org.jgap.impl
Class CompositeGene

java.lang.Object
  org.jgap.BaseGene
      org.jgap.impl.CompositeGene

All Implemented Interfaces:

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

public class CompositeGene
extends BaseGene
implements ICompositeGene, IPersistentRepresentation

Ordered container for multiple genes Has the same interface as a single gene and could be used accordingly. Use the addGene(Gene) method to add single genes (possibly CompositeGenes) after construction, an empty CompositeGene without genes makes no sense. Beware that there are two equalities defined for a CompositeGene in respect to its contained genes: a) Two genes are (only) equal if they are identical b) Two genes are (seen as) equal if their equals method returns true This influences several methods such as addGene. Notice that it is safer to use addGene(a_gene, false) than addGene(a_gene, true) because the second variant only allows to add genes not seen as equal to already added genes in respect to their equals function. But: the equals function returns true for two different DoubleGenes (e.g.) just after their creation. If no specific (and hopefully different) allele is set for these DoubleGenes they are seen as equal!

Since:

1.1

See Also:

Serialized Form

Field Summary

static java.lang.String	GENE_DELIMITER This field separates gene class name from the gene persistent representation string. '*' does not work properly with URLEncoder!
static java.lang.String	GENE_DELIMITER_CLOSING Represents the closing delimiter that is used to separate genes in the persistent representation of CompositeGene instances.
static java.lang.String	GENE_DELIMITER_HEADING Represents the heading delimiter that is used to separate genes in the persistent representation of CompositeGene instances.

Fields inherited from class org.jgap.BaseGene

DELTA, S_APPLICATION_DATA

Fields inherited from interface org.jgap.Gene

PERSISTENT_FIELD_DELIMITER

Constructor Summary

CompositeGene()
Default constructor.

CompositeGene(Configuration a_config)

CompositeGene(Configuration a_config, Gene a_geneTypeAllowed)
Allows to specify which Gene implementation is allowed to be added to the CompositeGene.

Method Summary

void	addGene(Gene a_gene) Adds a gene to the CompositeGene.
void	addGene(Gene a_gene, boolean a_strict) Adds a gene to the CompositeGene's container.
void	applyMutation(int a_index, double a_percentage) Don't use this method, is makes no sense here.
void	cleanup() Executed by the genetic engine when this Gene instance is no longer needed and should perform any necessary resource cleanup.
int	compareTo(java.lang.Object a_other) Compares this CompositeGene with the specified object for order.
boolean	containsGeneByIdentity(Gene gene) Checks whether a specific gene is already contained.
protected Gene	createGene(java.lang.String a_geneClassName, java.lang.String a_persistentRepresentation) Creates a new instance of gene.
Gene	geneAt(int a_index)
java.lang.Object	getAllele() Retrieves the value represented by this Gene.
java.lang.String	getBusinessKey()
java.util.List<Gene>	getGenes()
Gene	getGeneTypeAllowed()
protected java.lang.Object	getInternalValue() This method is not called internally because BaseGene.getAllele() is overridden here!
java.lang.String	getPersistentRepresentation() See interface Gene for description.
int	hashCode() Retrieves the hash code value for this Gene.
boolean	isEmpty()
protected Gene	newGeneInternal() Provides an implementation-independent means for creating new Gene instances.
boolean	removeGene(Gene a_gene) Removes the given gene from the collection of genes.
boolean	removeGeneByIdentity(Gene a_gene) Removes the given gene from the collection of genes.
void	setAllele(java.lang.Object a_newValue) Sets the value of the contained Genes to the new given value.
void	setToRandomValue(RandomGenerator a_numberGenerator) See interface Gene for description.
void	setValueFromPersistentRepresentation(java.lang.String a_representation) See interface Gene for description.
int	size()
protected static java.util.List	split(java.lang.String a_string) Splits a_string into individual gene representations.
java.lang.String	toString() Retrieves a string representation of this CompositeGene's value that may be useful for display purposes.

