Uses of Interface
org.jaga.definitions.Individual

Packages that use Individual

org.jaga.definitions
org.jaga.exampleApplications
org.jaga.fitnessEvaluation.largerNumbers
org.jaga.fitnessEvaluation.multiplexer
org.jaga.fitnessEvaluation.proteinLocation
org.jaga.hooks
org.jaga.individualRepresentation.booleanFormulas
org.jaga.individualRepresentation.greycodedNumbers
org.jaga.individualRepresentation.proteinLocation
org.jaga.masterAlgorithm
org.jaga.reproduction
org.jaga.reproduction.booleanFormulas
org.jaga.reproduction.greycodedNumbers
org.jaga.reproduction.proteinLocation
org.jaga.selection
org.jaga.util

Uses of Individual in org.jaga.definitions

Methods in org.jaga.definitions that return Individual

Individual	SelectionAlgorithm.select(Population population, int age, GAParameterSet params) Selects an individual from the specified population according to the fitness.
Individual[]	SelectionAlgorithm.select(Population population, int howMany, int age, GAParameterSet params) Selects a spacified number of individuals from the population according to their fitness.
Individual[]	ReproductionAlgorithm.reproduce(Individual[] parents, GAParameterSet params) Reproduces the specified individuals.
Individual[]	Population.getAllMembers() Gets an array of all individuals in the population.
Individual	Population.getMember(int index) Gets an individual at the specifies index from the population. If this population does not support an ordering, this method may throw an UnsupportedOperationException.
Individual	IndividualsFactory.createDefaultIndividual(GAParameterSet params) Creates a new default individual.
Individual	IndividualsFactory.createRandomIndividual(GAParameterSet params) Creates a random individual according to this factory's current internal settings and expariment paramanters.
Individual	IndividualsFactory.createSpecificIndividual(java.lang.Object init, GAParameterSet params) Creates a new individual and initialises it to the specified value(s).

Methods in org.jaga.definitions with parameters of type Individual

Individual[]	ReproductionAlgorithm.reproduce(Individual[] parents, GAParameterSet params) Reproduces the specified individuals.
void	Population.addAll(Individual[] individuals) Adds a list of individuals to the population.
void	Population.add(Individual individual) Adds a specified individual to the population.
Fitness	FitnessEvaluationAlgorithm.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params) Evaluates the fitness of a spscified individual.

Uses of Individual in org.jaga.exampleApplications

Methods in org.jaga.exampleApplications with parameters of type Individual

Fitness	Example2Fitness.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params)
Fitness	Example1Fitness.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params)

Uses of Individual in org.jaga.fitnessEvaluation.largerNumbers

Methods in org.jaga.fitnessEvaluation.largerNumbers with parameters of type Individual

Fitness

LargerDecimals.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params)

Uses of Individual in org.jaga.fitnessEvaluation.multiplexer

Methods in org.jaga.fitnessEvaluation.multiplexer with parameters of type Individual

Fitness

MultiplexerFitness.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params)

Uses of Individual in org.jaga.fitnessEvaluation.proteinLocation

Methods in org.jaga.fitnessEvaluation.proteinLocation with parameters of type Individual

Fitness

ProteinLocationTrainer.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params)

Uses of Individual in org.jaga.hooks

Methods in org.jaga.hooks with parameters of type Individual

void	SimpleGAHook.selectedForReproduction(SimpleGA caller, Individual[] selectedParents, Population pop, int age, GAResult result, GAParameterSet params)
void	SimpleGAHook.reproduced(SimpleGA caller, Individual[] children, Individual[] parents, Population pop, int age, GAResult result, GAParameterSet params)
void	SimpleGAHook.fitnessCalculated(SimpleGA caller, Individual updatedIndividual, Population pop, int age, GAParameterSet params)
protected void	DebugHook.printIndividuals(Individual[] inds)
void	DebugHook.selectedForReproduction(SimpleGA caller, Individual[] selectedParents, Population pop, int age, GAResult result, GAParameterSet params)
void	DebugHook.reproduced(SimpleGA caller, Individual[] children, Individual[] parents, Population pop, int age, GAResult result, GAParameterSet params)
void	DebugHook.fitnessCalculated(SimpleGA caller, Individual updatedIndividual, Population pop, int age, GAParameterSet params)
void	BetterResultHook.selectedForReproduction(SimpleGA caller, Individual[] selectedParents, Population pop, int age, GAResult result, GAParameterSet params)
void	BetterResultHook.reproduced(SimpleGA caller, Individual[] children, Individual[] parents, Population pop, int age, GAResult result, GAParameterSet params)
void	BetterResultHook.fitnessCalculated(SimpleGA caller, Individual updatedIndividual, Population pop, int age, GAParameterSet params)
void	AnalysisHook.selectedForReproduction(SimpleGA caller, Individual[] selectedParents, Population pop, int age, GAResult result, GAParameterSet params)
void	AnalysisHook.reproduced(SimpleGA caller, Individual[] children, Individual[] parents, Population pop, int age, GAResult result, GAParameterSet params)
void	AnalysisHook.fitnessCalculated(SimpleGA caller, Individual updatedIndividual, Population pop, int age, GAParameterSet params)

Uses of Individual in org.jaga.individualRepresentation.booleanFormulas

Classes in org.jaga.individualRepresentation.booleanFormulas that implement Individual

class

BooleanFormulaTree TODO: Complete these comments.

