A B C D E F G H I J K L M N O P Q R S T U V X Y

S

SelectionAlgorithm - interface org.jaga.definitions.SelectionAlgorithm.

Basis for all algorithms which perform selection for reproduction.

SimpleBinaryMutation - class org.jaga.reproduction.greycodedNumbers.SimpleBinaryMutation.

TODO: Complete these comments.

SimpleBinaryMutation() - Constructor for class org.jaga.reproduction.greycodedNumbers.SimpleBinaryMutation

SimpleBinaryMutation(double) - Constructor for class org.jaga.reproduction.greycodedNumbers.SimpleBinaryMutation

SimpleBinaryXOver - class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOver.

TODO: Complete these comments.

SimpleBinaryXOver() - Constructor for class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOver

SimpleBinaryXOver(double) - Constructor for class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOver

SimpleBinaryXOverWithMutation - class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOverWithMutation.

TODO: Complete these comments.

SimpleBinaryXOverWithMutation() - Constructor for class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOverWithMutation

SimpleBinaryXOverWithMutation(double, double) - Constructor for class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOverWithMutation

SimpleCollectionOfIndividuals - class org.jaga.util.SimpleCollectionOfIndividuals.

TODO: Complete these comments.

SimpleCollectionOfIndividuals() - Constructor for class org.jaga.util.SimpleCollectionOfIndividuals

SimpleGA - class org.jaga.masterAlgorithm.SimpleGA.

TODO: Complete these comments.

SimpleGA() - Constructor for class org.jaga.masterAlgorithm.SimpleGA

SimpleGAHook - class org.jaga.hooks.SimpleGAHook.

TODO: Complete these comments.

SimpleGAHook() - Constructor for class org.jaga.hooks.SimpleGAHook

SimpleImplementationDemo - class org.jaga.exampleApplications.SimpleImplementationDemo.

TODO: Complete these comments.

SimpleImplementationDemo() - Constructor for class org.jaga.exampleApplications.SimpleImplementationDemo

SimplifiedFastaFileParser - class org.jaga.individualRepresentation.proteinLocation.SimplifiedFastaFileParser.

TODO: Complete these comments.

SimplifiedFastaFileParser() - Constructor for class org.jaga.individualRepresentation.proteinLocation.SimplifiedFastaFileParser

SingleGap - class org.jaga.individualRepresentation.proteinLocation.SingleGap.

TODO: Complete these comments.

SingleGap() - Constructor for class org.jaga.individualRepresentation.proteinLocation.SingleGap

Small - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty

Small - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidPropertyFactory

SubcellularProteinLocation - class org.jaga.exampleApplications.proteinLocation.SubcellularProteinLocation.

TODO: Complete these comments.

SubcellularProteinLocation() - Constructor for class org.jaga.exampleApplications.proteinLocation.SubcellularProteinLocation

SubstitutionScoringMatrix - class org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix.

TODO: Complete these comments.

SubstitutionScoringMatrix() - Constructor for class org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix

saveProtein(DataSplitter.Protein[], String) - Method in class org.jaga.exampleApplications.proteinLocation.DataSplitter

saveProteins() - Method in class org.jaga.exampleApplications.proteinLocation.DataSplitter

scaleX(double) - Method in class org.jaga.hooks.AnalysisGraphPanel

scaleY(double) - Method in class org.jaga.hooks.AnalysisGraphPanel

scoringMatrix - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

select(Population, int, GAParameterSet) - Method in interface org.jaga.definitions.SelectionAlgorithm

Selects an individual from the specified population according to the fitness.

select(Population, int, int, GAParameterSet) - Method in interface org.jaga.definitions.SelectionAlgorithm

Selects a spacified number of individuals from the population according to their fitness.

select(Population, int, GAParameterSet) - Method in class org.jaga.selection.RouletteWheelSelection

select(Population, int, int, GAParameterSet) - Method in class org.jaga.selection.RouletteWheelSelection

select(Population, int, GAParameterSet) - Method in class org.jaga.selection.TournamentSelection

select(Population, int, int, GAParameterSet) - Method in class org.jaga.selection.TournamentSelection

select(Population, int, GAParameterSet) - Method in class org.jaga.selection.TwoTournamentProbabalisticSelection

select(Population, int, int, GAParameterSet) - Method in class org.jaga.selection.TwoTournamentProbabalisticSelection

selectForReproduction(Population, int, GAParameterSet) - Method in class org.jaga.masterAlgorithm.SimpleGA

selectRandomNode(GAParameterSet) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTree

selectRootNode() - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTree

selectedForReproduction(SimpleGA, Individual[], Population, int, GAResult, GAParameterSet) - Method in class org.jaga.hooks.AnalysisHook

selectedForReproduction(SimpleGA, Individual[], Population, int, GAResult, GAParameterSet) - Method in class org.jaga.hooks.BetterResultHook

selectedForReproduction(SimpleGA, Individual[], Population, int, GAResult, GAParameterSet) - Method in class org.jaga.hooks.DebugHook

selectedForReproduction(SimpleGA, Individual[], Population, int, GAResult, GAParameterSet) - Method in class org.jaga.hooks.SimpleGAHook

