/*
 * Java Genetic Algorithm Library (jenetics-8.3.0).
 * 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.engine;

import static java.lang.String.format;
import static java.util.Map.entry;
import static java.util.Objects.requireNonNull;
import static java.util.function.Function.identity;

import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Objects;
import java.util.function.Predicate;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import java.util.stream.DoubleStream;
import java.util.stream.IntStream;
import java.util.stream.LongStream;
import java.util.stream.Stream;

import io.jenetics.AnyChromosome;
import io.jenetics.AnyGene;
import io.jenetics.BitChromosome;
import io.jenetics.BitGene;
import io.jenetics.DoubleChromosome;
import io.jenetics.DoubleGene;
import io.jenetics.EnumGene;
import io.jenetics.Gene;
import io.jenetics.Genotype;
import io.jenetics.IntegerChromosome;
import io.jenetics.IntegerGene;
import io.jenetics.LongChromosome;
import io.jenetics.LongGene;
import io.jenetics.PermutationChromosome;
import io.jenetics.internal.util.Bits;
import io.jenetics.internal.util.Predicates;
import io.jenetics.internal.util.Requires;
import io.jenetics.util.DoubleRange;
import io.jenetics.util.ISeq;
import io.jenetics.util.IntRange;
import io.jenetics.util.LongRange;

/**
 * This class contains factory methods for creating common problem encodings.
 *
 * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
 * @since 3.2
 * @version 5.2
 */
public final class Codecs {

        private Codecs() {}

        /**
         * Return a scalar {@link InvertibleCodec} for the given range.
         *
         * @param domain the domain of the returned {@code Codec}
         * @return a new scalar {@code Codec} with the given domain.
         * @throws NullPointerException if the given {@code domain} is {@code null}
         */
        public static InvertibleCodec<Integer, IntegerGene>
        ofScalar(final IntRange domain) {
                requireNonNull(domain);

                return InvertibleCodec.of(
                        Genotype.of(IntegerChromosome.of(domain)),
                        gt -> gt.chromosome().gene().allele(),
                        val -> Genotype.of(IntegerChromosome.of(IntegerGene.of(val, domain)))
                );
        }

        /**
         * Return a scalar {@link InvertibleCodec} for the given range.
         *
         * @param domain the domain of the returned {@code Codec}
         * @return a new scalar {@code Codec} with the given domain.
         * @throws NullPointerException if the given {@code domain} is {@code null}
         */
        public static InvertibleCodec<Long, LongGene>
        ofScalar(final LongRange domain) {
                requireNonNull(domain);

                return InvertibleCodec.of(
                        Genotype.of(LongChromosome.of(domain)),
                        gt -> gt.gene().allele(),
                        val -> Genotype.of(LongChromosome.of(LongGene.of(val, domain)))
                );
        }

        /**
         * Return a scalar {@link InvertibleCodec} for the given range.
         *
         * @param domain the domain of the returned {@code Codec}
         * @return a new scalar {@code Codec} with the given domain.
         * @throws NullPointerException if the given {@code domain} is {@code null}
         */
        public static InvertibleCodec<Double, DoubleGene>
        ofScalar(final DoubleRange domain) {
                requireNonNull(domain);

                return InvertibleCodec.of(
                        Genotype.of(DoubleChromosome.of(domain)),
                        gt -> gt.gene().allele(),
                        val -> Genotype.of(DoubleChromosome.of(DoubleGene.of(val, domain)))
                );
        }

        /**
         * Return a scala {@link Codec} with the given allele {@link Supplier} and
         * allele {@code validator}. The {@code supplier} is responsible for
         * creating new random alleles, and the {@code validator} can verify it.
         * <p>
         * The following example shows a codec which creates and verifies
         * {@code BigInteger} objects.
         * {@snippet lang="java":
         * final Codec<BigInteger, AnyGene<BigInteger>> codec = Codecs.of(
         *     // Create new random 'BigInteger' object.
         *     () -> {
         *         final byte[] data = new byte[100];
         *         RandomRegistry.getRandom().nextBytes(data);
         *         return new BigInteger(data);
         *     },
         *     // Verify that bit 7 is set. (For illustration purpose.)
         *     bi -> bi.testBit(7)
         * );
         * }
         *
         * @see AnyGene#of(Supplier, Predicate)
         * @see AnyChromosome#of(Supplier, Predicate)
         *
         * @param <A> the allele type
         * @param supplier the allele-supplier which is used for creating new,
         *        random alleles
         * @param validator the validator used for validating the created gene. This
         *        predicate is used in the {@link AnyGene#isValid()} method.
         * @return a new {@code Codec} with the given parameters
         * @throws NullPointerException if one of the parameters is {@code null}
         */
        public static <A> Codec<A, AnyGene<A>> ofScalar(
                final Supplier<? extends A> supplier,
                final Predicate<? super A> validator
        ) {
                return Codec.of(
                        Genotype.of(AnyChromosome.of(supplier, validator)),
                        gt -> gt.gene().allele()
                );
        }

