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Jenetics - Java Genetic Algorithm Library
/*
* Java Genetic Algorithm Library (jenetics-3.2.0).
* Copyright (c) 2007-2015 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 ([email protected])
*/
package org.jenetics;
import static java.lang.String.format;
import static org.jenetics.internal.util.Equality.eq;
import java.io.Serializable;
import java.util.List;
import java.util.Objects;
import java.util.function.Function;
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.XmlElementWrapper;
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.Hash;
import org.jenetics.internal.util.jaxb;
import org.jenetics.internal.util.model.IndexedObject;
import org.jenetics.internal.util.reflect;
import org.jenetics.util.ISeq;
import org.jenetics.util.RandomRegistry;
/**
*
* Gene which holds enumerable (countable) genes. Will be used for combinatorial
* problems in combination with the {@link PermutationChromosome}.
*
* The following code shows how to create a combinatorial genotype factory which
* can be used when creating an {@link org.jenetics.engine.Engine} instance.
* {@code
* final ISeq alleles = ISeq.of(1, 2, 3, 4, 5, 6, 7, 8);
* final Factory>> gtf = Genotype.of(
* PermutationChromosome.of(alleles)
* );
* }
*
* The following code shows the assurances of the {@code EnumGene}.
* {@code
* final ISeq alleles = ISeq.of(1, 2, 3, 4, 5, 6, 7, 8);
* final EnumGene gene = new EnumGene<>(5, alleles);
*
* assert(gene.getAlleleIndex() == 5);
* assert(gene.getAllele() == gene.getValidAlleles().get(5));
* assert(gene.getValidAlleles() == alleles);
* }
*
* @see PermutationChromosome
*
* @author Franz Wilhelmstötter
* @since 1.0
* @version 2.0
*/
@XmlJavaTypeAdapter(EnumGene.Model.Adapter.class)
public final class EnumGene
implements
Gene>,
Comparable>,
Serializable
{
private static final long serialVersionUID = 2L;
private final ISeq _validAlleles;
private final int _alleleIndex;
/**
* Create a new enum gene from the given valid genes and the chosen allele
* index.
* @param alleleIndex the index of the allele for this gene.
* @param validAlleles the sequence of valid alleles.
* @throws IllegalArgumentException if the give valid alleles sequence is
* empty
* @throws NullPointerException if the valid alleles seq is {@code null}.
*/
EnumGene(final int alleleIndex, final ISeq validAlleles) {
if (validAlleles.length() == 0) {
throw new IllegalArgumentException(
"Array of valid alleles must be greater than zero."
);
}
if (alleleIndex < 0 || alleleIndex >= validAlleles.length()) {
throw new IndexOutOfBoundsException(format(
"Allele index is not in range [0, %d).", alleleIndex
));
}
_validAlleles = reflect.cast(validAlleles);
_alleleIndex = alleleIndex;
}
/**
* Return sequence of the valid alleles where this gene is a part of.
*
* @return the sequence of the valid alleles.
*/
public ISeq getValidAlleles() {
return _validAlleles;
}
/**
* Return the index of the allele this gene is representing.
*
* @return the index of the allele this gene is representing.
*/
public int getAlleleIndex() {
return _alleleIndex;
}
@Override
public A getAllele() {
return _validAlleles.get(_alleleIndex);
}
@Override
public boolean isValid() {
return _alleleIndex >= 0 && _alleleIndex < _validAlleles.length();
}
@Override
public EnumGene newInstance() {
return new EnumGene<>(
RandomRegistry.getRandom().nextInt(_validAlleles.length()),
_validAlleles
);
}
/**
* Create a new gene from the given {@code value} and the gene context.
*
* @since 1.6
* @param value the value of the new gene.
* @return a new gene with the given value.
*/
public EnumGene newInstance(final A value) {
return new EnumGene<>(
_validAlleles.indexOf(value),
_validAlleles
);
}
@Override
public int compareTo(final EnumGene gene) {
int result = 0;
if (_alleleIndex > gene._alleleIndex) {
result = 1;
} else if (_alleleIndex < gene._alleleIndex) {
result = -1;
}
return result;
}
@Override
public int hashCode() {
return Hash.of(EnumGene.class)
.and(_alleleIndex)
.and(_validAlleles).value();
}
@Override
public boolean equals(final Object obj) {
return obj instanceof EnumGene &&
eq(((EnumGene)obj)._alleleIndex, _alleleIndex) &&
eq(((EnumGene)obj)._validAlleles, _validAlleles);
}
@Override
public String toString() {
return Objects.toString(getAllele());
}
/* *************************************************************************
* Static object creation methods
* ************************************************************************/
/**
* Return a new enum gene with an allele randomly chosen from the given
* valid alleles.
*
* @param the allele type
* @param validAlleles the sequence of valid alleles.
* @return a new {@code EnumGene} with the given parameter
* @throws java.lang.IllegalArgumentException if the give valid alleles
* sequence is empty
* @throws NullPointerException if the valid alleles seq is {@code null}.
*/
public static EnumGene of(final ISeq validAlleles) {
return new EnumGene<>(
RandomRegistry.getRandom().nextInt(validAlleles.length()),
validAlleles
);
}
/**
* Create a new enum gene from the given valid genes and the chosen allele
* index.
*
* @param the allele type
* @param alleleIndex the index of the allele for this gene.
* @param validAlleles the array of valid alleles.
* @return a new {@code EnumGene} with the given parameter
* @throws java.lang.IllegalArgumentException if the give valid alleles
* array is empty of the allele index is out of range.
*/
@SafeVarargs
public static EnumGene of(
final int alleleIndex,
final A... validAlleles
) {
return new EnumGene<>(alleleIndex, ISeq.of(validAlleles));
}
/**
* Return a new enum gene with an allele randomly chosen from the given
* valid alleles.
*
* @param the allele type
* @param validAlleles the array of valid alleles.
* @return a new {@code EnumGene} with the given parameter
* @throws java.lang.IllegalArgumentException if the give valid alleles
* array is empty
*/
@SafeVarargs
public static EnumGene of(final A... validAlleles) {
return EnumGene.of(ISeq.of(validAlleles));
}
/* *************************************************************************
* JAXB object serialization
* ************************************************************************/
@XmlRootElement(name = "enum-gene")
@XmlType(name = "org.jenetics.EnumGene")
@XmlAccessorType(XmlAccessType.FIELD)
@SuppressWarnings({"unchecked", "rawtypes"})
final static class Model {
@XmlAttribute(name = "length", required = true)
public int length;
@XmlElementWrapper(name = "valid-alleles", required = true, nillable = false)
@XmlElement(name = "allele", required = true, nillable = false)
public List alleles;
@XmlElement(name = "allele", required = true, nillable = false)
public IndexedObject allele = new IndexedObject();
public static final class Adapter
extends XmlAdapter
{
@Override
public Model marshal(final EnumGene gene) {
final Function marshaller = jaxb.Marshaller(gene.getAllele());
final Model m = new Model();
m.length = gene.getValidAlleles().length();
m.allele.index = gene.getAlleleIndex();
m.allele.value = marshaller.apply(gene.getAllele());
m.alleles = gene.getValidAlleles()
.map(marshaller)
.asList();
return m;
}
@Override
public EnumGene unmarshal(final Model m) {
return new EnumGene<>(
m.allele.index,
ISeq.of(m.alleles)
.map(jaxb.Unmarshaller(m.allele.value))
);
}
}
}
}
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