# Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## A

A - Variable in class ec.eda.dovs.DOVSSpecies
  Constraint coefficients
A_AT - Static variable in class ec.eval.Slave
  The argument indicating the class where the resource is relative to.
A_AT - Static variable in class ec.Evolve
  The argument indicating the class where the resource is relative to.
A_CHECKPOINT - Static variable in class ec.Evolve
  The argument indicating that we're starting up from a checkpoint file.
A_FILE - Static variable in class ec.eval.Slave
  The argument indicating that we're starting fresh from a new parameter file.
A_FILE - Static variable in class ec.Evolve
  The argument indicating that we're starting fresh from a new parameter file.
A_FROM - Static variable in class ec.eval.Slave
  The argument indicating that we're starting fresh from a parameter file stored in a jar file or as some resource.
A_FROM - Static variable in class ec.Evolve
  The argument indicating that we're starting fresh from a parameter file stored in a jar file or as some resource.
A_HELP - Static variable in class ec.Evolve
  The argument indicating a request to print out the help message.
ACCESSED - Static variable in class ec.util.ParameterDatabaseEvent
activate(EvolutionState) - Method in class ec.neat.NEATNetwork
  Activates the net such that all outputs are active.
activateWithOverride() - Method in class ec.neat.NEATNode
  Set activation to the override value and turn off override.
activation - Variable in class ec.neat.NEATNode
  The total activation entering the node.
activationCount - Variable in class ec.neat.NEATNode
  Keeps track of which activation the node is currently in.
activeFlag - Variable in class ec.neat.NEATNode
  To make sure outputs are active.
activeSolutions - Variable in class ec.eda.dovs.DOVSSpecies
  activeSolutions contains all the samples that is on the boundary of the most promising area.
activeSum - Variable in class ec.neat.NEATNode
  The incoming activity before being processed.
adaptDistributionMultiplier(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
add(int) - Method in class ec.util.IntBag
addAll(int[]) - Method in class ec.util.IntBag
addAll(int, int[]) - Method in class ec.util.IntBag
addAll(int, IntBag) - Method in class ec.util.IntBag
addAll(IntBag) - Method in class ec.util.IntBag
addArgument(GrammarNode) - Method in class ec.gp.ge.GrammarFunctionNode
  Adds a given argument to the node.
addChoice(GrammarNode) - Method in class ec.gp.ge.GrammarRuleNode
  Adds a choice to the children of this node.
addDataPoint(int, double, double) - Method in class ec.display.chart.XYSeriesChartStatistics
addGene(NEATGene[]) - Method in class ec.neat.NEATIndividual
  We append new gene(s) to the current genome
addInnovation(NEATInnovation) - Method in class ec.neat.NEATSpecies
addInput(NEATNode) - Method in class ec.neat.NEATNetwork
  Add a new input node.
addLog(int, boolean) - Method in class ec.util.Output
  Creates a new log and adds it to Output.
addLog(int, int, boolean) - Method in class ec.util.Output
  Creates a new log of minimal verbosity verbosity and adds it to Output.
addLog(Log) - Method in class ec.util.Output
  Adds the given log to Output.
addLog(File, boolean) - Method in class ec.util.Output
  Creates a new log and adds it to Output.
addLog(File, boolean, boolean) - Method in class ec.util.Output
  Creates a new log and adds it to Output.
addLog(File, boolean, boolean, boolean) - Method in class ec.util.Output
  Creates a new log and adds it to Output.
addLog(File, int, boolean, boolean) - Method in class ec.util.Output
  Creates a new log of minimal verbosity verbosity and adds it to Output.
addLog(File, int, boolean, boolean, boolean) - Method in class ec.util.Output
  Creates a new log of minimal verbosity verbosity and adds it to Output.
addLog(Writer, LogRestarter, boolean, boolean) - Method in class ec.util.Output
  Creates a new log and adds it to Output.
addLog(Writer, LogRestarter, int, boolean, boolean) - Method in class ec.util.Output
  Creates a new log of minimal verbosity verbosity and adds it to Output.
addNewGenIndividual(NEATIndividual) - Method in class ec.neat.NEATSubspecies
  Add the individual to the next generation of this subspecies
addNodeMaxGenomeLength - Variable in class ec.neat.NEATSpecies
  Beyond this genome length, mutateAddNode does a pure random split rather than a bias.
addOutput(NEATNode) - Method in class ec.neat.NEATNetwork
  Add a new output node.
addParent(ParameterDatabase) - Method in class ec.util.ParameterDatabase
addRandomRule(EvolutionState, int) - Method in class ec.rule.RuleSet
  Add a random rule to the rule set
addRule(Rule) - Method in class ec.rule.RuleSet
  Add a rule directly to the rule set.
addSeries(String) - Method in class ec.display.chart.XYSeriesChartStatistics
addTreeModelListener(TreeModelListener) - Method in class ec.util.ReflectedObject
adf - Variable in class ec.gp.ADFContext
  The ADF/ADM node proper
ADF - Class in ec.gp
  An ADF is a GPNode which implements an "Automatically Defined Function", as described in Koza II.
ADF() - Constructor for class ec.gp.ADF
ADFArgument - Class in ec.gp
  An ADFArgument is a GPNode which represents an ADF's argument terminal, its counterpart which returns argument values in its associated function tree.
ADFArgument() - Constructor for class ec.gp.ADFArgument
ADFContext - Class in ec.gp
  ADFContext is the object pushed onto an ADF stack which represents the current context of an ADM or ADF function call, that is, how to get the argument values that argument_terminals need to return.
ADFContext() - Constructor for class ec.gp.ADFContext
ADFStack - Class in ec.gp
  ADFStack is a special data object used to hold ADF data.
ADFStack() - Constructor for class ec.gp.ADFStack
adjustedFitness - Variable in class ec.neat.NEATIndividual
  Fitness after the adjustment.
adjustedFitness() - Method in class ec.gp.koza.KozaFitness
  Returns the adjusted fitness metric, which recasts the fitness to the half-open interval (0,1], where 1 is ideal and 0 is worst.
adjustFitness(EvolutionState, int, double) - Method in class ec.neat.NEATSubspecies
  Adjust the fitness of the individuals within this subspecies.
ADM - Class in ec.gp
  An ADM is an ADF which doesn't evaluate its arguments beforehand, but instead only evaluates them (and possibly repeatedly) when necessary at runtime.
ADM() - Constructor for class ec.gp.ADM
afterCoevolutionaryEvaluation(EvolutionState, GroupedProblemForm) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
age - Variable in class ec.neat.NEATSubspecies
  Age of the current subspecies.
ageOfLastImprovement - Variable in class ec.neat.NEATSubspecies
  Record the last time the best fitness improved within the individuals of this subspecies If this is too long ago, the subspecies will goes extinct
ageSignificance - Variable in class ec.neat.NEATSpecies
  How much does age matter?
aggCovarMatrix - Variable in class ec.eda.amalgam.AMALGAMSpecies
ALL_MESSAGE_LOGS - Static variable in class ec.util.Output
allowOverEvaluation - Variable in class ec.coevolve.CompetitiveEvaluator
allValid(ArrayList<Individual>, int, int, EvolutionState, int) - Method in class ec.breed.CheckingPipeline
alpha - Variable in class ec.eda.pbil.PBILSpecies
alphaAMS - Variable in class ec.eda.amalgam.AMALGAMSpecies
altGeneratorTries - Variable in class ec.eda.cmaes.CMAESSpecies
  How many times should we try to generate a valid individual before we give up and use the useAltGenerator approach?
AMALGAMBreeder - Class in ec.eda.amalgam
AMALGAMBreeder() - Constructor for class ec.eda.amalgam.AMALGAMBreeder
AMALGAMDefaults - Class in ec.eda.amalgam
AMALGAMDefaults() - Constructor for class ec.eda.amalgam.AMALGAMDefaults
AMALGAMSpecies - Class in ec.eda.amalgam
  AMALGAMSpecies is a FloatVectorSpecies which implements a faithful version of the iAMaLGaM IDEA algorithm.
AMALGAMSpecies() - Constructor for class ec.eda.amalgam.AMALGAMSpecies
AnnealedSelection - Class in ec.select
  Returns an individual using a form of simulated annealing.
AnnealedSelection() - Constructor for class ec.select.AnnealedSelection
appendOnRestart - Variable in class ec.util.Log
  If the log writes to a file, should it append to the file on restart, or should it overwrite the file?
ARCHIVE_LOADED - Enum constant in enum class ec.multiobjective.nsga2.NSGA2Breeder.BreedingState
ARCHIVE_LOADED - Enum constant in enum class ec.multiobjective.spea2.SPEA2Breeder.BreedingState
argposition - Variable in class ec.gp.GPNode
  The argument position of the child in its parent.
argument - Variable in class ec.gp.ADFArgument
arguments - Variable in class ec.gp.ADFContext
  An array of GPData nodes (none of the null, when it's used) holding an ADF's arguments' return results
arity - Variable in class ec.gp.build.RandTree.ArityObject
ArityObject(int) - Constructor for class ec.gp.build.RandTree.ArityObject
assignFrontRanks(Subpopulation) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
  Divides inds into ranks and assigns each individual's rank to be the rank it was placed into.
associatedTree - Variable in class ec.gp.ADF
  The ADF's associated tree
atDepth() - Method in class ec.gp.GPNode
  Returns the depth at which I appear in the tree, which is a value >= 0.
author - Static variable in class ec.util.Version
authorEmail0 - Static variable in class ec.util.Version
authorEmail1 - Static variable in class ec.util.Version
authorEmail2 - Static variable in class ec.util.Version
authorURL - Static variable in class ec.util.Version
AUXILLARY_PREAMBLE - Static variable in class ec.pso.Particle

## B

b - Variable in class ec.eda.cmaes.CMAESSpecies
  The "B" matrix, eigendecomposed from the "C" covariance matrix of the distribution.
b - Variable in class ec.eda.dovs.DOVSSpecies
  Constratin coefficients
b - Variable in class ec.eda.pbil.PBILSpecies
babiesStolen - Variable in class ec.neat.NEATSpecies
  The number of babies to siphen off to the champions.
backupPopulation - Variable in class ec.simple.SimpleBreeder
BAD_TREE - Static variable in class ec.gp.ge.GEIndividual
BadParameterException - Exception Class in ec.util
  Thrown when you attempt to create a Parameter from bad path items.
BadParameterException(String) - Constructor for exception class ec.util.BadParameterException
BarChartStatistics - Class in ec.display.chart
BarChartStatistics() - Constructor for class ec.display.chart.BarChartStatistics
base - Variable in class ec.eval.MetaProblem
  The parameter base from which the MetaProblem was loaded.
base - Variable in class ec.exchange.InterPopulationExchange
  My parameter base -- I need to keep this in order to help the server reinitialize contacts
base - Variable in class ec.exchange.IslandExchange
  My parameter base -- I need to keep this in order to help the server reinitialize contacts
base - Variable in class ec.neat.NEATSpecies
base() - Static method in class ec.breed.BreedDefaults
  Returns the default base.
base() - Static method in class ec.ECDefaults
  Returns the default base.
base() - Static method in class ec.eda.amalgam.AMALGAMDefaults
  Returns the default base.
base() - Static method in class ec.eda.cmaes.CMAESDefaults
  Returns the default base.
base() - Static method in class ec.eda.dovs.DOVSDefaults
  Returns the default base.
base() - Static method in class ec.es.ESDefaults
  Returns the default base.
base() - Static method in class ec.gp.breed.GPBreedDefaults
  Returns the default base, which is built off of the GPDefaults base.
base() - Static method in class ec.gp.build.GPBuildDefaults
  Returns the default base.
base() - Static method in class ec.gp.ge.GEDefaults
  Returns the default base.
base() - Static method in class ec.gp.GPDefaults
  Returns the default base.
base() - Static method in class ec.gp.koza.GPKozaDefaults
  Returns the default base, which is built off of the GPDefaults base.
base() - Static method in class ec.gp.push.PushDefaults
  Returns the default base.
base() - Static method in class ec.multiobjective.MultiObjectiveDefaults
  Returns the default base.
base() - Static method in class ec.neat.NEATDefaults
base() - Static method in class ec.rule.RuleDefaults
  Returns the default base.
base() - Static method in class ec.select.SelectDefaults
  Returns the default base.
base() - Static method in class ec.simple.SimpleDefaults
  Returns the default base.
base() - Static method in class ec.spatial.SpatialDefaults
  Returns the default base.
base() - Static method in class ec.steadystate.SteadyStateDefaults
  Returns the default base.
base() - Static method in class ec.vector.VectorDefaults
  Returns the default base.
batchMode - Variable in class ec.eval.MasterProblem
bd - Variable in class ec.eda.cmaes.CMAESSpecies
  b x d
beforeCoevolutionaryEvaluation(EvolutionState, Population, GroupedProblemForm) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
best_of_run - Variable in class ec.simple.SimpleStatistics
  The best individual we've found so far
Best1BinDEBreeder - Class in ec.de
  Best1BinDEBreeder is a differential evolution breeding operator.
Best1BinDEBreeder() - Constructor for class ec.de.Best1BinDEBreeder
bestn - Variable in class ec.select.BestSelection
bestnFrac - Variable in class ec.select.BestSelection
bestOfGeneration - Variable in class ec.simple.SimpleShortStatistics
BestSelection - Class in ec.select
  Performs a tournament selection restricted to only the best, or worst, n indivdiuals in the population.
BestSelection() - Constructor for class ec.select.BestSelection
bestSoFar - Variable in class ec.simple.SimpleShortStatistics
bestSoFarIndex - Variable in class ec.de.DEBreeder
  the best individuals in each population (required by some DE breeders).
bestUnderlyingIndividual - Variable in class ec.eval.MetaProblem
  The best underlying individual array, one per subpopulation.
betterThan(Fitness) - Method in class ec.Fitness
  Should return true if this fitness is clearly better than _fitness; You may assume that _fitness is of the same class as yourself.
betterThan(Fitness) - Method in class ec.gp.koza.KozaFitness
betterThan(Fitness) - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns true if I'm better than _fitness.
betterThan(Fitness) - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
  We specify the tournament selection criteria, Rank (lower values are better) and Sparsity (higher values are better)
betterThan(Fitness) - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
  The selection criteria in SPEA2 uses the computed fitness, and not pareto dominance.
betterThan(Fitness) - Method in class ec.simple.SimpleFitness
betterThan(Individual, Individual, int, EvolutionState, int) - Method in class ec.parsimony.LexicographicTournamentSelection
betterThan(Individual, Individual, int, EvolutionState, int) - Method in class ec.parsimony.ProportionalTournamentSelection
betterThan(Individual, Individual, int, EvolutionState, int) - Method in class ec.select.TournamentSelection
  Returns true if *first* is a better (fitter, whatever) individual than *second*.
BIAS - Enum constant in enum class ec.neat.NEATNode.NodePlace
BIG_TREE_ERROR - Static variable in class ec.gp.ge.GESpecies
BitVectorIndividual - Class in ec.vector
  BitVectorIndividual is a VectorIndividual whose genome is an array of booleans.
BitVectorIndividual() - Constructor for class ec.vector.BitVectorIndividual
BitVectorSpecies - Class in ec.vector
  BitVectorSpecies is a subclass of VectorSpecies with special constraints for boolean vectors, namely BitVectorIndividual.
BitVectorSpecies() - Constructor for class ec.vector.BitVectorSpecies
BoltzmannSelection - Class in ec.select
  Similar to FitProportionateSelection, but with a Simulated Annealing style twist.
BoltzmannSelection() - Constructor for class ec.select.BoltzmannSelection
BOOLEAN_CONSTANT - Static variable in class ec.gp.ge.GrammarParser
boxA - Variable in class ec.eda.dovs.HyperboxSpecies
  boxA and boxB contain the current constraint hyperbox.
boxB - Variable in class ec.eda.dovs.HyperboxSpecies
  boxA and boxB contain the current constraint hyperbox.
BreedDefaults - Class in ec.breed
BreedDefaults() - Constructor for class ec.breed.BreedDefaults
breeder - Variable in class ec.EvolutionState
  The population breeder, a singleton object.
Breeder - Class in ec
  A Breeder is a singleton object which is responsible for the breeding process during the course of an evolutionary run.
Breeder() - Constructor for class ec.Breeder
breedIndividual(EvolutionState, int, int) - Method in class ec.steadystate.SteadyStateBreeder
BREEDING_COMPLETE - Enum constant in enum class ec.multiobjective.nsga2.NSGA2Breeder.BreedingState
BREEDING_COMPLETE - Enum constant in enum class ec.multiobjective.spea2.SPEA2Breeder.BreedingState
BreedingPipeline - Class in ec
  A BreedingPipeline is a BreedingSource which provides "fresh" individuals which can be used to fill a new population.
BreedingPipeline() - Constructor for class ec.BreedingPipeline
BreedingSource - Class in ec
  A BreedingSource is a Prototype which provides Individuals to populate new populations based on old ones.
BreedingSource() - Constructor for class ec.BreedingSource
breedNewPopulation(EvolutionState, int, int) - Method in class ec.neat.NEATSpecies
  Breed a new generation of population, this is done by first figure the expected offsprings for each subspecies, and then calls each subspecies to reproduce.
breedPopChunk(Population, EvolutionState, int[], int[], int) - Method in class ec.es.MuCommaLambdaBreeder
  A private helper function for breedPopulation which breeds a chunk of individuals in a subpopulation for a given thread.
breedPopChunk(Population, EvolutionState, int[], int[], int) - Method in class ec.simple.SimpleBreeder
  A private helper function for breedPopulation which breeds a chunk of individuals in a subpopulation for a given thread.
breedPopChunk(Population, EvolutionState, int[], int[], int) - Method in class ec.spatial.SpatialBreeder
breedPopChunkProduce(int) - Method in class ec.simple.SimpleBreeder
breedPopulation(EvolutionState) - Method in class ec.Breeder
  Breeds state.population, returning a new population.
breedPopulation(EvolutionState) - Method in class ec.de.DEBreeder
breedPopulation(EvolutionState) - Method in class ec.eda.amalgam.AMALGAMBreeder
  Updates the distribution given the current population, then replaces the population with new samples generated from the distribution.
breedPopulation(EvolutionState) - Method in class ec.eda.cmaes.CMAESBreeder
  Updates the CMA-ES distribution given the current population, then replaces the population with new samples generated from the distribution.
breedPopulation(EvolutionState) - Method in class ec.eda.dovs.DOVSBreeder
  This method have three major part, first identify the best indiviudal, and then call updateMostPromisingArea(...) to construct a hyperbox around this individual.
breedPopulation(EvolutionState) - Method in class ec.eda.pbil.PBILBreeder
  Updates the PBIL distribution given the current population, then replaces the population with new samples generated from the distribution.
breedPopulation(EvolutionState) - Method in class ec.es.MuCommaLambdaBreeder
breedPopulation(EvolutionState) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
  Use super's breeding, but also set our local state to record that breeding is complete.
breedPopulation(EvolutionState) - Method in class ec.multiobjective.spea2.SPEA2Breeder
  Use super's breeding, but also set our local state to record that breeding is complete.
breedPopulation(EvolutionState) - Method in class ec.neat.NEATBreeder
  This method simply call breedNewPopulation method in NEATSpecies，where all the critical work in done.
breedPopulation(EvolutionState) - Method in class ec.pso.PSOBreeder
breedPopulation(EvolutionState) - Method in class ec.simple.SimpleBreeder
  A simple breeder that doesn't attempt to do any cross- population breeding.
breedthreads - Variable in class ec.EvolutionState
  The requested number of threads to be used in breeding, excepting perhaps a "parent" thread which gathers the other threads.
BucketTournamentSelection - Class in ec.parsimony
  Does a tournament selection, limited to the subpopulation it's working in at the time.
BucketTournamentSelection() - Constructor for class ec.parsimony.BucketTournamentSelection
buffer - Variable in class ec.breed.BufferedBreedingPipeline
BufferedBreedingPipeline - Class in ec.breed
  If empty, a BufferedBreedingPipeline makes a request of exactly num-inds individuals from a single child source; it then uses these individuals to fill requests (returning min each time), until the buffer is emptied, at which time it grabs exactly num-inds more individuals, and so on.
BufferedBreedingPipeline() - Constructor for class ec.breed.BufferedBreedingPipeline
bufSize - Variable in class ec.breed.BufferedBreedingPipeline
buildArchive(EvolutionState, int) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
  Build the auxiliary fitness data and reduce the subpopulation to just the archive, which is returned.
buildDyckWord(int, int[], int[], EvolutionState, int) - Method in class ec.gp.build.RandTree
builder - Variable in class ec.gp.koza.MutationPipeline
  How the pipeline builds a new subtree
buildMisc(EvolutionState, int, int) - Method in class ec.Species
  Called whenever the Breeder calls produce(...) on a BreedingPipeline, in order to pass a new "misc" object.
buildNetwork(NEATIndividual) - Method in class ec.neat.NEATNetwork
  Create the phenotype (network) from the genotype (genome).
buildOutput() - Static method in class ec.Evolve
  Constructs and sets up an Output object which always issues errors in the traditional fashion rather than throwing them.
buildOutput(boolean) - Static method in class ec.Evolve
  Constructs and sets up an Output object.
buildTree(EvolutionState, int) - Method in class ec.gp.GPTree
  Builds a new randomly-generated rooted tree and attaches it to the GPTree.
buildTreeModel() - Method in class ec.util.ParameterDatabase
  Builds a TreeModel from the available property keys.
bypassFinalStatistics(EvolutionState, int) - Method in class ec.simple.SimpleStatistics
  Allows MultiObjectiveStatistics etc.
bypassPostEvaluationStatistics(EvolutionState) - Method in class ec.simple.SimpleStatistics
  Allows MultiObjectiveStatistics etc.
ByteVectorIndividual - Class in ec.vector
  ByteVectorIndividual is a VectorIndividual whose genome is an array of bytes.
ByteVectorIndividual() - Constructor for class ec.vector.ByteVectorIndividual

## C

c - Variable in class ec.eda.cmaes.CMAESSpecies
  The "C" covariance matrix of the distribution.
C_ANY_POINT - Static variable in class ec.vector.VectorSpecies
C_AUTO - Static variable in class ec.simple.SimpleEvaluator
C_CLASS - Static variable in class ec.util.ParameterDatabase
C_EXACTLY_ONE_FIFTH_BETTER - Static variable in class ec.es.MuCommaLambdaBreeder
C_FLIP_MUTATION - Static variable in class ec.vector.BitVectorSpecies
C_GAUSS_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
C_GEOMETRIC - Static variable in class ec.vector.VectorSpecies
C_HERE - Static variable in class ec.util.ParameterDatabase
C_INTEGER_RANDOM_WALK_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
C_INTEGER_RESET_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
C_INTERMED_RECOMB - Static variable in class ec.vector.VectorSpecies
C_LINE_RECOMB - Static variable in class ec.vector.VectorSpecies
C_NEIGHBORHOOD_RANDOM - Static variable in class ec.pso.PSOBreeder
C_NEIGHBORHOOD_RANDOM_EACH_TIME - Static variable in class ec.pso.PSOBreeder
C_NEIGHBORHOOD_TOROIDAL - Static variable in class ec.pso.PSOBreeder
C_NONE - Static variable in class ec.vector.VectorSpecies
C_ONE_POINT - Static variable in class ec.vector.VectorSpecies
C_ONE_POINT_NO_NOP - Static variable in class ec.vector.VectorSpecies
C_OVER_ONE_FIFTH_BETTER - Static variable in class ec.es.MuCommaLambdaBreeder
C_POLYNOMIAL_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
C_RANDOM_WALK_MUTATION - Static variable in class ec.vector.IntegerVectorSpecies
C_RESET_MUTATION - Static variable in class ec.vector.BitVectorSpecies
C_RESET_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
C_RESET_MUTATION - Static variable in class ec.vector.IntegerVectorSpecies
C_SIMULATED_BINARY - Static variable in class ec.vector.VectorSpecies
C_STARTED_FRESH - Static variable in class ec.EvolutionState
  "The population has started fresh (not from a checkpoint)."
C_STARTED_FROM_CHECKPOINT - Static variable in class ec.EvolutionState
  "The population started from a checkpoint."
C_TWO_POINT - Static variable in class ec.vector.VectorSpecies
C_TWO_POINT_NO_NOP - Static variable in class ec.vector.VectorSpecies
C_UNDER_ONE_FIFTH_BETTER - Static variable in class ec.es.MuCommaLambdaBreeder
C_UNIFORM - Static variable in class ec.vector.VectorSpecies
c1 - Variable in class ec.eda.cmaes.CMAESSpecies
  The c_1 rank-1 update learning rate.
CACHE_SIZE - Static variable in class ec.gp.build.PTCFunctionSet
cacheBest(int, EvolutionState, int) - Method in class ec.select.AnnealedSelection
cacheBest(int, EvolutionState, int) - Method in class ec.select.TopSelection
calculateDistancesFromIndividual(Individual, ArrayList<Individual>) - Method in class ec.multiobjective.spea2.SPEA2Breeder
canEvaluate() - Method in class ec.eval.MasterProblem
canEvaluate() - Method in class ec.gp.ge.GEProblem
canEvaluate() - Method in class ec.Problem
  Asynchronous Steady-State EC only: Returns true if the problem is ready to evaluate.
canEvaluate() - Method in class ec.steadystate.SteadyStateEvaluator
  Returns true if we're ready to evaluate an individual.
canPick() - Method in class ec.gp.GPNodeBuilder
  Returns true if some size distribution (either minSize and maxSize, or sizeDistribution) is set up by the user in order to pick sizes randomly.
cc - Variable in class ec.eda.cmaes.CMAESSpecies
  The c_c rank-one evolution path cumulation parameter.
champion - Variable in class ec.neat.NEATIndividual
  Marks the subspecies champion, which is the individual who has the highest fitness with the subspecies.
ChartableStatistics - Class in ec.display.chart
ChartableStatistics() - Constructor for class ec.display.chart.ChartableStatistics
chatty - Variable in class ec.exchange.InterPopulationExchange
CHECK_BOUNDARY - Static variable in class ec.gp.GPNodeBuilder
CHECKBOUNDARY - Static variable in class ec.util.RandomChoice
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class ec.gp.ADF
  Checks type-compatibility constraints between the ADF, its argument terminals, and the tree type of its associated tree, and also checks to make sure the tree exists, there aren't invalid argument terminals in it, and there are sufficient argument terminals (a warning).
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class ec.gp.GPNode
  You ought to override this method to check to make sure that the constraints are valid as best you can tell.
checkDyckWord(String) - Method in class ec.gp.build.RandTree
checkForHelp(String[], String, boolean) - Static method in class ec.Evolve
  Optionally prints the help message.
CheckingPipeline - Class in ec.breed
  CheckingPipeline is a BreedingPipeline which just passes through the individuals it receives from its source 0, but only if those individuals ALL pass a validation check (the method allValid(), which you must override).
CheckingPipeline() - Constructor for class ec.breed.CheckingPipeline
checkpoint - Variable in class ec.EvolutionState
  Should we checkpoint at all?
Checkpoint - Class in ec.util
  Checkpoints ec.EvolutionState objects out to checkpoint files, or restores the same from checkpoint files.
Checkpoint() - Constructor for class ec.util.Checkpoint
checkpointDirectory - Variable in class ec.EvolutionState
  The requested directory where checkpoints should be located.
checkpointModulo - Variable in class ec.EvolutionState
  The requested number of generations that should pass before we write out a checkpoint file.
checkpointPrefix - Variable in class ec.EvolutionState
  The requested prefix to start checkpoint filenames, not including a following period.
checkPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, then trims the line and checks the preamble.
checkTerminationConditions(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
child - Variable in class ec.gp.GPTree
  the root GPNode in the GPTree
CHILD_D - Variable in class ec.gp.build.Uniform
children - Variable in class ec.gp.ge.GrammarNode
children - Variable in class ec.gp.GPNode
children - Variable in class ec.Statistics
CHILDREN_UNKNOWN - Static variable in class ec.gp.GPNode
childtypes - Variable in class ec.gp.GPNodeConstraints
  The children types for a GPNode
chiN - Variable in class ec.eda.cmaes.CMAESSpecies
  An estimate of the expected size of the standard multivariate gaussian N(0,I).
choleskyLower - Variable in class ec.eda.amalgam.AMALGAMSpecies
chunksize - Variable in class ec.vector.VectorSpecies
  How big of chunks should we define for crossover?
clamp() - Method in class ec.vector.ByteVectorIndividual
  Clips each gene value to be within its specified [min,max] range.
clamp() - Method in class ec.vector.DoubleVectorIndividual
  Clips each gene value to be within its specified [min,max] range.
clamp() - Method in class ec.vector.FloatVectorIndividual
  Clips each gene value to be within its specified [min,max] range.
clamp() - Method in class ec.vector.IntegerVectorIndividual
  Clips each gene value to be within its specified [min,max] range.
clamp() - Method in class ec.vector.LongVectorIndividual
  Clips each gene value to be within its specified [min,max] range.
clamp() - Method in class ec.vector.ShortVectorIndividual
  Clips each gene value to be within its specified [min,max] range.
cleanup(EvolutionState) - Static method in class ec.Evolve
  Begins a fresh evolutionary run with a given state.
clear() - Method in class ec.Population
clear() - Method in class ec.Subpopulation
  Sets all Individuals in the Subpopulation to null, preparing it to be reused.
clear() - Method in class ec.util.IntBag
  Removes all numbers in the IntBag.
clearAnnouncements() - Method in class ec.util.Output
  Clears out announcements.
clearErrors() - Method in class ec.util.Output
  Clears the error flag.
clearEvaluationFlag(ArrayList<Individual>) - Method in class ec.neat.NEATSpecies
  Clear the evaluation flag in each individual.
clearGaussian() - Method in class ec.util.MersenneTwister
  Clears the internal gaussian variable from the RNG.
clearGaussian() - Method in class ec.util.MersenneTwisterFast
  Clears the internal gaussian variable from the RNG.
clearIncoming() - Method in class ec.neat.NEATNode
  Clear in incomgin links of this node, this is useful in create a new network from current genotype.
clientPort - Variable in class ec.exchange.IslandExchange
  The port of the client mailbox
Clique - Interface in ec
  Clique is a class pattern marking classes which create only a few instances, generally accessible through some global mechanism, and every single one of which gets its own distinct setup(...) call.
clone() - Method in class ec.breed.StubPipeline
clone() - Method in class ec.breed.UniquePipeline
clone() - Method in class ec.BreedingPipeline
clone() - Method in class ec.BreedingSource
clone() - Method in class ec.eda.amalgam.AMALGAMSpecies
clone() - Method in class ec.eda.cmaes.CMAESSpecies
clone() - Method in class ec.eda.pbil.PBILSpecies
clone() - Method in class ec.eval.MasterProblem
clone() - Method in class ec.Fitness
clone() - Method in class ec.gp.ADFContext
clone() - Method in class ec.gp.ADFStack
clone() - Method in class ec.gp.breed.InternalCrossoverPipeline
clone() - Method in class ec.gp.breed.MutateAllNodesPipeline
clone() - Method in class ec.gp.breed.MutateERCPipeline
clone() - Method in class ec.gp.breed.MutateOneNodePipeline
clone() - Method in class ec.gp.breed.SizeFairCrossoverPipeline
clone() - Method in class ec.gp.ge.GEProblem
clone() - Method in class ec.gp.ge.GESpecies
clone() - Method in class ec.gp.ge.GrammarParser
clone() - Method in class ec.gp.GPData
clone() - Method in class ec.gp.GPIndividual
  Deep-clones the GPIndividual.
clone() - Method in class ec.gp.GPNode
  Deep-clones the tree rooted at this node, and returns the entire copied tree.
clone() - Method in class ec.gp.GPNodeBuilder
clone() - Method in class ec.gp.GPProblem
clone() - Method in class ec.gp.GPTree
  Deep-clones the tree.
clone() - Method in class ec.gp.koza.CrossoverPipeline
clone() - Method in class ec.gp.koza.KozaNodeSelector
clone() - Method in class ec.gp.koza.MutationPipeline
clone() - Method in class ec.gp.push.PushInstruction
clone() - Method in class ec.gp.push.PushProblem
clone() - Method in class ec.Individual
clone() - Method in class ec.multiobjective.MultiObjectiveFitness
clone() - Method in class ec.neat.NEATGene
clone() - Method in class ec.neat.NEATIndividual
clone() - Method in class ec.neat.NEATInnovation
clone() - Method in class ec.neat.NEATNetwork
clone() - Method in class ec.neat.NEATNode
clone() - Method in class ec.neat.NEATSubspecies
clone() - Method in class ec.Problem
clone() - Method in interface ec.Prototype
  Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.
clone() - Method in class ec.pso.Particle
clone() - Method in class ec.rule.breed.RuleCrossoverPipeline
clone() - Method in class ec.rule.Rule
clone() - Method in class ec.rule.RuleIndividual
clone() - Method in class ec.rule.RuleSet
clone() - Method in class ec.select.MultiSelection
clone() - Method in class ec.Species
clone() - Method in class ec.util.IntBag
clone() - Method in class ec.util.MersenneTwister
clone() - Method in class ec.util.MersenneTwisterFast
clone() - Method in class ec.vector.BitVectorIndividual
clone() - Method in class ec.vector.breed.ListCrossoverPipeline
clone() - Method in class ec.vector.breed.MultipleVectorCrossoverPipeline
clone() - Method in class ec.vector.breed.VectorCrossoverPipeline
clone() - Method in class ec.vector.ByteVectorIndividual
clone() - Method in class ec.vector.DoubleVectorIndividual
clone() - Method in class ec.vector.FloatVectorIndividual
clone() - Method in class ec.vector.Gene
clone() - Method in class ec.vector.GeneVectorIndividual
clone() - Method in class ec.vector.IntegerVectorIndividual
clone() - Method in class ec.vector.LongVectorIndividual
clone() - Method in class ec.vector.ShortVectorIndividual
cloneGenes(Object) - Method in class ec.vector.GeneVectorIndividual
cloneGenes(Object) - Method in class ec.vector.VectorIndividual
  Clones the genes in pieces, and replaces the genes with their copies.
clonePipelineAndPopulation - Variable in class ec.simple.SimpleBreeder
cloneProblem - Variable in class ec.simple.SimpleEvaluator
cloneReplacing() - Method in class ec.gp.GPNode
  Deep-clones the tree rooted at this node, and returns the entire copied tree.
cloneReplacing(GPNode[], GPNode[]) - Method in class ec.gp.GPNode
  Deep-clones the tree rooted at this node, and returns the entire copied tree.
cloneReplacing(GPNode, GPNode) - Method in class ec.gp.GPNode
  Deep-clones the tree rooted at this node, and returns the entire copied tree.
cloneReplacingAtomic(GPNode[], GPNode[]) - Method in class ec.gp.GPNode
  Clones a new subtree, but with each node in oldNodes[] respectively (which may or may not be in the subtree) replaced with the equivalent nodes in newNodes[] (and not clones).
cloneReplacingAtomic(GPNode, GPNode) - Method in class ec.gp.GPNode
  Clones a new subtree, but with the single node oldNode (which may or may not be in the subtree) replaced with a newNode (not a clone of newNode).
cloneReplacingNoSubclone(GPNode, GPNode) - Method in class ec.gp.GPNode
  Deep-clones the tree rooted at this node, and returns the entire copied tree.
close() - Method in class ec.util.Output
  Closes the logs -- ONLY call this if you are preparing to quit
closeContacts(EvolutionState, int) - Method in class ec.eval.MasterProblem
  Gracefully close contacts with the slaves
closeContacts(EvolutionState, int) - Method in class ec.Evaluator
  Called to shut down remote evaluation network contacts when the run is completed.
closeContacts(EvolutionState, int) - Method in class ec.exchange.InterPopulationExchange
  Closes contacts with other processes, if that's what you're doing.
closeContacts(EvolutionState, int) - Method in class ec.exchange.IslandExchange
  Closes contacts with other processes, if that's what you're doing.
closeContacts(EvolutionState, int) - Method in class ec.Exchanger
  Closes contacts with other processes, if that's what you're doing.
closeContacts(EvolutionState, int) - Method in class ec.gp.ge.GEProblem
closeContacts(EvolutionState, int) - Method in class ec.Problem
  Called to shut down remote evaluation network contacts when the run is completed.
closeContacts(EvolutionState, int) - Method in class ec.simple.SimpleExchanger
  Doesn't do anything.
CMAESBreeder - Class in ec.eda.cmaes
  CMAESBreeder is a Breeder which overrides the breedPopulation method to first update CMA-ES's internal distribution, then replace all the individuals in the population with new samples generated from the distribution.
CMAESBreeder() - Constructor for class ec.eda.cmaes.CMAESBreeder
CMAESDefaults - Class in ec.eda.cmaes
  CMAESDefaults is the basic defaults class for the cmaes package.
CMAESDefaults() - Constructor for class ec.eda.cmaes.CMAESDefaults
CMAESInitializer - Class in ec.eda.cmaes
  CMAESInitializer is a SimpleInitializer which ensures that the subpopulations are all set to the provided or computed lambda values.
CMAESInitializer() - Constructor for class ec.eda.cmaes.CMAESInitializer
CMAESSpecies - Class in ec.eda.cmaes
  CMAESSpecies is a FloatVectorSpecies which implements a faithful version of the CMA-ES algorithm.
CMAESSpecies() - Constructor for class ec.eda.cmaes.CMAESSpecies
cmu - Variable in class ec.eda.cmaes.CMAESSpecies
  The c_{\mu} rank-mu update learning rate.
Code - Class in ec.util
  Code provides some simple wrapper functions for encoding and decoding basic data types for storage in a pseudo-Java source code strings format.
Code() - Constructor for class ec.util.Code
COLDGAUSSIAN - Enum constant in enum class ec.neat.NEATSpecies.MutationType
combine(EvolutionState, Fitness[], Fitness) - Method in class ec.eval.MetaProblem
  Combines fitness results from multiple runs into a final Fitness.
COMMENT - Static variable in class ec.gp.ge.GrammarParser
compareIndividuals(Individual, Individual) - Method in class ec.eda.amalgam.AMALGAMSpecies
compareTo(Individual) - Method in class ec.Individual
  Returns -1 if I am BETTER in some way than the other Individual, 1 if the other Individual is BETTER than me, and 0 if we are equivalent.
compareTo(Object) - Method in class ec.Fitness
  Returns -1 if I am FITTER than the other Fitness, 1 if I am LESS FIT than the other Fitness, and 0 if we are equivalent.
compareTo(Object) - Method in class ec.rule.Rule
  This function replaces the old gt and lt functions that Rule used to require as it implemented the SortComparator interface.
comparison - Variable in class ec.es.MuCommaLambdaBreeder
compatibility(NEATIndividual, NEATIndividual) - Method in class ec.neat.NEATSpecies
  This function gives a measure of compatibility between two Genomes by computing a linear combination of 3 characterizing variables of their compatibilty.
compatibleWith(GPInitializer, GPType) - Method in class ec.gp.GPAtomicType
compatibleWith(GPInitializer, GPType) - Method in class ec.gp.GPSetType
compatibleWith(GPInitializer, GPType) - Method in class ec.gp.GPType
  Am I compatible with ("fit" with) t? For two atomic types, this is done by direct pointer equality.
compatThreshold - Variable in class ec.neat.NEATSpecies
  Compatible threshold to determine if two individual are compatible.
CompetitiveEvaluator - Class in ec.coevolve
  CompetitiveEvaluator.java
CompetitiveEvaluator() - Constructor for class ec.coevolve.CompetitiveEvaluator
componentType() - Method in interface ec.util.Indexed
  Should return the base component type for this Indexed object, or null if the component type should be queried via getValue(index).getClass.getComponentType()
componentType() - Method in class ec.util.IntBag
compress - Variable in class ec.simple.SimpleStatistics
  Should we compress the file?
compressedCommunication - Variable in class ec.exchange.IslandExchange
  whether the communication is compressed or not
computeAMS(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
computeConstraintViolations(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
computeCovariance(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
computeMean(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
computeNonterminalSelectionProbabilities(int) - Method in class ec.gp.build.PTCFunctionSet
computePercentages() - Method in class ec.gp.build.Uniform
computeValidationData(EvolutionState, ArrayList<Individual>, int) - Method in class ec.vector.breed.ListCrossoverPipeline
  A hook called by ListCrossoverPipeline to allow subclasses to prepare for additional validation testing.
Console - Class in ec.display
Console(GraphicsConfiguration, String[]) - Constructor for class ec.display.Console
Console(String[]) - Constructor for class ec.display.Console
Console(String, GraphicsConfiguration, String[]) - Constructor for class ec.display.Console
Console(String, String[]) - Constructor for class ec.display.Console
constraintNumber - Variable in class ec.gp.GPNodeConstraints
  The byte value of the constraints -- we can only have 256 of them
constraintNumber - Variable in class ec.gp.GPTreeConstraints
  The byte value of the constraints -- we can only have 256 of them
constraintNumber - Variable in class ec.rule.RuleConstraints
  The byte value of the constraints -- we can only have 256 of them
constraintNumber - Variable in class ec.rule.RuleSetConstraints
  The byte value of the constraints -- we can only have 256 of them
constraints - Variable in class ec.gp.GPNode
  The GPNode's constraints.
constraints - Variable in class ec.gp.GPTree
  constraints on the GPTree -- don't access the constraints through this variable -- use the constraints() method instead, which will give the actual constraints object.
constraints - Variable in class ec.rule.Rule
  An index to a RuleConstraints
constraints - Variable in class ec.rule.RuleSet
  An index to a RuleSetConstraints
constraints(GPInitializer) - Method in class ec.gp.GPNode
constraints(GPInitializer) - Method in class ec.gp.GPTree
constraints(RuleInitializer) - Method in class ec.rule.Rule
constraints(RuleInitializer) - Method in class ec.rule.RuleSet
constraintsFor(String, EvolutionState) - Static method in class ec.gp.GPNodeConstraints
  You must guarantee that after calling constraintsFor(...) one or several times, you call state.output.exitIfErrors() once.
constraintsFor(String, EvolutionState) - Static method in class ec.gp.GPTreeConstraints
  You must guarantee that after calling constraintsFor(...) one or several times, you call state.output.exitIfErrors() once.
constraintsFor(String, EvolutionState) - Static method in class ec.rule.RuleConstraints
  You must guarantee that after calling constraintsFor(...) one or several times, you call state.output.exitIfErrors() once.
constraintsFor(String, EvolutionState) - Static method in class ec.rule.RuleSetConstraints
  You must guarantee that after calling constraintsFor(...) one or several times, you call state.output.exitIfErrors() once.
constraintViolations - Variable in class ec.eda.amalgam.AMALGAMSpecies
consumed(EvolutionState, GEIndividual, int) - Method in class ec.gp.ge.GESpecies
  Returns the number of elements consumed from the GEIndividual array to produce the tree, else returns -1 if an error occurs, specifically if all elements were consumed and the tree had still not been completed.
contains(boolean[], boolean) - Method in class ec.vector.VectorSpecies
  Utility method: returns the first array slot which contains the given value, else -1.
contains(double[], double) - Method in class ec.vector.VectorSpecies
  Utility method: returns the first array slot which contains the given value, else -1.
contains(int) - Method in class ec.util.IntBag
contains(int[], int) - Method in class ec.vector.VectorSpecies
  Utility method: returns the first array slot which contains the given value, else -1.
contains(long[], long) - Method in class ec.vector.VectorSpecies
  Utility method: returns the first array slot which contains the given value, else -1.
contains(GPNode) - Method in class ec.gp.GPNode
  Returns true if the subtree rooted at this node contains subnode.
containsNulls(Collection) - Static method in class ec.util.Misc
context - Variable in class ec.Fitness
  Auxiliary variable, used by coevolutionary processes, to store the individuals involved in producing this given Fitness value.
context_proto - Variable in class ec.gp.ADFStack
contextIsBetterThan(Fitness) - Method in class ec.Fitness
  Given another Fitness, returns true if the trial which produced my current context is "better" in fitness than the trial which produced his current context, and thus should be retained in lieu of his.
contributors - Static variable in class ec.util.Version
contributors2 - Static variable in class ec.util.Version
contributors3 - Static variable in class ec.util.Version
contributors4 - Static variable in class ec.util.Version
contributors5 - Static variable in class ec.util.Version
contributors6 - Static variable in class ec.util.Version
contributors7 - Static variable in class ec.util.Version
ControlPanel - Class in ec.display
ControlPanel(Console) - Constructor for class ec.display.ControlPanel
  This is the default constructor
copy(Serializable) - Static method in class ec.util.DataPipe
  A poor-man's clone for serializable but not cloneable objects: serializes an object to the pipe, then deserializes it.
copyIntoArray(int, int[], int, int) - Method in class ec.util.IntBag
  Copies 'len' elements from the Bag into the provided array.
copyNoClone(RuleSet) - Method in class ec.rule.RuleSet
  Clears out existing rules, and loads the rules from the other ruleset without cloning them.
copyright - Static variable in class ec.util.Version
copyTo(GPData) - Method in class ec.gp.GPData
  Modifies gpd so that gpd is equivalent to us.
CornerMap - Class in ec.eda.dovs
  CornerMap can help us to quickly identify the possible individuals that is able to form a hyperbox around best individual.
CornerMap() - Constructor for class ec.eda.dovs.CornerMap
CornerMap.Pair - Class in ec.eda.dovs
  Simple structure store the key and value from this CornerMap.
corners - Variable in class ec.eda.dovs.DOVSSpecies
  CornerMaps for the all the visisted individuals.
count - Variable in class ec.es.MuCommaLambdaBreeder
  Modified by multiple threads, don't fool with this
countdown - Variable in class ec.evolve.RandomRestarts
countOffspring(double) - Method in class ec.neat.NEATSubspecies
  Compute the collective offspring the entire species (the sum of all individual's offspring) is assigned skim is fractional offspring left over from a previous subspecies that was counted.
countOffspring(EvolutionState, int) - Method in class ec.neat.NEATSpecies
  Determine the offsprings for all the subspecies.
covarMatrix - Variable in class ec.eda.amalgam.AMALGAMSpecies
Cr - Variable in class ec.de.DEBreeder
  Probability of crossover per gene
CR_UNSPECIFIED - Static variable in class ec.de.DEBreeder
createIndividual(EvolutionState, int, int, int) - Method in class ec.de.Best1BinDEBreeder
createIndividual(EvolutionState, int, int, int) - Method in class ec.de.DEBreeder
createIndividual(EvolutionState, int, int, int) - Method in class ec.de.Rand1EitherOrDEBreeder
createNetwork() - Method in class ec.neat.NEATIndividual
createNodeCopyIfMissing(ArrayList<NEATNode>, NEATNode) - Method in class ec.neat.NEATIndividual
  Create the node if the nodeList do not have that node.The nodes in the nodeList is guarantee in ascending order according to node's nodeId.
crossover(EvolutionState, int, NEATIndividual) - Method in class ec.neat.NEATIndividual
  Crossover function.
crossover(EvolutionState, DoubleVectorIndividual, DoubleVectorIndividual, int) - Method in class ec.de.DEBreeder
  Crosses over child with target, storing the result in child and returning it.
crossoverDistributionIndex - Variable in class ec.vector.VectorSpecies
  What should the SBX distribution index be?
CrossoverPipeline - Class in ec.gp.koza
  CrossoverPipeline is a GPBreedingPipeline which performs a strongly-typed version of Koza-style "Subtree Crossover".
CrossoverPipeline() - Constructor for class ec.gp.koza.CrossoverPipeline
crossoverProbability - Variable in class ec.vector.VectorSpecies
  Probability that a gene will cross over -- ONLY used in V_ANY_POINT crossover
crossoverType - Variable in class ec.vector.breed.ListCrossoverPipeline
crossoverType - Variable in class ec.vector.VectorSpecies
  What kind of crossover do we have?
cs - Variable in class ec.eda.cmaes.CMAESSpecies
  The c_{\sigma} mutation rate evolution path learning rate.
currentDatabase - Variable in class ec.eval.MetaProblem
  This points to the database presently used by the underlying (base-level) evolutionary computation system.
currNodeId - Variable in class ec.neat.NEATSpecies
  Current node id that is available.
customInstructions - Variable in class ec.gp.push.Terminal
  A list of custom PushInstructions I can be set to.

