org.jgap

Class BaseChromosome

java.lang.Object

org.jgap.BaseChromosome

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable, IBusinessKey, IChromosome, IHandler, IInitializer, IPersistentRepresentation, IUniqueKey, ICloneable

Direct Known Subclasses:

Chromosome

public abstract class BaseChromosome
extends java.lang.Object
implements IChromosome, IInitializer, IPersistentRepresentation, IBusinessKey

Base class for any implementation of interface IChromosome.

Since:

3.0

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CHROM_DELIMITER Separates chromosome-related information.
static java.lang.String	GENE_DELIMITER This field separates gene class name from the gene persistent representation string.
static java.lang.String	GENE_DELIMITER_CLOSING Represents the closing delimiter that is used to separate genes in the persistent representation of Chromosome instances.
static java.lang.String	GENE_DELIMITER_HEADING Represents the heading delimiter that is used to separate genes in the persistent representation of Chromosome instances.

Fields inherited from interface org.jgap.IChromosome

S_ALLELES, S_APPLICATION_DATA, S_FITNESS_VALUE, S_SIZE

Constructor Summary

Constructors

Constructor and Description
BaseChromosome(Configuration a_configuration) The only constructor in this class.

Method Summary

Modifier and Type	Method and Description
abstract java.lang.Object	clone() Creates and returns a copy of this object.
int	getAge()
java.lang.String	getBusinessKey()
Configuration	getConfiguration()
Gene	getGene(int a_desiredLocus) Returns the Gene at the given index (locus) within the Chromosome.
Gene[]	getGenes() Retrieves the set of genes that make up this Chromosome.
java.lang.StringBuffer	getGenesPersistentRepresentation()
void	getGenesPersistentRepresentation(java.lang.StringBuffer a_buffer) Retrieves the persistent representation of the chromosome by considering its genes.
java.lang.String	getPersistentRepresentation() Returns a persistent representation of this chromosome, see interface Gene for description.
java.lang.String	getUniqueID()
java.lang.String	getUniqueIDTemplate(int a_index)
void	increaseAge() Increases the number of evolutionary rounds of chromosome in which it has not been changed by one.
void	increaseOperatedOn() Increase information of number of genetic operations performed on chromosome in current evolution round.
int	operatedOn()
void	resetAge() Reset age of chromosome because it has been changed.
void	resetOperatedOn() Resets the information of how many genetic operators have been performed on the chromosome in the current round of evolution.
void	setAge(int a_age)
void	setGene(int a_index, Gene a_gene)
void	setGenes(Gene[] a_genes) Sets the genes for the chromosome.
void	setUniqueIDTemplate(java.lang.String a_templateID, int a_index) A template is a chromosome that is the logical predecessor of the current chromosome.
void	setValueFromPersistentRepresentation(java.lang.String a_representation) Counterpart of getPersistentRepresentation.
int	size() Returns the size of this Chromosome (the number of genes it contains).

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.jgap.IChromosome

cleanup, getApplicationData, getFitnessValue, getFitnessValueDirectly, isSelectedForNextGeneration, setApplicationData, setConstraintChecker, setFitnessValue, setFitnessValueDirectly, setIsSelectedForNextGeneration

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.jgap.IHandler

isHandlerFor, perform

Field Detail

GENE_DELIMITER

public static final java.lang.String GENE_DELIMITER

This field separates gene class name from the gene persistent representation string. '*' does not work properly with URLEncoder!

See Also:

Constant Field Values

GENE_DELIMITER_HEADING

public static final java.lang.String GENE_DELIMITER_HEADING

Represents the heading delimiter that is used to separate genes in the persistent representation of Chromosome instances.

See Also:

Constant Field Values

GENE_DELIMITER_CLOSING

public static final java.lang.String GENE_DELIMITER_CLOSING

Represents the closing delimiter that is used to separate genes in the persistent representation of Chromosome instances.

See Also:

Constant Field Values

CHROM_DELIMITER

public static final java.lang.String CHROM_DELIMITER

Separates chromosome-related information.

See Also:

Constant Field Values

Constructor Detail

BaseChromosome

public BaseChromosome(Configuration a_configuration)
               throws InvalidConfigurationException

The only constructor in this class. Sets the immutable configuration.

Parameters:

a_configuration - the configuration to set

Throws:

InvalidConfigurationException - if configuration is null

Since:

3.0

Method Detail

getUniqueID

public java.lang.String getUniqueID()

Specified by:

getUniqueID in interface IUniqueKey

Returns:

unique ID of the chromosome, which allows to distinct this instance from others, in the best case worldwide

Since:

3.5

setUniqueIDTemplate

public void setUniqueIDTemplate(java.lang.String a_templateID,
                                int a_index)

A template is a chromosome that is the logical predecessor of the current chromosome. A template can occur in mutation or crossing over. In the latter case can be at least two template chromosomes. This is why in this setter method the parameter a_index exists.

