org.jgap
Class Chromosome

java.lang.Object
  org.jgap.BaseChromosome
      org.jgap.Chromosome

All Implemented Interfaces:

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

Direct Known Subclasses:

MyChromosome

public class Chromosome
extends BaseChromosome

Chromosomes represent potential solutions and consist of a fixed-length collection of genes. Each gene represents a discrete part of the solution. Each gene in the Chromosome may be backed by a different concrete implementation of the Gene interface, but all genes in a respective position (locus) must share the same concrete implementation across Chromosomes within a single population (genotype). In other words, gene 1 in a chromosome must share the same concrete implementation as gene 1 in all other chromosomes in the population.

Since:

1.0

See Also:

Serialized Form

Field Summary

protected double

m_fitnessValue Stores the fitness value of this Chromosome as determined by the active fitness function.

Fields inherited from class org.jgap.BaseChromosome

CHROM_DELIMITER, GENE_DELIMITER, GENE_DELIMITER_CLOSING, GENE_DELIMITER_HEADING

Fields inherited from interface org.jgap.IChromosome

S_ALLELES, S_APPLICATION_DATA, S_FITNESS_VALUE, S_SIZE

Constructor Summary

Chromosome()
Default constructor, only provided for dynamic instantiation.

Chromosome(Configuration a_configuration)
Constructor, provided for dynamic or minimal instantiation.

Chromosome(Configuration a_configuration, Gene[] a_initialGenes)
Constructs a Chromosome separate from any specific Configuration.

Chromosome(Configuration a_configuration, Gene[] a_initialGenes, IGeneConstraintChecker a_constraintChecker)
Constructs a Chromosome separate from any specific Configuration.

Chromosome(Configuration a_configuration, Gene a_sampleGene, int a_desiredSize)
Constructs a Chromosome of the given size separate from any specific Configuration.

Chromosome(Configuration a_configuration, Gene a_sampleGene, int a_desiredSize, IGeneConstraintChecker a_constraintChecker)

Chromosome(Configuration a_configuration, int a_desiredSize)
Constructor for specifying the number of genes.

Chromosome(Configuration a_configuration, java.lang.String a_persistentRepresentatuion)
Constructor, provided for instantiation via persistent representation.

Method Summary

protected double	calcFitnessValue()
protected void	checkGenes(Gene[] a_initialGenes) Helper: called by constructors only to verify the initial genes.
void	cleanup() Invoked when this Chromosome is no longer needed and should perform any necessary cleanup.
java.lang.Object	clone() Returns a copy of this Chromosome.
static java.lang.Object	cloneObject(Configuration a_config, java.lang.Object a_object, java.lang.Object a_master) Static convenience method.
protected java.lang.Object	cloneObject(java.lang.Object a_object) Clones an object by using clone handlers.
int	compareTo(java.lang.Object other) Compares the given Chromosome to this Chromosome.
boolean	equals(java.lang.Object other) Compares this Chromosome against the specified object.
java.lang.Object	getApplicationData() Retrieves the application-specific data that is attached to this Chromosome.
IGeneConstraintChecker	getConstraintChecker()
double	getFitnessValue() Retrieves the fitness value of this Chromosome, as determined by the active fitness function.
double	getFitnessValueDirectly()
java.util.List	getMultiObjectives()
int	hashCode() Retrieve a hash code for this Chromosome.
protected void	initFromGene(Gene a_sampleGene)
boolean	isCompareApplicationData()
boolean	isHandlerFor(java.lang.Object a_obj, java.lang.Class a_class) Determines whether the handler is suitable for the given object instance or class.
boolean	isSelectedForNextGeneration() Retrieves whether this Chromosome has been selected by the natural selector to continue to the next generation.
java.lang.Object	perform(java.lang.Object a_obj, java.lang.Class a_class, java.lang.Object a_params) Performs a task for the given object or class.
static IChromosome	randomInitialChromosome(Configuration a_configuration) Convenience method that returns a new Chromosome instance with its genes values (alleles) randomized.
void	setApplicationData(java.lang.Object a_newData) This sets the application-specific data that is attached to this Chromosome.
void	setCompareApplicationData(boolean a_doCompare) Should we also consider the application data when comparing?
void	setConstraintChecker(IGeneConstraintChecker a_constraintChecker) Sets the constraint checker to be used for this gene whenever method setAllele(Object) is called.
void	setFitnessValue(double a_newFitnessValue) Sets the fitness value of this Chromosome.
void	setFitnessValueDirectly(double a_newFitnessValue) Sets the fitness value of this Chromosome directly without any constraint checks, conversions or checks.
void	setGenes(Gene[] a_genes) Sets the genes for the chromosome.
void	setIsSelectedForNextGeneration(boolean a_isSelected) Sets whether this Chromosome has been selected by the natural selector to continue to the next generation or manually (e.g. via an add-method).
void	setMultiObjectives(java.util.List a_values)
java.lang.String	toString()
protected void	verify(IGeneConstraintChecker a_constraintChecker) Verifies the state of the chromosome.