## D

d - Variable in class ec.eda.cmaes.CMAESSpecies
  The "C" matrix, eigendecomposed from the "C" covariance matrix of the distribution.
d - Variable in class ec.util.DecodeReturn
  Stores floats, doubles
D_STDERR - Static variable in class ec.util.Log
  Specifies that the log should write to stderr (System.err)
D_STDOUT - Static variable in class ec.util.Log
  Specifies that the log should write to stdout (System.out)
damps - Variable in class ec.eda.cmaes.CMAESSpecies
  The d_{\sigma} dampening for the mutation rate update.
data - Variable in class ec.EvolutionState
  An array of HashMaps, indexed by the thread number you were given (or, if you're not in a multithreaded area, use 0).
data - Variable in class ec.util.DecodeReturn
  The DecodeReturn string that's read from.
DataPipe - Class in ec.util
DataPipe() - Constructor for class ec.util.DataPipe
dataset - Variable in class ec.display.chart.BarChartStatistics
dataset - Variable in class ec.display.chart.PieChartStatistics
date - Static variable in class ec.util.Version
DEBreeder - Class in ec.de
  DEBreeder provides a straightforward Differential Evolution (DE) breeder for the ECJ system.
DEBreeder() - Constructor for class ec.de.DEBreeder
decode(DecodeReturn) - Method in class ec.gp.ERC
  Decodes data into the ERC from dret.
decode(DecodeReturn) - Method in class ec.gp.push.Terminal
decode(DecodeReturn) - Static method in class ec.util.Code
  Decodes the next item out of a DecodeReturn and modifies the DecodeReturn to hold the results.
DecodeReturn - Class in ec.util
  DecodeReturn is used by Code to provide varied information returned when decoding.
DecodeReturn(String) - Constructor for class ec.util.DecodeReturn
  Use this to make a new DecodeReturn starting at position 0
DecodeReturn(String, int) - Constructor for class ec.util.DecodeReturn
  Use this to make a new DecodeReturn starting at some position
DEEvaluator - Class in ec.de
  DEEvaluator is a simple subclass of SimpleEvaluator which first evaluates the population, then compares each population member against the parent which had created it in Differential Evolution.
DEEvaluator() - Constructor for class ec.de.DEEvaluator
DEFAULT_ALT_GENERATOR_TRIES - Static variable in class ec.eda.cmaes.CMAESSpecies
  Default value (100) for altGeneratorTries.
DEFAULT_OUT_OF_BOUNDS_RETRIES - Static variable in class ec.vector.FloatVectorSpecies
DEFAULT_PROBABILITY - Static variable in class ec.gp.GPNodeConstraints
DEFAULT_REGEXES - Static variable in class ec.gp.ge.GrammarParser
  The default regular expressions for tokens in the parser.
defaultBase() - Method in class ec.breed.BufferedBreedingPipeline
defaultBase() - Method in class ec.breed.CheckingPipeline
defaultBase() - Method in class ec.breed.FirstCopyPipeline
defaultBase() - Method in class ec.breed.ForceBreedingPipeline
defaultBase() - Method in class ec.breed.GenerationSwitchPipeline
defaultBase() - Method in class ec.breed.InitializationPipeline
defaultBase() - Method in class ec.breed.MultiBreedingPipeline
defaultBase() - Method in class ec.breed.RepeatPipeline
defaultBase() - Method in class ec.breed.ReproductionPipeline
defaultBase() - Method in class ec.breed.StubPipeline
defaultBase() - Method in class ec.breed.UniquePipeline
defaultBase() - Method in class ec.eda.amalgam.AMALGAMSpecies
defaultBase() - Method in class ec.eda.cmaes.CMAESSpecies
defaultBase() - Method in class ec.eda.dovs.DOVSSpecies
defaultBase() - Method in class ec.es.ESSelection
defaultBase() - Method in class ec.gp.ADF
defaultBase() - Method in class ec.gp.ADFArgument
defaultBase() - Method in class ec.gp.ADFContext
defaultBase() - Method in class ec.gp.ADFStack
defaultBase() - Method in class ec.gp.breed.InternalCrossoverPipeline
defaultBase() - Method in class ec.gp.breed.MutateAllNodesPipeline
defaultBase() - Method in class ec.gp.breed.MutateDemotePipeline
defaultBase() - Method in class ec.gp.breed.MutateERCPipeline
defaultBase() - Method in class ec.gp.breed.MutateOneNodePipeline
defaultBase() - Method in class ec.gp.breed.MutatePromotePipeline
defaultBase() - Method in class ec.gp.breed.MutateSwapPipeline
defaultBase() - Method in class ec.gp.breed.RehangPipeline
defaultBase() - Method in class ec.gp.breed.SizeFairCrossoverPipeline
defaultBase() - Method in class ec.gp.build.PTC1
defaultBase() - Method in class ec.gp.build.PTC2
defaultBase() - Method in class ec.gp.build.RandomBranch
defaultBase() - Method in class ec.gp.build.RandTree
defaultBase() - Method in class ec.gp.build.Uniform
defaultBase() - Method in class ec.gp.ge.GESpecies
defaultBase() - Method in class ec.gp.ge.GrammarParser
defaultBase() - Method in class ec.gp.GPData
defaultBase() - Method in class ec.gp.GPIndividual
defaultBase() - Method in class ec.gp.GPNode
  The default base for GPNodes -- defined even though GPNode is abstract so you don't have to in subclasses.
defaultBase() - Method in class ec.gp.GPProblem
  GPProblem defines a default base so your subclass doesn't absolutely have to.
defaultBase() - Method in class ec.gp.GPSpecies
defaultBase() - Method in class ec.gp.GPTree
defaultBase() - Method in class ec.gp.koza.CrossoverPipeline
defaultBase() - Method in class ec.gp.koza.FullBuilder
defaultBase() - Method in class ec.gp.koza.GrowBuilder
defaultBase() - Method in class ec.gp.koza.HalfBuilder
defaultBase() - Method in class ec.gp.koza.KozaFitness
defaultBase() - Method in class ec.gp.koza.KozaNodeSelector
defaultBase() - Method in class ec.gp.koza.MutationPipeline
defaultBase() - Method in class ec.gp.push.PushBuilder
defaultBase() - Method in class ec.gp.push.PushInstruction
defaultBase() - Method in class ec.gp.push.Terminal
defaultBase() - Method in class ec.multiobjective.MultiObjectiveFitness
defaultBase() - Method in class ec.neat.NEATGene
defaultBase() - Method in class ec.neat.NEATIndividual
defaultBase() - Method in class ec.neat.NEATInnovation
defaultBase() - Method in class ec.neat.NEATNetwork
defaultBase() - Method in class ec.neat.NEATNode
defaultBase() - Method in class ec.neat.NEATSpecies
defaultBase() - Method in class ec.neat.NEATSubspecies
defaultBase() - Method in class ec.parsimony.BucketTournamentSelection
defaultBase() - Method in class ec.parsimony.DoubleTournamentSelection
defaultBase() - Method in class ec.parsimony.LexicographicTournamentSelection
defaultBase() - Method in class ec.parsimony.ProportionalTournamentSelection
defaultBase() - Method in class ec.parsimony.RatioBucketTournamentSelection
defaultBase() - Method in class ec.Problem
  Here's a nice default base for you -- you can change it if you like
defaultBase() - Method in interface ec.Prototype
  Returns the default base for this prototype.
defaultBase() - Method in class ec.rule.breed.RuleCrossoverPipeline
defaultBase() - Method in class ec.rule.breed.RuleMutationPipeline
defaultBase() - Method in class ec.rule.Rule
defaultBase() - Method in class ec.rule.RuleIndividual
defaultBase() - Method in class ec.rule.RuleSet
defaultBase() - Method in class ec.rule.RuleSpecies
defaultBase() - Method in class ec.select.AnnealedSelection
defaultBase() - Method in class ec.select.BestSelection
defaultBase() - Method in class ec.select.BoltzmannSelection
defaultBase() - Method in class ec.select.FirstSelection
defaultBase() - Method in class ec.select.FitProportionateSelection
defaultBase() - Method in class ec.select.GreedyOverselection
defaultBase() - Method in class ec.select.LexicaseSelection
defaultBase() - Method in class ec.select.MultiSelection
defaultBase() - Method in class ec.select.RandomSelection
defaultBase() - Method in class ec.select.SigmaScalingSelection
defaultBase() - Method in class ec.select.SUSSelection
defaultBase() - Method in class ec.select.TopSelection
defaultBase() - Method in class ec.select.TournamentSelection
defaultBase() - Method in class ec.simple.SimpleFitness
defaultBase() - Method in class ec.spatial.SpatialTournamentSelection
defaultBase() - Method in class ec.Subpopulation
defaultBase() - Method in class ec.vector.BitVectorIndividual
defaultBase() - Method in class ec.vector.breed.GeneDuplicationPipeline
defaultBase() - Method in class ec.vector.breed.ListCrossoverPipeline
defaultBase() - Method in class ec.vector.breed.MultipleVectorCrossoverPipeline
defaultBase() - Method in class ec.vector.breed.VectorCrossoverPipeline
defaultBase() - Method in class ec.vector.breed.VectorMutationPipeline
defaultBase() - Method in class ec.vector.ByteVectorIndividual
defaultBase() - Method in class ec.vector.DoubleVectorIndividual
defaultBase() - Method in class ec.vector.FloatVectorIndividual
defaultBase() - Method in class ec.vector.Gene
defaultBase() - Method in class ec.vector.GeneVectorIndividual
defaultBase() - Method in class ec.vector.IntegerVectorIndividual
defaultBase() - Method in class ec.vector.LongVectorIndividual
defaultBase() - Method in class ec.vector.ShortVectorIndividual
defaultBase() - Method in class ec.vector.VectorSpecies
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.BitVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.ByteVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.DoubleVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.FloatVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.GeneVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.IntegerVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.LongVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.ShortVectorIndividual
defaultCrossover(EvolutionState, int, VectorIndividual) - Method in class ec.vector.VectorIndividual
  Destructively crosses over the individual with another in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.neat.NEATIndividual
  Mutation function, determine which mutation is going to proceed with certain probabilities parameters.
defaultMutate(EvolutionState, int) - Method in class ec.vector.BitVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.ByteVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.DoubleVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.FloatVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.GeneVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.IntegerVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.LongVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.ShortVectorIndividual
  Destructively mutates the individual in some default manner.
defaultMutate(EvolutionState, int) - Method in class ec.vector.VectorIndividual
  Destructively mutates the individual in some default manner.
DefaultsForm - Interface in ec
  DefaultsForm is the interface which describes how Defaults objects should work.
delimiter - Variable in class ec.simple.SimpleShortStatistics
delimiter - Static variable in class ec.util.Parameter
deltaAMS - Variable in class ec.eda.amalgam.AMALGAMSpecies
deltaCoding(EvolutionState, int, ArrayList<NEATSubspecies>) - Method in class ec.neat.NEATSpecies
  Perform a delta coding.
depth() - Method in class ec.gp.GPNode
  Returns the depth of the tree, which is a value >= 1.
depth(int, NEATNetwork, int) - Method in class ec.neat.NEATNode
  Return the depth of this node in the network.
describe(EvolutionState, Individual, int, int, int) - Method in class ec.eval.MasterProblem
describe(EvolutionState, Individual, int, int, int) - Method in class ec.eval.MetaProblem
describe(EvolutionState, Individual, int, int, int) - Method in class ec.gp.ge.GEProblem
describe(EvolutionState, Individual, int, int, int) - Method in class ec.Problem
  Part of SimpleProblemForm.
describe(EvolutionState, Individual, int, int, int) - Method in interface ec.simple.SimpleProblemForm
  "Reevaluates" an individual, for the purpose of printing out interesting facts about the individual in the context of the Problem, and logs the results.
describe(Individual, EvolutionState, int, int, int, int) - Method in class ec.Problem
determineSeed(Output, ParameterDatabase, Parameter, long, int, boolean) - Static method in class ec.Evolve
  Loads a random generator seed.
determineThreads(Output, ParameterDatabase, Parameter) - Static method in class ec.Evolve
  Loads the number of threads.
disableControls() - Method in class ec.display.ControlPanel
disjointCoeff - Variable in class ec.neat.NEATSpecies
  Coefficient for disjoint gene in compatibility computation.
distanceTo(Individual) - Method in class ec.Individual
  Returns the metric distance to another individual, if such a thing can be measured.
distanceTo(Individual) - Method in class ec.vector.BitVectorIndividual
  Implements distance as hamming distance.
distanceTo(Individual) - Method in class ec.vector.ByteVectorIndividual
distanceTo(Individual) - Method in class ec.vector.DoubleVectorIndividual
distanceTo(Individual) - Method in class ec.vector.FloatVectorIndividual
distanceTo(Individual) - Method in class ec.vector.IntegerVectorIndividual
distanceTo(Individual) - Method in class ec.vector.LongVectorIndividual
distanceTo(Individual) - Method in class ec.vector.ShortVectorIndividual
distributionMultiplier - Variable in class ec.eda.amalgam.AMALGAMSpecies
distributionMultiplierDecrease - Variable in class ec.eda.amalgam.AMALGAMSpecies
distributionMultiplierIncrease - Variable in class ec.eda.amalgam.AMALGAMSpecies
doDepth - Variable in class ec.gp.koza.KozaShortStatistics
doDescription - Variable in class ec.simple.SimpleStatistics
doFinal - Variable in class ec.simple.SimpleStatistics
doGeneration - Variable in class ec.simple.SimpleStatistics
doHeader - Variable in class ec.simple.SimpleShortStatistics
doHypervolume - Variable in class ec.multiobjective.MultiObjectiveStatistics
doLengthFirst - Variable in class ec.parsimony.DoubleTournamentSelection
domain - Variable in class ec.eval.MetaProblem
  A list of domain information, one per parameter in the genome.
doMessage - Variable in class ec.simple.SimpleStatistics
doPerGenerationDescription - Variable in class ec.simple.SimpleStatistics
doSize - Variable in class ec.simple.SimpleShortStatistics
doSubpops - Variable in class ec.simple.SimpleShortStatistics
doTime - Variable in class ec.simple.SimpleShortStatistics
doubleArrayEquals(double[], double[], double) - Static method in class ec.util.Misc
doubleEquals(double, double, double) - Static method in class ec.util.Misc
DoubleTournamentSelection - Class in ec.parsimony
DoubleTournamentSelection() - Constructor for class ec.parsimony.DoubleTournamentSelection
DoubleVectorIndividual - Class in ec.vector
  DoubleVectorIndividual is a VectorIndividual whose genome is an array of doubles.
DoubleVectorIndividual() - Constructor for class ec.vector.DoubleVectorIndividual
DOVSBreeder - Class in ec.eda.dovs
  DOVSBreeder is a Breeder which overrides the breedPopulation method to first construct hyperbox around current best individual and replace the population with new individuals sampled from this hyperbox.
DOVSBreeder() - Constructor for class ec.eda.dovs.DOVSBreeder
DOVSDefaults - Class in ec.eda.dovs
  DOVSDefaults is the basic defaults class for the dovs package.
DOVSDefaults() - Constructor for class ec.eda.dovs.DOVSDefaults
DOVSEvaluator - Class in ec.eda.dovs
  The DOVSEvaluator is a SimpleEvaluator to evaluate the Individual.
DOVSEvaluator() - Constructor for class ec.eda.dovs.DOVSEvaluator
DOVSFitness - Class in ec.eda.dovs
  DOVSFitness is a subclass of Fitness which implements contains important statistics about simulation results of the individual.
DOVSFitness() - Constructor for class ec.eda.dovs.DOVSFitness
DOVSInitializer - Class in ec.eda.dovs
  DOVSInitializer is a SimpleInitializer which ensures that the subpopulations are create from an existing individual read from file.
DOVSInitializer() - Constructor for class ec.eda.dovs.DOVSInitializer
DOVSSpecies - Class in ec.eda.dovs
  DOVSSpecies is a IntegerVectorSpecies which implements DOVS algorithm.
DOVSSpecies() - Constructor for class ec.eda.dovs.DOVSSpecies
dropoffAge - Variable in class ec.neat.NEATSpecies
  Age where Species starts to be penalized.
duplicateRetries - Variable in class ec.vector.VectorSpecies
  How often do we retry until we get a non-duplicate gene?
duplicateRetries(int) - Method in class ec.vector.VectorSpecies
DYNAMIC_SOURCES - Static variable in class ec.BreedingPipeline
  Indicates that the number of sources is not hard coded but is determined by the user in the parameter file.
dynamicInitialSize - Variable in class ec.vector.VectorSpecies
  Was the initial size determined dynamically?

