws IllegalArgumentException if the genes string is empty.
         */
        public static CharacterChromosome of(
                final String alleles,
                final CharSeq validChars
        ) {
                final MSeq<CharacterGene> genes = MSeq.ofLength(alleles.length());
                for (int i = 0; i < alleles.length(); ++i) {
                        genes.set(i, CharacterGene.of(alleles.charAt(i), validChars));
                }

                return new CharacterChromosome(genes.toISeq(), IntRange.of(alleles.length()));
        }

        /**
         * Create a new chromosome from the given genes (given as string).
         *
         * @param alleles the character genes.
         * @return a new {@code CharacterChromosome} with the given parameter
         * @throws IllegalArgumentException if the genes string is empty.
         */
        public static CharacterChromosome of(final String alleles) {
                return of(alleles, DEFAULT_CHARACTERS);
        }


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

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

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

        void write(final DataOutput out) throws IOException {
                writeInt(lengthRange().min(), out);
                writeInt(lengthRange().max(), out);
                writeString(_validCharacters.toString(), out);
                writeString(toString(), out);
        }

        static CharacterChromosome read(final DataInput in) throws IOException {
                final var lengthRange = IntRange.of(readInt(in), readInt(in));
                final var validCharacters = new CharSeq(readString(in));
                final var chars = readString(in);

                final MSeq<CharacterGene> values = MSeq.ofLength(chars.length());
                for (int i = 0, n = chars.length(); i <  n; ++i) {
                        values.set(i, CharacterGene.of(chars.charAt(i), validCharacters));
                }

                return new CharacterChromosome(values.toISeq(), lengthRange);
        }

}