Methods in org.jaga.individualRepresentation.booleanFormulas that return Individual

Individual	BooleanFormulaTreeFactory.createDefaultIndividual(GAParameterSet params)
Individual	BooleanFormulaTreeFactory.createRandomIndividual(GAParameterSet params)
Individual	BooleanFormulaTreeFactory.createSpecificIndividual(java.lang.Object init, GAParameterSet params)

Uses of Individual in org.jaga.individualRepresentation.greycodedNumbers

Subinterfaces of Individual in org.jaga.individualRepresentation.greycodedNumbers

interface

BinaryEncodedIndividual TODO: Complete these comments.

Classes in org.jaga.individualRepresentation.greycodedNumbers that implement Individual

class	NDecimalsIndividual TODO: Complete these comments.
class	NNumbersGreycodedIndivudual TODO: Complete these comments.

Methods in org.jaga.individualRepresentation.greycodedNumbers that return Individual

Individual	NDecimalsIndividualSimpleFactory.createDefaultIndividual(GAParameterSet params)
Individual	NDecimalsIndividualSimpleFactory.createRandomIndividual(GAParameterSet params)
Individual	NDecimalsIndividualSimpleFactory.createSpecificIndividual(java.lang.Object init, GAParameterSet params)
Individual	NDecimalsIndividualSimpleFactory.createSpecificIndividual(NDecimalsIndividual initVal)
Individual	NDecimalsIndividualSimpleFactory.createSpecificIndividual(BitString initVal)
Individual	NDecimalsIndividualSimpleFactory.createSpecificIndividual(double[] initVal)

Uses of Individual in org.jaga.individualRepresentation.proteinLocation

Classes in org.jaga.individualRepresentation.proteinLocation that implement Individual

class

ProteinLocationClassifier TODO: Complete these comments.

Methods in org.jaga.individualRepresentation.proteinLocation that return Individual

Individual	ProteinLocationClassifierFactory.createDefaultIndividual(GAParameterSet params)
Individual	ProteinLocationClassifierFactory.createRandomIndividual(GAParameterSet params)
Individual	ProteinLocationClassifierFactory.createSpecificIndividual(java.lang.Object init, GAParameterSet params)
Individual	ProteinLocationClassifierFactory.createSpecificIndividual(ProteinLocationClassifier init, GAParameterSet params)
Individual	ProteinLocationClassifierFactory.createSpecificIndividual(PolypeptidePattern init, GAParameterSet params)
Individual	ProteinLocationClassifierFactory.createSpecificIndividual(java.lang.String init, GAParameterSet params)

Uses of Individual in org.jaga.masterAlgorithm

Methods in org.jaga.masterAlgorithm that return Individual

protected Individual[]	SimpleGA.selectForReproduction(Population pop, int age, GAParameterSet params)
protected Individual[]	SimpleGA.haveSex(Individual[] parents, GAParameterSet params)

Methods in org.jaga.masterAlgorithm with parameters of type Individual

protected Individual[]	SimpleGA.haveSex(Individual[] parents, GAParameterSet params)
protected void	SimpleGA.updateIndividualFitness(Individual indiv, Population pop, int genNum, GAParameterSet params)
protected void	SimpleGA.notifySelectedForReproduction(Individual[] selectedParents, Population pop, int age, GAResult result, GAParameterSet params)
protected void	SimpleGA.notifyReproduced(Individual[] children, Individual[] parents, Population pop, int age, GAResult result, GAParameterSet params)
protected void	SimpleGA.updateFitnessCalculated(Individual updated, Population pop, int age, GAParameterSet params)

Uses of Individual in org.jaga.reproduction

Methods in org.jaga.reproduction that return Individual

abstract Individual[]	XOver.reproduce(Individual[] parents, GAParameterSet params)
abstract Individual[]	Mutation.reproduce(Individual[] parents, GAParameterSet params)
Individual[]	CombinedReproductionAlgorithm.reproduce(Individual[] parents, GAParameterSet params)

Methods in org.jaga.reproduction with parameters of type Individual

abstract Individual[]	XOver.reproduce(Individual[] parents, GAParameterSet params)
abstract Individual[]	Mutation.reproduce(Individual[] parents, GAParameterSet params)
Individual[]	CombinedReproductionAlgorithm.reproduce(Individual[] parents, GAParameterSet params)