## E

ec - package ec
ec.breed - package ec.breed
ec.coevolve - package ec.coevolve
ec.de - package ec.de
ec.display - package ec.display
ec.display.chart - package ec.display.chart
ec.display.portrayal - package ec.display.portrayal
ec.eda.amalgam - package ec.eda.amalgam
ec.eda.cmaes - package ec.eda.cmaes
ec.eda.dovs - package ec.eda.dovs
ec.eda.pbil - package ec.eda.pbil
ec.es - package ec.es
ec.eval - package ec.eval
ec.evolve - package ec.evolve
ec.exchange - package ec.exchange
ec.gp - package ec.gp
ec.gp.breed - package ec.gp.breed
ec.gp.build - package ec.gp.build
ec.gp.ge - package ec.gp.ge
ec.gp.koza - package ec.gp.koza
ec.gp.push - package ec.gp.push
ec.multiobjective - package ec.multiobjective
ec.multiobjective.nsga2 - package ec.multiobjective.nsga2
ec.multiobjective.spea2 - package ec.multiobjective.spea2
ec.neat - package ec.neat
ec.parsimony - package ec.parsimony
ec.pso - package ec.pso
ec.rule - package ec.rule
ec.rule.breed - package ec.rule.breed
ec.select - package ec.select
ec.simple - package ec.simple
ec.spatial - package ec.spatial
ec.steadystate - package ec.steadystate
ec.util - package ec.util
ec.vector - package ec.vector
ec.vector.breed - package ec.vector.breed
ECDefaults - Class in ec
ECDefaults() - Constructor for class ec.ECDefaults
Ek - Variable in class ec.eda.dovs.DOVSSpecies
  This is the Ek in original paper, where is the collection all the individuals evaluated in generation k.
eliminate - Variable in class ec.neat.NEATIndividual
  Marker for destruction of inferior individual.
elite - Variable in class ec.simple.SimpleBreeder
  An array[subpop] of the number of elites to keep for that subpopulation
eliteFrac - Variable in class ec.simple.SimpleBreeder
  An array[subpop] of the *fraction* of elites to keep for that subpopulation
emptyAtGenerationBoundary - Variable in class ec.steadystate.SteadyStateEvolutionState
  If true, the population will be emptied after each "generation," so no replacement or breeding occurrs.
emptyClone() - Method in class ec.neat.NEATNode
  Return a clone of this node, but with a empty incomingGenes list.
emptyClone() - Method in class ec.neat.NEATSubspecies
  Return a clone of this subspecies, but with a empty individuals and newGenIndividuals list.
emptyClone() - Method in class ec.Population
  Returns an instance of Population just like it had been before it was populated with individuals.
emptyClone() - Method in class ec.Subpopulation
  Returns an instance of Subpopulation just like it had been before it was populated with individuals.
enable - Variable in class ec.neat.NEATGene
  Is the link this gene represent is enable in network activation.
enableControls() - Method in class ec.display.ControlPanel
encode() - Method in class ec.gp.ERC
  Encodes data from the ERC, using ec.util.Code.
encode() - Method in class ec.gp.push.Terminal
encode(boolean) - Static method in class ec.util.Code
  Encodes a boolean.
encode(byte) - Static method in class ec.util.Code
  Encodes a byte.
encode(char) - Static method in class ec.util.Code
  Encodes a character.
encode(double) - Static method in class ec.util.Code
  Encodes a double.
encode(float) - Static method in class ec.util.Code
  Encodes a float.
encode(int) - Static method in class ec.util.Code
  Encodes an int.
encode(long) - Static method in class ec.util.Code
  Encodes a long.
encode(short) - Static method in class ec.util.Code
  Encodes a short.
encode(String) - Static method in class ec.util.Code
  Encodes a String.
enteringInitialPopulationStatistics(SteadyStateEvolutionState) - Method in class ec.Statistics
  STEADY-STATE: called when we created an empty initial Population.
enteringInitialPopulationStatistics(SteadyStateEvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called when we created an empty initial Population.
enteringSteadyStateStatistics(int, SteadyStateEvolutionState) - Method in class ec.Statistics
  STEADY-STATE: called when a given Subpopulation is entering the Steady-State.
enteringSteadyStateStatistics(int, SteadyStateEvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called when we have filled the initial population and are entering the steady state.
enumerateGrammarTree(GrammarNode) - Method in class ec.gp.ge.GrammarParser
  Run BFS to enumerate the whole grammar tree into all necessary indices lists/hash-maps, we *need* to run BFS because the decoding of the "GE array to tree" works in a BFS fashion, so we need to stick with that; After enumeration, we will have four data-structures like these -- (1) productionRuleList (a flattened grammar tree): grammar-tree ==> {rule-0, rule-1, ,,, rule-(n-1)} (2) ruleToIndex: rule-0 --> 0 rule-1 --> 1 , , rule-(n-1) --> (n-1) (3) indexToRule (reverse of ruleToIndex): 0 --> rule-0 1 --> rule-1 , , n-1 --> rule-(n-1) and then, last but not the least, the relative rule index -- (4) absIndexToRelIndex: if we have two rules like " -> | " and " -> | " then, [rule] [absIndex] [relIndex] -> --> [0] --> [0] -> --> [1] --> [1] -> --> [2] --> [0] -> --> [3] --> [1] etc,
EPSILON_STABILITY - Static variable in class ec.eda.dovs.HyperboxSpecies
equals(Object) - Method in class ec.gp.ge.GrammarNode
  This is needed when we use a GrammarNode as a "key" in hash-map, see GrammarParser.java for details.
equals(Object) - Method in class ec.gp.GPIndividual
equals(Object) - Method in class ec.Individual
  Returns true if I am genetically "equal" to ind.
equals(Object) - Method in class ec.neat.NEATGene
equals(Object) - Method in class ec.neat.NEATIndividual
equals(Object) - Method in class ec.neat.NEATInnovation
equals(Object) - Method in class ec.neat.NEATNetwork
equals(Object) - Method in class ec.neat.NEATNode
equals(Object) - Method in class ec.pso.Particle
equals(Object) - Method in class ec.rule.Rule
  Unlike the standard form for Java, this function should return true if this rule is "genetically identical" to the other rule.
equals(Object) - Method in class ec.rule.RuleIndividual
equals(Object) - Method in class ec.rule.RuleSet
equals(Object) - Method in class ec.util.IIntPoint
equals(Object) - Method in class ec.util.ReflectedObject
equals(Object) - Method in class ec.vector.BitVectorIndividual
equals(Object) - Method in class ec.vector.ByteVectorIndividual
equals(Object) - Method in class ec.vector.DoubleVectorIndividual
equals(Object) - Method in class ec.vector.FloatVectorIndividual
equals(Object) - Method in class ec.vector.Gene
  Unlike the standard form for Java, this function should return true if this gene is "genetically identical" to the other gene.
equals(Object) - Method in class ec.vector.GeneVectorIndividual
equals(Object) - Method in class ec.vector.IntegerVectorIndividual
equals(Object) - Method in class ec.vector.LongVectorIndividual
equals(Object) - Method in class ec.vector.ShortVectorIndividual
EQUALS - Static variable in class ec.gp.ge.GrammarParser
equivalentTo(Fitness) - Method in class ec.Fitness
  Should return true if this fitness is in the same equivalence class as _fitness, that is, neither is clearly better or worse than the other.
equivalentTo(Fitness) - Method in class ec.gp.koza.KozaFitness
equivalentTo(Fitness) - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns true if I'm equivalent in fitness (neither better nor worse) to _fitness.
equivalentTo(Fitness) - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
equivalentTo(Fitness) - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
  The selection criteria in SPEA2 uses the computed fitness, and not pareto dominance.
equivalentTo(Fitness) - Method in class ec.simple.SimpleFitness
ERC - Class in ec.gp
  ERC is an abstract GPNode which implements Ephemeral Random Constants, as described in Koza I.
ERC() - Constructor for class ec.gp.ERC
ERC_NAMES - Static variable in class ec.gp.push.Terminal
ERC_PREAMBLE - Static variable in class ec.gp.ge.GEIndividual
ERCBank - Variable in class ec.gp.ge.GESpecies
  All the ERCs created so far, the ERCs are mapped as, "key --> list of ERC nodes", where the key = (genome[i] - minGene[i]); The ERCBank is "static", beacause we need one identical copy for all the individuals; Moreover, this copy may be sent to other sub-populations as well.
error(String) - Method in class ec.util.Output
  Posts a simple error.
error(String, Parameter) - Method in class ec.util.Output
  Posts a simple error.
error(String, Parameter, Parameter) - Method in class ec.util.Output
  Posts a simple error.
errorAboutNoNodeWithType(GPType, EvolutionState) - Method in class ec.gp.GPNodeBuilder
  Issues a fatal error that no node (nonterminal or terminal) was found with a return type of the given type, and that an algorithm had requested one.
errorInfo() - Method in class ec.gp.GPNode
  A convenience function for identifying a GPNode in an error message
ESDefaults - Class in ec.es
ESDefaults() - Constructor for class ec.es.ESDefaults
ESSelection - Class in ec.es
  ESSelection is a special SelectionMethod designed to be used with evolutionary strategies-type breeders.
ESSelection() - Constructor for class ec.es.ESSelection
etaP - Variable in class ec.eda.amalgam.AMALGAMSpecies
etaS - Variable in class ec.eda.amalgam.AMALGAMSpecies
eval(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem) - Method in class ec.gp.ADF
eval(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem) - Method in class ec.gp.ADFArgument
eval(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem) - Method in class ec.gp.ADM
eval(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem) - Method in class ec.gp.GPNode
  Evaluates the node with the given thread, state, individual, problem, and stack.
eval(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem) - Method in class ec.gp.push.Nonterminal
eval(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem) - Method in class ec.gp.push.Terminal
evalNRandomOneWay(EvolutionState, int[], int[], ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
evalNRandomOneWayPopChunk(EvolutionState, int, int, int, ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
evalNRandomTwoWay(EvolutionState, int[], int[], ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
evalNRandomTwoWayPopChunk(EvolutionState, int, int, int, ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
evalPopChunk(EvolutionState, int[], int[], int, Problem) - Method in class ec.simple.SimpleEvaluator
  A private helper function for evaluatePopulation which evaluates a chunk of individuals in a subpopulation for a given thread.
evalPopChunk(EvolutionState, int[], int[], int, Problem) - Method in class ec.simple.SimpleGroupedEvaluator
  This protected helper function for evaluatePopulation evaluates a chunk of individuals in a subpopulation for a given thread.
evalPopChunk(EvolutionState, int[], int[], int, SimpleProblemForm) - Method in class ec.eda.dovs.DOVSEvaluator
  For each of the iteration, we are not just evaluate the individuals in current population but also current best individual and individuals in activeSolutions.
evalRoundRobin(EvolutionState, int[], int[], ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
evalRoundRobinPopChunk(EvolutionState, int, int, int, ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
  A private helper function for evalutatePopulation which evaluates a chunk of individuals in a subpopulation for a given thread.
evalSingleElimination(EvolutionState, ArrayList<Individual>, int, GroupedProblemForm) - Method in class ec.coevolve.CompetitiveEvaluator
evalthreads - Variable in class ec.EvolutionState
  The requested number of threads to be used in evaluation, excepting perhaps a "parent" thread which gathers the other threads.
evaluate(EvolutionState, int, GPData, ADFStack, GPIndividual, Problem, int) - Method in class ec.gp.ADFContext
  Evaluates the argument number in the current context
evaluate(EvolutionState, Individual[], boolean[], boolean, int[], int) - Method in interface ec.coevolve.GroupedProblemForm
  Evaluates the individuals found in ind together.
evaluate(EvolutionState, Individual[], boolean[], boolean, int[], int) - Method in class ec.eval.MasterProblem
evaluate(EvolutionState, Individual[], boolean[], boolean, int[], int) - Method in class ec.gp.ge.GEProblem
  Default version assumes that every individual is a GEIndividual.
evaluate(EvolutionState, Individual, int, int) - Method in class ec.eval.MasterProblem
evaluate(EvolutionState, Individual, int, int) - Method in class ec.eval.MetaProblem
evaluate(EvolutionState, Individual, int, int) - Method in class ec.gp.ge.GEProblem
evaluate(EvolutionState, Individual, int, int) - Method in interface ec.simple.SimpleProblemForm
  Evaluates the individual in ind, if necessary (perhaps not evaluating them if their evaluated flags are true), and sets their fitness appropriately.
evaluated - Variable in class ec.Individual
  Has the individual been evaluated and its fitness determined yet?
EVALUATED_PREAMBLE - Static variable in class ec.Individual
  A string appropriate to put in front of whether or not the individual has been printed.
evaluatedIndividualAvailable() - Method in class ec.eval.MasterProblem
  This will only return true if (1) the EvolutionState is a SteadyStateEvolutionState and (2) an individual has returned from the system.
evaluatedIndividualAvailable() - Method in class ec.eval.SlaveMonitor
evaluateGroupedProblemForm(EvolutionState, boolean, DataInputStream, DataOutputStream) - Static method in class ec.eval.Slave
evaluateIndividual(EvolutionState, Individual, int) - Method in class ec.steadystate.SteadyStateEvaluator
  Submits an individual to be evaluated by the Problem, and adds it and its subpopulation to the queue.
evaluatePopulation(EvolutionState) - Method in class ec.coevolve.CompetitiveEvaluator
  An evaluator that performs coevolutionary evaluation.
evaluatePopulation(EvolutionState) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
evaluatePopulation(EvolutionState) - Method in class ec.de.DEEvaluator
evaluatePopulation(EvolutionState) - Method in class ec.Evaluator
  Evaluates the fitness of an entire population.
evaluatePopulation(EvolutionState) - Method in class ec.simple.SimpleEvaluator
  A simple evaluator that doesn't do any coevolutionary evaluation.
evaluateSimpleProblemForm(EvolutionState, boolean, DataInputStream, DataOutputStream, String[]) - Static method in class ec.eval.Slave
evaluations - Variable in class ec.EvolutionState
  The current number of evaluations which have transpired so far in the run.
evaluator - Variable in class ec.EvolutionState
  The population evaluator, a singleton object.
Evaluator - Class in ec
  An Evaluator is a singleton object which is responsible for the evaluation process during the course of an evolutionary run.
Evaluator() - Constructor for class ec.Evaluator
EvolutionState - Class in ec
  An EvolutionState object is a singleton object which holds the entire state of an evolutionary run.
EvolutionState() - Constructor for class ec.EvolutionState
  This will be called to create your evolution state; immediately after the constructor is called, the parameters, random, and output fields will be set for you.
EvolutionStateEvent - Class in ec.display
EvolutionStateEvent(Object) - Constructor for class ec.display.EvolutionStateEvent
EvolutionStateListener - Interface in ec.display
evolve() - Method in class ec.EvolutionState
evolve() - Method in class ec.exchange.IslandExchange
evolve() - Method in class ec.simple.SimpleEvolutionState
evolve() - Method in class ec.steadystate.SteadyStateEvolutionState
Evolve - Class in ec
  Evolve is the main entry class for an evolutionary computation run.
Evolve() - Constructor for class ec.Evolve
excessCoeff - Variable in class ec.neat.NEATSpecies
  Coefficient for excess genes in compatibility computation.
exchanger - Variable in class ec.EvolutionState
  The population exchanger, a singleton object.
Exchanger - Class in ec
  The Exchanger is a singleton object whose job is to (optionally) perform individual exchanges between subpopulations in the run, or exchange individuals with other concurrent evolutionary run processes, using sockets or whatever.
Exchanger() - Constructor for class ec.Exchanger
Execute(Interpreter) - Method in class ec.gp.push.PushInstruction
executeProgram(Program, Interpreter, int) - Method in class ec.gp.push.PushProblem
  Executes the given program for up to maxSteps steps.
exists(Parameter) - Method in class ec.util.ParameterDatabase
  Returns true if parameter exist in the database
exists(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Returns true if either parameter or defaultParameter exists in the database
exitIfErrors() - Method in class ec.util.Output
  Exits with a fatal error if the error flag has been raised.
expectedChildren() - Method in class ec.gp.ADFArgument
expectedChildren() - Method in class ec.gp.ERC
  Usually ERCs don't have children, and this default implementation makes certain of it.
expectedChildren() - Method in class ec.gp.GPNode
  Returns the number of children this node expects to have.
expectedChildren() - Method in class ec.gp.push.Terminal
expectedOffspring - Variable in class ec.neat.NEATIndividual
  Number of children this individual may have for next generation.
expectedOffspring - Variable in class ec.neat.NEATSubspecies
  Expected Offspring for next generation for this subspecies
expectedSize - Variable in class ec.gp.build.PTC1
  The default expected tree size for PTC1
extraBehavior - Variable in class ec.Subpopulation
  What is our fill behavior beyond files?

## F

F - Variable in class ec.de.DEBreeder
  Scaling factor for mutation
F_NOISE - Variable in class ec.de.Best1BinDEBreeder
  limits on uniform noise for F
f_prototype - Variable in class ec.Species
  The prototypical fitness for individuals of this species.
FAILURE - Static variable in class ec.util.Lexer
  An index which indicates that no further tokens were found.
fatal(String) - Method in class ec.util.Output
  Posts a fatal error.
fatal(String, Parameter) - Method in class ec.util.Output
  Posts a fatal error.
fatal(String, Parameter, Parameter) - Method in class ec.util.Output
  Posts a fatal error.
file - Variable in class ec.Population
file - Variable in class ec.Subpopulation
filename - Variable in class ec.util.Log
  A filename, if the writer writes to a file
fill(boolean[], boolean) - Method in class ec.vector.VectorSpecies
  Utility method: fills the array with the given value and returns it.
fill(double[], double) - Method in class ec.vector.VectorSpecies
  Utility method: fills the array with the given value and returns it.
fill(int) - Method in class ec.util.IntBag
  Replaces all elements in the bag with the provided int.
fill(int[], int) - Method in class ec.vector.VectorSpecies
  Utility method: fills the array with the given value and returns it.
fill(long[], long) - Method in class ec.vector.VectorSpecies
  Utility method: fills the array with the given value and returns it.
FILL - Static variable in class ec.Subpopulation
fillStubs(EvolutionState, BreedingSource) - Method in class ec.breed.StubPipeline
fillStubs(EvolutionState, BreedingSource) - Method in class ec.BreedingPipeline
fillStubs(EvolutionState, BreedingSource) - Method in class ec.BreedingSource
finalStatistics(EvolutionState, int) - Method in class ec.multiobjective.HypervolumeStatistics
  Logs the best individual of the run.
finalStatistics(EvolutionState, int) - Method in class ec.multiobjective.MultiObjectiveStatistics
  Logs the best individual of the run.
finalStatistics(EvolutionState, int) - Method in class ec.simple.SimpleStatistics
  Logs the best individual of the run.
finalStatistics(EvolutionState, int) - Method in class ec.Statistics
  Called immediately after the run has completed.
finalStatistics(EvolutionState, int) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately after the run has completed.
findBestSample(EvolutionState, Subpopulation) - Method in class ec.eda.dovs.DOVSSpecies
  To find the best sample for each generation, we need to go through each individual in the current population, and also best individual and individuals in actionSolutions.
findFairSizeNode(ArrayList, HashMap, GPNode, GPTree, EvolutionState, int) - Method in class ec.gp.breed.SizeFairCrossoverPipeline
  This method finds a node using the logic given in the langdon paper.
finish(int) - Method in class ec.EvolutionState
finish(int) - Method in class ec.exchange.IslandExchange
finish(int) - Method in class ec.simple.SimpleEvolutionState
finish(int) - Method in class ec.steadystate.SteadyStateEvolutionState
finisher - Variable in class ec.EvolutionState
  The population finisher, a singleton object.
Finisher - Class in ec
  Finisher is a singleton object which is responsible for cleaning up a population after a run has completed.
Finisher() - Constructor for class ec.Finisher
finishEvaluating(EvolutionState, int) - Method in class ec.eval.MasterProblem
finishEvaluating(EvolutionState, int) - Method in class ec.gp.ge.GEProblem
finishEvaluating(EvolutionState, int) - Method in class ec.Problem
  Will be called by the Evaluator after prepareToEvaluate(...) is called and then a series of individuals are evaluated.
finishEvaluationStatistics() - Method in class ec.steadystate.SteadyStateEvolutionState
finishPipelines(EvolutionState) - Method in class ec.steadystate.SteadyStateBreeder
finishPopulation(EvolutionState, int) - Method in class ec.Finisher
  Cleans up the population after the run has completed.
finishPopulation(EvolutionState, int) - Method in class ec.simple.SimpleFinisher
  Doesn't do anything.
finishProducing(EvolutionState, int, int) - Method in class ec.BreedingPipeline
finishProducing(EvolutionState, int, int) - Method in class ec.BreedingSource
  Called after produce(...), usually once a generation, or maybe only once if you're doing steady-state evolution (at the end of the run).
finishProducing(EvolutionState, int, int) - Method in class ec.select.BestSelection
finishProducing(EvolutionState, int, int) - Method in class ec.select.FitProportionateSelection
finishProducing(EvolutionState, int, int) - Method in class ec.select.GreedyOverselection
finishProducing(EvolutionState, int, int) - Method in class ec.SelectionMethod
  A default version of finishProducing, which does nothing.
fireUpServer(EvolutionState, Parameter) - Method in class ec.exchange.IslandExchange
  Fires up the server.
first() - Method in class ec.neat.NEATSubspecies
  Return the first individual in this subspecies
FirstCopyPipeline - Class in ec.breed
  FirstCopyPipeline is a BreedingPipeline similar to ReproductionPipeline, except that after a call to prepareToProduce(...), the immediate next child produced is produced from source 0, and all the remaining children in that produce() call and in subsequent produce() calls are produced from source 1.
FirstCopyPipeline() - Constructor for class ec.breed.FirstCopyPipeline
firstGeneration - Variable in class ec.eda.amalgam.AMALGAMSpecies
FirstSelection - Class in ec.select
  Always picks the first individual in the subpopulation.
FirstSelection() - Constructor for class ec.select.FirstSelection
firstTime - Variable in class ec.breed.FirstCopyPipeline
firstTime - Variable in class ec.steadystate.SteadyStateEvolutionState
  First time calling evolve
fitness - Variable in class ec.Individual
  The fitness of the Individual.
fitness - Variable in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
  Final SPEA2 fitness.
fitness() - Method in class ec.Fitness
  Should return an absolute fitness value ranging from negative infinity to infinity, NOT inclusive (thus infinity, negative infinity, and NaN are NOT valid fitness values).
fitness() - Method in class ec.gp.koza.KozaFitness
  Returns the adjusted fitness metric, which recasts the fitness to the half-open interval (0,1], where 1 is ideal and 0 is worst.
fitness() - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns the Max() of objectives, which adheres to Fitness.java's protocol for this method.
fitness() - Method in class ec.simple.SimpleFitness
Fitness - Class in ec
  Fitness is a prototype which describes the fitness of an individual.
Fitness() - Constructor for class ec.Fitness
FITNESS_POSTAMBLE - Static variable in class ec.multiobjective.MultiObjectiveFitness
FITNESS_PREAMBLE - Static variable in class ec.Fitness
  Basic preamble for printing Fitness values out
fitnesses - Variable in class ec.select.FitProportionateSelection
  Normalized, totalized fitnesses for the population
fitnesses - Variable in class ec.select.SUSSelection
  The distribution of fitnesses.
fitnessPressureProb - Variable in class ec.parsimony.ProportionalTournamentSelection
  The probability of having the tournament based on fitness
fitnessToString() - Method in class ec.Fitness
  Print to a string the fitness in a fashion intended to be parsed in again via readFitness(...).
fitnessToString() - Method in class ec.gp.koza.KozaFitness
fitnessToString() - Method in class ec.multiobjective.MultiObjectiveFitness
fitnessToString() - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
fitnessToString() - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
fitnessToString() - Method in class ec.simple.SimpleFitness
fitnessToStringForHumans() - Method in class ec.Fitness
  Print to a string the fitness in a fashion readable by humans, and not intended to be parsed in again.
fitnessToStringForHumans() - Method in class ec.gp.koza.KozaFitness
fitnessToStringForHumans() - Method in class ec.multiobjective.MultiObjectiveFitness
fitnessToStringForHumans() - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
fitnessToStringForHumans() - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
fitnessToStringForHumans() - Method in class ec.simple.SimpleFitness
fitnessVarianceTolerance - Variable in class ec.eda.amalgam.AMALGAMSpecies
FitProportionateSelection - Class in ec.select
  Picks individuals in a population in direct proportion to their fitnesses as returned by their fitness() methods.
FitProportionateSelection() - Constructor for class ec.select.FitProportionateSelection
flattenSexp(EvolutionState, int, GPTree) - Method in class ec.gp.ge.GESpecies
  Flattens an S-expression
FLOAT_ERC - Static variable in class ec.gp.push.Terminal
FloatVectorIndividual - Class in ec.vector
  FloatVectorIndividual is a VectorIndividual whose genome is an array of floats.
FloatVectorIndividual() - Constructor for class ec.vector.FloatVectorIndividual
FloatVectorSpecies - Class in ec.vector
  FloatVectorSpecies is a subclass of VectorSpecies with special constraints for floating-point vectors, namely FloatVectorIndividual and DoubleVectorIndividual.
FloatVectorSpecies() - Constructor for class ec.vector.FloatVectorSpecies
flush() - Method in class ec.neat.NEATNetwork
flush() - Method in class ec.neat.NEATNode
  Put all the field into initial status, this is useful in flushing the whole network.
flush() - Method in class ec.util.Output
  Flushes the logs
flushBack() - Method in class ec.neat.NEATNode
  Old flush code, used in C++ version.
ForceBreedingPipeline - Class in ec.breed
  ForceBreedingPipeline has one source.
ForceBreedingPipeline() - Constructor for class ec.breed.ForceBreedingPipeline
FOUND - Static variable in class ec.exchange.IslandExchange
  Found signal
FOUND_TIMEOUT - Static variable in class ec.exchange.IslandExchange
  How long we sleep between checking for FOUND messages
frontLog - Variable in class ec.multiobjective.MultiObjectiveStatistics
  The pareto front log
frozen - Variable in class ec.neat.NEATGene
  Is this gene frozen, a frozen gene's weight cannot get mutated in breeding procedure.
frozen - Variable in class ec.neat.NEATNode
  When it's true, the node cannot be mutated.
FullBuilder - Class in ec.gp.koza
  FullBuilder is a GPNodeBuilder which implements the FULL tree building method described in Koza I/II.
FullBuilder() - Constructor for class ec.gp.koza.FullBuilder
fullNode(EvolutionState, int, int, GPType, int, GPNodeParent, int, GPFunctionSet) - Method in class ec.gp.koza.KozaBuilder
  A private recursive method which builds a FULL-style tree for newRootedTree(...)
funcnodes - Variable in class ec.gp.build.Uniform
FUNCTION - Static variable in class ec.gp.ge.GrammarParser
functionset - Variable in class ec.gp.GPTreeConstraints
  The function set for nodes in the tree
functionSetFor(String, EvolutionState) - Static method in class ec.gp.GPFunctionSet
  Returns the function set for a given name.
functionSetRepository - Variable in class ec.gp.GPInitializer
functionsets - Variable in class ec.gp.build.Uniform
functionType - Variable in class ec.neat.NEATNode
  The activation function, use sigmoid for default, but can use some other choice, like ReLU.