Methods inherited from class org.jgap.BaseChromosome

createGene, decode, encode, getAge, getBusinessKey, getConfiguration, getGene, getGenes, getGenesPersistentRepresentation, getGenesPersistentRepresentation, getPersistentRepresentation, getUniqueID, getUniqueIDTemplate, increaseAge, increaseOperatedOn, operatedOn, resetAge, resetOperatedOn, setAge, setGene, setUniqueIDTemplate, setValueFromPersistentRepresentation, size, split

Methods inherited from class java.lang.Object

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

Field Detail

m_fitnessValue

protected double m_fitnessValue

Stores the fitness value of this Chromosome as determined by the active fitness function. A value of -1 indicates that this field has not yet been set with this Chromosome's fitness values (valid fitness values are always positive).

Since:

2.0 (until 1.1: type int)

Constructor Detail

Chromosome

public Chromosome()
           throws InvalidConfigurationException

Default constructor, only provided for dynamic instantiation.

Attention: The configuration used is the one set with the static method Genotype.setConfiguration.

Throws:

InvalidConfigurationException

Since:

2.4

Chromosome

public Chromosome(Configuration a_configuration)
           throws InvalidConfigurationException

Constructor, provided for dynamic or minimal instantiation.

Parameters:

a_configuration - the configuration to use

Throws:

InvalidConfigurationException

Since:

3.0

Chromosome

public Chromosome(Configuration a_configuration,
                  java.lang.String a_persistentRepresentatuion)
           throws InvalidConfigurationException,
                  UnsupportedRepresentationException

Constructor, provided for instantiation via persistent representation.

Parameters:

a_configuration - the configuration to use

a_persistentRepresentatuion - valid persistent representation that was most likely obtained via getPersistentRepresentation()

Throws:

InvalidConfigurationException

UnsupportedRepresentationException

Since:

3.2

Chromosome

public Chromosome(Configuration a_configuration,
                  int a_desiredSize)
           throws InvalidConfigurationException

Constructor for specifying the number of genes.

Parameters:

a_configuration - the configuration to use

a_desiredSize - number of genes the chromosome contains of

Throws:

InvalidConfigurationException

Since:

2.2

Chromosome

public Chromosome(Configuration a_configuration,
                  Gene a_sampleGene,
                  int a_desiredSize)
           throws InvalidConfigurationException

Constructs a Chromosome of the given size separate from any specific Configuration. This constructor will use the given sample Gene to construct a new Chromosome instance containing genes all of the same type as the sample Gene. This can be useful for constructing sample chromosomes that use the same Gene type for all of their genes and that are to be used to setup a Configuration object.

Parameters:

a_configuration - the configuration to use

a_sampleGene - a concrete sampleGene instance that will be used as a template for all of the genes in this Chromosome

a_desiredSize - the desired size (number of genes) of this Chromosome

Throws:

InvalidConfigurationException

Since:

1.0

Chromosome

public Chromosome(Configuration a_configuration,
                  Gene a_sampleGene,
                  int a_desiredSize,
                  IGeneConstraintChecker a_constraintChecker)
           throws InvalidConfigurationException

Throws:

InvalidConfigurationException

Chromosome

public Chromosome(Configuration a_configuration,
                  Gene[] a_initialGenes)
           throws InvalidConfigurationException

Constructs a Chromosome separate from any specific Configuration. This can be useful for constructing sample chromosomes that are to be used to setup a Configuration object.

Parameters:

a_configuration - the configuration to use

a_initialGenes - the initial genes of this Chromosome

Throws:

InvalidConfigurationException

Since:

1.0

Chromosome

public Chromosome(Configuration a_configuration,
                  Gene[] a_initialGenes,
                  IGeneConstraintChecker a_constraintChecker)
           throws InvalidConfigurationException

Constructs a Chromosome separate from any specific Configuration. This can be useful for constructing sample chromosomes that are to be used to setup a Configuration object. Additionally, a constraint checker can be specified. It is used right here to verify the validity of the gene types supplied.

Parameters:

a_configuration - the configuration to use

a_initialGenes - the initial genes of this Chromosome

a_constraintChecker - constraint checker to use

Throws:

InvalidConfigurationException - in case the constraint checker reports a configuration error

Since:

2.5

Method Detail

initFromGene

protected void initFromGene(Gene a_sampleGene)

checkGenes

protected void checkGenes(Gene[] a_initialGenes)

Helper: called by constructors only to verify the initial genes.