        /**
         * Return a scala {@link Codec} with the given allele {@link Supplier} and
         * allele {@code validator}. The {@code supplier} is responsible for
         * creating new random alleles.
         *
         * @see #ofScalar(Supplier, Predicate)
         * @see AnyGene#of(Supplier)
         * @see AnyChromosome#of(Supplier)
         *
         * @param <A> the allele type
         * @param supplier the allele-supplier which is used for creating new,
         *        random alleles
         * @return a new {@code Codec} with the given parameters
         * @throws NullPointerException if the parameter is {@code null}
         */
        public static <A> Codec<A, AnyGene<A>> ofScalar(
                final Supplier<? extends A> supplier
        ) {
                return Codec.of(
                        Genotype.of(AnyChromosome.of(supplier)),
                        gt -> gt.gene().allele()
                );
        }

        /**
         * Return a vector {@link InvertibleCodec} for the given range. All vector
         * values are restricted by the same domain.
         *
         * @param domain the domain of the vector values
         * @param length the vector length
         * @return a new vector {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<int[], IntegerGene> ofVector(
                final IntRange domain,
                final int length
        ) {
                return ofVector(domain, new IntRange(length));
        }

        /**
         * Return a vector {@link InvertibleCodec} for the given range. All vector
         * values are restricted by the same domain.
         *
         * @since 7.0
         *
         * @param domain the domain of the vector values
         * @param length the vector length range
         * @return a new vector {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<int[], IntegerGene> ofVector(
                final IntRange domain,
                final IntRange length
        ) {
                requireNonNull(domain);
                Requires.positive(length.min());

                return InvertibleCodec.of(
                        Genotype.of(IntegerChromosome.of(domain, length)),
                        gt -> gt.chromosome().as(IntegerChromosome.class).toArray(),
                        val -> Genotype.of(
                                IntegerChromosome.of(
                                        IntStream.of(val)
                                                .mapToObj(i -> IntegerGene.of(i, domain))
                                                .collect(ISeq.toISeq())
                                )
                        )
                );
        }

        /**
         * Return a vector {@link InvertibleCodec} for the given range. All vector
         * values are restricted by the same domain.
         *
         * @param domain the domain of the vector values
         * @param length the vector length
         * @return a new vector {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<long[], LongGene> ofVector(
                final LongRange domain,
                final int length
        ) {
                return ofVector(domain, new IntRange(length));
        }

        /**
         * Return a vector {@link InvertibleCodec} for the given range. All vector
         * values are restricted by the same domain.
         *
         * @since 7.0
         *
         * @param domain the domain of the vector values
         * @param length the vector length range
         * @return a new vector {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<long[], LongGene> ofVector(
                final LongRange domain,
                final IntRange length
        ) {
                requireNonNull(domain);
                Requires.positive(length.min());

                return InvertibleCodec.of(
                        Genotype.of(LongChromosome.of(domain, length)),
                        gt -> gt.chromosome().as(LongChromosome.class).toArray(),
                        val -> Genotype.of(
                                LongChromosome.of(
                                        LongStream.of(val)
                                                .mapToObj(l -> LongGene.of(l, domain))
                                                .collect(ISeq.toISeq())
                                )
                        )
                );
        }

        /**
         * Return a vector {@link InvertibleCodec} for the given range. All vector
         * values are restricted by the same domain. Use the following code if you
         * want to create {@code int[]} arrays and still using {@link DoubleGene}.
         * The {@code int[]} array elements are created by casting the {@code double}
         * values to {@code int} values.
         * {@snippet lang=java:
         * final Codec<int[], DoubleGene> codec = Codecs
         *     .ofVector(new DoubleRange(0, 100), 100)
         *     .map(ArrayConversions::doubleToIntArray);
         * }
         * If you want round the double values, you can use the following code.
         * {@snippet lang=java:
         * final Codec<int[], DoubleGene> codec = Codecs
         *     .ofVector(new DoubleRange(0, 100), 100)
         *     .map(ArrayConversions.doubleToIntArray(v -> (int)Math.round(v)));
         * }
         *
         * @param domain the domain of the vector values
         * @param length the vector length
         * @return a new vector {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<double[], DoubleGene> ofVector(
                final DoubleRange domain,
                final int length
        ) {
                return ofVector(domain, new IntRange(length));
        }

        /**
         * Return a vector {@link InvertibleCodec} for the given range. All vector
         * values are restricted by the same domain.
         *
         * @since 7.0
         *
         * @param domain the domain of the vector values
         * @param length the vector length range
         * @return a new vector {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<double[], DoubleGene> ofVector(
                final DoubleRange domain,
                final IntRange length
        ) {
                requireNonNull(domain);
                Requires.positive(length.min());

                return InvertibleCodec.of(
                        Genotype.of(DoubleChromosome.of(domain, length)),
                        gt -> gt.chromosome().as(DoubleChromosome.class).toArray(),
                        val -> Genotype.of(
                                DoubleChromosome.of(
                                        DoubleStream.of(val)
                                                .mapToObj(d -> DoubleGene.of(d, domain))
                                                .collect(ISeq.toISeq())
                                )
                        )
                );
        }