## G

gatherExtraPopStatistics(EvolutionState, int) - Method in class ec.simple.SimpleShortStatistics
gatherExtraSubpopStatistics(EvolutionState, int, int) - Method in class ec.gp.koza.KozaShortStatistics
gatherExtraSubpopStatistics(EvolutionState, int, int) - Method in class ec.simple.SimpleShortStatistics
gatherFirstSets(GrammarNode, GrammarNode) - Method in class ec.gp.ge.GrammarParser
  Generate the FIRST-SET for each production rule and store them in the global hash-table, this runs a DFS on the grammar tree, the returned ArrayList is discarded and the FIRST-SETs are organized in a hash-map called "ruleToFirstSet" as follows -- rule-0 --> {FIRST-SET-0} rule-1 --> {FIRST-SET-1} , , rule-(n-1) --> {FIRST-SET-(n-1)}
gatherFollowSets(GrammarNode, GrammarNode) - Method in class ec.gp.ge.GrammarParser
  We do not have any example grammar to test with FOLLOW-SETs, so the FOLLOW-SET is empty, we need to test with a grammar that contains post-fix notations; this needs to be implemented properly with a new grammar.
gatherNodeString(EvolutionState, int, GPNode, int) - Method in class ec.gp.ge.GESpecies
  Used by the above function
gatherPredictSets(GrammarNode, GrammarNode) - Method in class ec.gp.ge.GrammarParser
  Populate the PREDICT-SET from the FIRST-SETs and the FOLLOW-SETs, as we do not have FOLLOW-SET, so FIRST-SET == PREDICT-SET; this needs to be implemented, when the FOLLOW-SETs are done properly.
GAUSSIAN - Enum constant in enum class ec.neat.NEATSpecies.MutationType
gaussMutationStdev - Variable in class ec.vector.FloatVectorSpecies
  Standard deviation for Gaussian Mutation, per gene.
gaussMutationStdev(int) - Method in class ec.vector.FloatVectorSpecies
GEDefaults - Class in ec.gp.ge
  A static class that returns the base for "default values" which GE-style operators use, rather than making the user specify them all on a per- species basis.
GEDefaults() - Constructor for class ec.gp.ge.GEDefaults
GEIndividual - Class in ec.gp.ge
  GEIndividual is a simple subclass of IntegerVectorIndividual which not only prints out (for humans) the Individual as a int vector but also prints out the Individual's tree representation.
GEIndividual() - Constructor for class ec.gp.ge.GEIndividual
genCovarMatrix - Variable in class ec.eda.amalgam.AMALGAMSpecies
Gene - Class in ec.vector
  Gene is an abstract superclass of objects which may be used in the genome array of GeneVectorIndividuals.
Gene() - Constructor for class ec.vector.Gene
GeneDuplicationPipeline - Class in ec.vector.breed
  GeneDuplicationPipeline is designed to duplicate a sequence of genes from the chromosome and append them to the end of the chromosome.
GeneDuplicationPipeline() - Constructor for class ec.vector.breed.GeneDuplicationPipeline
genePrototype - Variable in class ec.vector.GeneVectorSpecies
generateMax - Variable in class ec.breed.GenerationSwitchPipeline
generateMax - Variable in class ec.breed.MultiBreedingPipeline
generation - Variable in class ec.EvolutionState
  The current generation of the population in the run.
generation - Variable in class ec.neat.NEATIndividual
  Tells which generation this individual is from.
generationBoundary - Variable in class ec.steadystate.SteadyStateEvolutionState
  Did we just start a new generation?
generationBoundaryStatistics(EvolutionState) - Method in class ec.Statistics
  STEADY-STATE: called each time the generation count increments
generationBoundaryStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called when the generation count increments
generationSize - Variable in class ec.steadystate.SteadyStateEvolutionState
  how big is a generation? Set to the size of subpopulation 0 of the initial population.
generationSwitch - Variable in class ec.breed.GenerationSwitchPipeline
GenerationSwitchPipeline - Class in ec.breed
  GenerationSwitchPipeline is a simple BreedingPipeline which switches its source depending on the generation.
GenerationSwitchPipeline() - Constructor for class ec.breed.GenerationSwitchPipeline
geneticNodeLabel - Variable in class ec.neat.NEATNode
  Distinguish the input node, hidden or output node.
GeneVectorIndividual - Class in ec.vector
  GeneVectorIndividual is a VectorIndividual whose genome is an array of Genes.
GeneVectorIndividual() - Constructor for class ec.vector.GeneVectorIndividual
GeneVectorSpecies - Class in ec.vector
  GeneVectorSpecies is a subclass of VectorSpecies with special constraints for GeneVectorIndividuals.
GeneVectorSpecies() - Constructor for class ec.vector.GeneVectorSpecies
genome - Variable in class ec.vector.BitVectorIndividual
genome - Variable in class ec.vector.ByteVectorIndividual
genome - Variable in class ec.vector.DoubleVectorIndividual
genome - Variable in class ec.vector.FloatVectorIndividual
genome - Variable in class ec.vector.GeneVectorIndividual
genome - Variable in class ec.vector.IntegerVectorIndividual
genome - Variable in class ec.vector.LongVectorIndividual
genome - Variable in class ec.vector.ShortVectorIndividual
genomeIncreaseProbability - Variable in class ec.vector.VectorSpecies
  With what probability would our genome be at least 1 larger than it is now during initialization?
genomeLength() - Method in class ec.vector.BitVectorIndividual
genomeLength() - Method in class ec.vector.ByteVectorIndividual
genomeLength() - Method in class ec.vector.DoubleVectorIndividual
genomeLength() - Method in class ec.vector.FloatVectorIndividual
genomeLength() - Method in class ec.vector.GeneVectorIndividual
genomeLength() - Method in class ec.vector.IntegerVectorIndividual
genomeLength() - Method in class ec.vector.LongVectorIndividual
genomeLength() - Method in class ec.vector.ShortVectorIndividual
genomeLength() - Method in class ec.vector.VectorIndividual
  Returns the length of the gene array.
genomeResizeAlgorithm - Variable in class ec.vector.VectorSpecies
  How should we reset the genome?
genomeSize - Variable in class ec.vector.VectorSpecies
  How big of a genome should we create on initialization?
genotypeToString() - Method in class ec.Individual
  Print to a string the genotype of the Individual in a fashion intended to be parsed in again via parseGenotype(...).
genotypeToString() - Method in class ec.neat.NEATIndividual
  This method is used to output a individual that is same as the format in start genome file.
genotypeToString() - Method in class ec.vector.BitVectorIndividual
genotypeToString() - Method in class ec.vector.ByteVectorIndividual
genotypeToString() - Method in class ec.vector.DoubleVectorIndividual
genotypeToString() - Method in class ec.vector.FloatVectorIndividual
genotypeToString() - Method in class ec.vector.GeneVectorIndividual
genotypeToString() - Method in class ec.vector.IntegerVectorIndividual
genotypeToString() - Method in class ec.vector.LongVectorIndividual
genotypeToString() - Method in class ec.vector.ShortVectorIndividual
genotypeToStringForHumans() - Method in class ec.Individual
  Print to a string the genotype of the Individual in a fashion readable by humans, and not intended to be parsed in again.
genotypeToStringForHumans() - Method in class ec.vector.BitVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.ByteVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.DoubleVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.FloatVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.GeneVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.IntegerVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.LongVectorIndividual
genotypeToStringForHumans() - Method in class ec.vector.ShortVectorIndividual
GEProblem - Class in ec.gp.ge
  GEProblem is a special replacement for Problem which performs GE mapping.
GEProblem() - Constructor for class ec.gp.ge.GEProblem
GESpecies - Class in ec.gp.ge
  GESpecies generates GPIndividuals from GEIndividuals through the application of a grammar parse graph computed by the GrammarParser.
GESpecies() - Constructor for class ec.gp.ge.GESpecies
get() - Method in class ec.gp.ADFStack
  Returns an ADFContext from the stack's reserve, or creates one fresh if there are none in reserve.
get(int) - Method in class ec.util.IntBag
getActivation() - Method in class ec.neat.NEATNode
  Return the activation status of this node.
getAllComponents() - Method in class ec.eval.MasterProblem
getAllowedComponents(ConstructiveIndividual) - Method in class ec.eval.MasterProblem
getArbitraryComponent(EvolutionState, int) - Method in class ec.eval.MasterProblem
getArgument(int) - Method in class ec.gp.ge.GrammarFunctionNode
  Returna given argument.
getAuxilliaryFitnessNames() - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns auxilliary fitness value names to be printed by the statistics object.
getAuxilliaryFitnessNames() - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
getAuxilliaryFitnessNames() - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
getAuxilliaryFitnessValues() - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns auxilliary fitness values to be printed by the statistics object.
getAuxilliaryFitnessValues() - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
getAuxilliaryFitnessValues() - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
getBestSoFar() - Method in class ec.simple.SimpleShortStatistics
getBestSoFar() - Method in class ec.simple.SimpleStatistics
getBoolean(Parameter, Parameter, boolean) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter; If the parameter does not exist, defaultValue is returned.
getChild(int) - Method in class ec.util.ReflectedObject
getChild(Object, int) - Method in class ec.util.ParameterDatabaseTreeModel
getChild(Object, int) - Method in class ec.util.ReflectedObject
getChildCount(Object) - Method in class ec.util.ParameterDatabaseTreeModel
getChildCount(Object) - Method in class ec.util.ReflectedObject
getChildren() - Method in class ec.util.ReflectedObject
getChoice(int) - Method in class ec.gp.ge.GrammarRuleNode
  Returns a given choice.
getClassForParameter(Parameter, Parameter, Class) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter.
getComponentFromString(String) - Method in class ec.eval.MasterProblem
getContext() - Method in class ec.Fitness
  Treat the Individual[] you receive from this as read-only.
getDouble(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
getDouble(Parameter, Parameter, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a double >= minValue.
getDouble(Parameter, Parameter, double, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a double >= minValue and invalid input: '<'= maxValue.
getDoubles(Parameter, Parameter, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of doubles, each of which is >= minValue, and which must be at least 1 number long.
getDoubles(Parameter, Parameter, double, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of doubles, each of which is >= minValue, and which must be exactly expectedLength (> 0) long.
getDoublesUnconstrained(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of doubles, and which must be at least 1 number long.
getDoublesUnconstrained(Parameter, Parameter, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of doubles, and which must be exactly expectedLength (> 0) long.
getDoublesWithMax(Parameter, Parameter, double, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of doubles, each of which is >= minValue and invalid input: '<'= maxValue, and which must be at least 1 number long.
getDoublesWithMax(Parameter, Parameter, double, double, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of doubles, each of which is >= minValue and invalid input: '<'= maxValue, and which must be exactly expectedLength (> 0) long.
getDoubleWithDefault(Parameter, Parameter, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, which must be a float.
getDoubleWithMax(Parameter, Parameter, double, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a double >= minValue and invalid input: '<'= maxValue.
getField(int) - Method in class ec.util.ReflectedObject
getFields() - Method in class ec.util.ReflectedObject
getFile(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through the databases to find a given parameter, whose value must be an absolute or relative path name.
getFloat(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
getFloat(Parameter, Parameter, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a float >= minValue.
getFloat(Parameter, Parameter, double, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a float >= minValue and invalid input: '<'= maxValue.
getFloatWithDefault(Parameter, Parameter, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, which must be a float.
getFloatWithMax(Parameter, Parameter, double, double) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a float >= minValue and invalid input: '<'= maxValue.
getFlush() - Method in class ec.util.Output
getGeneInnovationNumberSup() - Method in class ec.neat.NEATIndividual
  Get the upperbound for the innovation number, used in Initializer.
getGenome() - Method in class ec.vector.BitVectorIndividual
getGenome() - Method in class ec.vector.ByteVectorIndividual
getGenome() - Method in class ec.vector.DoubleVectorIndividual
getGenome() - Method in class ec.vector.FloatVectorIndividual
getGenome() - Method in class ec.vector.GeneVectorIndividual
getGenome() - Method in class ec.vector.IntegerVectorIndividual
getGenome() - Method in class ec.vector.LongVectorIndividual
getGenome() - Method in class ec.vector.ShortVectorIndividual
getGenome() - Method in class ec.vector.VectorIndividual
  Returns the gene array.
getGPNodePrototype() - Method in class ec.gp.ge.GrammarFunctionNode
  Returns the prototype without cloning it first.
getHead() - Method in class ec.gp.ge.GrammarNode
getIndex(int) - Method in interface ec.spatial.Space
  Functionality: retrieve the index for a specific threanum.
getIndex(int) - Method in class ec.spatial.Spatial1DSubpopulation
getIndexOfChild(Object, Object) - Method in class ec.util.ReflectedObject
getIndexRandomNeighbor(EvolutionState, int, int) - Method in interface ec.spatial.Space
  Input: the maximum distance for neighbors.
getIndexRandomNeighbor(EvolutionState, int, int) - Method in class ec.spatial.Spatial1DSubpopulation
  Returns a the index of a random neighbor.
getInnovation(NEATInnovation) - Method in class ec.neat.NEATSpecies
getInstanceForParameter(Parameter, Parameter, Class) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a full Class name, and the class must be a descendent of but not equal to mustCastTosuperclass .
getInstanceForParameterEq(Parameter, Parameter, Class) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a full Class name, and the class must be a descendent, or equal to, mustCastTosuperclass .
getInt(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be an integer.
getInt(Parameter, Parameter, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be an integer >= minValue.
getInterpreter(EvolutionState, GPIndividual, int) - Method in class ec.gp.push.PushProblem
  Builds a Push Interpreter suitable for interpreting the Program given in getProgram().
getInts(Parameter, Parameter, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of ints, each of which is >= minValue, and which must be at least 1 number long.
getInts(Parameter, Parameter, int, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of ints, each of which is >= minValue, and which must be exactly expectedLength (> 0) long.
getIntsUnconstrained(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of ints, and which must be at least 1 number long.
getIntsUnconstrained(Parameter, Parameter, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of ints, and which must be exactly expectedLength (> 0) long.
getIntsWithMax(Parameter, Parameter, int, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of ints, each of which is >= minValue and invalid input: '<'= maxValue, and which must be at least 1 number long.
getIntsWithMax(Parameter, Parameter, int, int, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a space- or tab-delimited list of ints, each of which is >= minValue and invalid input: '<'= maxValue, and which must be exactly expectedLength (> 0) long.
getIntWithDefault(Parameter, Parameter, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, which must be an integer.
getIntWithMax(Parameter, Parameter, int, int) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be an integer >= minValue and invalid input: '<'= maxValue.
getJobFilePrefix() - Method in class ec.display.ControlPanel
getKey() - Method in class ec.eda.dovs.CornerMap.Pair
getKeyFromNode(EvolutionState, int, GPNode, int) - Method in class ec.gp.ge.GESpecies
getLabel() - Method in class ec.util.ParameterDatabase
  Returns a String describing the location of the ParameterDatabase holding this parameter, or "" if there is none.
getLocalHost() - Static method in class ec.util.LocalHost
  Returns an `InetAddress` object encapsulating what is most likely the machine's LAN IP address.
getLocation(Parameter) - Method in class ec.util.ParameterDatabase
getLocation(String) - Method in class ec.util.ParameterDatabase
getLog(int) - Method in class ec.util.Output
  Returns the given log.
getLong(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a long.
getLong(Parameter, Parameter, long) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a long >= minValue.
getLong(Parameter, Parameter, long, long) - Method in class ec.util.ParameterDatabase
  Use getLongWithMax(...) instead.
getLongWithDefault(Parameter, Parameter, long) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, which must be a long.
getLongWithMax(Parameter, Parameter, long, long) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter, whose value must be a long >= minValue and = invalid input: '<' maxValue.
getMarginalDistribution(int) - Method in class ec.eda.pbil.PBILSpecies
getMatchingIndex() - Method in class ec.util.Lexer
  Returns the index of the regular expression which matched the most recent token.
getMatchingPosition() - Method in class ec.util.Lexer
  Returns the position in the String just beyond the most recent token.
getMatchingRule() - Method in class ec.util.Lexer
  Returns the regular expression which matched the most recent token.
getNextEvaluatedIndividual() - Method in class ec.eval.MasterProblem
  This method blocks until an individual is available from the slaves (which will cause evaluatedIndividualAvailable() to return true), at which time it returns the individual.
getNextEvaluatedIndividual(EvolutionState) - Method in class ec.steadystate.SteadyStateEvaluator
  Returns an evaluated individual is in the queue and ready to come back to us.
getNodeIdSup() - Method in class ec.neat.NEATIndividual
  Get the upperbound for the node id, used in Initializer.
getNumArguments() - Method in class ec.gp.ge.GrammarFunctionNode
  Returns the number of arguments.
getNumChildren() - Method in class ec.util.ReflectedObject
getNumChoices() - Method in class ec.gp.ge.GrammarRuleNode
  Returns the current number of choices to the node.
getNumFields() - Method in class ec.util.ReflectedObject
getNumJobs() - Method in class ec.display.ControlPanel
getNumObjectives() - Method in class ec.multiobjective.MultiObjectiveFitness
getObjective(int) - Method in class ec.multiobjective.MultiObjectiveFitness
getObjectives() - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns the objectives as an array.
getOutputResults() - Method in class ec.neat.NEATNetwork
  Produces an array of activation results, one per output node.
getOutstandingWorkers() - Method in class ec.util.ThreadPool
  Returns the total number of outstanding workers (those working on something right now).
getParameter() - Method in class ec.util.ParameterDatabaseEvent
getPooledWorkers() - Method in class ec.util.ThreadPool
  Returns the total number of pooled workers (those not working on something right now).
getProbability(Object) - Method in class ec.BreedingSource
getProbability(Object) - Method in interface ec.util.RandomChoiceChooser
  Returns obj's probability
getProbability(Object) - Method in interface ec.util.RandomChoiceChooserD
  Returns obj's probability
getProgram(EvolutionState, GPIndividual) - Method in class ec.gp.push.PushProblem
  Produces a Push Program from the provided GP Individual's tree.
getRandomIndividual(int, int, EvolutionState, int) - Method in class ec.select.TournamentSelection
  Produces the index of a (typically uniformly distributed) randomly chosen individual to fill the tournament.
getRandomIndividual(int, int, EvolutionState, int) - Method in class ec.spatial.SpatialTournamentSelection
getRankings(ArrayList<Individual>) - Static method in class ec.multiobjective.MultiObjectiveFitness
  Returns the Pareto rank for each individual.
getReferencePoint() - Method in class ec.multiobjective.HypervolumeStatistics
getRegexes() - Method in class ec.gp.ge.GrammarParser
  Returns the regular expressions to use for tokenizing these rules.
getResource(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through the databases to find a given parameter, whose value must be an absolute or relative path name.
getRoot() - Method in class ec.util.ReflectedObject
gets_n_percent - Variable in class ec.select.GreedyOverselection
getSeed(int, int) - Method in class ec.display.ControlPanel
getShadowedValues(Parameter) - Method in class ec.util.ParameterDatabase
getSortedParetoFront(ArrayList<Individual>) - Static method in class ec.multiobjective.MultiObjectiveFitness
  Returns the Pareto Front of the provided Individuals, sorted by objective 0, breaking ties with objective 1, and so on...
getStore() - Method in class ec.util.Output
getString(Parameter, Parameter) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter.
getStringWithDefault(Parameter, Parameter, String) - Method in class ec.util.ParameterDatabase
  Searches down through databases to find a given parameter.
getSubpopulationOfEvaluatedIndividual() - Method in class ec.steadystate.SteadyStateEvaluator
  Returns the subpopulation of the last evaluated individual returned by getNextEvaluatedIndividual, or potentially -1 if getNextEvaluatedIndividual was never called or hasn't returned an individual yet.
getThreadCount(String) - Method in class ec.display.ControlPanel
getThrowsErrors() - Method in class ec.util.Output
getTimeDelayActivation() - Method in class ec.neat.NEATNode
  Return the last step activation if this node is active at last step.
getTotalWorkers() - Method in class ec.util.ThreadPool
  Returns the total number of workers, both pooled and outstanding (working on something).
getTournamentSizeToUse(MersenneTwisterFast) - Method in class ec.select.TournamentSelection
  Returns a tournament size to use, at random, based on base size and probability of picking the size plus one.
getType() - Method in class ec.util.ParameterDatabaseEvent
getValue() - Method in class ec.display.ParameterValue
getValue() - Method in class ec.eda.dovs.CornerMap.Pair
getValue() - Method in class ec.util.ParameterDatabaseEvent
getValue(int) - Method in interface ec.util.Indexed
  Throws an IndexOutOfBoundsException if index is inappropriate.
getValue(int) - Method in class ec.util.IntBag
getVerbosity() - Method in class ec.util.Output
  Returns the Output object's general verbosity
getVisibleLeaves() - Method in class ec.util.ParameterDatabaseTreeModel
globalBest - Variable in class ec.pso.PSOBreeder
globalBestFitness - Variable in class ec.pso.PSOBreeder
globalCoeff - Variable in class ec.pso.PSOBreeder
GP_PREAMBLE - Static variable in class ec.gp.ge.GEIndividual
GPAtomicType - Class in ec.gp
  A GPAtomicType is a simple, atomic GPType.
GPAtomicType() - Constructor for class ec.gp.GPAtomicType
  Don't use this constructor unless you call setup(...) immediately after it.
GPAtomicType(String) - Constructor for class ec.gp.GPAtomicType
  Use this constructor for GPAtomic Type unless you know what you're doing
GPBreedDefaults - Class in ec.gp.breed
  A static class that returns the base for "default values" which various GP breeding operators use, rather than making the user specify them all on a per- species basis.
GPBreedDefaults() - Constructor for class ec.gp.breed.GPBreedDefaults
GPBreedingPipeline - Class in ec.gp
  A GPBreedingPipeline is a BreedingPipeline which produces only members of some subclass of GPSpecies.
GPBreedingPipeline() - Constructor for class ec.gp.GPBreedingPipeline
GPBuildDefaults - Class in ec.gp.build
GPBuildDefaults() - Constructor for class ec.gp.build.GPBuildDefaults
GPData - Class in ec.gp
  GPData is the parent class of data transferred between GPNodes.
GPData() - Constructor for class ec.gp.GPData
GPDefaults - Class in ec.gp
  A static class that returns the base for "default values" which GP-style operators use, rather than making the user specify them all on a per- species basis.
GPDefaults() - Constructor for class ec.gp.GPDefaults
GPFunctionSet - Class in ec.gp
  GPFunctionSet is a Clique which represents a set of GPNode prototypes forming a standard function set for forming certain trees in individuals.
GPFunctionSet() - Constructor for class ec.gp.GPFunctionSet
GPIndividual - Class in ec.gp
  GPIndividual is an Individual used for GP evolution runs.
GPIndividual() - Constructor for class ec.gp.GPIndividual
GPInitializer - Class in ec.gp
  GPInitializer is a SimpleInitializer which sets up all the Cliques, ( the initial [tree/node]constraints, types, and function sets) for the GP system.
GPInitializer() - Constructor for class ec.gp.GPInitializer
GPKozaDefaults - Class in ec.gp.koza
  A static class that returns the base for "default values" which Koza-style operators use, rather than making the user specify them all on a per- species basis.
GPKozaDefaults() - Constructor for class ec.gp.koza.GPKozaDefaults
GPNode - Class in ec.gp
  GPNode is a GPNodeParent which is the abstract superclass of all GP function nodes in trees.
GPNode() - Constructor for class ec.gp.GPNode
GPNodeBuilder - Class in ec.gp
  GPNodeBuilder is a Prototype which defines the superclass for objects which create ("grow") GP trees, whether for population initialization, subtree mutation, or whatnot.
GPNodeBuilder() - Constructor for class ec.gp.GPNodeBuilder
GPNodeConstraints - Class in ec.gp
  A GPNodeConstraints is a Clique which defines constraint information common to many different GPNode functions, namely return types, child types, and number of children.
GPNodeConstraints() - Constructor for class ec.gp.GPNodeConstraints
GPNodeGatherer - Class in ec.gp
  GPNodeGatherer is a small container object for the GPNode.nodeInPosition(...) method and GPNode.numNodes(...) method.
GPNodeGatherer() - Constructor for class ec.gp.GPNodeGatherer
GPNodeParent - Interface in ec.gp
  GPNodeParent is a Prototype which identifies objects which may be parents of GPNodes, namely: GPTrees and GPNodes.
GPNODEPRINTTAB - Static variable in class ec.gp.GPNode
GPNodeSelector - Interface in ec.gp
  GPNodeSelector is a Prototype which describes algorithms which select random nodes out of trees, typically marking them for mutation, crossover, or whatnot.
GPProblem - Class in ec.gp
  A GPProblem is a Problem which is meant to efficiently handle GP evaluation.
GPProblem() - Constructor for class ec.gp.GPProblem
GPSetType - Class in ec.gp
  A GPSetType is a GPType which contains GPAtomicTypes in a set, and is used as a generic GP type.
GPSetType() - Constructor for class ec.gp.GPSetType
  You should not construct new types.
gpspecies - Variable in class ec.gp.ge.GESpecies
  The GPSpecies subsidiary to GESpecies.
GPSpecies - Class in ec.gp
  GPSpecies is a simple individual which is suitable as a species for GP subpopulations.
GPSpecies() - Constructor for class ec.gp.GPSpecies
GPTree - Class in ec.gp
  GPTree is a GPNodeParent which holds the root GPNode of a tree of GPNodes.
GPTree() - Constructor for class ec.gp.GPTree
GPTreeConstraints - Class in ec.gp
  A GPTreeConstraints is a Clique which defines constraint information common to many different GPTree trees, namely the tree type, builder, and function set.
GPTreeConstraints() - Constructor for class ec.gp.GPTreeConstraints
GPType - Class in ec.gp
  GPType is a Clique which represents types in Strongly-Typed Genetic Programming (STGP).
GPType() - Constructor for class ec.gp.GPType
grammar - Variable in class ec.gp.ge.GESpecies
  The parsed grammars.
GrammarFunctionNode - Class in ec.gp.ge
  A GrammarNode representing a GPNode in the GE Grammar.
GrammarFunctionNode(GPFunctionSet, String) - Constructor for class ec.gp.ge.GrammarFunctionNode
  Determines the GPNode from the function set by the name.
GrammarFunctionNode(String) - Constructor for class ec.gp.ge.GrammarFunctionNode
GrammarNode - Class in ec.gp.ge
  The abstract superclass of nodes used by GrammarParser to construct a parse graph to generate GEIndividuals.
GrammarNode(String) - Constructor for class ec.gp.ge.GrammarNode
grammarParser - Variable in class ec.gp.ge.GESpecies
  Parser for each grammar -- khaled
GrammarParser - Class in ec.gp.ge
  A GrammarParser is the basic class for parsing a GE ruleset into a parse graph of GrammarNodes.
GrammarParser() - Constructor for class ec.gp.ge.GrammarParser
GrammarRuleNode - Class in ec.gp.ge
  A GrammarNode representing a Rule in the GE Grammar.
GrammarRuleNode(String) - Constructor for class ec.gp.ge.GrammarRuleNode
GreedyOverselection - Class in ec.select
  GreedyOverselection is a SelectionMethod which implements Koza-style fitness-proportionate greedy overselection.
GreedyOverselection() - Constructor for class ec.select.GreedyOverselection
GroupedProblemForm - Interface in ec.coevolve
  GroupedProblemForm.java
groupSize - Variable in class ec.coevolve.CompetitiveEvaluator
GrowBuilder - Class in ec.gp.koza
  GrowBuilder is a GPNodeBuilder which implements the GROW tree building method described in Koza I/II.
GrowBuilder() - Constructor for class ec.gp.koza.GrowBuilder
growNode(EvolutionState, int, int, GPType, int, GPNodeParent, int, GPFunctionSet) - Method in class ec.gp.koza.KozaBuilder
  A private function which recursively returns a GROW tree to newRootedTree(...)
gt(long, long) - Method in interface ec.util.SortComparatorL
  Returns true if a > b, else false
gt(Object, Object) - Method in interface ec.util.SortComparator
  Returns true if a > b, else false

## H

HalfBuilder - Class in ec.gp.koza
  HalfBuilder is a GPNodeBuilder which implements the RAMPED HALF-AND-HALF tree building method described in Koza I/II.
HalfBuilder() - Constructor for class ec.gp.koza.HalfBuilder
hasGene(ArrayList<Gene>, Gene) - Method in class ec.neat.NEATIndividual
  Test if a genome has certain gene.
hashCode() - Method in class ec.gp.ge.GrammarNode
  As usual
hashCode() - Method in class ec.gp.GPIndividual
hashCode() - Method in class ec.Individual
  Returns a hashcode for the individual, such that individuals which are equals(...) each other always return the same hash code.
hashCode() - Method in class ec.neat.NEATGene
  "Placeholder" method for generating a hashcode.
hashCode() - Method in class ec.neat.NEATIndividual
hashCode() - Method in class ec.neat.NEATInnovation
hashCode() - Method in class ec.neat.NEATNode
hashCode() - Method in class ec.pso.Particle
hashCode() - Method in class ec.rule.Rule
  Rulerates a hash code for this rule -- the rule for this is that the hash code must be the same for two rules that are equal to each other genetically.
hashCode() - Method in class ec.rule.RuleIndividual
hashCode() - Method in class ec.rule.RuleSet
  The hash code for the rule set.
hashCode() - Method in class ec.util.IIntPoint
hashCode() - Method in class ec.vector.BitVectorIndividual
hashCode() - Method in class ec.vector.ByteVectorIndividual
hashCode() - Method in class ec.vector.DoubleVectorIndividual
hashCode() - Method in class ec.vector.FloatVectorIndividual
hashCode() - Method in class ec.vector.Gene
  Generates a hash code for this gene -- the rule for this is that the hash code must be the same for two genes that are equal to each other genetically.
hashCode() - Method in class ec.vector.GeneVectorIndividual
hashCode() - Method in class ec.vector.IntegerVectorIndividual
hashCode() - Method in class ec.vector.LongVectorIndividual
hashCode() - Method in class ec.vector.ShortVectorIndividual
hasInnovation(NEATInnovation) - Method in class ec.neat.NEATSpecies
hasLarger(CornerMap.Pair) - Method in class ec.eda.dovs.CornerMap
  Test if we have another key value pair after parameter pair
hasNewGeneration() - Method in class ec.neat.NEATSubspecies
  Test if newGenIndividuals list is empty.
hasPath(EvolutionState, NEATNode, NEATNode, int) - Static method in class ec.neat.NEATNetwork
  This checks a POTENTIAL link between start from fromNode to toNode to use count and threshold to jump out in the case of an infinite loop.
hasPath(EvolutionState, NEATNode, NEATNode, HashSet<NEATNode>, int, int, boolean[]) - Static method in class ec.neat.NEATNetwork
  The helper function to check if there is a path from fromNode to toNode.
hasSmaller(CornerMap.Pair) - Method in class ec.eda.dovs.CornerMap
  Test if we have another key value pair before parameter pair
HIDDEN - Enum constant in enum class ec.neat.NEATNode.NodePlace
highestFitness - Variable in class ec.neat.NEATSpecies
  Used for delta coding, stagnation detector.
highestLastChanged - Variable in class ec.neat.NEATSpecies
  Used for delta coding, If too high, leads to delta coding.
highFit - Variable in class ec.neat.NEATIndividual
  debug variable, highest fitness of champion
hits - Variable in class ec.gp.koza.KozaFitness
  This auxillary measure is used in some problems for additional information.
homologous - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
HyperboxSpecies - Class in ec.eda.dovs
  HyperboxSpecies is a DOVSSpecies which contains method for updating promising sample area and also sample from that area.
HyperboxSpecies() - Constructor for class ec.eda.dovs.HyperboxSpecies
hypervolume(ArrayList<Individual>) - Method in class ec.multiobjective.HypervolumeStatistics
  Compute the hypervolume of the Pareto front induced by a collection of points, relative to the reference point that was provided to this class's setup() method.
hypervolume(ArrayList<Individual>, double[]) - Static method in class ec.multiobjective.HypervolumeStatistics
  Compute the hypervolume of the Pareto front induced by a collection of points, relative to the provided reference point.
HypervolumeStatistics - Class in ec.multiobjective
  Measures the hypervolume of a population's Pareto front.
HypervolumeStatistics() - Constructor for class ec.multiobjective.HypervolumeStatistics

## I

i_prototype - Variable in class ec.Species
  The prototypical individual for this species.
iAmServer - Variable in class ec.exchange.IslandExchange
  whether the server should be running on the current island or not
IIntPoint - Class in ec.util
  An immutable 2-dimensional point.
IIntPoint(int, int) - Constructor for class ec.util.IIntPoint
immigrantsSelectionMethod - Variable in class ec.exchange.IslandExchange
  the selection method for immigrants
includeSelf - Variable in class ec.pso.PSOBreeder
inclusiveHypervolume(Individual) - Method in class ec.multiobjective.HypervolumeStatistics
  Compute the hypervolume covered by a single individual, relative to the reference point that was provided to this class's setup() method.
inclusiveHypervolume(Individual, double[]) - Static method in class ec.multiobjective.HypervolumeStatistics
  Compute the hypervolume covered by a single individual, relative to the provided reference point.
incomingGenes - Variable in class ec.neat.NEATNode
  A list of incoming links, it is used to get activation status of the nodes on the other ends.
incrementEvaluations(int) - Method in class ec.EvolutionState
ind - Variable in class ec.steadystate.QueueIndividual
Indexed - Interface in ec.util
  A simple interface (simpler than List) for accessing random-access objects without changing their size.
indices - Variable in class ec.gp.push.Terminal
  For each PushInstruction, a pointer into instructions which gives the name of that instruction.
indices - Variable in class ec.select.SUSSelection
  An array of pointers to individuals in the population, shuffled along with the fitnesses array.
individual - Variable in class ec.breed.RepeatPipeline
individual - Variable in class ec.neat.NEATNetwork
  The neat individual we belong to
Individual - Class in ec
  An Individual is an item in the EC population stew which is evaluated and assigned a fitness which determines its likelihood of selection.
Individual() - Constructor for class ec.Individual
INDIVIDUAL_INDEX_PREAMBLE - Static variable in class ec.Subpopulation
IndividualPortrayal - Class in ec.display.portrayal
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.BreedingPipeline
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.parsimony.BucketTournamentSelection
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.parsimony.DoubleTournamentSelection
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.parsimony.RatioBucketTournamentSelection
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.select.FirstSelection
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.select.RandomSelection
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.select.TournamentSelection
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in class ec.steadystate.SteadyStateBreeder
  Called whenever individuals have been replaced by new individuals in the population.
individualReplaced(SteadyStateEvolutionState, int, int, int) - Method in interface ec.steadystate.SteadyStateBSourceForm
  Called whenever an individual has been replaced by another in the population.
individuals - Variable in class ec.neat.NEATSubspecies
  The individuals within this species
individuals - Variable in class ec.Subpopulation
  The subpopulation's individuals.
individualsBredStatistics(SteadyStateEvolutionState, Individual[]) - Method in class ec.Statistics
  STEADY-STATE: called each time new individuals are bred during the steady-state process.
individualsBredStatistics(SteadyStateEvolutionState, Individual[]) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called each time new individuals are bred during the steady-state process.
individualsEvaluatedStatistics(SteadyStateEvolutionState, Individual[], Individual[], int[], int[]) - Method in class ec.Statistics
  STEADY-STATE: called each time new individuals are evaluated during the steady-state process.
individualsEvaluatedStatistics(SteadyStateEvolutionState, Individual[], Individual[], int[], int[]) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called each time new individuals are evaluated during the steady-state process, NOT including the initial generation's individuals.
INDS_PRODUCED - Static variable in class ec.breed.BufferedBreedingPipeline
INDS_PRODUCED - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
INDS_PRODUCED - Static variable in class ec.gp.koza.CrossoverPipeline
INDS_PRODUCED - Static variable in class ec.gp.koza.MutationPipeline
INDS_PRODUCED - Static variable in class ec.rule.breed.RuleCrossoverPipeline
INDS_PRODUCED - Static variable in class ec.rule.breed.RuleMutationPipeline
INDS_PRODUCED - Static variable in class ec.SelectionMethod
indsToDieSelectionMethod - Variable in class ec.exchange.IslandExchange
  the selection method for individuals to be replaced by immigrants
informantCoeff - Variable in class ec.pso.PSOBreeder
init - Variable in class ec.gp.GPTreeConstraints
  The builder for the tree
INITIAL_STACK_SIZE - Static variable in class ec.gp.ADFStack
initialError(String, boolean) - Static method in class ec.util.Output
  Prints an initial error to System.err.
initialError(String, Parameter, boolean) - Static method in class ec.util.Output
  Prints an initial error to System.err.
initialError(String, Parameter, Parameter, boolean) - Static method in class ec.util.Output
  Prints an initial error to System.err.
InitializationPipeline - Class in ec.breed
  InitializationPipeline is a BreedingPipeline which simply generates a new random inidividual.
InitializationPipeline() - Constructor for class ec.breed.InitializationPipeline
initialize(ParameterDatabase, int) - Static method in class ec.Evolve
  Initializes an evolutionary run given the parameters and a random seed adjustment (added to each random seed).
initialize(ParameterDatabase, int, Output) - Static method in class ec.Evolve
  Initializes an evolutionary run given the parameters and a random seed adjustment (added to each random seed), with the Output pre-constructed.
initializeContacts(EvolutionState) - Method in class ec.eval.MasterProblem
  Initialize contacts with the slaves
initializeContacts(EvolutionState) - Method in class ec.Evaluator
  Called to set up remote evaluation network contacts when the run is started.
initializeContacts(EvolutionState) - Method in class ec.exchange.InterPopulationExchange
  Initializes contacts with other processes, if that's what you're doing.
initializeContacts(EvolutionState) - Method in class ec.exchange.IslandExchange
  Initializes contacts with other processes, if that's what you're doing.
initializeContacts(EvolutionState) - Method in class ec.Exchanger
  Initializes contacts with other processes, if that's what you're doing.
initializeContacts(EvolutionState) - Method in class ec.gp.ge.GEProblem
initializeContacts(EvolutionState) - Method in class ec.Problem
  Called to set up remote evaluation network contacts when the run is started.
initializeContacts(EvolutionState) - Method in class ec.simple.SimpleExchanger
  Doesn't do anything.
initializeGenomeSegmentsByEndIndices(EvolutionState, Parameter, Parameter, int) - Method in class ec.vector.VectorSpecies
  Looks up genome segments using end indices.
initializeGenomeSegmentsByStartIndices(EvolutionState, Parameter, Parameter, int) - Method in class ec.vector.VectorSpecies
  Looks up genome segments using start indices.
initializer - Variable in class ec.EvolutionState
  The population initializer, a singleton object.
Initializer - Class in ec
  The Initializer is a singleton object whose job is to initialize the population at the beginning of the run.
Initializer() - Constructor for class ec.Initializer
initialMessage(String) - Static method in class ec.util.Output
  Prints an initial message to System.err.
initialPopulation(EvolutionState, int) - Method in class ec.eda.dovs.DOVSInitializer
  In DOVS, we provide the algorithm with a start individual from file, this start individual is the start search point of the DOVS algorithm.
initialPopulation(EvolutionState, int) - Method in class ec.Initializer
  Creates and returns a new initial population for the evolutionary run.
initialPopulation(EvolutionState, int) - Method in class ec.neat.NEATInitializer
  In NEAT, we provide the algorithm with a start individual from file, after read the start individual from file, we populate the subpopulation with mutated version of that template individual.
initialPopulation(EvolutionState, int) - Method in class ec.simple.SimpleInitializer
  Creates, populates, and returns a new population by making a new population, calling setup(...) on it, and calling populate(...) on it, assuming an unthreaded environment (thread 0).
initialReps - Variable in class ec.eda.dovs.DOVSSpecies
  Base value of number evaluation for each individual.
initialSize - Variable in class ec.Subpopulation
  initial expected size of the subpopulation
initialWarning(String) - Static method in class ec.util.Output
  Prints an initial warning to System.err.
initialWarning(String, Parameter) - Static method in class ec.util.Output
  Prints an initial warning to System.err.
initialWarning(String, Parameter, Parameter) - Static method in class ec.util.Output
  Prints an initial warning to System.err.
initScheme - Variable in class ec.gp.ge.GESpecies
innerLevel - Variable in class ec.neat.NEATNode
  The depth of current node in current network, this field is used in counting max depth in a network.
inNode - Variable in class ec.neat.NEATGene
  The actual in node this gene connect to.
inNodeId - Variable in class ec.neat.NEATGene
  The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.
inNodeId - Variable in class ec.neat.NEATInnovation
  Two nodes specify where the link innovation took place : this is the input node.
innovationNum1 - Variable in class ec.neat.NEATInnovation
  The number assigned to the innovation.
innovationNum2 - Variable in class ec.neat.NEATInnovation
  If this is a new node innovation,then there are 2 innovations (links) added for the new node.
innovationNumber - Variable in class ec.EvolutionState
  Global birthday tracker number for genes in representations such as NEAT.
innovationNumber - Variable in class ec.neat.NEATGene
  The innovation number of this link.
innovationPrototype - Variable in class ec.neat.NEATSpecies
  The prototypical innovation for individuals in this species.
innovations - Variable in class ec.neat.NEATSpecies
  A Hashmap for easy tracking the innovation within species.
innovationType - Variable in class ec.neat.NEATInnovation
  Either NEWNODE (0) or NEWLINK (1).
inNumericalTypeRange(double) - Method in class ec.vector.FloatVectorSpecies
inNumericalTypeRange(double) - Method in class ec.vector.IntegerVectorSpecies
inNumericalTypeRange(long) - Method in class ec.vector.IntegerVectorSpecies
input - Variable in class ec.gp.GPProblem
  The GPProblem's GPData
input - Variable in class ec.util.DataPipe
  The input stream
INPUT - Enum constant in enum class ec.neat.NEATNode.NodePlace
inputs - Variable in class ec.neat.NEATNetwork
  A list of input nodes for this network.
inReserve - Variable in class ec.gp.ADFStack
insert(int, Individual) - Method in class ec.eda.dovs.CornerMap
  Insert a key and value pair into CornerMap
inssort(byte[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(char[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(double[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(float[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(int[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(int[], SortComparatorL) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(long[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(long[], SortComparatorL) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(short[]) - Static method in class ec.util.QuickSort
  Insertion Sort
inssort(Object[], SortComparator) - Static method in class ec.util.QuickSort
  Insertion Sort
instructions - Variable in class ec.gp.push.Terminal
  Names of all the Push instructions I can be set to.
IntBag - Class in ec.util
  Maintains a simple array (objs) of ints and the number of ints (numObjs) in the array (the array can be bigger than this number).
IntBag() - Constructor for class ec.util.IntBag
IntBag(int) - Constructor for class ec.util.IntBag
  Creates an IntBag with a given initial capacity.
IntBag(int[]) - Constructor for class ec.util.IntBag
  Creates an IntBag with the given elements.
IntBag(IntBag) - Constructor for class ec.util.IntBag
  Adds the ints from the other IntBag without copying them.
INTEGER_ERC - Static variable in class ec.gp.push.Terminal
IntegerVectorIndividual - Class in ec.vector
  IntegerVectorIndividual is a VectorIndividual whose genome is an array of ints.
IntegerVectorIndividual() - Constructor for class ec.vector.IntegerVectorIndividual
IntegerVectorSpecies - Class in ec.vector
  IntegerVectorSpecies is a subclass of VectorSpecies with special constraints for integral vectors, namely ByteVectorIndividual, ShortVectorIndividual, IntegerVectorIndividual, and LongVectorIndividual.
IntegerVectorSpecies() - Constructor for class ec.vector.IntegerVectorSpecies
InternalCrossoverPipeline - Class in ec.gp.breed
  InternalCrossoverPipeline picks two subtrees from somewhere within an individual, and crosses them over.
InternalCrossoverPipeline() - Constructor for class ec.gp.breed.InternalCrossoverPipeline
InterPopulationExchange - Class in ec.exchange
  InterPopulationExchange is an Exchanger which implements a simple exchanger between subpopulations.
InterPopulationExchange() - Constructor for class ec.exchange.InterPopulationExchange
interrupt() - Method in interface ec.util.ThreadPool.Worker
interspeciesMateRate - Variable in class ec.neat.NEATSpecies
  Probability of doing interspecies crossover.
intForNode(GPNode) - Method in class ec.gp.build.Uniform
invsqrtC - Variable in class ec.eda.cmaes.CMAESSpecies
  C^{-1/2}.
isCompleteSolution(ConstructiveIndividual) - Method in class ec.eval.MasterProblem
isEmpty() - Method in class ec.util.IntBag
isFloatStackEmpty(Interpreter) - Method in class ec.gp.push.PushProblem
  Tests to see if the interpreter's float stack is empty.
isGroupedProblem() - Method in class ec.eval.MasterProblem
  Returns true if the underlying class returns true for isGroupedProblem()
isGroupedProblem() - Method in class ec.gp.ge.GEProblem
isGroupedProblem() - Method in class ec.Problem
  Returns true if this method is meant to be a grouped problem.
isIdeal - Variable in class ec.simple.SimpleFitness
isIdealFitness() - Method in class ec.Fitness
  Should return true if this is a good enough fitness to end the run
isIdealFitness() - Method in class ec.gp.koza.KozaFitness
isIdealFitness() - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns true if this fitness is the "ideal" fitness.
isIdealFitness() - Method in class ec.simple.SimpleFitness
isIdealFitness(EvolutionState, Individual) - Method in class ec.steadystate.SteadyStateEvaluator
  The SimpleEvaluator determines that a run is complete by asking each individual in each population if he's optimal; if he finds an individual somewhere that's optimal, he signals that the run is complete.
isInRange() - Method in class ec.vector.ByteVectorIndividual
  Returns true if each gene value is within is specified [min,max] range.
isInRange() - Method in class ec.vector.DoubleVectorIndividual
  Returns true if each gene value is within is specified [min,max] range.
isInRange() - Method in class ec.vector.FloatVectorIndividual
  Returns true if each gene value is within is specified [min,max] range.
isInRange() - Method in class ec.vector.IntegerVectorIndividual
  Returns true if each gene value is within is specified [min,max] range.
isInRange() - Method in class ec.vector.LongVectorIndividual
  Returns true if each gene value is within is specified [min,max] range.
isInRange() - Method in class ec.vector.ShortVectorIndividual
  Returns true if each gene value is within is specified [min,max] range.
isIntStackEmpty(Interpreter) - Method in class ec.gp.push.PushProblem
  Tests to see if the interpreter's int stack is empty.
IslandExchange - Class in ec.exchange
  IslandExchange is an Exchanger which implements a simple but quite functional asynchronous island model for doing massive parallel distribution of evolution across beowulf clusters.
IslandExchange() - Constructor for class ec.exchange.IslandExchange
isLeaf(Object) - Method in class ec.util.ReflectedObject
isLoggingToSystemOut - Variable in class ec.util.Log
isMaximizing() - Method in class ec.multiobjective.MultiObjectiveFitness
isMaximizing(int) - Method in class ec.multiobjective.MultiObjectiveFitness
isRecurrent - Variable in class ec.neat.NEATGene
  Is the link this gene represent a recurrent link.
isTraversed - Variable in class ec.neat.NEATNode
  Indicate if this node has been traversed in max depth counting.
isValid(DoubleVectorIndividual) - Method in class ec.eda.amalgam.AMALGAMSpecies
isValidated(int[][], Object) - Method in class ec.vector.breed.ListCrossoverPipeline
  A hook called by ListCrossoverPipeline to allow subclasses to further validate children crossover points.
isViolated(ConstructiveIndividual, Component) - Method in class ec.eval.MasterProblem
iterator() - Method in class ec.gp.GPNode
  Returns an iterator over all the GPNodes in the subtree rooted by this GPNode.
iterator(int) - Method in class ec.gp.GPNode
  Returns an iterator over all the GPNodes in the subtree rooted by this GPNode, filtered by the provided nodesearch option (either NODSEARCH_TERMINALS, NODESEARCH_NONTERMINALS, or NODESEARCH_ALL)
iterator(GPNodeGatherer) - Method in class ec.gp.GPNode
  Returns an iterator over all the GPNodes in the subtree rooted by this GPNode, filtered by the provided GPNodeGatherer.

