evSOLve.JEvolution.chromosomes

Class IntChromosome

java.lang.Object

evSOLve.JEvolution.chromosomes.Chromosome

evSOLve.JEvolution.chromosomes.IntChromosome

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

PermChromosome

public class IntChromosome
extends Chromosome

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<java.lang.Integer>	bases The genetic information carrier.
protected int	high The largest integer encoded.
protected int	low The lowest integer encoded.

Fields inherited from class evSOLve.JEvolution.chromosomes.Chromosome

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

Constructor Summary

Constructors

Constructor and Description
IntChromosome() Creates a chromosome with default length.
IntChromosome(Element c) Creates an IntChromosome via XML.
IntChromosome(int length) Constructs a chromosome of given length.

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone() A proper clone, cloning the bases deeply by creating new objects.
void	doCrossover(Chromosome father) Standard 1-, or 2-Point Crossover.
void	doMutation() Mutate by randomly setting a base to a new integer value within 'low' and 'high' (both included).
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	getHigh() Gives higher bound of integer encoding.
int	getLow() Gives lower bound of integer encoding.
int	hashCode() An efficient hash code.
void	mixSoup() Initial creation of alleles.
void	setHigh(int high) Changes higher bound of integer encoding.
void	setLow(int low) Changes lower bound of integer encoding.
java.lang.String	toString() Convert chromosome to string.
Element	toXml(Element parent) Saves the current state to XML.

Methods inherited from class evSOLve.JEvolution.chromosomes.Chromosome

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

Methods inherited from class java.lang.Object

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

Field Detail

bases

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

The genetic information carrier.

low

protected int low

The lowest integer encoded.

high

protected int high

The largest integer encoded.

Constructor Detail

IntChromosome

public IntChromosome()

Creates a chromosome with default length.

IntChromosome

public IntChromosome(int length)

Constructs a chromosome of given length.

Parameters:

length - the number of bases

IntChromosome

public IntChromosome(Element c)

Creates an IntChromosome via XML.

Parameters:

c - an XML Chromosome element

Method Detail

clone

public java.lang.Object clone()

A proper clone, cloning the bases deeply by creating new objects.

Overrides:

clone in class Chromosome

Returns:

Object the cloned IntChromosome

equals

public boolean equals(java.lang.Object o)

An efficient check for equality. It only checks the bases, first, if the number of bases is equal, and then if the base values are the same.

Specified by:

equals in class Chromosome

Returns:

equal The equality of the passed object with this object.

hashCode

public int hashCode()

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

Specified by:

hashCode in class Chromosome

Returns:

hashCode A correct hash code.

doMutation

public void doMutation()

Mutate by randomly setting a base to a new integer value within 'low' and 'high' (both included). It may occur that the new value is equal to the old.

Specified by:

doMutation in class Chromosome

doCrossover

public void doCrossover(Chromosome father)

Standard 1-, or 2-Point Crossover.

Specified by:

doCrossover in class Chromosome

Parameters:

father - A parent Chromosome.

mixSoup

public void mixSoup()

Initial creation of alleles. Integers are randomly drawn from uniform distribution (eventually biased).

Specified by:

mixSoup in class Chromosome

getLow

public int getLow()

Gives lower bound of integer encoding.

Returns:

the smallest integer encoded

setLow

public void setLow(int low)

Changes lower bound of integer encoding.

Parameters:

low - the smallest integer encoded

getHigh

public int getHigh()

Gives higher bound of integer encoding.

Returns:

the largest integer encoded

setHigh

public void setHigh(int high)

Changes higher bound of integer encoding.

Parameters:

high - the largest integer encoded

getBases

public java.lang.Object getBases()

Return the genetic information.

Specified by:

getBases in class Chromosome

Returns:

bases The bases.

toString

public java.lang.String toString()

Convert chromosome to string. The first base (the rightmost) has index 0.

Specified by:

toString in class Chromosome

fromString

public void fromString(java.lang.String b)

Create bases from String. The syntax of the string must be like this: "1|2|3|4|", where the numbers are just examples, but the '|' character must be exactly at the given spots.

Specified by:

fromString in class Chromosome

Parameters:

b - a String describing the bases

toXml

public Element toXml(Element parent)

Saves the current state to XML.

Overrides:

toXml in class Chromosome

Parameters:

parent - the JDOM parent element

Returns:

the Chromosome element