        /**
         * Create a vector {@link InvertibleCodec} for the given ranges. Each vector
         * element might have a different domain. The vector length is equal to the
         * number of domains.
         *
         * @param domains the domain ranges
         * @return a new vector {@code Codec}
         * @throws NullPointerException if one of the arguments is {@code null}
         * @throws IllegalArgumentException if the {@code domains} array is empty
         */
        public static InvertibleCodec<int[], IntegerGene>
        ofVector(final IntRange... domains) {
                if (domains.length == 0) {
                        throw new IllegalArgumentException("Domains must not be empty.");
                }

                final ISeq<IntegerChromosome> chromosomes = Stream.of(domains)
                        .peek(Objects::requireNonNull)
                        .map(IntegerGene::of)
                        .map(IntegerChromosome::of)
                        .collect(ISeq.toISeq());

                return InvertibleCodec.of(
                        Genotype.of(chromosomes),
                        gt -> {
                                final int[] args = new int[gt.length()];
                                for (int i = gt.length(); --i >= 0;) {
                                        args[i] = gt.get(i).gene().intValue();
                                }
                                return args;
                        },
                        val -> Genotype.of(
                                IntStream.range(0, val.length)
                                        .mapToObj(i ->
                                                IntegerChromosome.of(IntegerGene.of(val[i], domains[i])))
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Create a vector {@link InvertibleCodec} for the given ranges. Each vector
         * element might have a different domain. The vector length is equal to the
         * number of domains.
         *
         * @param domains the domain ranges
         * @return a new vector {@code Codec}
         * @throws NullPointerException if one of the arguments is {@code null}
         * @throws IllegalArgumentException if the {@code domains} array is empty
         */
        public static InvertibleCodec<long[], LongGene>
        ofVector(final LongRange... domains) {
                if (domains.length == 0) {
                        throw new IllegalArgumentException("Domains must not be empty.");
                }

                final ISeq<LongChromosome> chromosomes = Stream.of(domains)
                        .peek(Objects::requireNonNull)
                        .map(LongGene::of)
                        .map(LongChromosome::of)
                        .collect(ISeq.toISeq());

                return InvertibleCodec.of(
                        Genotype.of(chromosomes),
                        gt -> {
                                final long[] args = new long[gt.length()];
                                for (int i = gt.length(); --i >= 0;) {
                                        args[i] = gt.get(i).gene().longValue();
                                }
                                return args;
                        },
                        val -> Genotype.of(
                                IntStream.range(0, val.length)
                                        .mapToObj(i ->
                                                LongChromosome.of(LongGene.of(val[i], domains[i])))
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Create a vector {@link InvertibleCodec} for the given ranges. Each vector
         * element might have a different domain. The vector length is equal to the
         * number of domains.
         *
         * @param domains the domain ranges
         * @return a new vector {@code Codec}
         * @throws NullPointerException if one of the arguments is {@code null}
         * @throws IllegalArgumentException if the {@code domains} array is empty
         */
        public static InvertibleCodec<double[], DoubleGene>
        ofVector(final DoubleRange... domains) {
                if (domains.length == 0) {
                        throw new IllegalArgumentException("Domains must not be empty.");
                }

                final ISeq<DoubleChromosome> chromosomes = Stream.of(domains)
                        .peek(Objects::requireNonNull)
                        .map(DoubleGene::of)
                        .map(DoubleChromosome::of)
                        .collect(ISeq.toISeq());

                return InvertibleCodec.of(
                        Genotype.of(chromosomes),
                        gt -> {
                                final double[] args = new double[gt.length()];
                                for (int i = gt.length(); --i >= 0;) {
                                        args[i] = gt.get(i).gene().doubleValue();
                                }
                                return args;
                        },
                        val -> Genotype.of(
                                IntStream.range(0, val.length)
                                        .mapToObj(i ->
                                                DoubleChromosome.of(DoubleGene.of(val[i], domains[i])))
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Return a scala {@link Codec} with the given allele {@link Supplier},
         * allele {@code validator} and {@code Chromosome} length. The
         * {@code supplier} is responsible for creating new random alleles, and the
         * {@code validator} can verify it.
         * <p>
         * The following example shows a codec which creates and verifies
         * {@code BigInteger} object arrays.
         * {@snippet lang="java":
         * final Codec<BigInteger[], AnyGene<BigInteger>> codec = Codecs.of(
         *     // Create new random 'BigInteger' object.
         *     () -> {
         *         final byte[] data = new byte[100];
         *         RandomRegistry.getRandom().nextBytes(data);
         *         return new BigInteger(data);
         *     },
         *     // Verify that bit 7 is set. (For illustration purpose.)
         *     bi -> bi.testBit(7),
         *     // The 'Chromosome' length.
         *     123
         * );
         * }
         *
         * @see AnyChromosome#of(Supplier, Predicate, Predicate, int)
         *
         * @param <A> the allele type
         * @param supplier the allele-supplier which is used for creating new,
         *        random alleles
         * @param alleleValidator the validator used for validating the created gene.
         *        This predicate is used in the {@link AnyGene#isValid()} method.
         * @param alleleSeqValidator the validator used for validating the created
         *        chromosome. This predicate is used in the
         *        {@link AnyChromosome#isValid()} method.
         * @param length the vector length
         * @return a new {@code Codec} with the given parameters
         * @throws NullPointerException if one of the parameters is {@code null}
         * @throws IllegalArgumentException if the length of the vector is smaller
         *         than one.
         */
        public static <A> Codec<ISeq<A>, AnyGene<A>> ofVector(
                final Supplier<? extends A> supplier,
                final Predicate<? super A> alleleValidator,
                final Predicate<? super ISeq<A>> alleleSeqValidator,
                final int length
        ) {
                requireNonNull(supplier);
                requireNonNull(alleleSeqValidator);
                requireNonNull(alleleSeqValidator);
                Requires.positive(length);