## J

job - Variable in class ec.EvolutionState
  Current job iteration variables, set by Evolve.
Job - Class in ec.eval
  Job.java This class stores information regarding a job submitted to a Slave: the individuals, the subpopulations in which they are stored, a scratch array for the individuals used internally, and various coevolutionary information (whether we should only count victories single-elimination-tournament style; which individuals should have their fitnesses updated).
Job() - Constructor for class ec.eval.Job
join(RuleSet) - Method in class ec.rule.RuleSet
  Makes a copy of the rules in another RuleSet and adds the rule copies.
join(ThreadPool.Worker) - Method in class ec.util.ThreadPool
  If the thread is presently running a Runnable of any kind, blocks until the Runnable has finished running.
join(ThreadPool.Worker, Runnable) - Method in class ec.util.ThreadPool
  Joins the given thread running the given Runnable.
join(Object[]) - Method in class ec.pso.Particle
join(Object[]) - Method in class ec.vector.BitVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.ByteVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.DoubleVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.FloatVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.GeneVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.IntegerVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.LongVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.ShortVectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
join(Object[]) - Method in class ec.vector.VectorIndividual
  Joins the n pieces and sets the genome to their concatenation.
joinAll() - Method in class ec.util.ThreadPool
  Waits until there are no outstanding workers: all pool workers are in the pool.

## K

key - Variable in class ec.eda.dovs.CornerMap.Pair
KEY_PARENTS - Static variable in class ec.gp.breed.InternalCrossoverPipeline
KEY_PARENTS - Static variable in class ec.gp.breed.MutateAllNodesPipeline
KEY_PARENTS - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
KEY_PARENTS - Static variable in class ec.gp.koza.CrossoverPipeline
KEY_PARENTS - Static variable in class ec.rule.breed.RuleCrossoverPipeline
KEY_PARENTS - Static variable in class ec.SelectionMethod
KEY_PARENTS - Static variable in class ec.vector.breed.ListCrossoverPipeline
KEY_PARENTS - Static variable in class ec.vector.breed.VectorCrossoverPipeline
killAll() - Method in class ec.util.ThreadPool
  Waits until there are no outstanding workers: all pool workers are in the pool.
killPooled() - Method in class ec.util.ThreadPool
  Kills all unused workers in the pool.
KozaBuilder - Class in ec.gp.koza
KozaBuilder() - Constructor for class ec.gp.koza.KozaBuilder
KozaFitness - Class in ec.gp.koza
  KozaFitness is a Fitness which stores an individual's fitness as described in Koza I.
KozaFitness() - Constructor for class ec.gp.koza.KozaFitness
KozaNodeSelector - Class in ec.gp.koza
  KozaNodeSelector is a GPNodeSelector which picks nodes in trees a-la Koza I, with the addition of having a probability of always picking the root.
KozaNodeSelector() - Constructor for class ec.gp.koza.KozaNodeSelector
KozaShortStatistics - Class in ec.gp.koza
  A Koza-style statistics generator, intended to be easily parseable with awk or other Unix tools.
KozaShortStatistics() - Constructor for class ec.gp.koza.KozaShortStatistics
kthNNDistance - Variable in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
  SPEA2 NN distance

## L

l - Variable in class ec.util.DecodeReturn
  Stores booleans (0=false), bytes, chars, shorts, ints, longs
lambda - Variable in class ec.eda.cmaes.CMAESSpecies
  The individuals generated from the distribution.
lambda - Variable in class ec.es.MuCommaLambdaBreeder
LARGE_NUMBER - Static variable in class ec.eda.dovs.HyperboxSpecies
lastActivation - Variable in class ec.neat.NEATNode
  Holds the previous step's activation for recurrence.
lastEigenDecompositionGeneration - Variable in class ec.eda.cmaes.CMAESSpecies
  The most recent generation where an eigendecomposition on C was performed into B and D
lastIndex - Variable in class ec.select.SUSSelection
  The index in the array of the last individual selected.
lastTime - Variable in class ec.simple.SimpleShortStatistics
Lexer - Class in ec.util
  A simple line-by-line String tokenizer.
Lexer(CharSequence, String[]) - Constructor for class ec.util.Lexer
  Builds a Lexer for the given input with the provided regular expressions.
LexicaseSelection - Class in ec.select
LexicaseSelection() - Constructor for class ec.select.LexicaseSelection
LexicographicTournamentSelection - Class in ec.parsimony
  Does a simple tournament selection, limited to the subpopulation it's working in at the time.
LexicographicTournamentSelection() - Constructor for class ec.parsimony.LexicographicTournamentSelection
lightClone() - Method in class ec.gp.GPIndividual
  Like clone(), but doesn't force the GPTrees to deep-clone themselves.
lightClone() - Method in class ec.gp.GPNode
lightClone() - Method in class ec.gp.GPTree
  Like clone() but doesn't copy the tree.
likelihood - Variable in class ec.BreedingPipeline
lineDistance - Variable in class ec.vector.VectorSpecies
  How far along the long a child can be located for line or intermediate recombination
lineNumber - Variable in class ec.util.DecodeReturn
  The Line number, if it has been posted.
list(PrintWriter) - Method in class ec.util.ParameterDatabase
  Prints out all the parameters in the database, but not shadowed parameters.
list(PrintWriter, boolean) - Method in class ec.util.ParameterDatabase
  Prints out all the parameters in the database.
listAccessed(PrintWriter) - Method in class ec.util.ParameterDatabase
  Prints out all the parameters marked as accessed ("gotten" by some getFoo(...) method), plus their values.
ListCrossoverPipeline - Class in ec.vector.breed
  ListCrossoverPipeline is a crossover pipeline for vector individuals whose length may be lengthened or shortened.
ListCrossoverPipeline() - Constructor for class ec.vector.breed.ListCrossoverPipeline
listGotten(PrintWriter) - Method in class ec.util.ParameterDatabase
  Prints out all the parameters marked as used, plus their values.
listNotAccessed(PrintWriter) - Method in class ec.util.ParameterDatabase
  Prints out all the parameters NOT marked as used, plus their values.
listNotGotten(PrintWriter) - Method in class ec.util.ParameterDatabase
  Prints out all the parameters NOT marked as used, plus their values.
loadDomain(EvolutionState, Parameter) - Method in class ec.eval.MetaProblem
loadElites(EvolutionState, Population) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
  Extract the elite individuals from the current population and both place in newpop and replace the current population with the archive.
loadElites(EvolutionState, Population) - Method in class ec.multiobjective.spea2.SPEA2Breeder
  Extract the elite individuals from the current population and both place in newpop and replace the current population with the archive.
loadElites(EvolutionState, Population) - Method in class ec.simple.SimpleBreeder
  A protected helper function for breedPopulation which loads elites into a subpopulation.
loadInds - Variable in class ec.Population
loadInds - Variable in class ec.Subpopulation
loadParameterDatabase(String[]) - Static method in class ec.Evolve
  Loads a ParameterDatabase from checkpoint if "-params" is in the command-line arguments.
loadParameters() - Method in class ec.display.ControlPanel
loadParametersForGene(EvolutionState, int, Parameter, Parameter, String) - Method in class ec.vector.BitVectorSpecies
  Called when VectorSpecies is setting up per-gene and per-segment parameters.
loadParametersForGene(EvolutionState, int, Parameter, Parameter, String) - Method in class ec.vector.FloatVectorSpecies
loadParametersForGene(EvolutionState, int, Parameter, Parameter, String) - Method in class ec.vector.IntegerVectorSpecies
loadParametersForGene(EvolutionState, int, Parameter, Parameter, String) - Method in class ec.vector.VectorSpecies
  Called when VectorSpecies is setting up per-gene and per-segment parameters.
loadSensors(double[]) - Method in class ec.neat.NEATNetwork
  Takes an array of sensor values and loads it into SENSOR inputs ONLY.
LocalHost - Class in ec.util
  Modified from apache mail-archives.
LocalHost() - Constructor for class ec.util.LocalHost
lock - Variable in class ec.eval.MetaProblem
  Acquire this lock before accessing bestUnderlyingIndividual
Log - Class in ec.util
  Defines a log to which Output outputs.
Log(int, boolean) - Constructor for class ec.util.Log
  Creates a log on stdout (descriptor == Log.D_STDOUT) or stderr (descriptor == Log.D_STDERR).
Log(File, boolean, boolean) - Constructor for class ec.util.Log
  Creates a log to a given filename; this file may or may not be appended to on restart, depending on _appendOnRestart.
Log(File, boolean, boolean, boolean) - Constructor for class ec.util.Log
  Creates a log to a given filename; this file may or may not be appended to on restart, depending on _appendOnRestart.
Log(Writer, LogRestarter, boolean, boolean) - Constructor for class ec.util.Log
  Creates a log on a given Writer and custom LogRestarter.
LogRestarter - Class in ec.util
  A LogRestarter is an abstract superclass of objects which are capable of restarting logs after a computer failure.
LogRestarter() - Constructor for class ec.util.LogRestarter
LongVectorIndividual - Class in ec.vector
  LongVectorIndividual is a VectorIndividual whose genome is an array of longs.
LongVectorIndividual() - Constructor for class ec.vector.LongVectorIndividual
lowerBound(int) - Method in class ec.eda.dovs.CornerMap
  This returns the smallest element whose key is equal to or bigger than the argument "key".
LPAREN - Static variable in class ec.gp.ge.GrammarParser
lt(long, long) - Method in interface ec.util.SortComparatorL
  Returns true if a invalid input: '<' b, else false
lt(Object, Object) - Method in interface ec.util.SortComparator
  Returns true if a invalid input: '<' b, else false

## M

main(String[]) - Static method in class ec.display.Console
main(String[]) - Static method in class ec.eval.Slave
main(String[]) - Static method in class ec.Evolve
  Top-level evolutionary loop.
main(String[]) - Static method in class ec.exchange.IslandExchange
main(String[]) - Static method in class ec.gp.ge.GrammarParser
  A simple testing facility.
main(String[]) - Static method in class ec.util.MersenneTwister
  Tests the code.
main(String[]) - Static method in class ec.util.MersenneTwisterFast
  Tests the code.
main(String[]) - Static method in class ec.util.ParameterDatabase
  Test the ParameterDatabase
main(String[]) - Static method in class ec.util.ThreadPool
make(int, EvolutionState, int) - Method in class ec.parsimony.DoubleTournamentSelection
  Produces the index of a person selected from among several by a tournament.
makeBar(int, double[]) - Method in class ec.display.chart.BarChartStatistics
makeChart() - Method in class ec.display.chart.BarChartStatistics
makeChart() - Method in class ec.display.chart.ChartableStatistics
makeChart() - Method in class ec.display.chart.PieChartStatistics
makeChart() - Method in class ec.display.chart.XYSeriesChartStatistics
makeCompressingInputStream(InputStream) - Static method in class ec.util.Output
  Returns a compressing input stream using JZLib (http://www.jcraft.com/jzlib/).
makeCompressingOutputStream(OutputStream) - Static method in class ec.util.Output
  Returns a compressing output stream using JZLib (http://www.jcraft.com/jzlib/).
makeCTree(boolean, boolean, boolean) - Method in class ec.gp.GPNode
  Producess a String consisting of the tree in pseudo-C form, given that the parent already will wrap the expression in parentheses (or not).
makeGraphvizSubtree(String) - Method in class ec.gp.GPNode
  Produces the inner code for a graphviz subtree.
makeGraphvizTree() - Method in class ec.gp.GPNode
  Produces the Graphviz code for a Graphviz tree of the subtree rooted at this node.
makeLatexTree() - Method in class ec.gp.GPNode
  Produces the LaTeX code for a LaTeX tree of the subtree rooted at this node, using the `epic` and `fancybox` packages, as described in sections 10.5.2 (page 307) and 10.1.3 (page 278) of The LaTeX Companion, respectively.
makeLispTree() - Method in class ec.gp.GPNode
makeLispTree(StringBuilder) - Method in class ec.gp.GPNode
  Produces a tree for human consumption in Lisp form similar to that generated by printTreeForHumans().
makeSector(int, double[]) - Method in class ec.display.chart.PieChartStatistics
makeTree(EvolutionState, int[], GPTree, int, int, int, HashMap) - Method in class ec.gp.ge.GESpecies
  makeTree, edits the tree that its given by adding a root (and all subtrees attached)
makeTrees(EvolutionState, int[], GPTree[], int, HashMap) - Method in class ec.gp.ge.GESpecies
makeTrees(EvolutionState, GEIndividual, GPTree[], int, HashMap) - Method in class ec.gp.ge.GESpecies
  creates all of an individual's trees
manhattanObjectiveDistance(MultiObjectiveFitness) - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns the Manhattan difference between two Fitnesses in Objective space.
map(EvolutionState, double[], FloatVectorSpecies, int) - Method in class ec.eval.MetaProblem
map(EvolutionState, GEIndividual, int, HashMap) - Method in class ec.gp.ge.GESpecies
  Returns a dummy GPIndividual with a single tree which was built by mapping over the elements of the given GEIndividual.
markReproducableIndividuals(double) - Method in class ec.neat.NEATSubspecies
  Mark the individual who can reproduce for this generation.
masterproblem - Variable in class ec.Evaluator
MasterProblem - Class in ec.eval
  MasterProblem.java
MasterProblem() - Constructor for class ec.eval.MasterProblem
mateMultipoint(EvolutionState, int, NEATIndividual, boolean) - Method in class ec.neat.NEATIndividual
  Doing crossover from two parent at multiple points in the genome.
mateMultipointAvgProb - Variable in class ec.neat.NEATSpecies
  Probability of doing multipoint crossover with averaging two genes.
mateMultipointProb - Variable in class ec.neat.NEATSpecies
  Probability of doing multipoint crossover.
mateOnlyProb - Variable in class ec.neat.NEATSpecies
  Probability of mating without mutation.
mateSinglepoint(EvolutionState, int, NEATIndividual) - Method in class ec.neat.NEATIndividual
  Deprecated.
mateSinglepointProb - Variable in class ec.neat.NEATSpecies
  Probability of doing single point crossover (not in used in this implementation, always set to 0).
MAX_TRIES_BEFORE_WARNING - Static variable in class ec.eda.cmaes.CMAESSpecies
maxarity - Variable in class ec.gp.build.Uniform
maxChildProduction() - Method in class ec.BreedingPipeline
  Returns the maximum among the typicalIndsProduced() for any children -- a function that's useful internally, not very useful for you to call externally.
maxCrossoverPercentage - Variable in class ec.vector.breed.ListCrossoverPipeline
maxDepth - Variable in class ec.gp.breed.InternalCrossoverPipeline
  The deepest tree the pipeline is allowed to form.
maxDepth - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  The deepest tree the pipeline is allowed to form.
maxDepth - Variable in class ec.gp.build.PTC1
  The largest maximum tree depth PTC1 can specify -- should be big.
maxDepth - Variable in class ec.gp.build.PTC2
  The largest maximum tree depth GROW can specify -- should be big.
maxDepth - Variable in class ec.gp.koza.CrossoverPipeline
  The deepest tree the pipeline is allowed to form.
maxDepth - Variable in class ec.gp.koza.KozaBuilder
  The largest maximum tree depth RAMPED HALF-AND-HALF can specify.
maxDepth() - Method in class ec.neat.NEATNetwork
  Find the maximum number of neurons between an output and an input.
maxFitnessEver - Variable in class ec.neat.NEATSubspecies
  The max fitness the an individual in this subspecies ever achieved.
maxFloatERC - Static variable in class ec.gp.push.Terminal
maxGene - Variable in class ec.vector.FloatVectorSpecies
  Max-gene value, per gene.
maxGene - Variable in class ec.vector.IntegerVectorSpecies
  Max-gene value, per gene.
maxGene(int) - Method in class ec.vector.FloatVectorSpecies
maxGene(int) - Method in class ec.vector.IntegerVectorSpecies
maxGeneratable - Variable in class ec.breed.GenerationSwitchPipeline
maxGeneratable - Variable in class ec.breed.MultiBreedingPipeline
maximize - Variable in class ec.multiobjective.MultiObjectiveFitness
  Maximization.
MAXIMUM_INTEGER_IN_DOUBLE - Static variable in class ec.vector.DoubleVectorIndividual
MAXIMUM_SHORT_IN_FLOAT - Static variable in class ec.vector.FloatVectorIndividual
maximumMuLambdaDivisor() - Method in class ec.es.MuCommaLambdaBreeder
  lambda should be no SMALLER than mu times this value.
maximumMuLambdaDivisor() - Method in class ec.es.MuPlusLambdaBreeder
maximumNoImprovementStretch - Variable in class ec.eda.amalgam.AMALGAMSpecies
maxInitialSize - Variable in class ec.vector.VectorSpecies
  What's the largest legal genome?
maxIntegerERC - Static variable in class ec.gp.push.Terminal
maxNetworkDepth - Variable in class ec.neat.NEATSpecies
  how deep a node can be in the network, measured by number of parents
maxObjective - Variable in class ec.multiobjective.MultiObjectiveFitness
  Desired maximum fitness values.
MAXPRINTBYTES - Static variable in class ec.gp.GPNode
maxSize - Variable in class ec.gp.GPNodeBuilder
  the minium possible size -- if unused, it's 0
maxSize - Variable in class ec.gp.koza.CrossoverPipeline
  The largest tree (measured as a nodecount) the pipeline is allowed to form.
maxSize - Variable in class ec.gp.koza.MutationPipeline
  The largest tree (measured as a nodecount) the pipeline is allowed to form.
maxSize - Variable in class ec.rule.RuleSetConstraints
maxtreesize - Variable in class ec.gp.build.Uniform
mean - Variable in class ec.eda.amalgam.AMALGAMSpecies
  The mean of the distribution.
mean - Variable in class ec.eda.dovs.DOVSFitness
  Mean fitness value of the current individual.
meanShift - Variable in class ec.eda.amalgam.AMALGAMSpecies
merge(EvolutionState, Fitness) - Method in class ec.Fitness
  Merges the other fitness into this fitness.
merge(EvolutionState, Individual) - Method in class ec.Individual
  Replaces myself with the other Individual, while merging our evaluation results together.
merge(GrammarRuleNode) - Method in class ec.gp.ge.GrammarRuleNode
  Adds to this node all the choices of another node.
MERGE_BEST - Static variable in class ec.simple.SimpleEvaluator
MERGE_MEAN - Static variable in class ec.simple.SimpleEvaluator
MERGE_MEDIAN - Static variable in class ec.simple.SimpleEvaluator
mergeForm - Variable in class ec.simple.SimpleEvaluator
MersenneTwister - Class in ec.util
  MersenneTwister and MersenneTwisterFast
MersenneTwister() - Constructor for class ec.util.MersenneTwister
  Constructor using the default seed.
MersenneTwister(int[]) - Constructor for class ec.util.MersenneTwister
  Constructor using an array of integers as seed.
MersenneTwister(long) - Constructor for class ec.util.MersenneTwister
  Constructor using a given seed.
MersenneTwisterFast - Class in ec.util
  MersenneTwister and MersenneTwisterFast
MersenneTwisterFast() - Constructor for class ec.util.MersenneTwisterFast
  Constructor using the default seed.
MersenneTwisterFast(int[]) - Constructor for class ec.util.MersenneTwisterFast
  Constructor using an array of integers as seed.
MersenneTwisterFast(long) - Constructor for class ec.util.MersenneTwisterFast
  Constructor using a given seed.
message() - Static method in class ec.util.Version
message(String) - Method in class ec.util.Output
  Posts a message.
MetaProblem - Class in ec.eval
  MetaProblem is a special class for implenting so-called "Meta-Evolutionary Algorithms", a topic related to "HyperHeuristics".
MetaProblem() - Constructor for class ec.eval.MetaProblem
MIN_QUEUE_SIZE - Static variable in class ec.gp.build.PTC2
minChildProduction() - Method in class ec.BreedingPipeline
  Returns the minimum among the typicalIndsProduced() for any children -- a function that's useful internally, not very useful for you to call externally.
minChildSize - Variable in class ec.vector.breed.ListCrossoverPipeline
minCrossoverPercentage - Variable in class ec.vector.breed.ListCrossoverPipeline
minDepth - Variable in class ec.gp.koza.KozaBuilder
  The smallest maximum tree depth RAMPED HALF-AND-HALF can specify.
minFloatERC - Static variable in class ec.gp.push.Terminal
minGene - Variable in class ec.vector.FloatVectorSpecies
  Min-gene value, per gene.
minGene - Variable in class ec.vector.IntegerVectorSpecies
  Min-gene value, per gene.
minGene(int) - Method in class ec.vector.FloatVectorSpecies
minGene(int) - Method in class ec.vector.IntegerVectorSpecies
minimumJavaVersion - Static variable in class ec.util.Version
minInitialSize - Variable in class ec.vector.VectorSpecies
  What's the smallest legal genome?
minIntegerERC - Static variable in class ec.gp.push.Terminal
minObjective - Variable in class ec.multiobjective.MultiObjectiveFitness
  Desired minimum fitness values.
minSize - Variable in class ec.gp.GPNodeBuilder
minSize - Variable in class ec.rule.RuleSetConstraints
Misc - Class in ec.util
  Miscellaneous static utility methods.
modifyParameters(EvolutionState, ParameterDatabase, int, Individual) - Method in class ec.eval.MetaProblem
  Override this method to revise the provided parameter database to reflect the "parameters" specified in the given meta-individual.
modulo - Variable in class ec.exchange.IslandExchange
  how often to send individuals
modulus - Variable in class ec.simple.SimpleShortStatistics
monitor - Variable in class ec.eval.MasterProblem
mostPromisingAreaSamples(EvolutionState, int) - Method in class ec.eda.dovs.DOVSSpecies
  Sample from the most promising area to get new generation of individual for evaluation.
mostPromisingAreaSamples(EvolutionState, int) - Method in class ec.eda.dovs.HyperboxSpecies
  Sample from the hyperbox to get new samples for evaluation.
moveFromSubstack(int) - Method in class ec.gp.ADFStack
  Moves n items onto the stack (popss them off the substack and pushes them onto the stack).
moveOntoSubstack(int) - Method in class ec.gp.ADFStack
  Moves n items onto the substack (pops them off the stack and pushes them onto the substack).
mu - Variable in class ec.eda.cmaes.CMAESSpecies
  The truncated individuals used to update the distribution.
mu - Variable in class ec.es.MuCommaLambdaBreeder
MuCommaLambdaBreeder - Class in ec.es
  MuCommaLambdaBreeder is a Breeder which, together with ESSelection, implements the (mu,lambda) breeding strategy and gathers the comparison data you can use to implement a 1/5-rule mutation mechanism.
MuCommaLambdaBreeder() - Constructor for class ec.es.MuCommaLambdaBreeder
mueff - Variable in class ec.eda.cmaes.CMAESSpecies
  The "mu_{eff}" constant in CMA-ES.
MULTI_FITNESS_POSTAMBLE - Static variable in class ec.multiobjective.MultiObjectiveFitness
MultiBreedingPipeline - Class in ec.breed
  MultiBreedingPipeline is a BreedingPipeline stores some n child sources; each time it must produce an individual or two, it picks one of these sources at random and has it do the production.
MultiBreedingPipeline() - Constructor for class ec.breed.MultiBreedingPipeline
MultiObjectiveDefaults - Class in ec.multiobjective
MultiObjectiveDefaults() - Constructor for class ec.multiobjective.MultiObjectiveDefaults
MultiObjectiveFitness - Class in ec.multiobjective
  MultiObjectiveFitness is a subclass of Fitness which implements basic multi-objective mechanisms suitable for being used with a variety of multi-objective selection mechanisms, including ones using pareto-optimality.
MultiObjectiveFitness() - Constructor for class ec.multiobjective.MultiObjectiveFitness
MultiObjectiveStatistics - Class in ec.multiobjective
MultiObjectiveStatistics() - Constructor for class ec.multiobjective.MultiObjectiveStatistics
MultipleVectorCrossoverPipeline - Class in ec.vector.breed
  MultipleVectorCrossoverPipeline is a BreedingPipeline which implements a uniform (any point) crossover between multiple vectors.
MultipleVectorCrossoverPipeline() - Constructor for class ec.vector.breed.MultipleVectorCrossoverPipeline
MultiPopCoevolutionaryEvaluator - Class in ec.coevolve
  MultiPopCoevolutionaryEvaluator.java
MultiPopCoevolutionaryEvaluator() - Constructor for class ec.coevolve.MultiPopCoevolutionaryEvaluator
MultiSelection - Class in ec.select
  MultiSelection is a SelectionMethod which stores some n subordinate SelectionMethods.
MultiSelection() - Constructor for class ec.select.MultiSelection
MuPlusLambdaBreeder - Class in ec.es
  MuPlusLambdaBreeder is a subclass of MuCommaLambdaBreeder which, together with ESSelection, implements the (mu + lambda) breeding strategy and gathers the comparison data you can use to implement a 1/5-rule mutation mechanism.
MuPlusLambdaBreeder() - Constructor for class ec.es.MuPlusLambdaBreeder
mutate(EvolutionState, int) - Method in class ec.rule.Rule
  Mutate the rule.
mutate(EvolutionState, int) - Method in class ec.rule.RuleIndividual
  Mutates the Individual.
mutate(EvolutionState, int) - Method in class ec.rule.RuleSet
  Mutates rules in the RuleSet independently with the given probability.
mutate(EvolutionState, int) - Method in class ec.vector.Gene
  Mutate the gene.
mutateAddLink(EvolutionState, int) - Method in class ec.neat.NEATIndividual
  Try to add a new gene (link) into the current genome.
mutateAddLinkProb - Variable in class ec.neat.NEATSpecies
  Probability of doing add-link mutation.
mutateAddNode(EvolutionState, int) - Method in class ec.neat.NEATIndividual
  Add a new node into this individual.
mutateAddNodeProb - Variable in class ec.neat.NEATSpecies
  Probability of doing add-node mutation.
MutateAllNodesPipeline - Class in ec.gp.breed
  MutateAllNodesPipeline implements the AllNodes mutation algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98.
MutateAllNodesPipeline() - Constructor for class ec.gp.breed.MutateAllNodesPipeline
MutateDemotePipeline - Class in ec.gp.breed
  MutateDemotePipeline works very similarly to the DemoteNode algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98, and is also similar to the "insertion" operator found in Una-May O'Reilly's thesis, "An Analysis of Genetic Programming".
MutateDemotePipeline() - Constructor for class ec.gp.breed.MutateDemotePipeline
mutateERC(EvolutionState, int) - Method in class ec.gp.ERC
  Mutates the node's "value".
MutateERCPipeline - Class in ec.gp.breed
  MutateERCPipeline works very similarly to the "Gaussian" algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98.
MutateERCPipeline() - Constructor for class ec.gp.breed.MutateERCPipeline
mutateERCs(GPNode, EvolutionState, int) - Method in class ec.gp.breed.MutateERCPipeline
mutateGeneReenable() - Method in class ec.neat.NEATIndividual
  Reenable a gene if it's disabled.
mutateGeneReenableProb - Variable in class ec.neat.NEATSpecies
  Probability of reenable a disabled gene.
mutateLinkWeights(EvolutionState, int, NEATSpecies, double, double, NEATSpecies.MutationType) - Method in class ec.neat.NEATIndividual
  Mutate the weights of the genes
mutateLinkWeightsProb - Variable in class ec.neat.NEATSpecies
  Probability of doing link weight mutate.
MutateOneNodePipeline - Class in ec.gp.breed
  MutateOneNodesPipeline implements the OneNode mutation algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98.
MutateOneNodePipeline() - Constructor for class ec.gp.breed.MutateOneNodePipeline
mutateOnlyProb - Variable in class ec.neat.NEATSpecies
  Probility of a non-mating reproduction.
MutatePromotePipeline - Class in ec.gp.breed
  MutatePromotePipeline works very similarly to the PromoteNode algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98, and is also similar to the "deletion" operator found in Una-May O'Reilly's thesis, "An Analysis of Genetic Programming".
MutatePromotePipeline() - Constructor for class ec.gp.breed.MutatePromotePipeline
MutateSwapPipeline - Class in ec.gp.breed
  MutateSwapPipeline works very similarly to the Swap algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98.
MutateSwapPipeline() - Constructor for class ec.gp.breed.MutateSwapPipeline
mutateToggleEnable(EvolutionState, int, int) - Method in class ec.neat.NEATIndividual
  Randomly enable or disable a gene.
mutateToggleEnableProb - Variable in class ec.neat.NEATSpecies
  Probability of changing the enable status of gene.
mutationDistributionIndex - Variable in class ec.vector.FloatVectorSpecies
  The distribution index for Polynomial Mutation, per gene.
mutationDistributionIndex(int) - Method in class ec.vector.FloatVectorSpecies
mutationIsBounded - Variable in class ec.vector.FloatVectorSpecies
  Whether mutation is bounded to the min- and max-gene values, per gene.
mutationIsBounded - Variable in class ec.vector.IntegerVectorSpecies
  Whether mutation is bounded to the min- and max-gene values, per gene.
mutationIsBounded(int) - Method in class ec.vector.FloatVectorSpecies
mutationIsBounded(int) - Method in class ec.vector.IntegerVectorSpecies
mutationNumber - Variable in class ec.neat.NEATGene
  The mutation number of this gene, Used to see how much mutation has changed.
MutationPipeline - Class in ec.gp.koza
  MutationPipeline is a GPBreedingPipeline which implements a strongly-typed version of the "Point Mutation" operator as described in Koza I.
MutationPipeline() - Constructor for class ec.gp.koza.MutationPipeline
mutationProbability - Variable in class ec.vector.VectorSpecies
  Probability that a gene will mutate, per gene.
mutationProbability(int) - Method in class ec.vector.VectorSpecies
mutationType - Variable in class ec.vector.BitVectorSpecies
  Mutation type, per gene.
mutationType - Variable in class ec.vector.FloatVectorSpecies
  Mutation type, per gene.
mutationType - Variable in class ec.vector.IntegerVectorSpecies
  Mutation type, per gene.
mutationType(int) - Method in class ec.vector.BitVectorSpecies
mutationType(int) - Method in class ec.vector.FloatVectorSpecies
mutationType(int) - Method in class ec.vector.IntegerVectorSpecies
mutDiffCoeff - Variable in class ec.neat.NEATSpecies
  Coefficient for mutational difference genes in compatibility computation.
mybase - Variable in class ec.BreedingPipeline
  My parameter base -- I keep it around so I can print some messages that are useful with it (not deep cloned)

