CharacterChromosome.java
/*
* 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.object.eq;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
import javax.xml.bind.annotation.adapters.XmlAdapter;
import javolution.text.CharArray;
import javolution.xml.XMLFormat;
import javolution.xml.XMLSerializable;
import javolution.xml.stream.XMLStreamException;
import org.jenetics.internal.util.HashBuilder;
import org.jenetics.internal.util.model.ModelType;
import org.jenetics.internal.util.model.ValueType;
import org.jenetics.util.Array;
import org.jenetics.util.CharSeq;
import org.jenetics.util.Factory;
import org.jenetics.util.Function;
import org.jenetics.util.ISeq;
/**
* CharacterChromosome which represents character sequences.
*
* @author <a href="mailto:franz.wilhelmstoetter@gmx.at">Franz Wilhelmstötter</a>
* @since 1.0
* @version 1.6 — <em>$Date: 2014-03-04 $</em>
*/
public class CharacterChromosome
extends
AbstractChromosome<CharacterGene>
implements
CharSequence,
XMLSerializable
{
private static final long serialVersionUID = 1L;
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.
*
* @deprecated Visibility will be changed to {@code protected}.
*/
@Deprecated
public 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;
}
/**
* Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
* char set as valid characters.
*
* @param length the {@code length} of the new chromosome.
* @throws IllegalArgumentException if the {@code length} is smaller than
* one.
*
* @deprecated Use {@link #of(int)} instead.
*/
@Deprecated
public CharacterChromosome(final int length) {
this(DEFAULT_CHARACTERS, length);
}
/**
* Create a new chromosome from the given genes (given as string).
*
* @param genes the character genes.
* @param validCharacters the valid characters.
* @throws IllegalArgumentException if the genes string is empty.
*
* @deprecated Use {@link #of(String, org.jenetics.util.CharSeq)} instead.
*/
@Deprecated
public CharacterChromosome(final String genes, final CharSeq validCharacters) {
super(
new Array<CharacterGene>(genes.length()).fill(new Factory<CharacterGene>() {
private int _index = 0;
@Override public CharacterGene newInstance() {
return CharacterGene.of(
genes.charAt(_index++), validCharacters
);
}
}).toISeq()
);
_validCharacters = validCharacters;
}
/**
* Create a new chromosome from the given genes (given as string).
*
* @param genes the character genes.
* @throws IllegalArgumentException if the genes string is empty.
*
* @deprecated Use {@link #of(String)} instead.
*/
@Deprecated
public CharacterChromosome(final String genes) {
this(genes, DEFAULT_CHARACTERS);
}
/**
* Return a more specific view of this chromosome factory.
*
* @return a more specific view of this chromosome factory.
*
* @deprecated No longer needed after adding new factory methods to the
* {@link Array} class.
*/
@Deprecated
@SuppressWarnings("unchecked")
public Factory<CharacterChromosome> asFactory() {
return (Factory<CharacterChromosome>)(Object)this;
}
@Override
public char charAt(final int index) {
return getGene(index).getAllele();
}
@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 HashBuilder.of(getClass()).
and(super.hashCode()).
and(_validCharacters).value();
}
@Override
public boolean equals(final Object obj) {
if (obj == this) {
return true;
}
if (obj == null || getClass() != obj.getClass()) {
return false;
}
final CharacterChromosome cc = (CharacterChromosome)obj;
return super.equals(obj) && eq(_validCharacters, cc._validCharacters);
}
@Override
public String toString() {
final StringBuilder out = new StringBuilder();
for (CharacterGene gene : this) {
out.append(gene);
}
return out.toString();
}
/**
* Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
* char set as valid characters.
*
* @param length the {@code length} of the new chromosome.
* @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.
* @throws IllegalArgumentException if the genes string is empty.