                return Codec.of(
                        Genotype.of(AnyChromosome
                                .of(supplier, alleleValidator, alleleSeqValidator, length)),
                        gt -> gt.chromosome().stream()
                                .map(Gene::allele)
                                .collect(ISeq.toISeq())
                );
        }

        /**
         * Return a scala {@link Codec} with the given allele {@link Supplier},
         * allele {@code validator} and {@code Chromosome} length. The
         * {@code supplier} is responsible for creating new random alleles, and the
         * {@code validator} can verify it.
         *
         * @param <A> the allele type
         * @param supplier the allele-supplier which is used for creating new,
         *        random alleles
         * @param validator the validator used for validating the created gene. This
         *        predicate is used in the {@link AnyGene#isValid()} method.
         * @param length the vector length
         * @return a new {@code Codec} with the given parameters
         * @throws NullPointerException if one of the parameters is {@code null}
         * @throws IllegalArgumentException if the length of the vector is smaller
         *         than one.
         */
        public static <A> Codec<ISeq<A>, AnyGene<A>> ofVector(
                final Supplier<? extends A> supplier,
                final Predicate<? super A> validator,
                final int length
        ) {
                return ofVector(
                        supplier,
                        validator,
                        Predicates.True(),
                        length
                );
        }

        /**
         * Return a scala {@link Codec} with the given allele {@link Supplier} and
         * {@code Chromosome} length. The {@code supplier} is responsible for
         * creating new random alleles.
         *
         * @param <A> the allele type
         * @param supplier the allele-supplier which is used for creating new,
         *        random alleles
         * @param length the vector length
         * @return a new {@code Codec} with the given parameters
         * @throws NullPointerException if one of the parameters is {@code null}
         * @throws IllegalArgumentException if the length of the vector is smaller
         *         than one.
         */
        public static <A> Codec<ISeq<A>, AnyGene<A>> ofVector(
                final Supplier<? extends A> supplier,
                final int length
        ) {
                return ofVector(supplier, Predicates.TRUE, length);
        }

        /**
         * Create a vector ({@link ISeq}) of domain objects, which are created with
         * the given {@code codec}.
         * {@snippet lang=java:
         * // Domain model of solution space.
         * record Path(WayPoint[] stops) {}
         *
         * // Codec fora single GPS point (latitude, longitude).
         * final Codec<WayPoint, DoubleGene> wpc = Codec.combine(
         *     Codecs.ofScalar(new DoubleRange(30, 50)), // latitude
         *     Codecs.ofScalar(new DoubleRange(69, 72)), // longitude
         *     WayPoint::of
         * );
         *
         * // Codec for the path object.
         * final Codec<Path, DoubleGene> pc = Codecs.ofVector(wpc, 10)
         *     .map(points -> points.toArray(WayPoint[]::new))
         *     .map(Path::new);
         *
         * final Path path = pc.decode(pc.encoding().newInstance());
         * }
         *
         * @since 8.1
         *
         * @param codec the codec for the <em>domain</em> object
         * @param length the length of the vector.
         * @return a codec for a sequence of domain objects
         * @param <S> the type of the domain object
         * @param <G> the encoding gene type
         * @throws NullPointerException if the given {@code codec} is {@code null}
         * @throws IllegalArgumentException if the length is smaller than 1
         */
        @SuppressWarnings("unchecked")
        public static <S, G extends Gene<?, G>> Codec<ISeq<S>, G>
        ofVector(final Codec<? extends S, G> codec, final int length) {
                requireNonNull(codec);
                if (length <= 0) {
                        throw new IllegalArgumentException("Length must be positive: " + length);
                }

                return Codec.combine(
                        IntStream.range(0, length)
                                .mapToObj(__ -> codec)
                                .collect(ISeq.toISeq()),
                        objects -> ISeq.of((S[])objects)
                );
        }

        /**
         * Create a permutation {@link InvertibleCodec} of integer in the range
         * {@code [0, length)}.
         *
         * @param length the number of permutation elements
         * @return a permutation {@code Codec} of integers
         * @throws IllegalArgumentException if the {@code length} is smaller than
         *         one.
         */
        public static InvertibleCodec<int[], EnumGene<Integer>>
        ofPermutation(final int length) {
                Requires.positive(length);

                final PermutationChromosome<Integer> chromosome =
                        PermutationChromosome.ofInteger(length);

                final Map<Integer, EnumGene<Integer>> genes = chromosome.stream()
                        .collect(Collectors.toMap(EnumGene::allele, identity()));

                return InvertibleCodec.of(
                        Genotype.of(chromosome),
                        gt -> gt.chromosome().stream()
                                .mapToInt(EnumGene::allele)
                                .toArray(),
                        val -> Genotype.of(
                                new PermutationChromosome<>(
                                        IntStream.of(val)
                                                .mapToObj(genes::get)
                                                .collect(ISeq.toISeq())
                                )
                        )
                );
        }

