org.jgap.impl
Class FixedBinaryGene

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

All Implemented Interfaces:

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

public class FixedBinaryGene
extends BaseGene
implements IPersistentRepresentation

A Gene implementation that supports two possible values (alleles, 1 and 0) with a fixed length of alleles.

NOTE: Since this Gene implementation only supports two different values (1 and 0), there's only a 50% chance that invocation of the setToRandomValue() method will actually change the value of this Gene (if it has a value). As a result, it may be desirable to use a higher overall mutation rate when this Gene implementation is in use.

Partly adapted stuff from the JAGA (Java API for Genetic Algorithms) package (see jaga).

Since:

2.0

See Also:

Serialized Form

Field Summary

Fields inherited from class org.jgap.BaseGene

DELTA, S_APPLICATION_DATA

Fields inherited from interface org.jgap.Gene

PERSISTENT_FIELD_DELIMITER

Constructor Summary

FixedBinaryGene(Configuration a_config, FixedBinaryGene a_toCopy)

FixedBinaryGene(Configuration a_config, int a_length)

Method Summary

void	applyMutation(int a_index, double a_percentage) Applies a mutation of a given intensity (percentage) onto the atomic element at given index
protected void	checkIndex(int a_index)
protected int	checkSubLength(int a_from, int a_to)
java.lang.Object	clone()
int	compareTo(java.lang.Object a_other) Compares this Gene with the specified object for order.
void	flip(int a_index)
java.lang.Object	getAllele() Retrieves the allele value represented by this Gene.
boolean	getBit(int a_index)
java.lang.String	getBusinessKey()
protected java.lang.Object	getInternalValue() Not called as getAllele() is overridden.
int[]	getIntValues()
int	getLength()
java.lang.String	getPersistentRepresentation() Returns a persistent representation of an entity (such as a chromosome or a gene).
protected boolean	getUnchecked(int a_index)
protected int[]	getValue()
int	hashCode() Modified hashCode() function to return different hashcodes for differently ordered genes in a chromosome --> does not work as internal value always initialized!
protected Gene	newGeneInternal()
void	setAllele(java.lang.Object a_newValue) Sets the value of this Gene to the new given value.
void	setBit(int a_index, boolean a_value)
void	setBit(int a_index, int a_value)
void	setBit(int a_from, int a_to, boolean a_value)
void	setBit(int a_from, int a_to, FixedBinaryGene a_values)
void	setToRandomValue(RandomGenerator a_numberGenerator) Sets the value of this Gene to a random legal value for the implementation.
void	setUnchecked(int a_index, boolean a_value)
void	setValueFromPersistentRepresentation(java.lang.String a_representation) Sets the value and internal state of this Gene from the string representation returned by a previous invocation of the getPersistentRepresentation() method.
int	size()
FixedBinaryGene	substring(int a_from, int a_to)
java.lang.String	toString() Retrieves a string representation of this Gene's value that may be useful for display purposes.

Methods inherited from class org.jgap.BaseGene

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

Methods inherited from class java.lang.Object

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

Constructor Detail

FixedBinaryGene

public FixedBinaryGene(Configuration a_config,
                       int a_length)
                throws InvalidConfigurationException

Parameters:

a_config - the configuration to use

a_length - the fixed length of the gene

Throws:

InvalidConfigurationException

Since:

2.0

FixedBinaryGene

public FixedBinaryGene(Configuration a_config,
                       FixedBinaryGene a_toCopy)
                throws InvalidConfigurationException

Throws:

InvalidConfigurationException

Method Detail

newGeneInternal

protected Gene newGeneInternal()

Specified by:

newGeneInternal in class BaseGene

getValue

protected int[] getValue()

getLength

public int getLength()

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

setAllele

public void setAllele(java.lang.Object a_newValue)

Description copied from interface: Gene

Sets the value of this Gene to the new given value. The actual type of the value is implementation-dependent.