## N

N_BUCKETS_DEFAULT - Static variable in class ec.parsimony.BucketTournamentSelection
  Default number of buckets
N_RULES - Static variable in class ec.rule.RuleSet
  The message to appear when printing the rule set
name - Variable in class ec.gp.ADF
  The "function name" of the ADF, to distinguish it from other GP functions you might provide.
name - Variable in class ec.gp.ADFArgument
  The "function name" of the ADFArgument, to distinguish it from other GP functions you might provide.
name - Variable in class ec.gp.GPFunctionSet
  Name of the GPFunctionSet
name - Variable in class ec.gp.GPNodeConstraints
  The name of the GPNodeConstraints object -- this is NOT the name of the GPNode
name - Variable in class ec.gp.GPTreeConstraints
name - Variable in class ec.gp.GPType
  The name of the type
name - Variable in class ec.rule.RuleConstraints
  The name of the RuleConstraints object
name - Variable in class ec.rule.RuleSetConstraints
  The name of the RuleSetConstraints object
name - Static variable in class ec.util.Version
name() - Method in class ec.gp.ADF
name() - Method in class ec.gp.ADFArgument
name() - Method in class ec.gp.ERC
  Returns the lowercase "name" of this ERC function class, some simple, short name which distinguishes this class from other ERC function classes you're using.
name() - Method in class ec.gp.GPNode
  Returns a Lisp-like atom for the node and any nodes of the same class.
name() - Method in class ec.gp.push.Terminal
NEATBreeder - Class in ec.neat
  NEATBreeder is a Breeder which overrides the breedPopulation method to first mark the individuals in each subspecies that are allow to reproduce, and replace the population with new individuals in each subspecies.
NEATBreeder() - Constructor for class ec.neat.NEATBreeder
NEATDefaults - Class in ec.neat
  NEATDefaults is the basic defaults class for the neat package.
NEATDefaults() - Constructor for class ec.neat.NEATDefaults
NEATGene - Class in ec.neat
  NEATGene is the combination of class Gene and class Link in original code.
NEATGene() - Constructor for class ec.neat.NEATGene
NEATIndividual - Class in ec.neat
  NEATIndividual is GeneVectorIndividual with NEATNetwork as phenotype.
NEATIndividual() - Constructor for class ec.neat.NEATIndividual
NEATInitializer - Class in ec.neat
  NEATInitializer is a SimpleInitializer which ensures that the subpopulations are all create from an existing template individual read from file.
NEATInitializer() - Constructor for class ec.neat.NEATInitializer
NEATInnovation - Class in ec.neat
  NEATInnovation is a class for recording the innovation information during the evolution of neat.
NEATInnovation() - Constructor for class ec.neat.NEATInnovation
NEATNetwork - Class in ec.neat
  NEATNetwork is the phenotype of NEATIndividual.
NEATNetwork() - Constructor for class ec.neat.NEATNetwork
NEATNode - Class in ec.neat
  NEATNode is the class to represent node in network, it stores status of the node in that network.
NEATNode() - Constructor for class ec.neat.NEATNode
NEATNode.FunctionType - Enum Class in ec.neat
  The activation function is used in for hidden node.
NEATNode.NodePlace - Enum Class in ec.neat
  The place this node could be.
NEATNode.NodeType - Enum Class in ec.neat
  The type of a node.
NEATSpecies - Class in ec.neat
  NEATSpecies is a GeneVectorSpecies which implements NEAT algorithm.
NEATSpecies() - Constructor for class ec.neat.NEATSpecies
NEATSpecies.MutationType - Enum Class in ec.neat
NEATSubspecies - Class in ec.neat
  NEATSubspecies is the actual Species in original code.
NEATSubspecies() - Constructor for class ec.neat.NEATSubspecies
neighborhood - Variable in class ec.pso.Particle
neighborhood - Variable in class ec.pso.PSOBreeder
neighborhoodBestFitness - Variable in class ec.pso.Particle
neighborhoodBestGenome - Variable in class ec.pso.Particle
neighborhoodSize - Variable in class ec.pso.PSOBreeder
networkPrototype - Variable in class ec.neat.NEATSpecies
  The prototypical network.
NEURON - Enum constant in enum class ec.neat.NEATNode.NodeType
newGenerationFirst() - Method in class ec.neat.NEATSubspecies
  Return the first individual in newGenIndividuals list.
newGenIndividuals - Variable in class ec.neat.NEATSubspecies
  The next generation individuals within this species
newIndividual(EvolutionState, int) - Method in class ec.eda.amalgam.AMALGAMSpecies
newIndividual(EvolutionState, int) - Method in class ec.eda.cmaes.CMAESSpecies
newIndividual(EvolutionState, int) - Method in class ec.eda.pbil.PBILSpecies
newIndividual(EvolutionState, int) - Method in class ec.gp.ge.GESpecies
  This is an ugly hack to simulate the "Sensible Initialization", First we create a GPIndividual, then reverse-map it to GEIndividuals, We do not need to call IntegerVectorSpecies.newIndividual() since it is overriden by the GPSpecies.newIndividual(); Moreover, as in the case for non-identical representations (i,e, GP-GE island models etc,), the grammar rules, tree constraints, ERC's etc, are supposed to be identical across all islands, so we are using the same "gpspecies" inside this class.
newIndividual(EvolutionState, int) - Method in class ec.gp.GPSpecies
newIndividual(EvolutionState, int) - Method in class ec.rule.RuleSpecies
newIndividual(EvolutionState, int) - Method in class ec.Species
  Provides a brand-new individual to fill in a population.
newIndividual(EvolutionState, int) - Method in class ec.vector.VectorSpecies
newIndividual(EvolutionState, int, ArrayList<NEATNode>, ArrayList<Gene>) - Method in class ec.neat.NEATSpecies
  Create a new individual with given nodes and genes
newIndividual(EvolutionState, DataInput) - Method in class ec.gp.GPSpecies
newIndividual(EvolutionState, DataInput) - Method in class ec.Species
  Provides an individual read from a DataInput source, including the fitness.
newIndividual(EvolutionState, LineNumberReader) - Method in class ec.gp.GPSpecies
newIndividual(EvolutionState, LineNumberReader) - Method in class ec.Species
  Provides an individual read from a stream, including the fitness; the individual will appear as it was written by printIndividual(...).
newIndividuals - Variable in class ec.es.MuCommaLambdaBreeder
newIndividuals - Variable in class ec.simple.SimpleBreeder
newLinkTries - Variable in class ec.neat.NEATSpecies
  Number of tries mutateAddLink will attempt to find an open link.
newNodeId - Variable in class ec.neat.NEATInnovation
  If a new node was created, this is its node id.
newNodeTries - Variable in class ec.neat.NEATSpecies
  Number of tries mutateAddNode will attempt to build a new node.
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.build.PTC1
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.build.PTC2
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.build.RandomBranch
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.build.RandTree
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.build.Uniform
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.GPNodeBuilder
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.koza.FullBuilder
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.koza.GrowBuilder
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.koza.HalfBuilder
newRootedTree(EvolutionState, GPType, int, GPNodeParent, GPFunctionSet, int, int) - Method in class ec.gp.push.PushBuilder
newWeight - Variable in class ec.neat.NEATInnovation
  If a link is added, this is its weight.
next(int) - Method in class ec.util.MersenneTwister
  Returns an integer with bits bits filled with a random number.
nextBoolean() - Method in class ec.util.MersenneTwister
  This method is missing from jdk 1.0.x and below.
nextBoolean() - Method in class ec.util.MersenneTwisterFast
nextBoolean(double) - Method in class ec.util.MersenneTwister
  This generates a coin flip with a probability `probability` of returning true, else returning false.
nextBoolean(double) - Method in class ec.util.MersenneTwisterFast
  This generates a coin flip with a probability `probability` of returning true, else returning false.
nextBoolean(float) - Method in class ec.util.MersenneTwister
  This generates a coin flip with a probability `probability` of returning true, else returning false.
nextBoolean(float) - Method in class ec.util.MersenneTwisterFast
  This generates a coin flip with a probability `probability` of returning true, else returning false.
nextByte() - Method in class ec.util.MersenneTwister
  For completeness' sake, though it's not in java.util.Random.
nextByte() - Method in class ec.util.MersenneTwisterFast
nextBytes(byte[]) - Method in class ec.util.MersenneTwister
  A bug fix for all versions of the JDK.
nextBytes(byte[]) - Method in class ec.util.MersenneTwisterFast
nextChar() - Method in class ec.util.MersenneTwister
  For completeness' sake, though it's not in java.util.Random.
nextChar() - Method in class ec.util.MersenneTwisterFast
nextDouble() - Method in class ec.util.MersenneTwister
  A bug fix for versions of JDK 1.1 and below.
nextDouble() - Method in class ec.util.MersenneTwisterFast
  Returns a random double in the half-open range from [0.0,1.0).
nextDouble(boolean, boolean) - Method in class ec.util.MersenneTwister
  Returns a double in the range from 0.0 to 1.0, possibly inclusive of 0.0 and 1.0 themselves.
nextDouble(boolean, boolean) - Method in class ec.util.MersenneTwisterFast
  Returns a double in the range from 0.0 to 1.0, possibly inclusive of 0.0 and 1.0 themselves.
nextFloat() - Method in class ec.util.MersenneTwister
  A bug fix for versions of JDK 1.1 and below.
nextFloat() - Method in class ec.util.MersenneTwisterFast
  Returns a random float in the half-open range from [0.0f,1.0f).
nextFloat(boolean, boolean) - Method in class ec.util.MersenneTwister
  Returns a float in the range from 0.0f to 1.0f, possibly inclusive of 0.0f and 1.0f themselves.
nextFloat(boolean, boolean) - Method in class ec.util.MersenneTwisterFast
  Returns a float in the range from 0.0f to 1.0f, possibly inclusive of 0.0f and 1.0f themselves.
nextGaussian() - Method in class ec.util.MersenneTwister
  A bug fix for all JDK code including 1.2.
nextGaussian() - Method in class ec.util.MersenneTwisterFast
nextInnovationNumber() - Method in class ec.neat.NEATSpecies
nextInt() - Method in class ec.util.MersenneTwisterFast
nextInt(int) - Method in class ec.util.MersenneTwister
  This method is missing from JDK 1.1 and below.
nextInt(int) - Method in class ec.util.MersenneTwisterFast
  Returns an integer drawn uniformly from 0 to n-1.
nextLong() - Method in class ec.util.MersenneTwisterFast
  Returns a long drawn uniformly from 0 to n-1.
nextLong(long) - Method in class ec.util.MersenneTwister
  This method is for completness' sake.
nextLong(long) - Method in class ec.util.MersenneTwisterFast
  Returns a long drawn uniformly from 0 to n-1.
nextShort() - Method in class ec.util.MersenneTwister
  For completeness' sake, though it's not in java.util.Random.
nextShort() - Method in class ec.util.MersenneTwisterFast
nextSubpopulationSize(EvolutionState, int) - Method in class ec.simple.SimpleBreeder
  Returns the next subpopulation size.
nextToken() - Method in class ec.util.Lexer
  Returns the next token as a string.
nextToken(boolean) - Method in class ec.util.Lexer
  Returns the next token as a string.
NO_LOGS - Static variable in class ec.util.Output
  When passed to print functions, doesn't do any printing
NO_PROBABILITY - Static variable in class ec.BreedingSource
NO_SIZE_LIMIT - Static variable in class ec.gp.koza.CrossoverPipeline
NO_SIZE_LIMIT - Static variable in class ec.gp.koza.MutationPipeline
NO_TREENUM - Static variable in class ec.gp.GPTree
nodeConstraintRepository - Variable in class ec.gp.GPInitializer
nodeConstraints - Variable in class ec.gp.GPInitializer
nodeEquals(GPNode) - Method in class ec.gp.ADF
  Determines node equality by comparing the class, associated tree, and function name of the nodes.
nodeEquals(GPNode) - Method in class ec.gp.ERC
  Implement this to do ERC-to-ERC comparisons.
nodeEquals(GPNode) - Method in class ec.gp.GPNode
  Returns true if I am the "genetically" identical to this node, and our children arrays are the same length, though we may have different parents and children.
nodeEquals(GPNode) - Method in class ec.gp.push.Terminal
nodeEquivalentTo(GPNode) - Method in class ec.gp.GPNode
  Returns true if I and the provided node are the same kind of node -- that is, we could have both been cloned() and reset() from the same prototype node.
nodeHashCode() - Method in class ec.gp.ADF
  Returns name.hashCode() + class.hashCode() + associatedTree.
nodeHashCode() - Method in class ec.gp.ERC
  Implement this to hash ERCs, along with other nodes, in such a way that two "equal" ERCs will usually hash to the same value.
nodeHashCode() - Method in class ec.gp.GPNode
  Returns a hashcode usually associated with all nodes that are equal to you (using nodeEquals(...)).
nodeId - Variable in class ec.neat.NEATNode
  Node id for this node.
nodeInPosition(int, int) - Method in class ec.gp.GPNode
  Returns the p'th node, constrained by nodesearch, in the subtree for which this GPNode is root.
nodeInPosition(int, GPNodeGatherer) - Method in class ec.gp.GPNode
  Returns the p'th node, constrained by nodesearch, in the subtree for which this GPNode is root.
nodePrototype - Variable in class ec.neat.NEATSpecies
  The prototypical node for individuals in this species.
nodes - Variable in class ec.gp.GPFunctionSet
  The nodes that our GPTree can use: nodes[type][thenodes].
nodes - Variable in class ec.gp.koza.KozaNodeSelector
  The number of nodes in the tree, -1 if unknown.
nodes - Variable in class ec.neat.NEATIndividual
  All the node of this individual.
nodes - Variable in class ec.neat.NEATNetwork
  A list of all nodes for this network.
nodes_h - Variable in class ec.gp.GPFunctionSet
  The nodes that our GPTree can use: arrays of nodes hashed by type.
nodesByArity - Variable in class ec.gp.GPFunctionSet
  Nodes == a given arity, that is: nodesByArity[type][arity][thenodes]
nodesByName - Variable in class ec.gp.GPFunctionSet
  The nodes that our GPTree can use, hashed by name().
NODESEARCH_ALL - Static variable in class ec.gp.GPNode
NODESEARCH_NONTERMINALS - Static variable in class ec.gp.GPNode
NODESEARCH_TERMINALS - Static variable in class ec.gp.GPNode
nodeselect - Variable in class ec.gp.breed.MutateAllNodesPipeline
  How the pipeline chooses a subtree to mutate
nodeselect - Variable in class ec.gp.breed.MutateERCPipeline
  How the pipeline chooses a subtree to mutate
nodeselect - Variable in class ec.gp.breed.MutateOneNodePipeline
  How the pipeline chooses a subtree to mutate
nodeselect - Variable in class ec.gp.koza.MutationPipeline
  How the pipeline chooses a subtree to mutate
nodeselect0 - Variable in class ec.gp.breed.InternalCrossoverPipeline
  How the pipeline chooses the first subtree
nodeselect1 - Variable in class ec.gp.breed.InternalCrossoverPipeline
  How the pipeline chooses the second subtree
nodeselect1 - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  How the pipeline selects a node from individual 1
nodeselect1 - Variable in class ec.gp.koza.CrossoverPipeline
  How the pipeline selects a node from individual 1
nodeselect2 - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  How the pipeline selects a node from individual 2
nodeselect2 - Variable in class ec.gp.koza.CrossoverPipeline
  How the pipeline selects a node from individual 2
noImprovementStretch - Variable in class ec.eda.amalgam.AMALGAMSpecies
Nonterminal - Class in ec.gp.push
  ECJ implements Push's s-expressions as trees of nonterminals and terminals.
Nonterminal() - Constructor for class ec.gp.push.Nonterminal
nonterminalProbabilities(int) - Method in class ec.gp.build.PTCFunctionSet
nonterminalProbabilities(int) - Method in interface ec.gp.build.PTCFunctionSetForm
  Returns an organized distribution (see ec.util.RandomChoice) of likelihoods that various nonterminals in the function set will be chosen over other nonterminals with the same return type.
nonterminalProbability - Variable in class ec.gp.koza.KozaNodeSelector
  The probability a nonterminal must be chosen.
nonterminals - Variable in class ec.gp.GPFunctionSet
  The nonterminals our GPTree can use: nonterminals[type][thenodes].
nonterminals - Variable in class ec.gp.koza.KozaNodeSelector
  The number of nonterminals in the tree, -1 if unknown.
nonterminals_h - Variable in class ec.gp.GPFunctionSet
  The nonterminals our GPTree can use: arrays of nonterminals hashed by type.
nonterminalSelectionProbabilities(int) - Method in class ec.gp.build.PTCFunctionSet
nonterminalSelectionProbabilities(int) - Method in interface ec.gp.build.PTCFunctionSetForm
  Returns an array (by return type) of the probability that PTC1 must pick a nonterminal over a terminal in order to guarantee the expectedTreeSize.
nonterminalsOverArity - Variable in class ec.gp.GPFunctionSet
  Nonterminals >= a given arity, that is: nonterminalsOverArity[type][arity][thenodes] -- this will be O(n^2).
nonterminalsUnderArity - Variable in class ec.gp.GPFunctionSet
  Nonterminals invalid input: '<'= a given arity, that is: nonterminalsUnderArity[type][arity][thenodes] -- this will be O(n^2).
NOSIZEGIVEN - Static variable in class ec.gp.GPNodeBuilder
  Produces a new rooted tree of GPNodes whose root's return type is swap-compatible with type.
NOT_SET - Static variable in class ec.select.BestSelection
NOT_SET - Static variable in class ec.simple.SimpleBreeder
notifyMonitor(Object) - Method in class ec.eval.SlaveMonitor
NSGA2_RANK_PREAMBLE - Static variable in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
NSGA2_SPARSITY_PREAMBLE - Static variable in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
NSGA2Breeder - Class in ec.multiobjective.nsga2
  This SimpleBreeder subclass breeds a set of children from the Population, then joins the original Population with the children in a (mu+mu) fashion.
NSGA2Breeder() - Constructor for class ec.multiobjective.nsga2.NSGA2Breeder
NSGA2Breeder.BreedingState - Enum Class in ec.multiobjective.nsga2
  We use a state variable to make sure that the nextSubpopulationSize() method is only called at the appropriate time.
NSGA2MultiObjectiveFitness - Class in ec.multiobjective.nsga2
  NSGA2MultiObjectiveFitness is a subclass of MultiObjeciveFitness which adds auxiliary fitness measures (sparsity, rank) largely used by MultiObjectiveStatistics.
NSGA2MultiObjectiveFitness() - Constructor for class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
NUM_INDIVIDUALS_PREAMBLE - Static variable in class ec.Subpopulation
NUM_SOURCES - Static variable in class ec.breed.BufferedBreedingPipeline
NUM_SOURCES - Static variable in class ec.breed.CheckingPipeline
NUM_SOURCES - Static variable in class ec.breed.FirstCopyPipeline
NUM_SOURCES - Static variable in class ec.breed.GenerationSwitchPipeline
NUM_SOURCES - Static variable in class ec.breed.InitializationPipeline
NUM_SOURCES - Static variable in class ec.breed.RepeatPipeline
NUM_SOURCES - Static variable in class ec.breed.ReproductionPipeline
NUM_SOURCES - Static variable in class ec.breed.UniquePipeline
NUM_SOURCES - Static variable in class ec.gp.breed.InternalCrossoverPipeline
NUM_SOURCES - Static variable in class ec.gp.breed.MutateAllNodesPipeline
NUM_SOURCES - Static variable in class ec.gp.breed.MutateDemotePipeline
NUM_SOURCES - Static variable in class ec.gp.breed.MutateERCPipeline
NUM_SOURCES - Static variable in class ec.gp.breed.MutateOneNodePipeline
NUM_SOURCES - Static variable in class ec.gp.breed.MutatePromotePipeline
NUM_SOURCES - Static variable in class ec.gp.breed.MutateSwapPipeline
NUM_SOURCES - Static variable in class ec.gp.breed.RehangPipeline
NUM_SOURCES - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
NUM_SOURCES - Static variable in class ec.gp.koza.CrossoverPipeline
NUM_SOURCES - Static variable in class ec.gp.koza.MutationPipeline
NUM_SOURCES - Static variable in class ec.rule.breed.RuleCrossoverPipeline
NUM_SOURCES - Static variable in class ec.rule.breed.RuleMutationPipeline
NUM_SOURCES - Static variable in class ec.vector.breed.GeneDuplicationPipeline
NUM_SOURCES - Static variable in class ec.vector.breed.ListCrossoverPipeline
NUM_SOURCES - Static variable in class ec.vector.breed.VectorCrossoverPipeline
NUM_SOURCES - Static variable in class ec.vector.breed.VectorMutationPipeline
NUM_SUBPOPS_PREAMBLE - Static variable in class ec.Population
numAtomicTypes - Variable in class ec.gp.GPInitializer
numCharts - Variable in class ec.display.StatisticsChartPane
numChildPermutations(GPInitializer, int, GPNode, int, int, int) - Method in class ec.gp.build.Uniform
NUMCHILDPERMUTATIONS - Variable in class ec.gp.build.Uniform
numComponents() - Method in class ec.eval.MasterProblem
numCurrent - Variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
numDuplicateRetries - Variable in class ec.breed.UniquePipeline
numDuplicateRetries - Variable in class ec.Subpopulation
  Do we allow duplicates?
numElites(EvolutionState, int) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
numElites(EvolutionState, int) - Method in class ec.multiobjective.spea2.SPEA2Breeder
  Return the number of individuals that we aim to see in the elitist archive.
numElites(EvolutionState, int) - Method in class ec.simple.SimpleBreeder
NUMERIC_CONSTANT - Static variable in class ec.gp.ge.GrammarParser
numEvaluations - Variable in class ec.EvolutionState
  The number of evaluations the evolutionary computation system will run until it ends (up to the next generation boundary), or UNDEFINED
numfuncnodes - Variable in class ec.gp.build.Uniform
numGenerations - Variable in class ec.EvolutionState
  The number of generations the evolutionary computation system will run until it ends, or UNDEFINED
numGuru - Variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
numInds - Variable in class ec.breed.ForceBreedingPipeline
numLogs() - Method in class ec.util.Output
  Returns the number of logs currently posted.
numNodeConstraints - Variable in class ec.gp.GPInitializer
numNodes(int) - Method in class ec.gp.GPNode
  Returns the number of nodes, constrained by nodesearch, in the subtree for which this GPNode is root.
numNodes(GPNodeGatherer) - Method in class ec.gp.GPNode
  Returns the number of nodes, constrained by g.test(...) in the subtree for which this GPNode is root.
numObjs - Variable in class ec.util.IntBag
numOfObservations - Variable in class ec.eda.dovs.DOVSFitness
  Number of evaluation have been performed on this individual.
numOfObservations() - Method in class ec.eda.dovs.DOVSFitness
  Return the number of simulation have done with current individual.
numOfTotalSamples - Variable in class ec.eda.dovs.DOVSSpecies
  This is for future using.
numPrev - Variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
numRead() - Method in class ec.util.DataPipe
  Returns the number of elements read from the buffer so far (after the last reset()).
numRuleConstraints - Variable in class ec.rule.RuleInitializer
numRules - Variable in class ec.rule.RuleSet
  How many rules are there used in the rules array
numRules() - Method in class ec.rule.RuleSet
  How many rules are there used in the rules array
numRuleSetConstraints - Variable in class ec.rule.RuleInitializer
numRulesForReset(RuleSet, EvolutionState, int) - Method in class ec.rule.RuleSetConstraints
  Returns a stochastic value picked to specify the number of rules to generate when calling reset() on this kind of Rule.
numSetTypes - Variable in class ec.gp.GPInitializer
numShuffled - Variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
numSources() - Method in class ec.breed.BufferedBreedingPipeline
numSources() - Method in class ec.breed.CheckingPipeline
numSources() - Method in class ec.breed.FirstCopyPipeline
numSources() - Method in class ec.breed.ForceBreedingPipeline
numSources() - Method in class ec.breed.GenerationSwitchPipeline
numSources() - Method in class ec.breed.InitializationPipeline
numSources() - Method in class ec.breed.MultiBreedingPipeline
numSources() - Method in class ec.breed.RepeatPipeline
numSources() - Method in class ec.breed.ReproductionPipeline
numSources() - Method in class ec.breed.UniquePipeline
numSources() - Method in class ec.BreedingPipeline
  Returns the number of sources to this pipeline.
numSources() - Method in class ec.gp.breed.InternalCrossoverPipeline
numSources() - Method in class ec.gp.breed.MutateAllNodesPipeline
numSources() - Method in class ec.gp.breed.MutateDemotePipeline
numSources() - Method in class ec.gp.breed.MutateERCPipeline
numSources() - Method in class ec.gp.breed.MutateOneNodePipeline
numSources() - Method in class ec.gp.breed.MutatePromotePipeline
numSources() - Method in class ec.gp.breed.MutateSwapPipeline
numSources() - Method in class ec.gp.breed.RehangPipeline
numSources() - Method in class ec.gp.breed.SizeFairCrossoverPipeline
numSources() - Method in class ec.gp.koza.CrossoverPipeline
numSources() - Method in class ec.gp.koza.MutationPipeline
numSources() - Method in class ec.rule.breed.RuleCrossoverPipeline
  Returns 2
numSources() - Method in class ec.rule.breed.RuleMutationPipeline
  Returns 1
numSources() - Method in class ec.vector.breed.GeneDuplicationPipeline
numSources() - Method in class ec.vector.breed.ListCrossoverPipeline
numSources() - Method in class ec.vector.breed.MultipleVectorCrossoverPipeline
  Returns the number of parents
numSources() - Method in class ec.vector.breed.VectorCrossoverPipeline
  Returns 2
numSources() - Method in class ec.vector.breed.VectorMutationPipeline
  Returns 1
numTests - Variable in class ec.simple.SimpleEvaluator
numTreeConstraints - Variable in class ec.gp.GPInitializer
numTreesOfType(GPInitializer, int, int, int) - Method in class ec.gp.build.Uniform
NUMTREESOFTYPE - Variable in class ec.gp.build.Uniform
numTreesRootedByNode(GPInitializer, int, GPNode, int) - Method in class ec.gp.build.Uniform
NUMTREESROOTEDBYNODE - Variable in class ec.gp.build.Uniform
numTries - Variable in class ec.gp.breed.InternalCrossoverPipeline
  How many times the pipeline attempts to pick nodes until it gives up.
numTries - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  How many times the pipeline attempts to pick nodes until it gives up.
numTries - Variable in class ec.gp.koza.CrossoverPipeline
  How many times the pipeline attempts to pick nodes until it gives up.
numTries - Variable in class ec.vector.breed.ListCrossoverPipeline
numWritten() - Method in class ec.util.DataPipe
  Returns the number of elements written to the buffer so far (after the last reset()).

## O

objectives - Variable in class ec.multiobjective.MultiObjectiveFitness
  The various fitnesses.
objs - Variable in class ec.util.IntBag
obtainERC(EvolutionState, int, int, GPNode, HashMap) - Method in class ec.gp.ge.GESpecies
  Loads an ERC from the ERCBank given the value in the genome.
offset - Variable in class ec.exchange.IslandExchange
  after how many generations to start sending individuals
offset - Variable in class ec.select.SUSSelection
  The floating point value to consider for the next selected individual.
OKAY - Static variable in class ec.exchange.IslandExchange
  Okay signal
oldInnovationNum - Variable in class ec.neat.NEATInnovation
  If a new node was created, this is the innovation number of the gene's link it is being stuck inside.
oneShot - Static variable in class ec.eval.Slave
onStack - Variable in class ec.gp.ADFStack
onSubstack - Variable in class ec.gp.ADFStack
optimalIndex - Variable in class ec.eda.dovs.DOVSSpecies
  This integer indicate the index of optimal individual in the visited array.
organizeDistribution(double[]) - Static method in class ec.util.RandomChoice
  Same as organizeDistribution(probabilities, false);
organizeDistribution(double[], boolean) - Static method in class ec.util.RandomChoice
  Normalizes probabilities, then converts them into continuing sums.
organizeDistribution(float[]) - Static method in class ec.util.RandomChoice
  Same as organizeDistribution(probabilities, false);
organizeDistribution(float[], boolean) - Static method in class ec.util.RandomChoice
  Normalizes probabilities, then converts them into continuing sums.
organizeDistribution(Object[], RandomChoiceChooser) - Static method in class ec.util.RandomChoice
  Same as organizeDistribution(objs, chooser, false);
organizeDistribution(Object[], RandomChoiceChooserD) - Static method in class ec.util.RandomChoice
  Same as organizeDistribution(objs, chooser, false);
organizeDistribution(Object[], RandomChoiceChooserD, boolean) - Static method in class ec.util.RandomChoice
  Normalizes the probabilities associated with an array of objects, then converts them into continuing sums.
organizeDistribution(Object[], RandomChoiceChooser, boolean) - Static method in class ec.util.RandomChoice
  Normalizes the probabilities associated with an array of objects, then converts them into continuing sums.
outgoingIds - Variable in class ec.exchange.IslandExchange
outNode - Variable in class ec.neat.NEATGene
  The actual out node this gene connect to.
outNodeId - Variable in class ec.neat.NEATGene
  The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.
outNodeId - Variable in class ec.neat.NEATInnovation
  Two nodes specify where the link innovation took place : this is the output node.
outOfBoundsRetries - Variable in class ec.vector.FloatVectorSpecies
  The number of times Polynomial Mutation or Gaussian Mutation retry for valid numbers until they get one.
outOfRangeRetryLimitReached(EvolutionState) - Method in class ec.vector.FloatVectorSpecies
output - Variable in class ec.EvolutionState
  The output and logging facility (threadsafe).
output - Variable in class ec.util.DataPipe
  The output stream
Output - Class in ec.util
  Outputs and logs system messages, errors, and other various items printed as a result of a run.
Output(boolean) - Constructor for class ec.util.Output
  Creates a new, verbose, empty Output object.
Output(boolean, int) - Constructor for class ec.util.Output
  Creates a new, verbose, empty Output object.
OUTPUT - Enum constant in enum class ec.neat.NEATNode.NodePlace
Output.OutputExitException - Exception Class in ec.util
OutputException - Exception Class in ec.util
  Thrown whenever a problem occurs when attempting to output to a Log.
OutputException(String) - Constructor for exception class ec.util.OutputException
OutputExitException(String) - Constructor for exception class ec.util.Output.OutputExitException
outputOff() - Method in class ec.neat.NEATNetwork
  Check if not all output are active.
outputs - Variable in class ec.neat.NEATNetwork
  A list of output nodes for this network.
override - Variable in class ec.neat.NEATNode
  Indicates if the value of current node has been override by method other than network's activation.
overrideOutput(double) - Method in class ec.neat.NEATNode
  Force an output value on the node.
overrideValue - Variable in class ec.neat.NEATNode
  Contains the activation value that will override this node's activation.
owner - Variable in class ec.gp.GPTree
  the owner of the GPTree
ownId - Variable in class ec.exchange.IslandExchange
  the id of the current island

