/*
* Java Genetic Algorithm Library (@__identifier__@).
* Copyright (c) @__year__@ 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@gmx.at)
*/
package org.jenetics;
import static org.jenetics.CharacterGene.DEFAULT_CHARACTERS;
import static org.jenetics.internal.util.Equality.eq;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.function.Supplier;
import java.util.stream.Collectors;
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.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.util.CharSeq;
import org.jenetics.util.ISeq;
import org.jenetics.util.MSeq;
/**
* CharacterChromosome which represents character sequences.
*
* @author <a href="mailto:franz.wilhelmstoetter@gmx.at">Franz Wilhelmstötter</a>
* @since 1.0
* @version 3.0
*/
@XmlJavaTypeAdapter(CharacterChromosome.Model.Adapter.class)
public class CharacterChromosome
extends
AbstractChromosome<CharacterGene>
implements
CharSequence,
Serializable
{
private static final long serialVersionUID = 2L;
private transient CharSeq _validCharacters;
/**
* Create a new chromosome from the given {@code genes} array. The genes
* array is copied, so changes to the given genes array doesn't effect the
* genes of this chromosome.
*
* @param genes the genes that form 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) {
super(genes);
_validCharacters = genes.get(0).getValidCharacters();
}
/**
* Create a new chromosome with the {@code validCharacters} char set as
* valid characters.
*
* @param validCharacters the valid characters for this chromosome.
* @param length the length of the new chromosome.
* @throws NullPointerException if the {@code validCharacters} is
* {@code null}.
* @throws IllegalArgumentException if the {@code length} is smaller than
* one.
*/
public CharacterChromosome(final CharSeq validCharacters, final int length) {
this(CharacterGene.seq(validCharacters, length));
_valid = true;
}
@Override
public char charAt(final int index) {
return getGene(index).charValue();
}
@Override
public CharacterChromosome subSequence(final int start, final int end) {
return new CharacterChromosome(_genes.subSeq(start, end));
}
/**
* @throws NullPointerException if the given gene array is {@code null}.
*/
@Override
public CharacterChromosome newInstance(final ISeq<CharacterGene> genes) {
return new CharacterChromosome(genes);
}
/**
* Create a new, <em>random</em> chromosome.
*/
@Override
public CharacterChromosome newInstance() {
return new CharacterChromosome(_validCharacters, length());
}
@Override
public int hashCode() {
return Hash.of(getClass())
.and(super.hashCode())
.and(_validCharacters).value();
}
@Override
public boolean equals(final Object obj) {
return Equality.of(this, obj).test(cc ->
super.equals(obj) &&
eq(_validCharacters, cc._validCharacters)
);
}
@Override
public String toString() {
return toSeq().stream()
.map(Object::toString)
.collect(Collectors.joining());
}
/**
* Returns an char array containing all of the elements in this chromosome
* in 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 chromosomes 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 an char array containing all of the elements in this chromosome
* in proper sequence.
*
* @since 3.0
*
* @return an array containing the elements of this chromosome
*/
public char[] toArray() {
return toArray(new char[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 new CharacterChromosome(
CharacterGene.seq(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 IntRef index = new IntRef();
final Supplier<CharacterGene> geneFactory = () -> CharacterGene.of(
alleles.charAt(index.value++), validChars
);
final ISeq<CharacterGene> genes =
MSeq.<CharacterGene>ofLength(alleles.length())
.fill(geneFactory)
.toISeq();
return new CharacterChromosome(genes);
}
/**
* 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
* ************************************************************************/
private void writeObject(final ObjectOutputStream out)
throws IOException
{
out.defaultWriteObject();
out.writeInt(length());
out.writeObject(_validCharacters);
for (CharacterGene gene : _genes) {
out.writeChar(gene.getAllele());
}
}
private void readObject(final ObjectInputStream in)
throws IOException, ClassNotFoundException
{
in.defaultReadObject();
final int length = in.readInt();
_validCharacters = (CharSeq)in.readObject();
final MSeq<CharacterGene> genes = MSeq.ofLength(length);
for (int i = 0; i < length; ++i) {
final CharacterGene gene = CharacterGene.of(
in.readChar(),
_validCharacters
);
genes.set(i, gene);
}
_genes = genes.toISeq();
}
/* *************************************************************************
* JAXB object serialization
* ************************************************************************/
@XmlRootElement(name = "character-chromosome")
@XmlType(name = "org.jenetics.CharacterChromosome")
@XmlAccessorType(XmlAccessType.FIELD)
final static class Model {
@XmlAttribute(name = "length", required = true)
public int length;
@XmlElement(name = "valid-alleles", required = true, nillable = false)
public String validCharacters;
@XmlElement(name = "alleles", required = true, nillable = false)
public String genes;
public final static class Adapter
extends XmlAdapter<Model, CharacterChromosome>
{
@Override
public Model marshal(final CharacterChromosome value) {
final Model m = new Model();
m.length = value.length();
m.validCharacters = value._validCharacters.toString();
m.genes = value.toString();
return m;
}
@Override
public CharacterChromosome unmarshal(final Model m) {
return CharacterChromosome.of(
m.genes,
new CharSeq(m.validCharacters)
);
}
}
}
}