sensitivity(int) - Method in class org.jaga.exampleApplications.proteinLocation.Locator

sensitivity - Variable in class org.jaga.selection.ClassifierFitness

sequence - Variable in class org.jaga.exampleApplications.proteinLocation.DataSplitter.Protein

sequence - Variable in class org.jaga.individualRepresentation.proteinLocation.Protein

set(int, boolean) - Method in class org.jaga.util.BitString

set(int, int, boolean) - Method in class org.jaga.util.BitString

set(int, int, BitString) - Method in class org.jaga.util.BitString

setAllowConstants(boolean) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

setAllowedNodeTypes(Class[]) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

setAminoAcidChance(int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setAminoAcid_cloneChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setAminoAcid_deleteChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setAminoAcid_generaliseToGroupChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setAminoAcid_generaliseToPropertyChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setAminoAcid_mutateChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setAnalyseBestFitness(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseGenAge(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseGenAverageFit(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseGenDump(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseGenFitStdDeviation(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseGenMaxFit(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseGenMinFit(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseRunTime(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalyseTotalFitEvals(boolean) - Method in class org.jaga.hooks.AnalysisHook

setAnalysisHookForCooperation(AnalysisHook) - Method in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

setBadProportion(double) - Method in class org.jaga.masterAlgorithm.ElitistGA

setBetterCandidateProbability(double) - Method in class org.jaga.selection.TournamentSelection

setBetterCandidateProbability(double) - Method in class org.jaga.selection.TwoTournamentProbabalisticSelection

setBitStringRepresentation(BitString) - Method in interface org.jaga.individualRepresentation.greycodedNumbers.BinaryEncodedIndividual

setBitStringRepresentation(BitString) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NNumbersGreycodedIndivudual

setChild(int, BooleanFormulaTreeNode) - Method in class org.jaga.reproduction.booleanFormulas.nodes.OperatorNode

setClassifierName(String) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setClassifiers(ProteinLocationClassifier, ProteinLocationClassifier, ProteinLocationClassifier, ProteinLocationClassifier) - Method in class org.jaga.exampleApplications.proteinLocation.Locator

setClearBitCode(int, BitString) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NNumbersGreycodedIndivudual

setCompetitors(int) - Method in class org.jaga.selection.TournamentSelection

setConstraint(int, RangeConstraint) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividualSimpleFactory

Sets the constraints for individuals' variable at the specified index.

setDecimalScale(int) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividualSimpleFactory

setDefaultvalues() - Method in class org.jaga.util.DefaultParameterSet

setDepth(int) - Method in class org.jaga.reproduction.booleanFormulas.nodes.BooleanFormulaTreeNode

setDoubleValue(int, double) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividual

setEliteProportion(double) - Method in class org.jaga.masterAlgorithm.ElitistGA

setFitness(Fitness) - Method in interface org.jaga.definitions.Individual

Sets the fitness.

setFitness(Fitness) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTree

setFitness(Fitness) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NNumbersGreycodedIndivudual

setFitness(Fitness) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifier

setFitnessEvaluationAlgorithm(FitnessEvaluationAlgorithm) - Method in interface org.jaga.definitions.GAParameterSet

setFitnessEvaluationAlgorithm(FitnessEvaluationAlgorithm) - Method in class org.jaga.util.DefaultParameterSet

setFittestIndividual(Individual) - Method in class org.jaga.util.FittestIndividualResult

setGroupChance(int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setGroup_addChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_cloneChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_deleteChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onEmptyDeleteChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onEmptyReplaceChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onLargeDontActChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onLargeReplaceChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onLargeSplitChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onLargeTriggerLength(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onPropertyReplaceProb(double) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onPropertyTriggerPercent(double) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_onSingleReplaceProb(double) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_substractChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setGroup_swapChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setHandle(Long) - Method in class org.jaga.reproduction.booleanFormulas.nodes.BooleanFormulaTreeNode

setHeight(int) - Method in class org.jaga.reproduction.booleanFormulas.nodes.BooleanFormulaTreeNode

setIndividualSize(int) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividualSimpleFactory

setIndividualsFactory(IndividualsFactory) - Method in interface org.jaga.definitions.GAParameterSet

setIndividualsFactory(IndividualsFactory) - Method in class org.jaga.util.DefaultParameterSet

setInitialPopulation(Object[]) - Method in class org.jaga.masterAlgorithm.InitialPopulationGA

setLogStream(PrintStream) - Method in class org.jaga.hooks.AnalysisHook

setMaxBadReproductionAttempts(int) - Method in interface org.jaga.definitions.GAParameterSet

setMaxBadReproductionAttempts(int) - Method in class org.jaga.util.DefaultParameterSet

setMaxGenerationNumber(int) - Method in interface org.jaga.definitions.GAParameterSet

setMaxGenerationNumber(int) - Method in class org.jaga.util.DefaultParameterSet

setMaxGroupLength(int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setMaxPatternLength(int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setMaxTreeDepth(int) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