Methods inherited from class org.jgap.BaseGene

compareApplicationData, decode, encode, equals, getApplicationData, getConfiguration, getConstraintChecker, getEnergy, getUniqueID, getUniqueIDTemplate, isCompareApplicationData, newGene, setApplicationData, setCompareApplicationData, setConstraintChecker, setEnergy, setUniqueIDTemplate

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.jgap.Gene

getApplicationData, getConfiguration, getEnergy, isCompareApplicationData, newGene, setApplicationData, setCompareApplicationData, setConstraintChecker, setEnergy

Methods inherited from interface org.jgap.IUniqueKey

getUniqueID, getUniqueIDTemplate, setUniqueIDTemplate

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 CompositeGene 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 CompositeGene instances.

See Also:

Constant Field Values

Constructor Detail

CompositeGene

public CompositeGene()
              throws InvalidConfigurationException

Default constructor.

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

Throws:

InvalidConfigurationException

Since:

1.1

CompositeGene

public CompositeGene(Configuration a_config)
              throws InvalidConfigurationException

Parameters:

a_config - the configuration to use

Throws:

InvalidConfigurationException

Since:

3.0

CompositeGene

public CompositeGene(Configuration a_config,
                     Gene a_geneTypeAllowed)
              throws InvalidConfigurationException

Allows to specify which Gene implementation is allowed to be added to the CompositeGene.

Parameters:

a_config - the configuration to use

a_geneTypeAllowed - the class of Genes to be allowed to be added to the CompositeGene

Throws:

InvalidConfigurationException

Since:

2.0

Method Detail

addGene

public void addGene(Gene a_gene)

Adds a gene to the CompositeGene.

Specified by:

addGene in interface ICompositeGene

Parameters:

a_gene - the gene to add

getGeneTypeAllowed

public Gene getGeneTypeAllowed()

Returns:

the gene type allowed, or null if any type allowed

Since:

2.4

addGene

public void addGene(Gene a_gene,
                    boolean a_strict)

Adds a gene to the CompositeGene's container. See comments in class header for additional details about equality (concerning "strict" param.)

Parameters:

a_gene - the gene to be added

a_strict - false: add the given gene except the gene itself already is contained within the CompositeGene's container. true: add the gene if there is no other gene being equal to the given gene in request to the Gene's equals method

Since:

1.1

removeGeneByIdentity

public boolean removeGeneByIdentity(Gene a_gene)

Removes the given gene from the collection of genes. The gene is only removed if an object of the same identity is contained. The equals method is not used here intentionally.

Parameters:

a_gene - the gene to be removed

Returns:

true: given gene found and removed

Since:

1.1

removeGene

public boolean removeGene(Gene a_gene)

Removes the given gene from the collection of genes. The gene is removed if another gene exists that is equal to the given gene in respect to the equals method of the gene.

Parameters:

a_gene - the gene to be removed

Returns:

true: given gene found and removed

Since:

1.1

cleanup

public void cleanup()

Executed by the genetic engine when this Gene instance is no longer needed and should perform any necessary resource cleanup.

Specified by:

cleanup in interface Gene

Overrides:

cleanup in class BaseGene

Since:

1.1

setToRandomValue

public void setToRandomValue(RandomGenerator a_numberGenerator)

See interface Gene for description.

Specified by:

setToRandomValue in interface Gene

Parameters:

a_numberGenerator - the random number generator that should be used to create any random values. It's important to use this generator to maintain the user's flexibility to configure the genetic engine to use the random number generator of their choice

Since:

1.1

setValueFromPersistentRepresentation

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

See interface Gene for description.

Specified by:

setValueFromPersistentRepresentation in interface Gene

Specified by:

setValueFromPersistentRepresentation in interface IPersistentRepresentation

Parameters:

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

Throws:

UnsupportedRepresentationException

Since:

1.1

createGene

protected Gene createGene(java.lang.String a_geneClassName,
                          java.lang.String a_persistentRepresentation)
                   throws java.lang.Exception

Creates a new instance of gene.