## P

P_A - Static variable in class ec.eda.dovs.DOVSSpecies
p_add - Variable in class ec.rule.RuleSetConstraints
P_ADD_NODE_MAX_GENOME_LENGTH - Static variable in class ec.neat.NEATSpecies
P_ADD_PROB - Static variable in class ec.rule.RuleSetConstraints
P_ADF - Static variable in class ec.gp.ADF
P_ADF - Static variable in class ec.gp.ADFStack
P_ADFARGUMENT - Static variable in class ec.gp.ADFArgument
P_ADFCONTEXT - Static variable in class ec.gp.ADFContext
P_ADFSTACK - Static variable in class ec.gp.ADFStack
P_AGE_SIGNIFICANCE - Static variable in class ec.neat.NEATSpecies
P_ALPHA - Static variable in class ec.eda.pbil.PBILSpecies
P_ALPHA_AMS - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_ALTERNATIVE_GENERATOR - Static variable in class ec.eda.cmaes.CMAESSpecies
P_ALTERNATIVE_GENERATOR_TRIES - Static variable in class ec.eda.cmaes.CMAESSpecies
P_ALTERNATIVE_TERMINATION - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_ALTERNATIVE_TERMINATION - Static variable in class ec.eda.cmaes.CMAESSpecies
P_AMALGAM - Static variable in class ec.eda.amalgam.AMALGAMDefaults
P_AMALGAM_SPECIES - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_ANNEALED - Static variable in class ec.select.AnnealedSelection
  Default base
P_ARGUMENT - Static variable in class ec.gp.ADFArgument
P_ASSOCIATEDTREE - Static variable in class ec.gp.ADF
P_ATOMIC - Static variable in class ec.gp.GPInitializer
P_B - Static variable in class ec.eda.dovs.DOVSSpecies
P_B - Static variable in class ec.eda.pbil.PBILSpecies
P_BABIES_STOLEN - Static variable in class ec.neat.NEATSpecies
P_BEST - Static variable in class ec.select.BestSelection
  Default base
P_BITVECTORINDIVIDUAL - Static variable in class ec.vector.BitVectorIndividual
P_BOLTZMANN - Static variable in class ec.select.BoltzmannSelection
  Default base
P_BREED - Static variable in class ec.breed.BreedDefaults
P_BREED - Static variable in class ec.gp.breed.GPBreedDefaults
P_BREEDER - Static variable in class ec.EvolutionState
P_BREEDTHREADS - Static variable in class ec.Evolve
  breedthreads parameter
P_BUCKETS - Static variable in class ec.parsimony.BucketTournamentSelection
  The number of buckets
P_BUFFERED - Static variable in class ec.breed.BufferedBreedingPipeline
P_BUFSIZE - Static variable in class ec.breed.BufferedBreedingPipeline
P_BUILD - Static variable in class ec.gp.build.GPBuildDefaults
P_BUILDER - Static variable in class ec.gp.koza.MutationPipeline
P_BYTEVECTORINDIVIDUAL - Static variable in class ec.vector.ByteVectorIndividual
P_C1 - Static variable in class ec.eda.cmaes.CMAESSpecies
P_CACHE - Static variable in class ec.select.AnnealedSelection
P_CACHE - Static variable in class ec.select.TopSelection
P_CC - Static variable in class ec.eda.cmaes.CMAESSpecies
P_CHATTY - Static variable in class ec.exchange.InterPopulationExchange
  Whether or not we're chatty
P_CHATTY - Static variable in class ec.exchange.IslandExchange
  Whether or not we're chatty
P_CHECK - Static variable in class ec.breed.CheckingPipeline
P_CHECKPOINT - Static variable in class ec.EvolutionState
P_CHECKPOINTDIRECTORY - Static variable in class ec.EvolutionState
P_CHECKPOINTMODULO - Static variable in class ec.EvolutionState
P_CHECKPOINTPREFIX - Static variable in class ec.EvolutionState
P_CHILD - Static variable in class ec.gp.GPNodeConstraints
P_CHILD - Static variable in class ec.Statistics
P_CHUNK_SIZE - Static variable in class ec.simple.SimpleEvaluator
P_CHUNKSIZE - Static variable in class ec.vector.VectorSpecies
P_CLIENT_PORT - Static variable in class ec.exchange.IslandExchange
  The client port
P_CLONE_PIPELINE_AND_POPULATION - Static variable in class ec.simple.SimpleBreeder
P_CLONE_PROBLEM - Static variable in class ec.simple.SimpleEvaluator
P_CMAES - Static variable in class ec.eda.cmaes.CMAESDefaults
P_CMAES_SPECIES - Static variable in class ec.eda.cmaes.CMAESSpecies
P_CMU - Static variable in class ec.eda.cmaes.CMAESSpecies
P_COMPAT_THRESH - Static variable in class ec.neat.NEATSpecies
P_COMPETE_STYLE - Static variable in class ec.coevolve.CompetitiveEvaluator
P_COMPRESS - Static variable in class ec.simple.SimpleShortStatistics
P_COMPRESS - Static variable in class ec.simple.SimpleStatistics
  compress?
P_COMPRESSED_COMMUNICATION - Static variable in class ec.exchange.IslandExchange
  Whether the communication is compressed or not
P_CONSTRAINTS - Static variable in class ec.rule.Rule
P_CONSTRAINTS - Static variable in class ec.rule.RuleSet
  The constraint for the rule set
P_CONSTRAINTS_SIZE - Static variable in class ec.eda.dovs.DOVSSpecies
P_CONTEXT - Static variable in class ec.gp.ADFStack
P_COOLING_RATE - Static variable in class ec.select.BoltzmannSelection
  Cooling rate parameter
P_COVARIANCE - Static variable in class ec.eda.cmaes.CMAESSpecies
P_Cr - Static variable in class ec.de.DEBreeder
P_CROSSOVER - Static variable in class ec.gp.koza.CrossoverPipeline
P_CROSSOVER - Static variable in class ec.rule.breed.RuleCrossoverPipeline
P_CROSSOVER - Static variable in class ec.vector.breed.MultipleVectorCrossoverPipeline
  default base
P_CROSSOVER - Static variable in class ec.vector.breed.VectorCrossoverPipeline
P_CROSSOVER_DISTRIBUTION_INDEX - Static variable in class ec.vector.VectorSpecies
P_CROSSOVERPROB - Static variable in class ec.rule.breed.RuleCrossoverPipeline
P_CROSSOVERPROB - Static variable in class ec.vector.VectorSpecies
P_CROSSOVERTYPE - Static variable in class ec.vector.VectorSpecies
P_CS - Static variable in class ec.eda.cmaes.CMAESSpecies
P_CUTDOWN - Static variable in class ec.select.AnnealedSelection
P_DAMPS - Static variable in class ec.eda.cmaes.CMAESSpecies
P_DATA - Static variable in class ec.gp.GPProblem
p_database - Variable in class ec.eval.MetaProblem
  A prototypical parameter database for the underlying (base-level) evolutionary computation system.
P_DEBUG_INFO - Static variable in class ec.eval.MasterProblem
P_DEFAULT_SUBPOP - Static variable in class ec.Population
p_del - Variable in class ec.rule.RuleSetConstraints
P_DEL_PROB - Static variable in class ec.rule.RuleSetConstraints
P_DELIMITER - Static variable in class ec.simple.SimpleShortStatistics
P_DELTA_AMS - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_DESELECTOR - Static variable in class ec.steadystate.SteadyStateBreeder
P_DEST - Static variable in class ec.exchange.InterPopulationExchange
  The prefix for destinations
P_DEST_FOR_SUBPOP - Static variable in class ec.exchange.InterPopulationExchange
  The number of destinations from current island
P_DISJOINT_COEFF - Static variable in class ec.neat.NEATSpecies
P_DO_DEPTH - Static variable in class ec.gp.koza.KozaShortStatistics
P_DO_DESCRIPTION - Static variable in class ec.simple.SimpleStatistics
P_DO_FINAL - Static variable in class ec.simple.SimpleStatistics
P_DO_GENERATION - Static variable in class ec.simple.SimpleStatistics
P_DO_HEADER - Static variable in class ec.simple.SimpleShortStatistics
P_DO_HYPERVOLUME - Static variable in class ec.multiobjective.MultiObjectiveStatistics
P_DO_MESSAGE - Static variable in class ec.simple.SimpleStatistics
P_DO_PER_GENERATION_DESCRIPTION - Static variable in class ec.simple.SimpleStatistics
P_DO_SIZE - Static variable in class ec.simple.SimpleShortStatistics
P_DO_SUBPOPS - Static variable in class ec.simple.SimpleShortStatistics
P_DO_TIME - Static variable in class ec.simple.SimpleShortStatistics
P_DOLENGTHFIRST - Static variable in class ec.parsimony.DoubleTournamentSelection
P_DOUBLEVECTORINDIVIDUAL - Static variable in class ec.vector.DoubleVectorIndividual
P_DOVS - Static variable in class ec.eda.dovs.DOVSDefaults
P_DOVS_SPECIES - Static variable in class ec.eda.dovs.DOVSSpecies
P_DROPOFF_AGE - Static variable in class ec.neat.NEATSpecies
P_DUPLICATE_RETRIES - Static variable in class ec.vector.VectorSpecies
P_DUPLICATION - Static variable in class ec.vector.breed.GeneDuplicationPipeline
P_EC - Static variable in class ec.ECDefaults
P_ELITE - Static variable in class ec.simple.SimpleBreeder
P_ELITE_FRAC - Static variable in class ec.simple.SimpleBreeder
P_EMPTY_AT_GEN - Static variable in class ec.steadystate.SteadyStateEvolutionState
P_EQUALSIZE - Static variable in class ec.gp.koza.MutationPipeline
P_ES - Static variable in class ec.es.ESDefaults
P_ESSELECT - Static variable in class ec.es.ESSelection
P_ETA_DEC - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_ETA_SHIFT - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_ETA_SIGMA - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_EVALCOMPRESSION - Static variable in class ec.eval.Slave
P_EVALCOMPRESSION - Static variable in class ec.eval.SlaveMonitor
P_EVALMASTERHOST - Static variable in class ec.eval.Slave
P_EVALMASTERPORT - Static variable in class ec.eval.Slave
P_EVALMASTERPORT - Static variable in class ec.eval.SlaveMonitor
P_EVALNODELAY - Static variable in class ec.eval.Slave
P_EVALNODELAY - Static variable in class ec.eval.SlaveMonitor
P_EVALRECVBUFFER - Static variable in class ec.eval.Slave
P_EVALRECVBUFFER - Static variable in class ec.eval.SlaveMonitor
P_EVALSENDBUFER - Static variable in class ec.eval.Slave
P_EVALSENDBUFER - Static variable in class ec.eval.SlaveMonitor
P_EVALSLAVENAME - Static variable in class ec.eval.Slave
P_EVALTHREADS - Static variable in class ec.Evolve
  evalthreads parameter
P_EVALUATIONS - Static variable in class ec.EvolutionState
P_EVALUATOR - Static variable in class ec.EvolutionState
P_EXCESS_COEFF - Static variable in class ec.neat.NEATSpecies
P_EXCHANGER - Static variable in class ec.EvolutionState
P_EXPECTED - Static variable in class ec.gp.build.PTC1
P_EXTRA_BEHAVIOR - Static variable in class ec.Subpopulation
P_F - Static variable in class ec.de.DEBreeder
P_FILE - Static variable in class ec.eval.MetaProblem
P_FILE - Static variable in class ec.gp.ge.GESpecies
P_FILE - Static variable in class ec.Population
P_FILE - Static variable in class ec.Subpopulation
P_FINISHER - Static variable in class ec.EvolutionState
P_FIRST - Static variable in class ec.select.FirstSelection
  default base
P_FIRST_COPY - Static variable in class ec.breed.FirstCopyPipeline
P_FITNESS - Static variable in class ec.Fitness
  base parameter for defaults
P_FITNESS - Static variable in class ec.Species
P_FITNESSPROPORTIONATE - Static variable in class ec.select.FitProportionateSelection
  Default base
P_FLOAT - Static variable in class ec.gp.push.Terminal
P_FloatVectorIndividual - Static variable in class ec.vector.FloatVectorIndividual
P_FNOISE - Static variable in class ec.de.Best1BinDEBreeder
P_FORCE - Static variable in class ec.breed.ForceBreedingPipeline
P_FULL - Static variable in class ec.simple.SimpleShortStatistics
P_FULLBUILDER - Static variable in class ec.gp.koza.FullBuilder
P_FUNC - Static variable in class ec.gp.GPFunctionSet
P_FUNC - Static variable in class ec.gp.push.Terminal
P_FUNCTIONNAME - Static variable in class ec.gp.ADF
P_FUNCTIONNAME - Static variable in class ec.gp.ADFArgument
P_FUNCTIONSET - Static variable in class ec.gp.GPTreeConstraints
P_FUNCTIONSETS - Static variable in class ec.gp.GPInitializer
P_GE - Static variable in class ec.gp.ge.GEDefaults
P_GEN_MAX - Static variable in class ec.breed.GenerationSwitchPipeline
P_GEN_MAX - Static variable in class ec.breed.MultiBreedingPipeline
P_GEN_MAX - Static variable in class ec.breed.UniquePipeline
P_GENE - Static variable in class ec.neat.NEATGene
P_GENE - Static variable in class ec.vector.Gene
P_GENE - Static variable in class ec.vector.GeneVectorSpecies
P_GENERATIONS - Static variable in class ec.EvolutionState
P_GENEVECTORINDIVIDUAL - Static variable in class ec.vector.GeneVectorIndividual
P_GENOMESIZE - Static variable in class ec.vector.VectorSpecies
P_GEOMETRIC_PROBABILITY - Static variable in class ec.vector.VectorSpecies
P_GESPECIES - Static variable in class ec.gp.ge.GESpecies
P_GETS - Static variable in class ec.select.GreedyOverselection
P_GLOBAL_COEFFICIENT - Static variable in class ec.pso.PSOBreeder
P_GP - Static variable in class ec.gp.GPDefaults
P_GPDATA - Static variable in class ec.gp.GPData
P_GPPROBLEM - Static variable in class ec.gp.GPProblem
P_GPSPECIES - Static variable in class ec.gp.ge.GESpecies
P_GPSPECIES - Static variable in class ec.gp.GPSpecies
P_GREEDY - Static variable in class ec.select.GreedyOverselection
P_GROUP_SIZE - Static variable in class ec.coevolve.CompetitiveEvaluator
P_GROWBUILDER - Static variable in class ec.gp.koza.GrowBuilder
P_HALFBUILDER - Static variable in class ec.gp.koza.HalfBuilder
P_HOMOLOGOUS - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
P_IAMSLAVE - Static variable in class ec.Evaluator
P_INCLUDE_SELF - Static variable in class ec.pso.PSOBreeder
P_IND_COMPETES - Static variable in class ec.spatial.SpatialTournamentSelection
  Some models assume an individual is always selected to compete for breeding a child that would take its location in space.
P_INDIVIDUAL - Static variable in class ec.Individual
  A reasonable parameter base element for individuals
P_INDIVIDUAL - Static variable in class ec.Species
P_INFORMANT_COEFFICIENT - Static variable in class ec.pso.PSOBreeder
P_INIT - Static variable in class ec.breed.InitializationPipeline
P_INIT - Static variable in class ec.gp.GPTreeConstraints
P_INITIAL_REPETITION - Static variable in class ec.eda.dovs.DOVSSpecies
P_INITIALIZER - Static variable in class ec.EvolutionState
P_INITSCHEME - Static variable in class ec.gp.ge.GESpecies
P_INNOVATION - Static variable in class ec.neat.NEATInnovation
P_INNOVATION - Static variable in class ec.neat.NEATSpecies
P_INNOVATIONNUMBER - Static variable in class ec.EvolutionState
P_INSTRUCTION - Static variable in class ec.gp.push.PushInstruction
P_INSTRUCTION - Static variable in class ec.gp.push.Terminal
P_INTEGER - Static variable in class ec.gp.push.Terminal
P_INTEGERVECTORINDIVIDUAL - Static variable in class ec.vector.IntegerVectorIndividual
P_INTERNALCROSSOVER - Static variable in class ec.gp.breed.InternalCrossoverPipeline
P_INTERSPECIES_MATE_PROB - Static variable in class ec.neat.NEATSpecies
P_IS_SERVER - Static variable in class ec.exchange.IslandExchange
  Whether the server is also on this island
P_JOB_SIZE - Static variable in class ec.eval.MasterProblem
P_K - Static variable in class ec.multiobjective.spea2.SPEA2Breeder
P_KILL_PROPORTION - Static variable in class ec.parsimony.TarpeianStatistics
  one in n individuals are killed
P_KOZA - Static variable in class ec.gp.koza.GPKozaDefaults
P_KOZAFITNESS - Static variable in class ec.gp.koza.KozaFitness
P_LAMBDA - Static variable in class ec.eda.cmaes.CMAESSpecies
P_LAMBDA - Static variable in class ec.es.MuCommaLambdaBreeder
P_LEXICASESELECT - Static variable in class ec.select.LexicaseSelection
P_LIKELIHOOD - Static variable in class ec.BreedingPipeline
  Indicates the probability that the Breeding Pipeline will perform its mutative action instead of just doing reproduction.
P_LINEDISTANCE - Static variable in class ec.vector.VectorSpecies
P_LIST_CROSSOVER - Static variable in class ec.vector.breed.ListCrossoverPipeline
P_LONGVECTORINDIVIDUAL - Static variable in class ec.vector.LongVectorIndividual
P_MASTERPROBLEM - Static variable in class ec.Evaluator
P_MATE_MULTIPOINT_AVG_PROB - Static variable in class ec.neat.NEATSpecies
P_MATE_MULTIPOINT_PROB - Static variable in class ec.neat.NEATSpecies
P_MATE_ONLY_PROB - Static variable in class ec.neat.NEATSpecies
P_MATE_SINGLE_POINT_PROB - Static variable in class ec.neat.NEATSpecies
P_MAX - Static variable in class ec.gp.push.Terminal
P_MAX_CROSSOVER_PERCENT - Static variable in class ec.vector.breed.ListCrossoverPipeline
P_MAX_NETWORK_DEPTH - Static variable in class ec.neat.NEATSpecies
P_MAXDEPTH - Static variable in class ec.gp.breed.InternalCrossoverPipeline
P_MAXDEPTH - Static variable in class ec.gp.breed.MutateDemotePipeline
P_MAXDEPTH - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
P_MAXDEPTH - Static variable in class ec.gp.build.PTC1
P_MAXDEPTH - Static variable in class ec.gp.build.PTC2
P_MAXDEPTH - Static variable in class ec.gp.koza.CrossoverPipeline
P_MAXDEPTH - Static variable in class ec.gp.koza.KozaBuilder
P_MAXDEPTH - Static variable in class ec.gp.koza.MutationPipeline
P_MAXGENE - Static variable in class ec.vector.FloatVectorSpecies
P_MAXGENE - Static variable in class ec.vector.IntegerVectorSpecies
P_MAXIMIZE - Static variable in class ec.multiobjective.MultiObjectiveFitness
  Is higher better?
P_MAXIMUMNUMBEROFCONCURRENTJOBSPERSLAVE - Static variable in class ec.eval.SlaveMonitor
P_MAXOBJECTIVE - Static variable in class ec.multiobjective.MultiObjectiveFitness
  parameter for max fitness values
P_MAXSIZE - Static variable in class ec.gp.GPNodeBuilder
P_MAXSIZE - Static variable in class ec.gp.koza.CrossoverPipeline
P_MAXSIZE - Static variable in class ec.gp.koza.MutationPipeline
P_MAXSIZE - Static variable in class ec.rule.RuleSetConstraints
P_MEAN - Static variable in class ec.eda.cmaes.CMAESSpecies
P_MEMBER - Static variable in class ec.gp.GPSetType
P_MERGE - Static variable in class ec.simple.SimpleEvaluator
P_MIN - Static variable in class ec.gp.push.Terminal
P_MIN_CHILD_SIZE - Static variable in class ec.vector.breed.ListCrossoverPipeline
P_MIN_CROSSOVER_PERCENT - Static variable in class ec.vector.breed.ListCrossoverPipeline
P_MINDEPTH - Static variable in class ec.gp.koza.KozaBuilder
P_MINGENE - Static variable in class ec.vector.FloatVectorSpecies
P_MINGENE - Static variable in class ec.vector.IntegerVectorSpecies
P_MINOBJECTIVE - Static variable in class ec.multiobjective.MultiObjectiveFitness
  parameter for min fitness values
P_MINSIZE - Static variable in class ec.gp.GPNodeBuilder
P_MINSIZE - Static variable in class ec.rule.RuleSetConstraints
P_MODULO - Static variable in class ec.exchange.InterPopulationExchange
  The parameter for the modulo (how many generations should pass between consecutive sendings of individuals
P_MU - Static variable in class ec.eda.cmaes.CMAESSpecies
P_MU - Static variable in class ec.es.MuCommaLambdaBreeder
P_MU_FRACTION - Static variable in class ec.es.MuCommaLambdaBreeder
P_MULTI - Static variable in class ec.multiobjective.MultiObjectiveDefaults
P_MULTIBREED - Static variable in class ec.breed.GenerationSwitchPipeline
P_MULTIBREED - Static variable in class ec.breed.MultiBreedingPipeline
P_MULTISELECT - Static variable in class ec.select.MultiSelection
P_MUT_DIFF_COEFF - Static variable in class ec.neat.NEATSpecies
P_MUTATE_ADD_LINK_PROB - Static variable in class ec.neat.NEATSpecies
P_MUTATE_ADD_NODE_PROB - Static variable in class ec.neat.NEATSpecies
P_MUTATE_GENE_REENABLE_PROB - Static variable in class ec.neat.NEATSpecies
P_MUTATE_LINK_WEIGHT_PROB - Static variable in class ec.neat.NEATSpecies
P_MUTATE_ONLY_PROB - Static variable in class ec.neat.NEATSpecies
P_MUTATE_TOGGLE_ENABLE_PROB - Static variable in class ec.neat.NEATSpecies
P_MUTATEALLNODES - Static variable in class ec.gp.breed.MutateAllNodesPipeline
P_MUTATEDEMOTE - Static variable in class ec.gp.breed.MutateDemotePipeline
P_MUTATEERC - Static variable in class ec.gp.breed.MutateERCPipeline
P_MUTATEONENODE - Static variable in class ec.gp.breed.MutateOneNodePipeline
P_MUTATEPROMOTE - Static variable in class ec.gp.breed.MutatePromotePipeline
P_MUTATESWAP - Static variable in class ec.gp.breed.MutateSwapPipeline
P_MUTATION - Static variable in class ec.gp.koza.MutationPipeline
P_MUTATION - Static variable in class ec.rule.breed.RuleMutationPipeline
P_MUTATION - Static variable in class ec.vector.breed.VectorMutationPipeline
P_MUTATION_BOUNDED - Static variable in class ec.vector.FloatVectorSpecies
P_MUTATION_BOUNDED - Static variable in class ec.vector.IntegerVectorSpecies
P_MUTATION_DISTRIBUTION_INDEX - Static variable in class ec.vector.FloatVectorSpecies
P_MUTATIONPROB - Static variable in class ec.vector.VectorSpecies
P_MUTATIONTYPE - Static variable in class ec.vector.BitVectorSpecies
P_MUTATIONTYPE - Static variable in class ec.vector.FloatVectorSpecies
P_MUTATIONTYPE - Static variable in class ec.vector.IntegerVectorSpecies
P_MUZZLE - Static variable in class ec.eval.MetaProblem
P_MUZZLE - Static variable in class ec.eval.Slave
P_MUZZLE - Static variable in class ec.Statistics
P_N - Static variable in class ec.select.BestSelection
P_N_FRACTION - Static variable in class ec.select.BestSelection
P_N_SIZE - Static variable in class ec.spatial.SpatialTournamentSelection
  The size of the neighborhood from where parents are selected.
P_NAME - Static variable in class ec.gp.GPFunctionSet
P_NAME - Static variable in class ec.gp.GPNodeConstraints
P_NAME - Static variable in class ec.gp.GPTreeConstraints
P_NAME - Static variable in class ec.gp.GPType
P_NAME - Static variable in class ec.rule.RuleConstraints
P_NAME - Static variable in class ec.rule.RuleSetConstraints
  The size of a byte
P_NEAT - Static variable in class ec.neat.NEATDefaults
P_NEIGHBORHOOD - Static variable in class ec.pso.PSOBreeder
P_NEIGHBORHOOD_SIZE - Static variable in class ec.pso.PSOBreeder
P_NETWORK - Static variable in class ec.neat.NEATNetwork
P_NETWORK - Static variable in class ec.neat.NEATSpecies
P_NEW_LINK_TRIES - Static variable in class ec.neat.NEATSpecies
P_NEW_NODE_TRIES - Static variable in class ec.neat.NEATSpecies
P_NIS_MAX - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_NODE - Static variable in class ec.gp.GPNode
P_NODE - Static variable in class ec.neat.NEATNode
P_NODE - Static variable in class ec.neat.NEATSpecies
P_NODECONSTRAINTS - Static variable in class ec.gp.GPInitializer
P_NODECONSTRAINTS - Static variable in class ec.gp.GPNode
P_NODESELECTOR - Static variable in class ec.gp.GPBreedingPipeline
  Standard parameter for node-selectors associated with a GPBreedingPipeline
P_NODESELECTOR - Static variable in class ec.gp.koza.KozaNodeSelector
P_NONTERMINAL_PROBABILITY - Static variable in class ec.gp.koza.KozaNodeSelector
P_NORMALIZE - Static variable in class ec.multiobjective.spea2.SPEA2Breeder
P_NUM_GURU - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_NUM_IND - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_NUM_INSTRUCTIONS - Static variable in class ec.gp.push.Terminal
P_NUM_PARAMS - Static variable in class ec.eval.MetaProblem
P_NUM_RAND_IND - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_NUM_SEGMENTS - Static variable in class ec.vector.IntegerVectorSpecies
P_NUM_SEGMENTS - Static variable in class ec.vector.VectorSpecies
P_NUM_SHUFFLED - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_NUM_TESTS - Static variable in class ec.simple.SimpleEvaluator
P_NUM_TRIES - Static variable in class ec.gp.breed.InternalCrossoverPipeline
P_NUM_TRIES - Static variable in class ec.gp.breed.MutateDemotePipeline
P_NUM_TRIES - Static variable in class ec.gp.breed.MutatePromotePipeline
P_NUM_TRIES - Static variable in class ec.gp.breed.MutateSwapPipeline
P_NUM_TRIES - Static variable in class ec.gp.breed.RehangPipeline
P_NUM_TRIES - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
P_NUM_TRIES - Static variable in class ec.gp.koza.CrossoverPipeline
P_NUM_TRIES - Static variable in class ec.gp.koza.MutationPipeline
P_NUM_TRIES - Static variable in class ec.vector.breed.ListCrossoverPipeline
P_NUM_VALS - Static variable in class ec.eval.MetaProblem
P_NUMCHILDREN - Static variable in class ec.Statistics
P_NUMINDS - Static variable in class ec.breed.ForceBreedingPipeline
P_NUMOBJECTIVES - Static variable in class ec.multiobjective.MultiObjectiveFitness
  parameter for size of objectives
P_NUMRULESETS - Static variable in class ec.rule.RuleIndividual
P_NUMSELECTS - Static variable in class ec.select.MultiSelection
P_NUMSIZES - Static variable in class ec.gp.GPNodeBuilder
P_NUMSIZES - Static variable in class ec.rule.RuleSetConstraints
P_NUMSOURCES - Static variable in class ec.BreedingPipeline
  Standard parameter for number of sources (only used if numSources returns DYNAMIC_SOURCES)
P_NUMTIMES - Static variable in class ec.breed.CheckingPipeline
P_NUMTREES - Static variable in class ec.gp.GPIndividual
P_OFFSET - Static variable in class ec.exchange.InterPopulationExchange
  How many generations to pass at the beginning of the evolution before the first emigration from the current subpopulation
P_ONESHOT - Static variable in class ec.eval.Slave
  Should slave go into an infinite loop looking for new masters after the master has quit, or not?
P_OUT_OF_BOUNDS_RETRIES - Static variable in class ec.de.DEBreeder
P_OUTOFBOUNDS_RETRIES - Static variable in class ec.vector.FloatVectorSpecies
P_OVER_EVAL - Static variable in class ec.coevolve.CompetitiveEvaluator
P_OWN_ID - Static variable in class ec.exchange.IslandExchange
  The id of the island
P_PARAM - Static variable in class ec.eval.MetaProblem
P_PARAMETER_MISSING - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_PARETO_FRONT_FILE - Static variable in class ec.multiobjective.MultiObjectiveStatistics
  front file parameter
P_PARSER - Static variable in class ec.gp.ge.GESpecies
P_PARSER - Static variable in class ec.gp.ge.GrammarParser
P_PASSES - Static variable in class ec.gp.ge.GESpecies
P_PBIL_SPECIES - Static variable in class ec.eda.pbil.PBILSpecies
P_PERSONAL_COEFFICIENT - Static variable in class ec.pso.PSOBreeder
P_PF - Static variable in class ec.de.Rand1EitherOrDEBreeder
P_PICKGROWPROBABILITY - Static variable in class ec.gp.koza.HalfBuilder
P_PICKWORST - Static variable in class ec.parsimony.BucketTournamentSelection
  If the worst individual should be picked in the tournament
P_PICKWORST - Static variable in class ec.parsimony.DoubleTournamentSelection
P_PICKWORST - Static variable in class ec.parsimony.RatioBucketTournamentSelection
  if the worst individual should be picked in the tournament
P_PICKWORST - Static variable in class ec.select.BestSelection
P_PICKWORST - Static variable in class ec.select.TournamentSelection
P_PICKWORST2 - Static variable in class ec.parsimony.DoubleTournamentSelection
P_PIPE - Static variable in class ec.Species
P_POLYNOMIAL_ALTERNATIVE - Static variable in class ec.vector.FloatVectorSpecies
P_POP - Static variable in class ec.Initializer
  parameter for a new population
P_PRINT_STYLE - Static variable in class ec.gp.GPTree
P_PRINTACCESSEDPARAMETERS - Static variable in class ec.Evolve
P_PRINTALLPARAMETERS - Static variable in class ec.Evolve
P_PRINTUNACCESSEDPARAMETERS - Static variable in class ec.Evolve
P_PRINTUNUSEDPARAMETERS - Static variable in class ec.Evolve
P_PRINTUSEDPARAMETERS - Static variable in class ec.Evolve
P_PROB - Static variable in class ec.BreedingSource
P_PROBABILITY - Static variable in class ec.gp.GPNodeConstraints
P_PROBABILITY - Static variable in class ec.parsimony.ProportionalTournamentSelection
  The parameter for the probability of having the tournament based on fitness
p_problem - Variable in class ec.Evaluator
P_PROBLEM - Static variable in class ec.Evaluator
P_PROBLEM - Static variable in class ec.gp.ge.GEProblem
P_PROBLEM - Static variable in class ec.Problem
P_PROPORTIONAL_TOURNAMENT - Static variable in class ec.parsimony.ProportionalTournamentSelection
  default base
P_PTC1 - Static variable in class ec.gp.build.PTC1
P_PTC2 - Static variable in class ec.gp.build.PTC2
P_PUSH - Static variable in class ec.gp.push.PushDefaults
P_PUSHBUILDER - Static variable in class ec.gp.push.PushBuilder
P_QUITONRUNCOMPLETE - Static variable in class ec.EvolutionState
P_RAND_ORDER_PROB - Static variable in class ec.rule.RuleSetConstraints
P_RANDOM - Static variable in class ec.select.RandomSelection
  default base
P_RANDOM_WALK_PROBABILITY - Static variable in class ec.vector.FloatVectorSpecies
P_RANDOM_WALK_PROBABILITY - Static variable in class ec.vector.IntegerVectorSpecies
P_RANDOMBRANCH - Static variable in class ec.gp.build.RandomBranch
P_RANDOMBRANCH - Static variable in class ec.gp.build.RandTree
p_randorder - Variable in class ec.rule.RuleSetConstraints
P_RATIO - Static variable in class ec.parsimony.RatioBucketTournamentSelection
  The value of RATIO: each step, the worse 1/RATIO individuals are assigned the same fitness
P_RATIO_BUCKET_TOURNAMENT - Static variable in class ec.parsimony.RatioBucketTournamentSelection
  default base
P_RECUR_ONLY_PROB - Static variable in class ec.neat.NEATSpecies
P_REEVALUATE_ELITES - Static variable in class ec.simple.SimpleBreeder
P_REEVALUATE_INDIVIDUALS - Static variable in class ec.eval.MetaProblem
P_REFERENCE_POINT - Static variable in class ec.multiobjective.HypervolumeStatistics
P_REFERENCE_POINT - Static variable in class ec.multiobjective.MultiObjectiveStatistics
P_REHANG - Static variable in class ec.gp.breed.RehangPipeline
P_REPEAT - Static variable in class ec.breed.RepeatPipeline
P_REPLACEMENT_PROBABILITY - Static variable in class ec.steadystate.SteadyStateEvolutionState
P_REPRODUCE - Static variable in class ec.breed.ReproductionPipeline
P_RESCHEDULELOSTJOBS - Static variable in class ec.eval.SlaveMonitor
P_RESETMAXSIZE - Static variable in class ec.rule.RuleSetConstraints
P_RESETMINSIZE - Static variable in class ec.rule.RuleSetConstraints
P_RESETSIZE - Static variable in class ec.rule.RuleSetConstraints
P_RESTART_TYPE - Static variable in class ec.evolve.RandomRestarts
P_RESTART_UPPERBOUND - Static variable in class ec.evolve.RandomRestarts
P_RETRIES - Static variable in class ec.breed.UniquePipeline
P_RETRIES - Static variable in class ec.Subpopulation
P_RETURNINDIVIDUALS - Static variable in class ec.eval.Slave
P_RETURNS - Static variable in class ec.gp.GPNodeConstraints
P_RETURNS - Static variable in class ec.gp.GPTreeConstraints
P_ROOT_PROBABILITY - Static variable in class ec.gp.koza.KozaNodeSelector
P_RULE - Static variable in class ec.rule.Rule
P_RULE - Static variable in class ec.rule.RuleDefaults
P_RULE - Static variable in class ec.rule.RuleSetConstraints
  num rulesets
P_RULECONSTRAINTS - Static variable in class ec.rule.RuleInitializer
P_RULESET - Static variable in class ec.rule.RuleIndividual
P_RULESET - Static variable in class ec.rule.RuleSet
P_RULESETCONSTRAINTS - Static variable in class ec.rule.RuleInitializer
P_RULESPECIES - Static variable in class ec.rule.RuleSpecies
P_RUNEVOLVE - Static variable in class ec.eval.Slave
  Should slave run its own evolutionary process?
P_RUNS - Static variable in class ec.eval.MetaProblem
P_RUNTIME - Static variable in class ec.eval.Slave
  Time to run evolution on the slaves in seconds
P_SCALED_FITNESS_FLOOR - Static variable in class ec.select.SigmaScalingSelection
  Scaled fitness floor
P_SEED - Static variable in class ec.Evolve
  seed parameter
P_SEGMENT - Static variable in class ec.vector.IntegerVectorSpecies
P_SEGMENT - Static variable in class ec.vector.VectorSpecies
P_SEGMENT_END - Static variable in class ec.vector.IntegerVectorSpecies
P_SEGMENT_END - Static variable in class ec.vector.VectorSpecies
P_SEGMENT_START - Static variable in class ec.vector.IntegerVectorSpecies
P_SEGMENT_START - Static variable in class ec.vector.VectorSpecies
P_SEGMENT_TYPE - Static variable in class ec.vector.IntegerVectorSpecies
P_SEGMENT_TYPE - Static variable in class ec.vector.VectorSpecies
P_SELECT - Static variable in class ec.select.MultiSelection
P_SELECT - Static variable in class ec.select.SelectDefaults
P_SELECT_METHOD - Static variable in class ec.exchange.InterPopulationExchange
  The selection method for sending individuals to other islands
P_SELECT_METHOD - Static variable in class ec.exchange.IslandExchange
  The selection method for sending individuals to other islands
P_SELECT_TO_DIE_METHOD - Static variable in class ec.exchange.InterPopulationExchange
  The selection method for deciding individuals to be replaced by immigrants
P_SELECT_TO_DIE_METHOD - Static variable in class ec.exchange.IslandExchange
  The selection method for deciding individuals to be replaced by immigrants
P_SELECTION_METHOD_CURRENT - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_SELECTION_METHOD_PREV - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_SEQUENTIAL_BREEDING - Static variable in class ec.simple.SimpleBreeder
P_SERVER_ADDRESS - Static variable in class ec.exchange.IslandExchange
  The server address
P_SERVER_PORT - Static variable in class ec.exchange.IslandExchange
  The server port
P_SET - Static variable in class ec.gp.GPInitializer
P_SET_RANDOM - Static variable in class ec.eval.MetaProblem
P_SHORTVECTORINDIVIDUAL - Static variable in class ec.vector.ShortVectorIndividual
P_SHUFFLE - Static variable in class ec.select.SUSSelection
P_SIGMA - Static variable in class ec.eda.cmaes.CMAESSpecies
P_SIGMA_SCALING - Static variable in class ec.select.SigmaScalingSelection
  Default base
P_SILENT - Static variable in class ec.eval.Slave
P_SILENT - Static variable in class ec.Evolve
  Should we muzzle stdout and stderr?
P_SILENT - Static variable in class ec.Statistics
P_SILENT_FILE - Static variable in class ec.Statistics
P_SILENT_FRONT_FILE - Static variable in class ec.multiobjective.MultiObjectiveStatistics
P_SILENT_PRINT - Static variable in class ec.Statistics
P_SIMPLE - Static variable in class ec.simple.SimpleDefaults
P_SIZE - Static variable in class ec.exchange.InterPopulationExchange
  The number of emigrants to be sent
P_SIZE - Static variable in class ec.gp.GPFunctionSet
P_SIZE - Static variable in class ec.gp.GPInitializer
P_SIZE - Static variable in class ec.gp.GPNodeBuilder
P_SIZE - Static variable in class ec.gp.GPNodeConstraints
P_SIZE - Static variable in class ec.gp.GPSetType
P_SIZE - Static variable in class ec.gp.GPTreeConstraints
P_SIZE - Static variable in class ec.parsimony.BucketTournamentSelection
  Tournament size parameter
P_SIZE - Static variable in class ec.parsimony.DoubleTournamentSelection
  size parameter
P_SIZE - Static variable in class ec.parsimony.RatioBucketTournamentSelection
  size parameter
P_SIZE - Static variable in class ec.Population
P_SIZE - Static variable in class ec.rule.RuleInitializer
P_SIZE - Static variable in class ec.select.BestSelection
P_SIZE - Static variable in class ec.select.TournamentSelection
  size parameter
P_SIZE2 - Static variable in class ec.parsimony.DoubleTournamentSelection
P_SIZEFAIR - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
P_SOURCE - Static variable in class ec.BreedingPipeline
  Standard parameter for individual-selectors associated with a BreedingPipeline
P_SPATIAL - Static variable in class ec.spatial.SpatialDefaults
P_SPECIES - Static variable in class ec.neat.NEATSpecies
P_SPECIES - Static variable in class ec.Subpopulation
P_STACK - Static variable in class ec.gp.GPProblem
P_START - Static variable in class ec.evolve.RandomRestarts
P_STARTING_TEMPERATURE - Static variable in class ec.select.BoltzmannSelection
  Starting temperature parameter
P_STATE - Static variable in class ec.Evolve
  state parameter
P_STATISTICS - Static variable in class ec.EvolutionState
P_STATISTICS_FILE - Static variable in class ec.simple.SimpleShortStatistics
P_STATISTICS_FILE - Static variable in class ec.simple.SimpleStatistics
  log file parameter
P_STATISTICS_MODULUS - Static variable in class ec.simple.SimpleShortStatistics
P_STDEV - Static variable in class ec.vector.FloatVectorSpecies
P_STEADYSTATE - Static variable in class ec.steadystate.SteadyStateDefaults
P_STOCHASTIC - Static variable in class ec.eda.dovs.DOVSSpecies
P_STUB - Static variable in class ec.breed.StubPipeline
P_STUB_PIPELINE - Static variable in class ec.breed.StubPipeline
P_SUBPOP - Static variable in class ec.coevolve.MultiPopCoevolutionaryEvaluator
P_SUBPOP - Static variable in class ec.exchange.InterPopulationExchange
  The subpopulation delimiter
P_SUBPOP - Static variable in class ec.Population
P_SUBPOPSIZE - Static variable in class ec.Subpopulation
P_SUBPOPULATION - Static variable in class ec.Subpopulation
P_SUBSPECIES - Static variable in class ec.neat.NEATSpecies
P_SUBSPECIES - Static variable in class ec.neat.NEATSubspecies
P_SURVIVIAL_THRESH - Static variable in class ec.neat.NEATSpecies
P_SUS - Static variable in class ec.select.SUSSelection
  Default base
P_SWITCHAT - Static variable in class ec.breed.GenerationSwitchPipeline
P_TAU - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_TEMPERATURE - Static variable in class ec.select.AnnealedSelection
P_TERMINAL_PROBABILITY - Static variable in class ec.gp.koza.KozaNodeSelector
P_THETA_SDR - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_TITLE - Static variable in class ec.display.chart.ChartableStatistics
P_TOP - Static variable in class ec.select.GreedyOverselection
P_TOP - Static variable in class ec.select.TopSelection
  Default base
P_TOROIDAL - Static variable in class ec.spatial.Spatial1DSubpopulation
  This parameter stipulates whether the world is toroidal or not.
P_TOSS - Static variable in class ec.gp.breed.SizeFairCrossoverPipeline
P_TOSS - Static variable in class ec.gp.koza.CrossoverPipeline
P_TOSS - Static variable in class ec.rule.breed.RuleCrossoverPipeline
P_TOSS - Static variable in class ec.vector.breed.ListCrossoverPipeline
P_TOSS - Static variable in class ec.vector.breed.VectorCrossoverPipeline
P_TOURNAMENT - Static variable in class ec.parsimony.BucketTournamentSelection
  Default base
P_TOURNAMENT - Static variable in class ec.parsimony.DoubleTournamentSelection
  default base
P_TOURNAMENT - Static variable in class ec.parsimony.LexicographicTournamentSelection
  default base
P_TOURNAMENT - Static variable in class ec.select.TournamentSelection
  default base
P_TREE - Static variable in class ec.gp.GPBreedingPipeline
  Standard parameter for tree fixing
P_TREE - Static variable in class ec.gp.GPIndividual
P_TREE - Static variable in class ec.gp.GPTree
P_TREECONSTRAINTS - Static variable in class ec.gp.GPInitializer
P_TREECONSTRAINTS - Static variable in class ec.gp.GPTree
P_TRUEDISTRIBUTION - Static variable in class ec.gp.build.Uniform
P_TYPE - Static variable in class ec.eval.MetaProblem
P_TYPE - Static variable in class ec.gp.GPInitializer
P_TYPE - Static variable in class ec.spatial.SpatialTournamentSelection
  Selection procedure.
P_UNIFORM - Static variable in class ec.gp.build.Uniform
P_UNIFORM_MAX - Static variable in class ec.vector.VectorSpecies
P_UNIFORM_MIN - Static variable in class ec.vector.VectorSpecies
P_UNIQUE - Static variable in class ec.breed.UniquePipeline
P_USEC - Static variable in class ec.gp.GPTree
P_USEGRAPHVIZ - Static variable in class ec.gp.GPTree
P_USELATEX - Static variable in class ec.gp.GPTree
P_USEOPS - Static variable in class ec.gp.GPTree
P_USEVARS - Static variable in class ec.gp.GPTree
P_VAL - Static variable in class ec.eval.MetaProblem
P_VARIANCE_TOLERANCE - Static variable in class ec.eda.amalgam.AMALGAMSpecies
P_VECTOR - Static variable in class ec.vector.VectorDefaults
P_VECTORSPECIES - Static variable in class ec.vector.VectorSpecies
P_VELOCITY_COEFFICIENT - Static variable in class ec.pso.PSOBreeder
P_WARM_UP - Static variable in class ec.eda.dovs.DOVSSpecies
P_WEIGHT_MUT_POWER - Static variable in class ec.neat.NEATSpecies
P_WEIGHTS - Static variable in class ec.eda.cmaes.CMAESSpecies
P_XAXIS - Static variable in class ec.display.chart.ChartableStatistics
p_y - Variable in class ec.gp.build.PTCFunctionSet
  cache of nonterminal selection probabilities -- dense array [size-1][type].
