org.jenetics

Class Genotype<G extends Gene<?,G>>

java.lang.Object

org.jenetics.Genotype<G>

All Implemented Interfaces:

Serializable, Iterable<Chromosome<G>>, Factory<Genotype<G>>, Verifiable

public final class Genotype<G extends Gene<?,G>>
extends Object
implements Factory<Genotype<G>>, Iterable<Chromosome<G>>, Verifiable, Serializable

The central class the GA is working with, is the Genotype. It is the structural representative of an individual. This class is the encoded problem solution with one to many Chromosome.

The chromosomes of a genotype doesn't have to have necessarily the same size. It is only required that all genes are from the same type and the genes within a chromosome have the same constraints; e. g. the same min- and max values for number genes.

final Genotype<DoubleGene> genotype = Genotype.of( DoubleChromosome.of(0.0, 1.0, 8), DoubleChromosome.of(1.0, 2.0, 10), DoubleChromosome.of(0.0, 10.0, 9), DoubleChromosome.of(0.1, 0.9, 5) );

The code snippet above creates a genotype with the same structure as shown in the figure above. In this example the DoubleGene has been chosen as gene type.

Since:

1.0

Version:

3.0

Author:

Franz Wilhelmstötter

See Also:

Serialized Form

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
G	get(int chromosomeIndex, int geneIndex) Return the gene from the given chromosome- and gene index.
Chromosome<G>	getChromosome() Return the first chromosome.
Chromosome<G>	getChromosome(int index) Return the chromosome at the given index.
G	getGene() Return the first Gene of the first Chromosome of this Genotype.
int	getNumberOfGenes() Return the number of genes this genotype consists of.
int	hashCode()
boolean	isValid() Test if this genotype is valid.
Iterator<Chromosome<G>>	iterator()
int	length() Getting the number of chromosomes of this genotype.
Genotype<G>	newInstance() Return a new, random genotype by creating new, random chromosomes (calling the Factory.newInstance() method) from the chromosomes of this genotype.
static <G extends Gene<?,G>> Genotype<G>	of(Chromosome<G> first, Chromosome<G>... rest) Create a new Genotype from a given array of Chromosomes.
static <G extends Gene<?,G>> Genotype<G>	of(Factory<? extends Chromosome<G>> factory, int n) Create a new Genotype which consists of n chromosomes, which are created by the given factory.
static <G extends Gene<?,G>> Genotype<G>	of(Iterable<? extends Chromosome<G>> chromosomes) Create a new Genotype from a given array of chromosomes.
Stream<Chromosome<G>>	stream() Returns a sequential Stream of chromosomes with this genotype as its source.
ISeq<Chromosome<G>>	toSeq()
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.jenetics.util.Factory

instances

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Method Detail

getChromosome

public Chromosome<G> getChromosome(int index)

Return the chromosome at the given index. It is guaranteed, that the returned chromosome is not null.

Parameters:

index - Chromosome index.

Returns:

The Chromosome.

Throws:

IndexOutOfBoundsException - if (index < 0 || index >= _length).

getChromosome

public Chromosome<G> getChromosome()

Return the first chromosome. This is a shortcut for

final Genotype<DoubleGene>; gt = ... final Chromosome<DoubleGene> chromosome = gt.getChromosome(0);

Returns:

The first chromosome.

getGene

public G getGene()

Return the first Gene of the first Chromosome of this Genotype. This is a shortcut for

final Genotype<DoubleGene> gt = ... final DoubleGene gene = gt.getChromosome(0).getGene(0);

Returns:

the first Gene of the first Chromosome of this Genotype.

get

public G get(int chromosomeIndex,
             int geneIndex)

Return the gene from the given chromosome- and gene index. This is a shortcut for gt.getChromosome(chromosomeIndex).getGene(geneIndex).

Parameters:

chromosomeIndex - the chromosome index

geneIndex - the gene index within the chromosome

Returns:

the gene with the given indexes

Throws:

IndexOutOfBoundsException - if the given indexes are not within the allowed range

Since:

3.0

toSeq

public ISeq<Chromosome<G>> toSeq()

iterator

public Iterator<Chromosome<G>> iterator()

Specified by:

iterator in interface Iterable<Chromosome<G extends Gene<?,G>>>

stream

public Stream<Chromosome<G>> stream()

Returns a sequential Stream of chromosomes with this genotype as its source.

Returns:

a sequential Stream of chromosomes

Since:

3.4

length

public int length()

Getting the number of chromosomes of this genotype.

Returns:

number of chromosomes.

getNumberOfGenes

public int getNumberOfGenes()

Return the number of genes this genotype consists of. This is the sum of the number of genes of the genotype chromosomes.

Returns:

Return the number of genes this genotype consists of.

isValid

public boolean isValid()

Test if this genotype is valid. A genotype is valid if all its Chromosomes are valid.

Specified by:

isValid in interface Verifiable

Returns:

true if this genotype is valid, false otherwise.

newInstance

public Genotype<G> newInstance()

Return a new, random genotype by creating new, random chromosomes (calling the Factory.newInstance() method) from the chromosomes of this genotype.

Specified by:

newInstance in interface Factory<Genotype<G extends Gene<?,G>>>

Returns:

a new instance of type T

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

of

@SafeVarargs
public static <G extends Gene<?,G>> Genotype<G> of(Chromosome<G> first,
                                                                Chromosome<G>... rest)

Create a new Genotype from a given array of Chromosomes.

Type Parameters:

G - the gene type

Parameters:

first - the first Chromosome of the Genotype

rest - the rest of the genotypes chromosomes.

Returns:

a new Genotype from the given chromosomes

Throws:

NullPointerException - if chromosomes is null or one of its element.

Since:

3.0

of

public static <G extends Gene<?,G>> Genotype<G> of(Factory<? extends Chromosome<G>> factory,
                                                   int n)

Create a new Genotype which consists of n chromosomes, which are created by the given factory. This method can be used for easily creating a gene matrix. The following example will create a 10x5 DoubleGene matrix.

final Genotype<DoubleGene> gt = Genotype .of(DoubleChromosome.of(0.0, 1.0, 10), 5);

Type Parameters:

G - the gene type

Parameters:

factory - the factory which creates the chromosomes this genotype consists of

n - the number of chromosomes this genotype consists of

Returns:

new Genotype containing n chromosomes

Throws:

IllegalArgumentException - if n < 1.

NullPointerException - if the factory is null.

Since:

3.0

of

public static <G extends Gene<?,G>> Genotype<G> of(Iterable<? extends Chromosome<G>> chromosomes)

Create a new Genotype from a given array of chromosomes.

Type Parameters:

G - the gene type

Parameters:

chromosomes - the Chromosomes the returned genotype consists of

Returns:

a new Genotype from the given chromosomes

Throws:

NullPointerException - if chromosomes is null or one of its element.

IllegalArgumentException - if chromosome.length() < 1.

Since:

3.0