        /**
         * Create a permutation {@link InvertibleCodec} with the given alleles.
         *
         * @param alleles the alleles of the permutation
         * @param <T> the allele type
         * @return a new permutation {@code Codec}
         * @throws IllegalArgumentException if the given allele array is empty
         * @throws NullPointerException if one of the alleles is {@code null}
         */
        public static <T> InvertibleCodec<ISeq<T>, EnumGene<T>>
        ofPermutation(final ISeq<? extends T> alleles) {
                if (alleles.isEmpty()) {
                        throw new IllegalArgumentException(
                                "Empty allele array is not allowed."
                        );
                }

                final Map<T, EnumGene<T>> genes =
                        IntStream.range(0, alleles.length())
                                .mapToObj(i -> EnumGene.<T>of(i, alleles))
                                .collect(Collectors.toMap(EnumGene::allele, identity()));

                return InvertibleCodec.of(
                        Genotype.of(new PermutationChromosome<>(ISeq.of(genes.values()))),
                        gt -> gt.chromosome().stream()
                                .map(EnumGene::allele)
                                .collect(ISeq.toISeq()),
                        val -> Genotype.of(
                                new PermutationChromosome<>(
                                        val.stream()
                                                .map(genes::get)
                                                .collect(ISeq.toISeq())
                                )
                        )
                );
        }

        /**
         * Return a 2-dimensional matrix {@link InvertibleCodec} for the given range.
         * All matrix values are restricted by the same domain. The dimension of the
         * returned matrix is {@code int[rows][cols]}.
         *
         * @since 4.4
         *
         * @param domain the domain of the matrix values
         * @param rows the number of rows of the matrix
         * @param cols the number of columns of the matrix
         * @return a new matrix {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code rows} or {@code cols} are
         *         smaller than one.
         */
        public static InvertibleCodec<int[][], IntegerGene> ofMatrix(
                final IntRange domain,
                final int rows,
                final int cols
        ) {
                requireNonNull(domain);
                Requires.positive(rows);
                Requires.positive(cols);

                return InvertibleCodec.of(
                        Genotype.of(
                                IntegerChromosome.of(domain, cols).instances()
                                        .limit(rows)
                                        .collect(ISeq.toISeq())
                        ),
                        gt -> gt.stream()
                                .map(ch -> ch.as(IntegerChromosome.class).toArray())
                                .toArray(int[][]::new),
                        matrix -> Genotype.of(
                                Stream.of(matrix)
                                        .map(row ->
                                                IntegerChromosome.of(
                                                        IntStream.of(row)
                                                                .mapToObj(v -> IntegerGene.of(v, domain))
                                                                .collect(ISeq.toISeq())
                                                ))
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Return a 2-dimensional matrix {@link InvertibleCodec} for the given range.
         * All matrix values are restricted by the same domain. The dimension of the
         * returned matrix is {@code long[rows][cols]}.
         *
         * @since 4.4
         *
         * @param domain the domain of the matrix values
         * @param rows the number of rows of the matrix
         * @param cols the number of columns of the matrix
         * @return a new matrix {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code rows} or {@code cols} are
         *         smaller than one.
         */
        public static InvertibleCodec<long[][], LongGene> ofMatrix(
                final LongRange domain,
                final int rows,
                final int cols
        ) {
                requireNonNull(domain);
                Requires.positive(rows);
                Requires.positive(cols);

                return InvertibleCodec.of(
                        Genotype.of(
                                LongChromosome.of(domain, cols).instances()
                                        .limit(rows)
                                        .collect(ISeq.toISeq())
                        ),
                        gt -> gt.stream()
                                .map(ch -> ch.as(LongChromosome.class).toArray())
                                .toArray(long[][]::new),
                        matrix -> Genotype.of(
                                Stream.of(matrix)
                                        .map(row ->
                                                LongChromosome.of(
                                                        LongStream.of(row)
                                                                .mapToObj(v -> LongGene.of(v, domain))
                                                                .collect(ISeq.toISeq())
                                                ))
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Return a 2-dimensional matrix {@link InvertibleCodec} for the given range.
         * All matrix values are restricted by the same domain. The dimension of the
         * returned matrix is {@code double[rows][cols]}.
         *
         * @since 4.4
         *
         * @param domain the domain of the matrix values
         * @param rows the number of rows of the matrix
         * @param cols the number of columns of the matrix
         * @return a new matrix {@code Codec}
         * @throws NullPointerException if the given {@code domain} is {@code null}
         * @throws IllegalArgumentException if the {@code rows} or {@code cols} are
         *         smaller than one.
         */
        public static InvertibleCodec<double[][], DoubleGene> ofMatrix(
                final DoubleRange domain,
                final int rows,
                final int cols
        ) {
                requireNonNull(domain);
                Requires.positive(rows);
                Requires.positive(cols);