*/
public static CharacterChromosome of(
final String alleles,
final CharSeq validChars
) {
final Array<CharacterGene> genes = new Array<>(alleles.length());
genes.fill(GeneFactory(alleles, validChars));
return new CharacterChromosome(genes.toISeq());
}
private static Factory<CharacterGene>
GeneFactory(final String alleles, final CharSeq validChars) {
return new Factory<CharacterGene>() {
private int _index = 0;
@Override
public CharacterGene newInstance() {
return CharacterGene.of(
alleles.charAt(_index++), validChars
);
}
};
}
/**
* Create a new chromosome from the given genes (given as string).
*
* @param alleles the character genes.
* @throws IllegalArgumentException if the genes string is empty.
*/
public static CharacterChromosome of(final String alleles) {
return of(alleles, DEFAULT_CHARACTERS);
}
/* *************************************************************************
* Property access methods
* ************************************************************************/
/**
* Return a {@link Function} which returns the gene array from this
* {@link Chromosome}.
*/
public static final Function<Chromosome<CharacterGene>, ISeq<CharacterGene>>
Genes = AbstractChromosome.genes();
/**
* Return a {@link Function} which returns the first {@link Gene} from this
* {@link Chromosome}.
*/
public static final Function<Chromosome<CharacterGene>, CharacterGene>
Gene = AbstractChromosome.gene();
/**
* Return a {@link Function} which returns the {@link Gene} with the given
* {@code index} from this {@link Chromosome}.
*/
public static Function<Chromosome<CharacterGene>, CharacterGene>
Gene(final int index)
{
return AbstractChromosome.gene(index);
}
/* *************************************************************************
* 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().charValue());
}
}
private void readObject(final ObjectInputStream in)
throws IOException, ClassNotFoundException
{
in.defaultReadObject();
final int length = in.readInt();
_validCharacters = (CharSeq)in.readObject();
final Array<CharacterGene> genes = new Array<>(length);
for (int i = 0; i < length; ++i) {
final CharacterGene gene = CharacterGene.of(
in.readChar(),
_validCharacters
);
genes.set(i, gene);
}
_genes = genes.toISeq();
}
/* *************************************************************************
* XML object serialization
* ************************************************************************/
static final XMLFormat<CharacterChromosome>
XML = new XMLFormat<CharacterChromosome>(CharacterChromosome.class)
{
private static final String LENGTH = "length";
private static final String VALID_CHARS = "valid-characters";
@Override
public CharacterChromosome newInstance(
final Class<CharacterChromosome> cls, final InputElement xml
)
throws XMLStreamException
{
final int length = xml.getAttribute(LENGTH, 0);
final CharSeq validCharacters = new CharSeq(xml.getAttribute(
VALID_CHARS, CharacterGene.DEFAULT_CHARACTERS.toString()
));
final Array<CharacterGene> array = new Array<>(length);
final CharArray values = xml.getText();
for (int i = 0; i < length; ++i) {
array.set(i, CharacterGene.of(values.charAt(i), validCharacters));
}
return new CharacterChromosome(array.toISeq());
}
@Override
public void write(final CharacterChromosome chromosome, final OutputElement xml)
throws XMLStreamException
{
xml.setAttribute(LENGTH, chromosome.length());
xml.setAttribute(VALID_CHARS, chromosome._validCharacters.toString());
final StringBuilder out = new StringBuilder(chromosome.length());
for (CharacterGene gene : chromosome) {
out.append(gene.getAllele().charValue());
}
xml.addText(out.toString());
}
@Override
public void read(final InputElement element, final CharacterChromosome chromosome) {
}
};
/* *************************************************************************
* JAXB object serialization
* ************************************************************************/
@XmlRootElement(name = "org.jenetics.CharacterChromosome")
@XmlType(name = "org.jenetics.CharacterChromosome")
@XmlAccessorType(XmlAccessType.FIELD)
final static class Model {
@XmlAttribute
public int length;
@XmlAttribute(name = "valid-characters")
public String validCharacters;
@XmlValue
public String genes;
@ValueType(CharacterChromosome.class)
@ModelType(Model.class)
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)
);
}
}
}
}