Parameters:

a_geneClassName - name of the gene class

a_persistentRepresentation - persistent representation of the gene to create (could be obtained via getPersistentRepresentation)

Returns:

newly created gene

Throws:

java.lang.Exception

getPersistentRepresentation

public java.lang.String getPersistentRepresentation()
                                             throws java.lang.UnsupportedOperationException

See interface Gene for description.

Specified by:

getPersistentRepresentation in interface Gene

Specified by:

getPersistentRepresentation in interface IPersistentRepresentation

Returns:

string representation of this Gene's current state

Throws:

java.lang.UnsupportedOperationException

Since:

1.1

getAllele

public java.lang.Object getAllele()

Retrieves the value represented by this Gene. All values returned by this class will be Vector instances. Each element of the Vector represents the allele of the corresponding gene in the CompositeGene's container

Specified by:

getAllele in interface Gene

Overrides:

getAllele in class BaseGene

Returns:

the value of this Gene

Since:

1.1

setAllele

public void setAllele(java.lang.Object a_newValue)

Sets the value of the contained Genes to the new given value. This class expects the value to be of a Vector type. Each element of the Vector must conform with the type of the gene in the CompositeGene's container at the corresponding position.

Specified by:

setAllele in interface Gene

Parameters:

a_newValue - the new value of this Gene instance

Since:

1.1

newGeneInternal

protected Gene newGeneInternal()

Provides an implementation-independent means for creating new Gene instances.

Specified by:

newGeneInternal in class BaseGene

Returns:

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

Since:

1.1

compareTo

public int compareTo(java.lang.Object a_other)

Compares this CompositeGene with the specified object for order. A false value is considered to be less than a true value. A null value is considered to be less than any non-null value.

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

a_other - the CompositeGene to be compared

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object

Throws:

java.lang.ClassCastException - if the specified object's type prevents it from being compared to this CompositeGene

Since:

1.1

toString

public java.lang.String toString()

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

Specified by:

toString in interface Gene

Overrides:

toString in class BaseGene

Returns:

string representation of this CompositeGene's value. Every contained gene's string representation is delimited by the given delimiter

Since:

1.1

isEmpty

public boolean isEmpty()

Returns:

true: no genes contained, false otherwise

Since:

1.1

geneAt

public Gene geneAt(int a_index)

Specified by:

geneAt in interface ICompositeGene

Parameters:

a_index - index to return the gene at

Returns:

the gene at the given index

Since:

1.1

getGenes

public java.util.List<Gene> getGenes()

Returns:

list of genes contained in the CompositeGene

Since:

3.2.2

size

public int size()

Specified by:

size in interface Gene

Overrides:

size in class BaseGene

Returns:

the number of genes contained

Since:

1.1

containsGeneByIdentity

public boolean containsGeneByIdentity(Gene gene)

Checks whether a specific gene is already contained. The determination will be done by checking for identity and not using the equal method!

Parameters:

gene - the gene under test

Returns:

true: the given gene object is contained

Since:

1.1

applyMutation

public void applyMutation(int a_index,
                          double a_percentage)

Don't use this method, is makes no sense here. It is just there to satisfy the Gene interface. Instead, loop over all contained genes and call their applyMutation method.

Specified by:

applyMutation in interface Gene

Parameters:

a_index - does not matter here

a_percentage - does not matter here

Since:

1.1

split

protected static final java.util.List split(java.lang.String a_string)
                                     throws UnsupportedRepresentationException

Splits a_string into individual gene representations.

Parameters:

a_string - the string to split

Returns:

the elements of the returned array are the persistent representation strings of the gene's components

Throws:

UnsupportedRepresentationException

Since:

2.0

hashCode

public int hashCode()

Retrieves the hash code value for this Gene.

Overrides:

hashCode in class BaseGene

Returns:

this Gene's hash code

Since:

2.2

getInternalValue

protected java.lang.Object getInternalValue()

This method is not called internally because BaseGene.getAllele() is overridden here!

Specified by:

getInternalValue in class BaseGene

Returns:

always null

getBusinessKey

public java.lang.String getBusinessKey()

Specified by:

getBusinessKey in interface IBusinessKey

Overrides:

getBusinessKey in class BaseGene

Returns:

business key