                return InvertibleCodec.of(
                        Genotype.of(
                                DoubleChromosome.of(domain, cols).instances()
                                        .limit(rows)
                                        .collect(ISeq.toISeq())
                        ),
                        gt -> gt.stream()
                                .map(ch -> ch.as(DoubleChromosome.class).toArray())
                                .toArray(double[][]::new),
                        matrix -> Genotype.of(
                                Stream.of(matrix)
                                        .map(row ->
                                                DoubleChromosome.of(
                                                        DoubleStream.of(row)
                                                                .mapToObj(v -> DoubleGene.of(v, domain))
                                                                .collect(ISeq.toISeq())
                                                ))
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Create a codec, which creates a mapping from the elements given in the
         * {@code source} sequence to the elements given in the {@code target}
         * sequence. The returned mapping can be seen as a function which maps every
         * element of the {@code target} set to an element of the {@code source} set.
         * {@snippet lang="java":
         * final ISeq<Integer> numbers = ISeq.of(1, 2, 3, 4, 5);
         * final ISeq<String> strings = ISeq.of("1", "2", "3");
         *
         * final Codec<Map<Integer, String>, EnumGene<Integer>> codec =
         *     Codecs.ofMapping(numbers, strings, HashMap::new);
         * }
         *
         * If {@code source.size() > target.size()}, the created mapping is
         * <a href="https://en.wikipedia.org/wiki/Surjective_function">surjective</a>,
         * if {@code source.size() < target.size()}, the mapping is
         * <a href="https://en.wikipedia.org/wiki/Injective_function">injective</a>
         * and if both sets have the same size, the returned mapping is
         * <a href="https://en.wikipedia.org/wiki/Bijection">bijective</a>.
         *
         * @since 4.3
         *
         * @param source the source elements. Will be the <em>keys</em> of the
         *        encoded {@code Map}.
         * @param target the target elements. Will be the <em>values</em> of the
         *            encoded {@code Map}.
         * @param mapSupplier a function which returns a new, empty Map into which
         *        the mapping will be inserted
         * @param <A> the type of the source elements
         * @param <B> the type of the target elements
         * @param <M> the type of the encoded Map
         * @return a new mapping codec
         * @throws IllegalArgumentException if the {@code target} sequences are empty
         * @throws NullPointerException if one of the arguments is {@code null}
         */
        public static <A, B, M extends Map<A, B>> InvertibleCodec<M, EnumGene<Integer>>
        ofMapping(
                final ISeq<? extends A> source,
                final ISeq<? extends B> target,
                final Supplier<M> mapSupplier
        ) {
                requireNonNull(source);
                requireNonNull(target);
                requireNonNull(mapSupplier);

                final Map<A, Integer> smap = IntStream.range(0, source.length())
                        .mapToObj(i -> entry(source.get(i), i))
                        .collect(Collectors.toMap(Entry::getKey, Entry::getValue));

                final Map<B, Integer> tmap = IntStream.range(0, target.length())
                        .mapToObj(i -> entry(target.get(i), i))
                        .collect(Collectors.toMap(Entry::getKey, Entry::getValue));

                final PermutationChromosome<Integer> chromosome =
                        PermutationChromosome.ofInteger(target.size());

                final Map<Integer, EnumGene<Integer>> genes = chromosome.stream()
                        .collect(Collectors.toMap(EnumGene::allele, identity()));

                final Codec<int[], EnumGene<Integer>> codec = Codec.of(
                        Genotype.of(chromosome),
                        gt -> gt.chromosome().stream()
                                .mapToInt(EnumGene::allele)
                                .toArray()
                );

                return codec
                        .map(permutation -> toMapping(permutation, source, target, mapSupplier))
                        .toInvertibleCodec(mapping -> toEncoding(mapping, smap,tmap, genes));
        }

        private static <A, B, M extends Map<A, B>> M toMapping(
                final int[] perm,
                final ISeq<? extends A> source,
                final ISeq<? extends B> target,
                final Supplier<M> mapSupplier
        ) {
                return IntStream.range(0, source.size())
                        .mapToObj(i -> entry(source.get(i), target.get(perm[i%perm.length])))
                        .collect(Collectors.toMap(
                                Entry::getKey, Entry::getValue,
                                (u,v) -> {throw new IllegalStateException("Duplicate key " + u);},
                                mapSupplier));
        }

        private static <A, B> Genotype<EnumGene<Integer>> toEncoding(
                final Map<A, B> mapping,
                final Map<A, Integer> source,
                final Map<B, Integer> target,
                final Map<Integer, EnumGene<Integer>> genes
        ) {
                final int[] perm = new int[target.size()];
                source.forEach((key, value) -> {
                        final int i = value;
                        final int j = target.get(mapping.get(key));
                        perm[i%perm.length] = j;
                });

                // If the target size is greater the source size, only the first
                // elements (source size) are filled. The rest of the 'perm' array
                // has to be filled with unique elements.
                if (target.size() > source.size()) {
                        final int[] indexes = new int[target.size()];

                        // Initialize the index set with all target indexes: O(|t|)
                        for (int i = 0; i < target.size(); ++i) {
                                indexes[i] = i;
                        }

                        // Mark existing permutations in the index array: O(|s|*log(|t|))
                        for (int i = 0; i < source.size(); ++i) {
                                final int si = Arrays.binarySearch(indexes, perm[i]);
                                if (si >= 0) {
                                        indexes[si] = -1;
                                }
                        }

                        // Fill the 'perm' array with the remaining, non-duplicate indexes:
                        // O(|t|)
                        int j = 0;
                        int next;
                        for (int i = source.size(); i < target.size(); ++i) {
                                while ((next = indexes[j++]) == -1);
                                perm[i] = next;
                        }
                }

                return  Genotype.of(
                        new PermutationChromosome<>(
                                IntStream.of(perm)
                                        .mapToObj(genes::get)
                                        .collect(ISeq.toISeq())
                        )
                );
        }

        /**
         * Create a codec, which creates a mapping from the elements given in the
         * {@code source} sequence to the elements given in the {@code target}
         * sequence. The returned mapping can be seen as a function which maps every
         * element of the {@code target} set to an element of the {@code source} set.
         * {@snippet lang="java":
         * final ISeq<Integer> numbers = ISeq.of(1, 2, 3, 4, 5);
         * final ISeq<String> strings = ISeq.of("1", "2", "3");
         *
         * final Codec<Map<Integer, String>, EnumGene<Integer>> codec =
         *     Codecs.ofMapping(numbers, strings);
         * }
         *
         * If {@code source.size() > target.size()}, the created mapping is
         * <a href="https://en.wikipedia.org/wiki/Surjective_function">surjective</a>,
         * if {@code source.size() < target.size()}, the mapping is
         * <a href="https://en.wikipedia.org/wiki/Injective_function">injective</a>
         * and if both sets have the same size, the returned mapping is
         * <a href="https://en.wikipedia.org/wiki/Bijection">bijective</a>.
         *
         * @since 4.3
         *
         * @param source the source elements. Will be the <em>keys</em> of the
         *        encoded {@code Map}.
         * @param target the target elements. Will be the <em>values</em> of the
         *            encoded {@code Map}.
         * @param <A> the type of the source elements
         * @param <B> the type of the target elements
         * @return a new mapping codec
         * @throws IllegalArgumentException if the {@code target} sequences are empty
         * @throws NullPointerException if one of the arguments is {@code null}
         */
        public static <A, B> InvertibleCodec<Map<A, B>, EnumGene<Integer>>
        ofMapping(final ISeq<? extends A> source, final ISeq<? extends B> target) {
                return ofMapping(source, target, HashMap::new);
        }

        /**
         * The subset {@link InvertibleCodec} can be used for problems where it is
         * required to find the best <b>variable-sized</b> subset from a given basic
         * set. A typical usage example of the returned {@code Codec} is the
         * Knapsack problem.
         * <p>
         * The following code snippet shows a simplified variation of the Knapsack
         * problem.
         * {@snippet lang="java":
         * public final class Main {
         *      // The basic set from where to choose an 'optimal' subset.
         *      private final static ISeq<Integer> SET =
         *          ISeq.of(1, 2, 3, 4, 5, 6, 7, 8, 9, 10);
         *
         *      // Fitness function directly takes an 'int' value.
         *      private static int fitness(final ISeq<Integer> subset) {
         *          assert(subset.size() <= SET.size());
         *          final int size = subset.stream()
         *             .mapToInt(Integer::intValue)
         *             .sum();
         *          return size <= 20 ? size : 0;
         *      }
         *
         *      public static void main(final String[] args) {
         *          final Engine<BitGene, Double> engine = Engine
         *              .builder(Main::fitness, codec.ofSubSet(SET))
         *              .build();
         *          // ...
         *      }
         *  }
         * }
         *
         * @param <T> the element type of the basic set
         * @param basicSet the basic set, from where to choose the <i>optimal</i>
         *        subset.
         * @return a new codec which can be used for modelling <i>subset</i>
         *         problems.
         * @throws NullPointerException if the given {@code basicSet} is
         *         {@code null}; {@code null} elements are allowed.
         * @throws IllegalArgumentException if the {@code basicSet} size is smaller
         *         than one.
         */
        public static <T> InvertibleCodec<ISeq<T>, BitGene>
        ofSubSet(final ISeq<? extends T> basicSet) {
                requireNonNull(basicSet);
                Requires.positive(basicSet.length());

                return InvertibleCodec.of(
                        Genotype.of(BitChromosome.of(basicSet.length())),
                        gt -> gt.chromosome()
                                .as(BitChromosome.class).ones()
                                .<T>mapToObj(basicSet)
                                .collect(ISeq.toISeq()),
                        values -> {
                                final byte[] bits = Bits.newArray(basicSet.size());