setMinFitness(double) - Method in class org.jaga.selection.RouletteWheelSelection

setMinOverlap(int) - Method in class org.jaga.fitnessEvaluation.proteinLocation.ProteinLocationTrainer

setMutationProbability(double) - Method in class org.jaga.reproduction.Mutation

setMutationProbability(double) - Method in class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOverWithMutation

setName(String) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

setName(String) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifier

setNegativeGroup(ProteinGroup) - Method in class org.jaga.fitnessEvaluation.proteinLocation.ProteinLocationTrainer

setNumberOfParameters(int) - Method in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

setParent(OperatorNode) - Method in class org.jaga.reproduction.booleanFormulas.nodes.BooleanFormulaTreeNode

setPattern(PolypeptidePattern) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifier

setPlotFrameTitle(String) - Method in class org.jaga.hooks.AnalysisHook

setPlotGraph(boolean) - Method in class org.jaga.hooks.AnalysisHook

setPopulationSize(int) - Method in interface org.jaga.definitions.GAParameterSet

setPopulationSize(int) - Method in class org.jaga.util.DefaultParameterSet

setPositiveGroup(ProteinGroup) - Method in class org.jaga.fitnessEvaluation.proteinLocation.ProteinLocationTrainer

setPrecision(int) - Method in class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividualSimpleFactory

setPressForShortFactor(double) - Method in class org.jaga.fitnessEvaluation.multiplexer.MultiplexerFitness

setPropertyChance(int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setProperty_cloneChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setProperty_deleteChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setProperty_expandChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setProperty_expandGroupSize(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setProperty_expandSamePropCount(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setProperty_mutateChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setRandomGenerator(RandomGenerator) - Method in interface org.jaga.definitions.GAParameterSet

setRandomGenerator(RandomGenerator) - Method in class org.jaga.util.DefaultParameterSet

setRange(double, double) - Method in class org.jaga.individualRepresentation.greycodedNumbers.RangeConstraint

setReproductionAlgorithm(ReproductionAlgorithm) - Method in interface org.jaga.definitions.GAParameterSet

setReproductionAlgorithm(int, ReproductionAlgorithm) - Method in class org.jaga.reproduction.CombinedReproductionAlgorithm

setReproductionAlgorithm(ReproductionAlgorithm) - Method in class org.jaga.util.DefaultParameterSet

setScoringMatrix(SubstitutionScoringMatrix) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setSeed(long) - Method in interface org.jaga.definitions.RandomGenerator

setSelectionAlgorithm(SelectionAlgorithm) - Method in interface org.jaga.definitions.GAParameterSet

setSelectionAlgorithm(SelectionAlgorithm) - Method in class org.jaga.util.DefaultParameterSet

setSingleGapChance(int) - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

setSingleGap_cloneChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setSingleGap_deleteChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setSingleGap_expandChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setSingleGap_expandGroupSize(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setSingleGap_mutateChance(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

setTerminalIndex(int) - Method in class org.jaga.reproduction.booleanFormulas.nodes.TerminalNode

setUnchecked(int, boolean) - Method in class org.jaga.util.BitString

setUpdateDelay(long) - Method in class org.jaga.hooks.AnalysisHook

setUseMainAlgorithmHooks(boolean) - Method in interface org.jaga.definitions.GAParameterSet

setUseMainAlgorithmHooks(boolean) - Method in class org.jaga.util.DefaultParameterSet

setXOverPoints(int) - Method in class org.jaga.reproduction.proteinLocation.PolypeptidePatternXOver

setXOverProbability(double) - Method in class org.jaga.reproduction.XOver

setXOverProbability(double) - Method in class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOverWithMutation

singleGapChance - Variable in class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory

singleGap_cloneChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

singleGap_deleteChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

singleGap_expandChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

singleGap_expandGroupSize - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

singleGap_mutateChance - Variable in class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation

size - Variable in class org.jaga.individualRepresentation.greycodedNumbers.NNumbersGreycodedIndivudual

size() - Method in class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup

size() - Method in class org.jaga.individualRepresentation.proteinLocation.ProteinGroup

smallAminoAcids - Static variable in class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory

sourceFiles - Static variable in class org.jaga.exampleApplications.proteinLocation.DataSplitter

specificity(int) - Method in class org.jaga.exampleApplications.proteinLocation.Locator

specificity - Variable in class org.jaga.selection.ClassifierFitness

spinRoulette(double, Population, GAParameterSet) - Method in class org.jaga.selection.RouletteWheelSelection

splitPane - Variable in class org.jaga.hooks.GAAnalysisFrame

startBoost(GAParameterSet) - Method in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

startedTime - Variable in class org.jaga.hooks.AnalysisHook

statsText - Variable in class org.jaga.hooks.GAAnalysisFrame

stopBoost(GAParameterSet) - Method in class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

stopLogStream() - Method in class org.jaga.hooks.AnalysisHook

stoppersWithConsts - Static variable in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

stoppersWithoutConsts - Static variable in class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory

substring(int, int) - Method in class org.jaga.util.BitString

swapResidue(int, AminoAcid) - Method in class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup