Uses of Interface
org.jaga.definitions.GAParameterSet

Packages that use GAParameterSet

org.jaga.definitions
org.jaga.exampleApplications
org.jaga.exampleApplications.proteinLocation
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 GAParameterSet in org.jaga.definitions

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

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	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).
GAResult	GeneticAlgorithm.exec(GAParameterSet parameters) Runs this master algorithm with the specified experimet paramenters.
Fitness	FitnessEvaluationAlgorithm.evaluateFitness(Individual individual, int age, Population population, GAParameterSet params) Evaluates the fitness of a spscified individual.

Uses of GAParameterSet in org.jaga.exampleApplications

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

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

Uses of GAParameterSet in org.jaga.exampleApplications.proteinLocation

Methods in org.jaga.exampleApplications.proteinLocation with parameters of type GAParameterSet

private void	ProgressiveTestGroupSizeHook.startBoost(GAParameterSet params)
private void	ProgressiveTestGroupSizeHook.stopBoost(GAParameterSet params)
void	ProgressiveTestGroupSizeHook.foundNewResult(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	ProgressiveTestGroupSizeHook.generationChanged(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)

Constructors in org.jaga.exampleApplications.proteinLocation with parameters of type GAParameterSet

ProgressiveTestGroupSizeHook(ProteinGroup allPositives, ProteinGroup allNegatives, ProteinGroup testPositives, ProteinGroup testNegatives, int initialTestSetSize, int testSetSizeDelta, double triggerFitness, double mutationBoost, int boostStartTimeout, int boostStopTimeout, GAParameterSet params)

Uses of GAParameterSet in org.jaga.fitnessEvaluation.largerNumbers

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

Fitness

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

Uses of GAParameterSet in org.jaga.fitnessEvaluation.multiplexer

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

Fitness

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

Uses of GAParameterSet in org.jaga.fitnessEvaluation.proteinLocation

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

Fitness

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

Uses of GAParameterSet in org.jaga.hooks

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

void	SimpleGAHook.initialisationDone(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	SimpleGAHook.foundNewResult(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	SimpleGAHook.generationChanged(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	SimpleGAHook.terminationConditionApplies(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
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)
void	DebugHook.initialisationDone(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	DebugHook.foundNewResult(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	DebugHook.generationChanged(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet paramss)
void	DebugHook.terminationConditionApplies(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
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.generationChanged(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet paramss)
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.initialisationDone(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	AnalysisHook.populationReinitialised(Population pop, int age, GAResult result, GAParameterSet params)
void	AnalysisHook.foundNewResult(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
void	AnalysisHook.generationChanged(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet paramss)
void	AnalysisHook.terminationConditionApplies(SimpleGA caller, Population pop, int age, GAResult result, 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 GAParameterSet in org.jaga.individualRepresentation.booleanFormulas

Methods in org.jaga.individualRepresentation.booleanFormulas with parameters of type GAParameterSet

Individual	BooleanFormulaTreeFactory.createDefaultIndividual(GAParameterSet params)
Individual	BooleanFormulaTreeFactory.createRandomIndividual(GAParameterSet params)
Individual	BooleanFormulaTreeFactory.createSpecificIndividual(java.lang.Object init, GAParameterSet params)
BooleanFormulaTree	BooleanFormulaTreeFactory.clone(BooleanFormulaTree template, GAParameterSet params)
BooleanFormulaTreeNode	BooleanFormulaTreeFactory.createRandomNode(int thisDepth, GAParameterSet params)
private BooleanFormulaTreeNode	BooleanFormulaTreeFactory.createRandomStopNode(GAParameterSet params)
private BooleanFormulaTreeNode	BooleanFormulaTreeFactory.createOneNodeOfRandomType(java.lang.Class[] nodeTypes, GAParameterSet params)
java.lang.Long	BooleanFormulaTree.selectRandomNode(GAParameterSet params)

Uses of GAParameterSet in org.jaga.individualRepresentation.greycodedNumbers

Methods in org.jaga.individualRepresentation.greycodedNumbers with parameters of type GAParameterSet

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

Uses of GAParameterSet in org.jaga.individualRepresentation.proteinLocation

Methods in org.jaga.individualRepresentation.proteinLocation with parameters of type GAParameterSet

AminoAcid	SubstitutionScoringMatrix.chooseProbabalisticMutation(AminoAcid aminoAcid, GAParameterSet params)
AminoAcid	SubstitutionScoringMatrix.chooseProbabalisticMutation(java.lang.String aminoAcid, GAParameterSet params)
PolypeptidePattern	ProteinLocationClassifierFactory.createRandomPattern(GAParameterSet params)
PolypeptidePattern	ProteinLocationClassifierFactory.createRandomPattern(int length, GAParameterSet params)
PolypeptidePatternItem	ProteinLocationClassifierFactory.createRandomPatternItem(GAParameterSet params)
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)
static AminoAcidProperty	AminoAcidPropertyFactory.getRandomProperty(GAParameterSet params)
static AminoAcid	AminoAcidFactory.getRandomResidueByProperty(int property, GAParameterSet params)
static AminoAcid	AminoAcidFactory.getRandomResidue(GAParameterSet params)

Uses of GAParameterSet in org.jaga.masterAlgorithm

Fields in org.jaga.masterAlgorithm declared as GAParameterSet

private GAParameterSet

ReusableSimpleGA.parameters

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

GAResult	SimpleGA.exec(GAParameterSet params)
protected Population	SimpleGA.generateNextPopulation(Population oldPop, int age, GAResult result, GAParameterSet params)
protected boolean	SimpleGA.checkForBetterResult(GAResult oldResult, Population newPop, GAParameterSet params)
protected Population	SimpleGA.createInitialPopulation(GAParameterSet params)
protected Population	SimpleGA.createEmptyPopulation(GAParameterSet params)
protected boolean	SimpleGA.terminationConditionApplies(Population pop, int genNum, GAResult result, GAParameterSet params)
protected Individual[]	SimpleGA.selectForReproduction(Population pop, int age, GAParameterSet params)
protected Individual[]	SimpleGA.haveSex(Individual[] parents, GAParameterSet params)
protected void	SimpleGA.updateIndividualFitness(Individual indiv, Population pop, int genNum, GAParameterSet params)
protected void	SimpleGA.notifyInitialisationDone(Population pop, int age, GAResult result, GAParameterSet params)
protected void	SimpleGA.notifyFoundNewResult(Population pop, int age, GAResult result, GAParameterSet params)
protected void	SimpleGA.notifyGenerationChanged(Population pop, int age, GAResult result, GAParameterSet params)
protected void	SimpleGA.notifyTerminationConditionApplies(Population pop, int age, GAResult result, 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)
protected Population	InitialPopulationGA.createInitialPopulation(GAParameterSet params)
protected Population	ElitistGA.generateNextPopulation(Population oldPop, int age, GAResult result, GAParameterSet params)

Constructors in org.jaga.masterAlgorithm with parameters of type GAParameterSet

ReusableSimpleGA(GAParameterSet parameters)

InitialPopulationGA(GAParameterSet parameters, double eliteProportion)

InitialPopulationGA(GAParameterSet parameters, double eliteProportion, double badProportion)

InitialPopulationGA(java.lang.Object[] initData, GAParameterSet parameters, double eliteProportion)

InitialPopulationGA(java.lang.Object[] initData, GAParameterSet parameters, double eliteProportion, double badProportion)

ElitistGA(GAParameterSet parameters, double eliteProportion)

ElitistGA(GAParameterSet parameters, double eliteProportion, double badProportion)

Uses of GAParameterSet in org.jaga.reproduction

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

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 GAParameterSet in org.jaga.reproduction.booleanFormulas

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

Individual[]	FunctionTreeXOver.reproduce(Individual[] parents, GAParameterSet params)
private Individual[]	FunctionTreeXOver.copyParents(Individual[] parents, GAParameterSet params)
Individual[]	FunctionTreeMutation.reproduce(Individual[] parents, GAParameterSet params)
private BooleanFormulaTree	FunctionTreeMutation.mutate(BooleanFormulaTree parent, GAParameterSet params)
private BooleanFormulaTree	FunctionTreeMutation.createSpecificIndividual(java.lang.Object init, GAParameterSet params)
private BooleanFormulaTreeFactory	FunctionTreeMutation.fetchFactory(GAParameterSet params)

Uses of GAParameterSet in org.jaga.reproduction.greycodedNumbers

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

Individual[]	SimpleBinaryXOver.reproduce(Individual[] parents, GAParameterSet params)
protected Individual[]	SimpleBinaryXOver.makeCopyOfParents(Individual[] parents, GAParameterSet params)
private boolean	SimpleBinaryXOver.kidsSatisfyConstraints(NDecimalsIndividual[] kids, GAParameterSet params)
private NDecimalsIndividual[]	SimpleBinaryXOver.createKidsFromEncoding(GAParameterSet params, BitString c1, BitString c2)
Individual[]	SimpleBinaryMutation.reproduce(Individual[] parents, GAParameterSet params)

Uses of GAParameterSet in org.jaga.reproduction.proteinLocation

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

Individual[]	PolypeptidePatternXOver.reproduce(Individual[] parents, GAParameterSet params)
private PolypeptidePatternItem[]	PolypeptidePatternMutation.mutateItem(AminoAcid aAcid, GAParameterSet params)
private PolypeptidePatternItem[]	PolypeptidePatternMutation.mutateItem(AminoAcidGroup group, GAParameterSet params)
private PolypeptidePatternItem[]	PolypeptidePatternMutation.mutateItem(AminoAcidProperty property, GAParameterSet params)
private PolypeptidePatternItem[]	PolypeptidePatternMutation.mutateItem(SingleGap gap, GAParameterSet params)
private PolypeptidePatternItem[]	PolypeptidePatternMutation.mutatePatternItem(PolypeptidePatternItem item, 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 GAParameterSet in org.jaga.selection

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

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)

Uses of GAParameterSet in org.jaga.util

Classes in org.jaga.util that implement GAParameterSet

class

DefaultParameterSet TODO: Complete these comments.