                                int i = 0;
                                for (T v : values) {
                                        while (i < basicSet.size() && !Objects.equals(basicSet.get(i), v)) {
                                                ++i;
                                        }
                                        if (i >= basicSet.size()) {
                                                throw new IllegalArgumentException(
                                                        "Invalid subset; input values were not created by " +
                                                                "'decode' method."
                                                );
                                        }

                                        Bits.set(bits, i);
                                }

                                return Genotype.of(new BitChromosome(bits, 0, basicSet.size()));
                        }
                );
        }

        /**
         * The subset {@link InvertibleCodec} can be used for problems where it is
         * required to find the best <b>fixed-size</b> subset from a given basic set.
         *
         * @since 3.4
         *
         * @see PermutationChromosome
         * @see PermutationChromosome#of(ISeq, int)
         *
         * @param <T> the element type of the basic set
         * @param basicSet the basic set, from where to choose the <i>optimal</i>
         *        subset.
         * @param size the length of the desired subsets
         * @return a new codec which can be used for modelling <i>subset</i>
         *         problems.
         * @throws NullPointerException if the given {@code basicSet} is
         *         {@code null}; {@code null} elements are allowed.
         * @throws IllegalArgumentException if {@code basicSet.size() < size},
         *         {@code size <= 0} or {@code basicSet.size()*size} will cause an
         *         integer overflow.
         */
        public static <T> InvertibleCodec<ISeq<T>, EnumGene<T>> ofSubSet(
                final ISeq<? extends T> basicSet,
                final int size
        ) {
                requireNonNull(basicSet);

                final Map<T, EnumGene<T>> genes =
                        IntStream.range(0, basicSet.length())
                                .mapToObj(i -> EnumGene.<T>of(i, basicSet))
                                .collect(Collectors.toMap(EnumGene::allele, identity()));

                return InvertibleCodec.of(
                        Genotype.of(PermutationChromosome.of(basicSet, size)),
                        gt -> gt.chromosome().stream()
                                .map(EnumGene::allele)
                                .collect(ISeq.toISeq()),
                        values -> {
                                if (values.size() != size) {
                                        throw new IllegalArgumentException(format(
                                                "Expected sub-set size of %d, but got %d,",
                                                size, values.size()
                                        ));
                                }

                                return Genotype.of(
                                        new PermutationChromosome<>(
                                                values.stream()
                                                        .map(genes::get)
                                                        .collect(ISeq.toISeq())
                                        )
                                );
                        }
                );
        }

//      /**
//       * Creates a codec for a 2-dimensional affine transformation. The composed
//       * order of the transformation is: <i>R&bull;Sc&bull;Sh&bull;T</i>
//       *
//       * @param sx the scale factor range in x direction
//       * @param sy the scale factor range in y direction
//       * @param tx the translation range in x direction
//       * @param ty the translation range in y direction
//       * @param th the rotation range (in radians)
//       * @param kx the shear range in x direction
//       * @param ky the shear range in x direction
//       * @return the affine transformation codec
//       * @throws NullPointerException if one of the arguments is {@code null}
//       */
//      static Codec<AffineTransform, DoubleGene> ofAffineTransform(
//              final DoubleRange sx, final DoubleRange sy,
//              final DoubleRange tx, final DoubleRange ty,
//              final DoubleRange th,
//              final DoubleRange kx, final DoubleRange ky
//      ) {
//              return Codec.of(
//                      Genotype.of(
//                              // Scale
//                              DoubleChromosome.of(sx), DoubleChromosome.of(sy),
//                              // Translation
//                              DoubleChromosome.of(tx), DoubleChromosome.of(ty),
//                              // Rotation
//                              DoubleChromosome.of(th),
//                              // Shear
//                              DoubleChromosome.of(kx), DoubleChromosome.of(ky)
//                      ),
//                      gt -> {
//                              final AffineTransform at = new AffineTransform();
//
//                              at.translate(
//                                      gt.getChromosome(2).getGene().doubleValue(),
//                                      gt.getChromosome(3).getGene().doubleValue()
//                              );
//                              at.shear(
//                                      gt.getChromosome(5).getGene().doubleValue(),
//                                      gt.getChromosome(6).getGene().doubleValue()
//                              );
//                              at.scale(
//                                      gt.getChromosome(0).getGene().doubleValue(),
//                                      gt.getChromosome(1).getGene().doubleValue()
//                              );
//                              at.rotate(gt.getChromosome(4).getGene().doubleValue());
//
//                              return at;
//                      }
//              );
//      }
//
//      /**
//       * Creates a codec for a 2-dimensional affine transformation. The composed
//       * order of the transformation is: <i>R&bull;Sc&bull;Sh&bull;T</i>
//       *
//       * @param s the scale factor range in x and y direction
//       * @param t the translation range in x and y direction
//       * @param th the rotation angle range
//       * @param k the shear range in x and y direction
//       * @return the affine transformation codec
//       * @throws NullPointerException if one of the arguments is {@code null}
//       */
//      static Codec<AffineTransform, DoubleGene> ofAffineTransform(
//              final DoubleRange s,
//              final DoubleRange t,
//              final DoubleRange th,
//              final DoubleRange k
//      ) {
//              return ofAffineTransform(s, s, t, t, th, k, k);
//      }

}