Specified by:

setUniqueIDTemplate in interface IUniqueKey

Parameters:

a_templateID - the unique ID of the template

a_index - the index of the template, e.g. in crossing over for the second candidate chromosome this is 2

Since:

3.5

getUniqueIDTemplate

public java.lang.String getUniqueIDTemplate(int a_index)

Specified by:

getUniqueIDTemplate in interface IUniqueKey

Parameters:

a_index - the index of the template to retrieve the key for

Returns:

String

Since:

3.5

getConfiguration

public Configuration getConfiguration()

Specified by:

getConfiguration in interface IChromosome

Returns:

the configuration used

Since:

3.0

clone

public abstract java.lang.Object clone()

Creates and returns a copy of this object.

Specified by:

clone in interface ICloneable

Overrides:

clone in class java.lang.Object

Returns:

a clone of this instance

Throws:

java.lang.IllegalStateException - instead of CloneNotSupportedException

Since:

3.0

increaseAge

public void increaseAge()

Increases the number of evolutionary rounds of chromosome in which it has not been changed by one.

Specified by:

increaseAge in interface IChromosome

Since:

3.2

resetAge

public void resetAge()

Reset age of chromosome because it has been changed.

Specified by:

resetAge in interface IChromosome

Since:

3.2

getAge

public int getAge()

Specified by:

getAge in interface IChromosome

Returns:

0: Chromosome newly created in this generation. This means it does not need being crossed over with another newly created one

Since:

3.2

setAge

public void setAge(int a_age)

Specified by:

setAge in interface IChromosome

Parameters:

a_age - set the age of the chromosome, see BestChromosomesSelector for a use-case

Since:

3.3.3

increaseOperatedOn

public void increaseOperatedOn()

Increase information of number of genetic operations performed on chromosome in current evolution round.

Specified by:

increaseOperatedOn in interface IChromosome

Since:

3.2

resetOperatedOn

public void resetOperatedOn()

Resets the information of how many genetic operators have been performed on the chromosome in the current round of evolution.

Specified by:

resetOperatedOn in interface IChromosome

Since:

3.2

operatedOn

public int operatedOn()

Specified by:

operatedOn in interface IChromosome

Returns:

number of genetic operations performed on chromosome in current evolution round

Since:

3.2

getGenes

public Gene[] getGenes()

Retrieves the set of genes that make up this Chromosome. This method exists primarily for the benefit of GeneticOperators that require the ability to manipulate Chromosomes at a low level.

Specified by:

getGenes in interface IChromosome

Returns:

an array of the Genes contained within this Chromosome

Since:

1.0

setGenes

public void setGenes(Gene[] a_genes)
              throws InvalidConfigurationException

Sets the genes for the chromosome.

Specified by:

setGenes in interface IChromosome

Parameters:

a_genes - the genes to set for the chromosome

Throws:

InvalidConfigurationException - in case constraint checker is provided

Since:

3.2 (previously in class Chromosome)

getGene

public Gene getGene(int a_desiredLocus)

Returns the Gene at the given index (locus) within the Chromosome. The first gene is at index zero and the last gene is at the index equal to the size of this Chromosome - 1.

Specified by:

getGene in interface IChromosome

Parameters:

a_desiredLocus - index of the gene value to be returned

Returns:

Gene at the given index

Since:

1.0

setGene

public void setGene(int a_index,
                    Gene a_gene)

size

public int size()

Returns the size of this Chromosome (the number of genes it contains). A Chromosome's size is constant and will not change, until setGenes(...) is used.

Specified by:

size in interface IChromosome

Returns:

number of genes contained within this Chromosome instance

Since:

1.0

getPersistentRepresentation

public java.lang.String getPersistentRepresentation()

Returns a persistent representation of this chromosome, see interface Gene for description. Similar to CompositeGene's routine. But does not include all information of the chromosome (yet).

Specified by:

getPersistentRepresentation in interface IPersistentRepresentation

Returns:

string representation of this Chromosome's relevant parts of its current state

Throws:

java.lang.UnsupportedOperationException

Since:

3.2

getGenesPersistentRepresentation

public java.lang.StringBuffer getGenesPersistentRepresentation()

Returns:

the persistent representation of the chromosome by considering its genes.

getBusinessKey

public java.lang.String getBusinessKey()

Specified by:

getBusinessKey in interface IBusinessKey

Returns:

business key of the chromosome

Since:

3.2

getGenesPersistentRepresentation

public void getGenesPersistentRepresentation(java.lang.StringBuffer a_buffer)

Retrieves the persistent representation of the chromosome by considering its genes.

Parameters:

a_buffer - the variable to store the persistent representation in

setValueFromPersistentRepresentation

public void setValueFromPersistentRepresentation(java.lang.String a_representation)
                                          throws UnsupportedRepresentationException

Counterpart of getPersistentRepresentation.

Specified by:

setValueFromPersistentRepresentation in interface IPersistentRepresentation

Parameters:

a_representation - the string representation retrieved from a prior call to the getPersistentRepresentation() method

Throws:

UnsupportedRepresentationException

Since:

3.2