Uses of Individual in org.jaga.reproduction.booleanFormulas

Methods in org.jaga.reproduction.booleanFormulas that return Individual

Individual[]	FunctionTreeXOver.reproduce(Individual[] parents, GAParameterSet params)
private Individual[]	FunctionTreeXOver.copyParents(Individual[] parents, GAParameterSet params)
Individual[]	FunctionTreeMutation.reproduce(Individual[] parents, GAParameterSet params)

Methods in org.jaga.reproduction.booleanFormulas with parameters of type Individual

Individual[]	FunctionTreeXOver.reproduce(Individual[] parents, GAParameterSet params)
private Individual[]	FunctionTreeXOver.copyParents(Individual[] parents, GAParameterSet params)
Individual[]	FunctionTreeMutation.reproduce(Individual[] parents, GAParameterSet params)

Uses of Individual in org.jaga.reproduction.greycodedNumbers

Methods in org.jaga.reproduction.greycodedNumbers that return Individual

Individual[]	SimpleBinaryXOver.reproduce(Individual[] parents, GAParameterSet params)
protected Individual[]	SimpleBinaryXOver.makeCopyOfParents(Individual[] parents, GAParameterSet params)
Individual[]	SimpleBinaryMutation.reproduce(Individual[] parents, GAParameterSet params)

Methods in org.jaga.reproduction.greycodedNumbers with parameters of type Individual

Individual[]	SimpleBinaryXOver.reproduce(Individual[] parents, GAParameterSet params)
protected Individual[]	SimpleBinaryXOver.makeCopyOfParents(Individual[] parents, GAParameterSet params)
private int	SimpleBinaryXOver.checkParentsTypeAndLength(Individual[] parents)
Individual[]	SimpleBinaryMutation.reproduce(Individual[] parents, GAParameterSet params)
private void	SimpleBinaryMutation.fireIllegalParentException(Individual[] parents, int i)

Uses of Individual in org.jaga.reproduction.proteinLocation

Methods in org.jaga.reproduction.proteinLocation that return Individual

Individual[]	PolypeptidePatternXOver.reproduce(Individual[] parents, GAParameterSet params)
Individual	PolypeptidePatternMutation.reproduce(Individual parent, GAParameterSet params)
Individual[]	PolypeptidePatternMutation.reproduce(Individual[] parents, GAParameterSet params)
Individual	PolypeptidePatternElongation.reproduce(Individual parent, GAParameterSet params)
Individual[]	PolypeptidePatternElongation.reproduce(Individual[] parents, GAParameterSet params)

Methods in org.jaga.reproduction.proteinLocation with parameters of type Individual

Individual[]	PolypeptidePatternXOver.reproduce(Individual[] parents, GAParameterSet params)
Individual	PolypeptidePatternMutation.reproduce(Individual parent, GAParameterSet params)
Individual[]	PolypeptidePatternMutation.reproduce(Individual[] parents, GAParameterSet params)
Individual	PolypeptidePatternElongation.reproduce(Individual parent, GAParameterSet params)
Individual[]	PolypeptidePatternElongation.reproduce(Individual[] parents, GAParameterSet params)

Uses of Individual in org.jaga.selection

Methods in org.jaga.selection that return Individual

Individual	TwoTournamentProbabalisticSelection.select(Population population, int age, GAParameterSet params)
Individual[]	TwoTournamentProbabalisticSelection.select(Population population, int howMany, int age, GAParameterSet params)
Individual	TournamentSelection.select(Population population, int age, GAParameterSet params)
Individual[]	TournamentSelection.select(Population population, int howMany, int age, GAParameterSet params)
Individual	RouletteWheelSelection.select(Population population, int age, GAParameterSet params)
Individual[]	RouletteWheelSelection.select(Population population, int howMany, int age, GAParameterSet params)
private Individual	RouletteWheelSelection.spinRoulette(double cumSum, Population pop, GAParameterSet params)

Methods in org.jaga.selection with parameters of type Individual

private double

RouletteWheelSelection.getRelativeFitnessValue(Individual indv)

Uses of Individual in org.jaga.util

Fields in org.jaga.util declared as Individual

private Individual

FittestIndividualResult.fittest

Methods in org.jaga.util that return Individual

Individual[]	SimpleCollectionOfIndividuals.getAllMembers()
Individual	SimpleCollectionOfIndividuals.getMember(int index)
Individual	FittestIndividualResult.getFittestIndividual()

Methods in org.jaga.util with parameters of type Individual

void	SimpleCollectionOfIndividuals.addAll(Individual[] individuals)
void	SimpleCollectionOfIndividuals.add(Individual individual)
void	FittestIndividualResult.setFittestIndividual(Individual fittest)