evSOLve.JEvolution.chromosomes

Class BitChromosome

java.lang.Object

evSOLve.JEvolution.chromosomes.Chromosome

evSOLve.JEvolution.chromosomes.BitChromosome

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

VariableBitChromosome

public class BitChromosome
extends Chromosome

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<java.lang.Boolean>	bases The carrier of genetic information.

Fields inherited from class evSOLve.JEvolution.chromosomes.Chromosome

BIASED, crossoverPoints, crossoverRate, LAPLACE, length, mutationRate, soupType

Constructor Summary

Constructors

Constructor and Description
BitChromosome() The standard constructor with default length.
BitChromosome(Element c) Creates a BitChromosome via XML.
BitChromosome(int length) Constructs a chromosome of given length.

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone() A proper clone.
void	doCrossover(Chromosome father) k-point Crossover.
void	doMutation() Bit flip mutation.
boolean	equals(java.lang.Object o) An efficient check for equality.
void	fromString(java.lang.String b) Create bases from String.
java.lang.Object	getBases() Return the genetic information.
int	hashCode() An efficient hash code.
void	mixSoup() Initial creation of alleles.
java.lang.String	toString() Convert chromosome to string.

Methods inherited from class evSOLve.JEvolution.chromosomes.Chromosome

create, getCrossoverPoints, getCrossoverRate, getLength, getMutationRate, getSoupType, setCrossoverPoints, setCrossoverRate, setLength, setMutationRate, setSoupType, toXml

Methods inherited from class java.lang.Object

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

Field Detail

bases

protected java.util.List<java.lang.Boolean> bases

The carrier of genetic information.

Constructor Detail

BitChromosome

public BitChromosome()

The standard constructor with default length.

BitChromosome

public BitChromosome(int length)

Constructs a chromosome of given length.

Parameters:

length - the number of bases

BitChromosome

public BitChromosome(Element c)

Creates a BitChromosome via XML.

Parameters:

c - an XML Chromosome element

Method Detail

clone

public java.lang.Object clone()

A proper clone.

Overrides:

clone in class Chromosome

Returns:

Object The clone.

equals

public boolean equals(java.lang.Object o)

An efficient check for equality. Uses List.equals().

Specified by:

equals in class Chromosome

Returns:

the equality of the passed object with this object.

hashCode

public int hashCode()

An efficient hash code. Uses BitSet.hashCode().

Specified by:

hashCode in class Chromosome

Returns:

hashCode A correct hash code.

doMutation

public void doMutation()

Bit flip mutation.

Specified by:

doMutation in class Chromosome

doCrossover

public void doCrossover(Chromosome father)

k-point Crossover. By now k may be only 1 or 2!!

Specified by:

doCrossover in class Chromosome

Parameters:

father - A parent Chromosome (technically already a child).

mixSoup

public void mixSoup()

Initial creation of alleles.

Specified by:

mixSoup in class Chromosome

getBases

public java.lang.Object getBases()

Return the genetic information.

Specified by:

getBases in class Chromosome

Returns:

bases a BitSet

toString

public java.lang.String toString()

Convert chromosome to string. The MSB has index 0.

Specified by:

toString in class Chromosome

fromString

public void fromString(java.lang.String b)

Create bases from String.

Specified by:

fromString in class Chromosome

Parameters:

b - a String describing the bases