Parameters:

a_initialGenes - the initial genes of this Chromosome to verify

Since:

2.5

clone

public java.lang.Object clone()

Returns a copy of this Chromosome. The returned instance can evolve independently of this instance. Note that, if possible, this method will first attempt to acquire a Chromosome instance from the active ChromosomePool (if any) and set its value appropriately before returning it. If that is not possible, then a new Chromosome instance will be constructed and its value set appropriately before returning.

Specified by:

clone in interface ICloneable

Specified by:

clone in class BaseChromosome

Returns:

copy of this Chromosome

Throws:

java.lang.IllegalStateException - instead of CloneNotSupportedException

Since:

1.0

cloneObject

protected java.lang.Object cloneObject(java.lang.Object a_object)
                                throws java.lang.Exception

Clones an object by using clone handlers. If no deep cloning possible, then return the reference.

Parameters:

a_object - the object to clone

Returns:

the cloned object, or the object itself if no coning supported

Throws:

java.lang.Exception

Since:

2.6

cloneObject

public static java.lang.Object cloneObject(Configuration a_config,
                                           java.lang.Object a_object,
                                           java.lang.Object a_master)
                                    throws java.lang.Exception

Static convenience method. Clones an object by using clone handlers. If no deep cloning possible, then return the reference.

Parameters:

a_config - a valid configuration to obtain the JGAPFactory from

a_object - the object to clone

a_master - the super object of a_object, e.g. a chromosome in case of application to be cloned

Returns:

the cloned object, or the object itself if no coning supported

Throws:

java.lang.Exception

Since:

3.5

getFitnessValue

public double getFitnessValue()

Retrieves the fitness value of this Chromosome, as determined by the active fitness function. If a bulk fitness function is in use and has not yet assigned a fitness value to this Chromosome, then -1 is returned.

Attention: should not be called from toString() as the fitness value would be computed if it was initial!

Returns:

a positive double value representing the fitness of this Chromosome, or -1 if a bulk fitness function is in use and has not yet assigned a fitness value to this Chromosome

Since:

2.0

getFitnessValueDirectly

public double getFitnessValueDirectly()

Returns:

the lastly computed fitness value, or FitnessFunction.NO_FITNESS_VALUE in case no value has been computed yet.

calcFitnessValue

protected double calcFitnessValue()

Returns:

fitness value of this chromosome determined via the registered fitness function

Since:

2.4

setFitnessValue

public void setFitnessValue(double a_newFitnessValue)

Sets the fitness value of this Chromosome. This method is for use by bulk fitness functions and should not be invokved from anything else (except test cases).

Parameters:

a_newFitnessValue - a positive integer representing the fitness of this Chromosome

Since:

1.0

setFitnessValueDirectly

public void setFitnessValueDirectly(double a_newFitnessValue)

Sets the fitness value of this Chromosome directly without any constraint checks, conversions or checks. Only use if you know what you do.

Parameters:

a_newFitnessValue - a positive integer representing the fitness of this Chromosome

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this Chromosome, useful for display purposes

Since:

1.0

randomInitialChromosome

public static IChromosome randomInitialChromosome(Configuration a_configuration)
                                           throws InvalidConfigurationException

Convenience method that returns a new Chromosome instance with its genes values (alleles) randomized. Note that, if possible, this method will acquire a Chromosome instance from the active ChromosomePool (if any) and then randomize its gene values before returning it. If a Chromosome cannot be acquired from the pool, then a new instance will be constructed and its gene values randomized before returning it.

Parameters:

a_configuration - the configuration to use

Returns:

randomly initialized Chromosome

Throws:

InvalidConfigurationException - if the given Configuration instance is invalid

java.lang.IllegalArgumentException - if the given Configuration instance is null

Since:

1.0

equals

public boolean equals(java.lang.Object other)

Compares this Chromosome against the specified object. The result is true if and the argument is an instance of the Chromosome class and has a set of genes equal to this one.

Overrides:

equals in class java.lang.Object

Parameters:

other - the object to compare against

Returns:

true: if the objects are the same, false otherwise

Since:

1.0

hashCode

public int hashCode()

Retrieve a hash code for this Chromosome. Does not considers the order of the Genes for all cases (especially when gene is empty).

Overrides:

hashCode in class java.lang.Object

Returns:

the hash code of this Chromosome

Since:

1.0

compareTo

public int compareTo(java.lang.Object other)

Compares the given Chromosome to this Chromosome. This chromosome is considered to be "less than" the given chromosome if it has a fewer number of genes or if any of its gene values (alleles) are less than their corresponding gene values in the other chromosome.

