org.jgap

Class BaseGene

java.lang.Object

org.jgap.BaseGene

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, Gene, IBusinessKey, IUniqueKey

Direct Known Subclasses:

AbstractSupergene, BooleanGene, CompositeGene, FixedBinaryGene, MapGene, NumberGene, SetGene, StringGene

public abstract class BaseGene
extends java.lang.Object
implements Gene, IBusinessKey

Abstract base class for all genes. Provides default implementations.

Since:

2.2

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static double	DELTA Delta, useful for comparing doubles and floats.
static java.lang.String	S_APPLICATION_DATA Constants for toString()

Fields inherited from interface org.jgap.Gene

PERSISTENT_FIELD_DELIMITER

Constructor Summary

Constructors

Constructor and Description
BaseGene(Configuration a_configuration)

Method Summary

Modifier and Type	Method and Description
void	cleanup() Executed by the genetic engine when this Gene instance is no longer needed and should perform any necessary resource cleanup.
boolean	equals(java.lang.Object a_other) Compares this Gene with the given object and returns true if the other object is a Gene of the same type and has the same value (allele) as this Gene.
java.lang.Object	getAllele() Retrieves the allele value represented by this Gene.
java.lang.Object	getApplicationData() Retrieves the application-specific data that is attached to this Gene.
java.lang.String	getBusinessKey()
Configuration	getConfiguration()
IGeneConstraintChecker	getConstraintChecker()
double	getEnergy()
java.lang.String	getUniqueID()
java.lang.String	getUniqueIDTemplate(int a_index)
int	hashCode() Retrieves the hash code value for a Gene.
boolean	isCompareApplicationData()
Gene	newGene() Provides implementation-independent means for creating new Gene instances.
void	setApplicationData(java.lang.Object a_newData) This sets the application-specific data that is attached to this Gene.
void	setCompareApplicationData(boolean a_doCompare) Should we also consider the application data when comparing? Default is "false" as "true" means a Gene is losing its identity when application data is set differently!
void	setConstraintChecker(IGeneConstraintChecker a_constraintChecker) Sets the constraint checker to be used for this gene whenever method setAllele(Object) is called.
void	setEnergy(double a_energy) Sets the energy of the gene
void	setUniqueIDTemplate(java.lang.String a_templateID, int a_index) A template is a gene that is the logical predecessor of the current gene.
int	size()
java.lang.String	toString() Retrieves a string representation of this Gene's value that may be useful for display purposes.

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.jgap.Gene

applyMutation, getPersistentRepresentation, setAllele, setToRandomValue, setValueFromPersistentRepresentation

Methods inherited from interface java.lang.Comparable

compareTo

Field Detail

S_APPLICATION_DATA

public static final java.lang.String S_APPLICATION_DATA

Constants for toString()

See Also:

Constant Field Values

DELTA

public static final double DELTA

Delta, useful for comparing doubles and floats.

See Also:

Constant Field Values

Constructor Detail

BaseGene

public BaseGene(Configuration a_configuration)
         throws InvalidConfigurationException

Parameters:

a_configuration - the configuration to use

Throws:

InvalidConfigurationException

Since:

3.0

Method Detail

getAllele

public java.lang.Object getAllele()

Retrieves the allele value represented by this Gene.

Specified by:

getAllele in interface Gene

Returns:

the allele value of this Gene

Since:

1.0

hashCode

public int hashCode()

Retrieves the hash code value for a Gene. Override if another hashCode() implementation is necessary or more appropriate than this default implementation.

Overrides:

hashCode in class java.lang.Object

Returns:

this Gene's hash code

Since:

1.0

cleanup

public void cleanup()

Executed by the genetic engine when this Gene instance is no longer needed and should perform any necessary resource cleanup. If you need a special cleanup, override this method.

Specified by:

cleanup in interface Gene

Since:

1.0

toString

public java.lang.String toString()

Retrieves a string representation of this Gene's value that may be useful for display purposes.

Specified by:

toString in interface Gene

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this Gene's value

Since:

1.0

size

public int size()

Specified by:

size in interface Gene

Returns:

the size of the gene, i.e the number of atomic elements. Always 1 for non-composed Gene types. Override for composed Gene types

Since:

1.0

equals

public boolean equals(java.lang.Object a_other)

Compares this Gene with the given object and returns true if the other object is a Gene of the same type and has the same value (allele) as this Gene. Otherwise it returns false.

Overrides:

equals in class java.lang.Object

Parameters:

a_other - the object to compare to this Gene for equality

Returns:

true if this Gene is equal to the given object, false otherwise

Since:

1.1

getEnergy

public double getEnergy()

Specified by:

getEnergy in interface Gene

Returns:

energy of the gene

Since:

2.3

setEnergy

public void setEnergy(double a_energy)

Sets the energy of the gene

Specified by:

setEnergy in interface Gene

Parameters:

a_energy - the energy to set

Since:

2.3

setApplicationData

public void setApplicationData(java.lang.Object a_newData)

This sets the application-specific data that is attached to this Gene. Attaching application-specific data may be useful for some applications when it comes time to distinguish a Gene from another. JGAP ignores this data functionally.

Specified by:

setApplicationData in interface Gene

Parameters:

a_newData - the new application-specific data to attach to this Gene

Since:

2.4

getApplicationData

public java.lang.Object getApplicationData()

Retrieves the application-specific data that is attached to this Gene. Attaching application-specific data may be useful for some applications when it comes time to distinguish a Gene from another. JGAP ignores this data functionally.

Specified by:

getApplicationData in interface Gene

Returns:

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

Since:

2.4

setCompareApplicationData

public void setCompareApplicationData(boolean a_doCompare)

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

Specified by:

setCompareApplicationData in interface Gene

Parameters:

a_doCompare - true: consider application data in method compareTo

Since:

2.4

isCompareApplicationData

public boolean isCompareApplicationData()

Specified by:

isCompareApplicationData in interface Gene

setConstraintChecker

public void setConstraintChecker(IGeneConstraintChecker a_constraintChecker)

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

Specified by:

setConstraintChecker in interface Gene

Parameters:

a_constraintChecker - the constraint checker to be set

Since:

2.5 (moved from CompositeGene, where it was since 2.0)

getConstraintChecker

public IGeneConstraintChecker getConstraintChecker()

Returns:

IGeneConstraintChecker the constraint checker to be used whenever method setAllele(Object) is called.

Since:

2.5 (moved from CompositeGene, where it was since 2.0)

newGene

public Gene newGene()

Provides implementation-independent means for creating new Gene instances. The new instance that is created and returned should be setup with any implementation-dependent configuration that this Gene instance is setup with (aside from the actual value, of course). For example, if this Gene were setup with bounds on its value, then the Gene instance returned from this method should also be setup with those same bounds. This is important, as the JGAP core will invoke this method on each Gene in the sample Chromosome in order to create each new Gene in the same respective gene position for a new Chromosome.

Specified by:

newGene in interface Gene

Returns:

a new Gene instance of the same type and with the same setup as this concrete Gene

Since:

2.6 (since 1.0 in IntegerGene)

getConfiguration

public Configuration getConfiguration()

Specified by:

getConfiguration in interface Gene

Returns:

the configuration set

Since:

3.0

getBusinessKey

public java.lang.String getBusinessKey()

Specified by:

getBusinessKey in interface IBusinessKey

Returns:

business key

getUniqueID

public java.lang.String getUniqueID()

Specified by:

getUniqueID in interface IUniqueKey

Returns:

unique ID of the gene, 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 gene that is the logical predecessor of the current gene. A template can occur in mutation or crossing over. In the latter case can be at least two template genes. 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 gene 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