Specified by:

setAllele in interface Gene

Parameters:

a_newValue - the new value of this Gene instance

getAllele

public java.lang.Object getAllele()

Description copied from class: BaseGene

Retrieves the allele value represented by this Gene.

Specified by:

getAllele in interface Gene

Overrides:

getAllele in class BaseGene

Returns:

the allele value of this Gene

getIntValues

public int[] getIntValues()

Returns:

internal representation of the gene's state. Use getBit for reading bits!

getBit

public boolean getBit(int a_index)

setBit

public void setBit(int a_index,
                   boolean a_value)

setBit

public void setBit(int a_index,
                   int a_value)

setBit

public void setBit(int a_from,
                   int a_to,
                   boolean a_value)

setBit

public void setBit(int a_from,
                   int a_to,
                   FixedBinaryGene a_values)

substring

public FixedBinaryGene substring(int a_from,
                                 int a_to)

flip

public void flip(int a_index)

checkSubLength

protected int checkSubLength(int a_from,
                             int a_to)

checkIndex

protected void checkIndex(int a_index)

getUnchecked

protected boolean getUnchecked(int a_index)

setUnchecked

public void setUnchecked(int a_index,
                         boolean a_value)

getPersistentRepresentation

public java.lang.String getPersistentRepresentation()

Description copied from interface: IPersistentRepresentation

Returns a persistent representation of an entity (such as a chromosome or a gene).

Specified by:

getPersistentRepresentation in interface Gene

Specified by:

getPersistentRepresentation in interface IPersistentRepresentation

Returns:

string representation of current state

setValueFromPersistentRepresentation

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

Sets the value and internal state of this Gene from the string representation returned by a previous invocation of the getPersistentRepresentation() method. This is an optional method but, if not implemented, XML persistence and possibly other features will not be available. An UnsupportedOperationException should be thrown if no implementation is provided.

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 - if this Gene implementation does not support the given string representation

Since:

2.0

setToRandomValue

public void setToRandomValue(RandomGenerator a_numberGenerator)

Description copied from interface: Gene

Sets the value of this Gene to a random legal value for the implementation. This method exists for the benefit of mutation and other operations that simply desire to randomize the value of a gene.

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

toString

public java.lang.String toString()

Description copied from class: BaseGene

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 BaseGene

Returns:

String representation

Since:

2.0

getBusinessKey

public java.lang.String getBusinessKey()

Specified by:

getBusinessKey in interface IBusinessKey

Overrides:

getBusinessKey in class BaseGene

Returns:

business key

size

public int size()

Specified by:

size in interface Gene

Overrides:

size in class BaseGene

Returns:

the size of the gene, i.e the number of atomic elements

Since:

2.0

applyMutation

public void applyMutation(int a_index,
                          double a_percentage)

Applies a mutation of a given intensity (percentage) onto the atomic element at given index

Specified by:

applyMutation in interface Gene

Parameters:

a_index - index of atomic element, between 0 and size()-1

a_percentage - percentage of mutation (greater than -1 and smaller than 1)

Since:

2.0

compareTo

public int compareTo(java.lang.Object a_other)

Compares this Gene with the specified object for order. A 0 value is considered to be less than a 1 value. A null value is considered to be less than any non-null value. A Gene is greater than another one of the same length if it has more 1's than the other one. If there is the same number of 1's the Gene with the highest value (binary to int) is greater.

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

a_other - the FixedBinaryGene 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 Gene

Since:

2.0

getInternalValue

protected java.lang.Object getInternalValue()

Not called as getAllele() is overridden.

Specified by:

getInternalValue in class BaseGene

Returns:

same as getAllele()

hashCode

public int hashCode()

Modified hashCode() function to return different hashcodes for differently ordered genes in a chromosome --> does not work as internal value always initialized!

Overrides:

hashCode in class BaseGene

Returns:

this Gene's hash code

Since:

2.2