Parameters:

other - the Chromosome against which to compare this chromosome

Returns:

a negative number if this chromosome is "less than" the given chromosome, zero if they are equal to each other, and a positive number if this chromosome is "greater than" the given chromosome

Since:

1.0

setIsSelectedForNextGeneration

public void setIsSelectedForNextGeneration(boolean a_isSelected)

Sets whether this Chromosome has been selected by the natural selector to continue to the next generation or manually (e.g. via an add-method).

Parameters:

a_isSelected - true if this Chromosome has been selected, false otherwise

Since:

1.0

isSelectedForNextGeneration

public boolean isSelectedForNextGeneration()

Retrieves whether this Chromosome has been selected by the natural selector to continue to the next generation.

Returns:

true if this Chromosome has been selected, false otherwise

Since:

1.0

cleanup

public void cleanup()

Invoked when this Chromosome is no longer needed and should perform any necessary cleanup. Note that this method will attempt to release this Chromosome instance to the active ChromosomePool, if any.

Since:

1.0

setApplicationData

public void setApplicationData(java.lang.Object a_newData)

This sets the application-specific data that is attached to this Chromosome. Attaching application-specific data may be useful for some applications when it comes time to evaluate this Chromosome in the fitness function. JGAP ignores this data, except for cloning and comparison (latter only if opted in via setCompareApplicationData(..))

Parameters:

a_newData - the new application-specific data to attach to this Chromosome. Should be an instance of IApplicationData

Since:

1.1

getApplicationData

public java.lang.Object getApplicationData()

Retrieves the application-specific data that is attached to this Chromosome. Attaching application-specific data may be useful for some applications when it comes time to evaluate this Chromosome in the fitness function. JGAP ignores this data functionally.

Returns:

the application-specific data previously attached to this Chromosome, or null if there is no data attached

Since:

1.1

setGenes

public void setGenes(Gene[] a_genes)
              throws InvalidConfigurationException

Sets the genes for the chromosome.

Specified by:

setGenes in interface IChromosome

Overrides:

setGenes in class BaseChromosome

Parameters:

a_genes - the genes to set for the chromosome

Throws:

InvalidConfigurationException - in case constraint checker is provided

setCompareApplicationData

public void setCompareApplicationData(boolean a_doCompare)

Should we also consider the application data when comparing? Default is "false" as "true" means a Chromosome is losing its identity when application data is set differently!

Parameters:

a_doCompare - true: consider application data in method compareTo

Since:

2.2

isCompareApplicationData

public boolean isCompareApplicationData()

setConstraintChecker

public void setConstraintChecker(IGeneConstraintChecker a_constraintChecker)
                          throws InvalidConfigurationException

Sets the constraint checker to be used for this gene whenever method setAllele(Object) is called.

Parameters:

a_constraintChecker - the constraint checker to be set

Throws:

InvalidConfigurationException

Since:

2.5

getConstraintChecker

public IGeneConstraintChecker getConstraintChecker()

Returns:

IGeneConstraintChecker the constraint checker to be used whenever method setGenes(Gene[]) is called.

Since:

2.5

verify

protected void verify(IGeneConstraintChecker a_constraintChecker)
               throws InvalidConfigurationException

Verifies the state of the chromosome. Especially takes care of the given constraint checker.

Parameters:

a_constraintChecker - the constraint checker to verify

Throws:

InvalidConfigurationException

Since:

2.5

isHandlerFor

public boolean isHandlerFor(java.lang.Object a_obj,
                            java.lang.Class a_class)

Determines whether the handler is suitable for the given object instance or class.

Parameters:

a_obj - the object instance to check

a_class - the class to check, alternatively if no object instance is available (some handlers could need to get an object and would always return false if only a class is provided)

Returns:

true: handler suitable for given object or class

perform

public java.lang.Object perform(java.lang.Object a_obj,
                                java.lang.Class a_class,
                                java.lang.Object a_params)
                         throws java.lang.Exception

Performs a task for the given object or class. For some handlers, additional parameters are necessary, which could be provided.

Parameters:

a_obj - the object instance to perform the handler task for

a_class - the class to perform the handler task for, in case no object instance is available (some handlers could need to get an object and would always throw an exception if only a class is provided)

a_params - optional parameters needed for the handler to perform its task

Returns:

Object

Throws:

java.lang.Exception - in case of any error

setMultiObjectives

public void setMultiObjectives(java.util.List a_values)

getMultiObjectives

public java.util.List getMultiObjectives()