P_YAXIS - Static variable in class ec.display.chart.ChartableStatistics
Pair() - Constructor for class ec.eda.dovs.CornerMap.Pair
param - Variable in class ec.util.Parameter
ParamClassLoadException - Exception Class in ec.util
  This exception is thrown by the Parameter Database when it fails to locate and load a class specified by a given parameter as requested.
ParamClassLoadException(String) - Constructor for exception class ec.util.ParamClassLoadException
Parameter - Class in ec.util
  A Parameter is an object which the ParameterDatabase class uses as a key to associate with strings, forming a key-value pair.
Parameter(String) - Constructor for class ec.util.Parameter
  Creates a new parameter from the single path item in s.
Parameter(String[]) - Constructor for class ec.util.Parameter
  Creates a new parameter by joining the path items in s into a single path.
Parameter(String, String[]) - Constructor for class ec.util.Parameter
  Creates a new parameter from the path item in s, plus the path items in s2.
ParameterDatabase - Class in ec.util
  This extension of the Properties class allows you to set, get, and delete Parameters in a hierarchical tree-like database.
ParameterDatabase() - Constructor for class ec.util.ParameterDatabase
  Creates an empty parameter database.
ParameterDatabase(File) - Constructor for class ec.util.ParameterDatabase
  Creates a new parameter database tree from a given database file and its parent files.
ParameterDatabase(File, String[]) - Constructor for class ec.util.ParameterDatabase
  Creates a new parameter database from a given database file and argv list.
ParameterDatabase(InputStream) - Constructor for class ec.util.ParameterDatabase
  Creates a new parameter database loaded from the given stream.
ParameterDatabase(String, Class) - Constructor for class ec.util.ParameterDatabase
  Creates a new parameter database loaded from a parameter file located relative to a class file, wherever the class file may be (such as in a jar).
ParameterDatabase(String, Class, String[]) - Constructor for class ec.util.ParameterDatabase
  Creates a new parameter database from a given database file and argv list.
ParameterDatabase(Dictionary) - Constructor for class ec.util.ParameterDatabase
  Creates a new parameter database from the given Dictionary.
ParameterDatabaseEvent - Class in ec.util
ParameterDatabaseEvent(Object, Parameter, String, int) - Constructor for class ec.util.ParameterDatabaseEvent
  For ParameterDatabase events.
ParameterDatabaseTreeModel - Class in ec.util
ParameterDatabaseTreeModel(TreeNode) - Constructor for class ec.util.ParameterDatabaseTreeModel
ParameterDatabaseTreeModel(TreeNode, boolean) - Constructor for class ec.util.ParameterDatabaseTreeModel
parameters - Variable in class ec.EvolutionState
  The parameter database (threadsafe).
ParametersPanel - Class in ec.display
ParametersPanel(Console) - Constructor for class ec.display.ParametersPanel
  This is the default constructor
ParameterValue - Class in ec.display
ParameterValue(String) - Constructor for class ec.display.ParameterValue
parent - Variable in class ec.gp.GPNode
  The GPNode's parent.
parentPopulation - Variable in class ec.es.MuCommaLambdaBreeder
parents - Variable in class ec.breed.RepeatPipeline
parents - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  Temporary holding place for parents
parents - Variable in class ec.gp.koza.CrossoverPipeline
  Temporary holding place for parents
parents - Variable in class ec.vector.breed.ListCrossoverPipeline
parentType(GPInitializer) - Method in class ec.gp.GPNode
  Returns the argument type of the slot that I fit into in my parent.
paretoDominates(MultiObjectiveFitness) - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns true if I'm better than _fitness.
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.gp.GPIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.Individual
  This method is used only by the default version of readIndividual(state,reader), and it is intended to be overridden to parse in that part of the individual that was outputted in the genotypeToString() method.
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.neat.NEATIndividual
  This method is used to read a gene in start genome from file.
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.rule.RuleIndividual
  Overridden for the RuleIndividual genotype.
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.BitVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.ByteVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.DoubleVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.FloatVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.GeneVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.IntegerVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.LongVectorIndividual
parseGenotype(EvolutionState, LineNumberReader) - Method in class ec.vector.ShortVectorIndividual
parseNodes(EvolutionState, LineNumberReader) - Method in class ec.neat.NEATIndividual
  Create the nodes from the reader, and calls readNode method on each node.
parser_prototype - Variable in class ec.gp.ge.GESpecies
  The prototypical parser used to parse the grammars.
parseRules(EvolutionState, BufferedReader, GPFunctionSet) - Method in class ec.gp.ge.GrammarParser
  Parses the rules from a grammar and returns the resulting GrammarRuleNode root.
parseSexp(ArrayList, GrammarParser) - Method in class ec.gp.ge.GESpecies
  The LL(1) parsing algorithm to parse the lisp tree, the lisp tree is actually fed as a flattened list, the parsing code uses the "exact" (and as-is) procedure described in the dragon book.
Particle - Class in ec.pso
  Particle is a DoubleVectorIndividual with additional statistical information necessary to perform Particle Swarm Optimization.
Particle() - Constructor for class ec.pso.Particle
partitionIntoParetoFront(ArrayList<Individual>, ArrayList<Individual>, ArrayList<Individual>) - Static method in class ec.multiobjective.MultiObjectiveFitness
  Divides an array of Individuals into the Pareto front and the "nonFront" (everyone else).
partitionIntoRanks(ArrayList<Individual>) - Static method in class ec.multiobjective.MultiObjectiveFitness
  Divides inds into pareto front ranks (each an ArrayList), and returns them, in order, stored in an ArrayList.
passes - Variable in class ec.gp.ge.GESpecies
  The number of passes permitted through the genome if we're wrapping.
pathLength(int) - Method in class ec.gp.GPNode
  Returns the path length of the tree, which is the sum of all paths from all nodes to the root.
PBILBreeder - Class in ec.eda.pbil
  PBILBreeder is a Breeder which overrides the breedPopulation method to first update PBIL's internal distribution, then replace all the individuals in the population with new samples generated from the distribution.
PBILBreeder() - Constructor for class ec.eda.pbil.PBILBreeder
PBILSpecies - Class in ec.eda.pbil
  PBILSpecies is an IntegerVectorSpecies which implements a faithful version of the PBIL algorithm.
PBILSpecies() - Constructor for class ec.eda.pbil.PBILSpecies
pc - Variable in class ec.eda.cmaes.CMAESSpecies
  The p_c evolution path vector.
pdf - Variable in class ec.display.chart.ChartableStatistics
PDF - Static variable in class ec.display.chart.ChartableStatistics
performCoevolutionaryEvaluation(EvolutionState, Population, GroupedProblemForm) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
personalBestFitness - Variable in class ec.pso.Particle
personalBestGenome - Variable in class ec.pso.Particle
personalCoeff - Variable in class ec.pso.PSOBreeder
PF - Variable in class ec.de.Rand1EitherOrDEBreeder
pickFromDistribution(double[], double) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of probabilities, normalized and summed as follows: For example, if four probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.
pickFromDistribution(double[], double, int) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of probabilities, normalized and summed as follows: For example, if four probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.
pickFromDistribution(float[], float) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of probabilities, normalized and summed as follows: For example, if four probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.
pickFromDistribution(float[], float, int) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of probabilities, normalized and summed as follows: For example, if four probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.
pickFromDistribution(Object[], RandomChoiceChooserD, double) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of objects, each with an associated probability that is accessed by taking an object and passing it to chooser.getProbability(obj).
pickFromDistribution(Object[], RandomChoiceChooserD, double, int) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of objects, each with an associated probability that is accessed by taking an object and passing it to chooser.getProbability(obj).
pickFromDistribution(Object[], RandomChoiceChooser, float) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of objects, each with an associated probability that is accessed by taking an object and passing it to chooser.getProbability(obj).
pickFromDistribution(Object[], RandomChoiceChooser, float, int) - Static method in class ec.util.RandomChoice
  Picks a random item from an array of objects, each with an associated probability that is accessed by taking an object and passing it to chooser.getProbability(obj).
pickGrowProbability - Variable in class ec.gp.koza.HalfBuilder
  The likelihood of using GROW over FULL.
pickNode(EvolutionState, int, int, GPIndividual, GPTree) - Method in interface ec.gp.GPNodeSelector
  Picks a node at random from tree and returns it.
pickNode(EvolutionState, int, int, GPIndividual, GPTree) - Method in class ec.gp.koza.KozaNodeSelector
pickRandom(BreedingSource[], double) - Static method in class ec.BreedingSource
  Picks a random source from an array of sources, with their probabilities normalized and summed as follows: For example, if four breeding source probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.
pickSize(EvolutionState, int) - Method in class ec.gp.GPNodeBuilder
  Assuming that either minSize and maxSize, or sizeDistribution, is defined, picks a random size from minSize...maxSize inclusive, or randomly from sizeDistribution.
pickSize(EvolutionState, int) - Method in class ec.rule.RuleSetConstraints
  Assuming that either resetMinSize and resetMaxSize, or sizeDistribution, is defined, picks a random size from resetMinSize...resetMaxSize inclusive, or randomly from sizeDistribution.
pickSize(EvolutionState, int, int, int) - Method in class ec.gp.build.Uniform
pickWorst - Variable in class ec.parsimony.BucketTournamentSelection
  Do we pick the worst instead of the best?
pickWorst - Variable in class ec.parsimony.DoubleTournamentSelection
  Do we pick the worst instead of the best?
pickWorst - Variable in class ec.parsimony.RatioBucketTournamentSelection
  Do we pick the worst instead of the best?
pickWorst - Variable in class ec.select.BestSelection
  Do we pick the worst instead of the best?
pickWorst - Variable in class ec.select.TournamentSelection
  Do we pick the worst instead of the best?
pickWorst2 - Variable in class ec.parsimony.DoubleTournamentSelection
PieChartStatistics - Class in ec.display.chart
PieChartStatistics() - Constructor for class ec.display.chart.PieChartStatistics
PIPE - Static variable in class ec.gp.ge.GrammarParser
pipe_prototype - Variable in class ec.Species
  The prototypical breeding pipeline for this species.
polynomialIsAlternative - Variable in class ec.vector.FloatVectorSpecies
  Whether the Polynomial Mutation method is the "alternative" method, per gene.
polynomialIsAlternative(int) - Method in class ec.vector.FloatVectorSpecies
polynomialMutate(EvolutionState, MersenneTwisterFast, double, boolean, boolean) - Method in class ec.vector.DoubleVectorIndividual
  This function is broken out to keep it identical to NSGA-II's mutation.c code.
polynomialMutate(EvolutionState, MersenneTwisterFast, float, boolean, boolean) - Method in class ec.vector.FloatVectorIndividual
  This function is broken out to keep it identical to NSGA-II's mutation.c code.
pool - Static variable in class ec.eval.Slave
pool - Variable in class ec.simple.SimpleBreeder
pool - Variable in class ec.simple.SimpleEvaluator
pop() - Method in class ec.util.IntBag
  Returns 0 if the IntBag is empty, else removes and returns the topmost int.
pop() - Method in class ec.util.Parameter
  Returns a new parameter with one path item popped off the end.
pop(int) - Method in class ec.gp.ADFStack
  Pops off n items from the stack, if possible.
popChampion - Variable in class ec.neat.NEATIndividual
  Marks the best individual in current generation of the population.
popChampionChild - Variable in class ec.neat.NEATIndividual
  Marks the duplicate child of a champion (for tracking purposes).
popn(int) - Method in class ec.util.Parameter
  Returns a new parameter with n path items popped off the end.
populate(EvolutionState, int) - Method in class ec.Population
  Populates the population with new random individuals.
populate(EvolutionState, int) - Method in class ec.Subpopulation
populatePredictiveParseTable(GrammarNode) - Method in class ec.gp.ge.GrammarParser
  Now populate the predictive-parse table, this procedure reads hash-maps/tables for the grammar-rule indices, PREDICT-SETs etc, and assigns the corresponding values in the predictive-parse table.
population - Variable in class ec.EvolutionState
  The current population.
Population - Class in ec
  A Population is the repository for all the Individuals being bred or evaluated in the evolutionary run at a given time.
Population() - Constructor for class ec.Population
populationStagnation(EvolutionState, int, ArrayList<NEATSubspecies>) - Method in class ec.neat.NEATSpecies
  Determine if the whole subpopulation get into stagnation.
portrayIndividual(EvolutionState, Individual) - Method in class ec.display.portrayal.IndividualPortrayal
portrayIndividual(EvolutionState, Individual) - Method in class ec.display.portrayal.SimpleIndividualPortrayal
pos - Variable in class ec.util.DecodeReturn
  The DecodeReturn new position in the string.
possiblyRestoreFromCheckpoint(String[]) - Static method in class ec.Evolve
  Restores an EvolutionState from checkpoint if "-checkpoint FILENAME" is in the command-line arguments.
postAnnouncements - Variable in class ec.util.Log
  Should the log post announcements?
postBreedingExchangePopulation(EvolutionState) - Method in class ec.exchange.InterPopulationExchange
postBreedingExchangePopulation(EvolutionState) - Method in class ec.exchange.IslandExchange
postBreedingExchangePopulation(EvolutionState) - Method in class ec.Exchanger
  Performs exchanges after the population has been bred but before it has been evaluated, once every generation (or pseudogeneration).
postBreedingExchangePopulation(EvolutionState) - Method in class ec.simple.SimpleExchanger
  Simply returns state.population.
postBreedingStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
postBreedingStatistics(EvolutionState) - Method in class ec.Statistics
  GENERATIONAL: Called immediately after breeding occurs.
postCheckpointStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately after checkpointing occurs.
postCheckpointStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately after checkpointing occurs.
postEvaluationGlobalUpdate(EvolutionState) - Method in class ec.Evaluator
  Called to update some state by considering the current population.
postEvaluationLocalUpdate(EvolutionState, Individual, int) - Method in class ec.Evaluator
  Called to update some state by considering a single Individual.
postEvaluationStatistics(EvolutionState) - Method in class ec.multiobjective.HypervolumeStatistics
postEvaluationStatistics(EvolutionState) - Method in class ec.multiobjective.MultiObjectiveStatistics
postEvaluationStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
  Prints out the statistics, but does not end with a println -- this lets overriding methods print additional statistics on the same line
postEvaluationStatistics(EvolutionState) - Method in class ec.simple.SimpleStatistics
postEvaluationStatistics(EvolutionState) - Method in class ec.Statistics
  GENERATIONAL: Called immediately after evaluation occurs.
postEvolution(EvolutionStateEvent) - Method in interface ec.display.EvolutionStateListener
postEvolution(EvolutionStateEvent) - Method in class ec.display.SubpopulationPanel
postInitializationStatistics(EvolutionState) - Method in class ec.gp.koza.KozaShortStatistics
postInitializationStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
postInitializationStatistics(EvolutionState) - Method in class ec.simple.SimpleStatistics
postInitializationStatistics(EvolutionState) - Method in class ec.Statistics
  GENERATIONAL: Called immediately after population initialization occurs.
postPostBreedingExchangeStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately after the post-breeding exchange occurs.
postPostBreedingExchangeStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately after the post-breeding exchange occurs.
postPreBreedingExchangeStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately after the pre-breeding exchange occurs.
postPreBreedingExchangeStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately after the pre-breeding exchange occurs.
postProcess(EvolutionState) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
postProcess(EvolutionState) - Method in class ec.multiobjective.spea2.SPEA2Breeder
postProcess(EvolutionState) - Method in class ec.simple.SimpleBreeder
  A hook to do final modifications as necessary to the population after breeding has concluded.
postProcess(Population, Population, EvolutionState) - Method in class ec.es.MuCommaLambdaBreeder
  A hook for Mu+Lambda, not used in Mu,Lambda
postProcess(Population, Population, EvolutionState) - Method in class ec.es.MuPlusLambdaBreeder
postProcessFunctionSet() - Method in class ec.gp.GPFunctionSet
  Sets up the arrays based on the hashtables
postprocessIndividual(EvolutionState, int) - Method in class ec.rule.RuleIndividual
  Called by pipelines after they've modified the individual and it might need to be "fixed" -- basically a hook for you to override.
postprocessPopulation(EvolutionState, Population, boolean[], boolean) - Method in interface ec.coevolve.GroupedProblemForm
  Finish processing the population (such as fitness information) after evaluation.
postprocessPopulation(EvolutionState, Population, boolean[], boolean) - Method in class ec.eval.MasterProblem
postprocessPopulation(EvolutionState, Population, boolean[], boolean) - Method in class ec.gp.ge.GEProblem
postprocessRules(EvolutionState, int) - Method in class ec.rule.RuleSet
  Should be called by pipelines to "fix up" the rulesets after they have been mutated or crossed over.
postProcessSetType(int) - Method in class ec.gp.GPSetType
  Sets up the packed and sparse arrays based on the hashtable
postProcessTypes() - Method in class ec.gp.GPInitializer
  Assigns unique integers to each atomic type, and sets up compatibility arrays for set types.
preBreedingExchangePopulation(EvolutionState) - Method in class ec.exchange.InterPopulationExchange
preBreedingExchangePopulation(EvolutionState) - Method in class ec.exchange.IslandExchange
preBreedingExchangePopulation(EvolutionState) - Method in class ec.Exchanger
  Performs exchanges after the population has been evaluated but before it has been bred, once every generation (or pseudogeneration).
preBreedingExchangePopulation(EvolutionState) - Method in class ec.simple.SimpleExchanger
  Simply returns state.population.
preBreedingStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
preBreedingStatistics(EvolutionState) - Method in class ec.Statistics
  GENERATIONAL: Called immediately before breeding occurs.
preCheckpointStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately before checkpointing occurs.
preCheckpointStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately before checkpointing occurs.
preEvaluationStatistics(EvolutionState) - Method in class ec.evolve.RandomRestarts
  Checks the clock; if it's time to restart, we repopulate the population.
preEvaluationStatistics(EvolutionState) - Method in class ec.parsimony.TarpeianStatistics
  Marks a proportion (killProportion) of individuals with above-average size (within their own subpopulation) to a minimum value.
preEvaluationStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
preEvaluationStatistics(EvolutionState) - Method in class ec.Statistics
  GENERATIONAL: Called immediately before evaluation occurs.
preInitializationStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
preInitializationStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately before population initialization occurs.
prepareADF(ADF, GPProblem) - Method in class ec.gp.ADFContext
  Increases arguments to accommodate space if necessary.
prepareADM(ADM) - Method in class ec.gp.ADFContext
  Sets adf to a
prepareDEBreeder(EvolutionState) - Method in class ec.de.DEBreeder
preparePipeline(Object) - Method in class ec.BreedingPipeline
preparePipeline(Object) - Method in class ec.BreedingSource
  A hook which should be passed to all your subsidiary breeding sources.
preparePipeline(Object) - Method in class ec.select.MultiSelection
prepareStatistics(EvolutionState) - Method in class ec.gp.koza.KozaShortStatistics
prepareStatistics(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
prepareToBreed(EvolutionState, int) - Method in class ec.steadystate.SteadyStateBreeder
prepareToEvaluate(EvolutionState, int) - Method in class ec.eval.MasterProblem
prepareToEvaluate(EvolutionState, int) - Method in class ec.gp.ge.GEProblem
prepareToEvaluate(EvolutionState, int) - Method in class ec.Problem
  May be called by the Evaluator prior to a series of individuals to evaluate, and then ended with a finishEvaluating(...).
prepareToEvaluate(EvolutionState, int) - Method in class ec.steadystate.SteadyStateEvaluator
prepareToProduce(EvolutionState, int, int) - Method in class ec.breed.BufferedBreedingPipeline
prepareToProduce(EvolutionState, int, int) - Method in class ec.breed.FirstCopyPipeline
prepareToProduce(EvolutionState, int, int) - Method in class ec.breed.RepeatPipeline
prepareToProduce(EvolutionState, int, int) - Method in class ec.breed.UniquePipeline
prepareToProduce(EvolutionState, int, int) - Method in class ec.BreedingPipeline
prepareToProduce(EvolutionState, int, int) - Method in class ec.BreedingSource
  Called before produce(...), usually once a generation, or maybe only once if you're doing steady-state evolution, to let the breeding source "warm up" prior to producing.
prepareToProduce(EvolutionState, int, int) - Method in class ec.es.ESSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.parsimony.BucketTournamentSelection
  Prepare to produce: create the buckets!!!!
prepareToProduce(EvolutionState, int, int) - Method in class ec.parsimony.RatioBucketTournamentSelection
  Prepare to produce: create the buckets!!!!
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.AnnealedSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.BestSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.BoltzmannSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.FitProportionateSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.GreedyOverselection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.MultiSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.SigmaScalingSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.SUSSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.select.TopSelection
prepareToProduce(EvolutionState, int, int) - Method in class ec.SelectionMethod
  A default version of prepareToProduce which does nothing.
prependParent(ParameterDatabase) - Method in class ec.util.ParameterDatabase
prePostBreedingExchangeStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately before the post-breeding exchange occurs.
prePostBreedingExchangeStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately before the post-breeding exchange occurs.
prePreBreedingExchangeStatistics(EvolutionState) - Method in class ec.Statistics
  Called immediately before the pre-breeding exchange occurs.
prePreBreedingExchangeStatistics(EvolutionState) - Method in interface ec.steadystate.SteadyStateStatisticsForm
  Called immediately before the pre-breeding exchange occurs.
preprocess(EvolutionState, int) - Method in class ec.gp.build.Uniform
preprocessIndividual(EvolutionState, int) - Method in class ec.rule.RuleIndividual
  Called by pipelines before they've modified the individual and it might need to be "fixed" -- basically a hook for you to override.
preprocessPopulation(EvolutionState, Population, boolean[], boolean) - Method in interface ec.coevolve.GroupedProblemForm
  Set up the population `pop` (such as fitness information) prior to evaluation.
preprocessPopulation(EvolutionState, Population, boolean[], boolean) - Method in class ec.eval.MasterProblem
preprocessPopulation(EvolutionState, Population, boolean[], boolean) - Method in class ec.gp.ge.GEProblem
preprocessRules(EvolutionState, int) - Method in class ec.rule.RuleSet
  Should be called by pipelines to "fix up" the rulesets before they have been mutated or crossed over.
previousLastActivation - Variable in class ec.neat.NEATNode
  Holds the activation BEFORE the previous step's This is necessary for a special recurrent case when the inNode of a recurrent link is one time step ahead of the outNode.
previousPopulation - Variable in class ec.de.DEBreeder
  the previous population is stored in order to have parents compete directly with their children
prevMean - Variable in class ec.eda.amalgam.AMALGAMSpecies
primeGenerator(MersenneTwisterFast) - Static method in class ec.Evolve
  Primes the generator.
print(String, int) - Method in class ec.util.Output
  Prints a non-announcement message to a given log.
print(String, int[]) - Method in class ec.util.Output
  Prints a non-announcement message to the given logs, with a certain verbosity.
print(String, int, int) - Method in class ec.util.Output
  Prints a non-announcement message to a given log, with a certain verbosity.
print(String, int, int[]) - Method in class ec.util.Output
  Prints a non-announcement message to the given logs, with a certain verbosity.
print(String, int, Log) - Method in class ec.util.Output
  Prints a non-announcement message to a given log, with a certain verbosity.
PRINT_PARAMS - Static variable in class ec.util.ParameterDatabase
PRINT_STYLE_C - Static variable in class ec.gp.GPTree
PRINT_STYLE_DOT - Static variable in class ec.gp.GPTree
PRINT_STYLE_LATEX - Static variable in class ec.gp.GPTree
PRINT_STYLE_LISP - Static variable in class ec.gp.GPTree
printExtraPopStatisticsAfter(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
printExtraPopStatisticsBefore(EvolutionState) - Method in class ec.gp.koza.KozaShortStatistics
printExtraPopStatisticsBefore(EvolutionState) - Method in class ec.simple.SimpleShortStatistics
printExtraSubpopStatisticsAfter(EvolutionState, int) - Method in class ec.simple.SimpleShortStatistics
printExtraSubpopStatisticsBefore(EvolutionState, int) - Method in class ec.gp.koza.KozaShortStatistics
printExtraSubpopStatisticsBefore(EvolutionState, int) - Method in class ec.simple.SimpleShortStatistics
printFitness(EvolutionState, int) - Method in class ec.Fitness
  Should print the fitness out in a computer-readable fashion, with a verbosity of Output.V_NO_GENERAL.
printFitness(EvolutionState, int, int) - Method in class ec.Fitness
  Should print the fitness out in a computer-readable fashion, using state.output.println(...,verbosity,log).
printFitness(EvolutionState, PrintWriter) - Method in class ec.Fitness
  Should print the fitness out in a computer-readable fashion, using writer.println(...).
printFitnessForHumans(EvolutionState, int) - Method in class ec.Fitness
  Should print the fitness out fashion pleasing for humans to read, with a verbosity of Output.V_NO_GENERAL.
printFitnessForHumans(EvolutionState, int, int) - Method in class ec.Fitness
  Should print the fitness out fashion pleasing for humans to read, using state.output.println(...,verbosity,log).
printGene(EvolutionState, int, int) - Method in class ec.vector.Gene
  Prints the gene in a way that can be read by readGene().
printGene(EvolutionState, PrintWriter) - Method in class ec.vector.Gene
  Prints the gene in a way that can be read by readGene().
printGeneForHumans(EvolutionState, int, int) - Method in class ec.vector.Gene
  Nice printing.
printGeneToString() - Method in class ec.neat.NEATGene
  This method is used to output a gene that is same as the format in start genome file.
printGeneToString() - Method in class ec.vector.Gene
  Prints the gene to a string in a fashion readable by readGeneFromString and parseable by readGene(state, reader).
printGeneToStringForHumans() - Method in class ec.neat.NEATGene
printGeneToStringForHumans() - Method in class ec.vector.Gene
  Prints the gene to a string in a human-readable fashion.
printIndividual(EvolutionState, int) - Method in class ec.gp.GPIndividual
printIndividual(EvolutionState, int) - Method in class ec.Individual
  Should print the individual in a way that can be read by computer, including its fitness, with a verbosity of Output.V_NO_GENERAL.
printIndividual(EvolutionState, int) - Method in class ec.pso.Particle
printIndividual(EvolutionState, int) - Method in class ec.rule.RuleIndividual
printIndividual(EvolutionState, int, int) - Method in class ec.Individual
  Should print the individual in a way that can be read by computer, including its fitness, using state.output.println(...,verbosity,log) You can get fitness to print itself at the appropriate time by calling fitness.printFitness(state,log,verbosity);
printIndividual(EvolutionState, PrintWriter) - Method in class ec.gp.GPIndividual
printIndividual(EvolutionState, PrintWriter) - Method in class ec.Individual
  Should print the individual in a way that can be read by computer, including its fitness.
printIndividual(EvolutionState, PrintWriter) - Method in class ec.pso.Particle
printIndividual(EvolutionState, PrintWriter) - Method in class ec.rule.RuleIndividual
  Overridden for the RuleIndividual genotype, writing each ruleset in turn.
printIndividualForHumans(EvolutionState, int) - Method in class ec.gp.ge.GEIndividual
printIndividualForHumans(EvolutionState, int) - Method in class ec.gp.GPIndividual
printIndividualForHumans(EvolutionState, int) - Method in class ec.Individual
  Should print the individual out in a pleasing way for humans, with a verbosity of Output.V_NO_GENERAL.
printIndividualForHumans(EvolutionState, int) - Method in class ec.rule.RuleIndividual
printIndividualForHumans(EvolutionState, int, int) - Method in class ec.Individual
  Should print the individual out in a pleasing way for humans, including its fitness, using state.output.println(...,verbosity,log) You can get fitness to print itself at the appropriate time by calling fitness.printFitnessForHumans(state,log,verbosity);
println(String, int) - Method in class ec.util.Output
  Prints a non-announcement message to the given logs, with a verbosity of V_NO_GENERAL.
println(String, int, boolean) - Method in class ec.util.Output
  Prints a message to a given log.
println(String, int, int) - Method in class ec.util.Output
  Prints a non-announcement message to the given logs, with a certain verbosity.
println(String, int, int[]) - Method in class ec.util.Output
  Prints a non-announcement message to the given logs, with a certain verbosity.
printNode(EvolutionState, int) - Method in class ec.gp.GPNode
  Prints out a COMPUTER-readable and Lisp-like atom for the node, which is also suitable for readNode to read, and returns the number of bytes in the string that you sent to the log (use print(), not println()).
printNode(EvolutionState, int, int) - Method in class ec.gp.GPNode
  Prints out a COMPUTER-readable and Lisp-like atom for the node, which is also suitable for readNode to read, and returns the number of bytes in the string that you sent to the log (use print(), not println()).
printNode(EvolutionState, PrintWriter) - Method in class ec.gp.GPNode
  Prints out a COMPUTER-readable and Lisp-like atom for the node, which is also suitable for readNode to read, and returns the number of bytes in the string that you sent to the log (use print(), not println()).
printNodeForHumans(EvolutionState, int) - Method in class ec.gp.GPNode
  Prints out a human-readable and Lisp-like atom for the node, and returns the number of bytes in the string that you sent to the log (use print(), not println()).
printNodeForHumans(EvolutionState, int, int) - Method in class ec.gp.GPNode
  Prints out a human-readable and Lisp-like atom for the node, and returns the number of bytes in the string that you sent to the log (use print(), not println()).
printNodeToString() - Method in class ec.neat.NEATNode
  This method is used to output a gene that is same as the format in start genome file.
printPopulation(EvolutionState, int) - Method in class ec.Population
  Prints an entire population in a form readable by humans but also parseable by the computer using readPopulation(EvolutionState, LineNumberReader), with a verbosity of Output.V_NO_GENERAL.
printPopulation(EvolutionState, int, int) - Method in class ec.Population
  Prints an entire population in a form readable by humans but also parseable by the computer using readPopulation(EvolutionState, LineNumberReader).
printPopulation(EvolutionState, PrintWriter) - Method in class ec.Population
  Prints an entire population in a form readable by humans but also parseable by the computer using readPopulation(EvolutionState, LineNumberReader).
printPopulationForHumans(EvolutionState, int) - Method in class ec.Population
  Prints an entire population in a form readable by humans, with a verbosity of Output.V_NO_GENERAL.
printPopulationForHumans(EvolutionState, int, int) - Method in class ec.Population
  Prints an entire population in a form readable by humans.
printRootedTree(EvolutionState, int, int) - Method in class ec.gp.GPNode
  Prints out the tree on a single line, with no ending \n, in a fashion that can be read in later by computer.
printRootedTree(EvolutionState, int, int, int) - Method in class ec.gp.GPNode
  Prints out the tree on a single line, with no ending \n, in a fashion that can be read in later by computer.
printRootedTree(EvolutionState, PrintWriter, int) - Method in class ec.gp.GPNode
  Prints out the tree on a single line, with no ending \n, in a fashion that can be read in later by computer.
printRootedTreeForHumans(EvolutionState, int, int, int) - Method in class ec.gp.GPNode
  Prints out the tree in a readable Lisp-like multi-line fashion.
printRootedTreeForHumans(EvolutionState, int, int, int, int) - Method in class ec.gp.GPNode
  Prints out the tree in a readable Lisp-like multi-line fashion.
printRule(EvolutionState, int) - Method in class ec.rule.Rule
  Prints the rule in a way that can be read by readRule().
printRule(EvolutionState, int, int) - Method in class ec.rule.Rule
  Prints the rule in a way that can be read by readRule().
printRule(EvolutionState, PrintWriter) - Method in class ec.rule.Rule
  Prints the rule in a way that can be read by readRule().
printRuleForHumans(EvolutionState, int) - Method in class ec.rule.Rule
  Nice printing.
printRuleForHumans(EvolutionState, int, int) - Method in class ec.rule.Rule
  Nice printing.
printRuleSet(EvolutionState, int) - Method in class ec.rule.RuleSet
  Prints the rule set such that the computer can read it later
printRuleSet(EvolutionState, int, int) - Method in class ec.rule.RuleSet
  Prints the rule set such that the computer can read it later
printRuleSet(EvolutionState, PrintWriter) - Method in class ec.rule.RuleSet
  Prints the rule set such that the computer can read it later
printRuleSetForHumans(EvolutionState, int) - Method in class ec.rule.RuleSet
  Prints out the rule set in a readable fashion.
printRuleSetForHumans(EvolutionState, int, int) - Method in class ec.rule.RuleSet
  Prints out the rule set in a readable fashion.
printRuleToString() - Method in class ec.rule.Rule
  Prints the rule to a string in a fashion readable by readRuleFromString.
printRuleToString(EvolutionState) - Method in class ec.rule.Rule
  Prints the rule to a string in a fashion readable by readRuleFromString.
printRuleToStringForHumans() - Method in class ec.rule.Rule
  Nice printing to a string.
printState - Variable in class ec.util.ParameterDatabase
printStyle - Variable in class ec.gp.GPTree
  The print style of the GPTree.
printSubpopulation(EvolutionState, int) - Method in class ec.Subpopulation
  Prints an entire subpopulation in a form readable by humans but also parseable by the computer using readSubpopulation(EvolutionState, LineNumberReader) with a verbosity of Output.V_NO_GENERAL.
printSubpopulation(EvolutionState, int, int) - Method in class ec.Subpopulation
  Prints an entire subpopulation in a form readable by humans but also parseable by the computer using readSubpopulation(EvolutionState, LineNumberReader).
printSubpopulation(EvolutionState, PrintWriter) - Method in class ec.Subpopulation
  Prints an entire subpopulation in a form readable by humans but also parseable by the computer using readSubpopulation(EvolutionState, LineNumberReader).
printSubpopulationForHumans(EvolutionState, int) - Method in class ec.Subpopulation
printSubpopulationForHumans(EvolutionState, int, int) - Method in class ec.Subpopulation
  Prints an entire subpopulation in a form readable by humans.
printTerminalsAsVariablesInC - Variable in class ec.gp.GPTree
  When using c to print for humans, do we print terminals as variables? (as opposed to zero-argument functions)?
printTree(EvolutionState, int) - Method in class ec.gp.GPTree
  Prints out the tree in single-line fashion suitable for reading in later by computer.
printTree(EvolutionState, int, int) - Method in class ec.gp.GPTree
  Prints out the tree in single-line fashion suitable for reading in later by computer.
printTree(EvolutionState, PrintWriter) - Method in class ec.gp.GPTree
  Prints out the tree in single-line fashion suitable for reading in later by computer.
printTreeForHumans(EvolutionState, int) - Method in class ec.gp.GPTree
  Prints out the tree in a readable Lisp-like fashion.
printTreeForHumans(EvolutionState, int, int) - Method in class ec.gp.GPTree
  Prints out the tree in a readable Lisp-like fashion.
printTrees(EvolutionState, int) - Method in class ec.gp.GPIndividual
  Prints just the trees of the GPIndividual.
printTwoArgumentNonterminalsAsOperatorsInC - Variable in class ec.gp.GPTree
  When using c to print for humans, do we print two-argument nonterminals in operator form "a op b"? (as opposed to functions "op(a, b)")?
probability - Variable in class ec.BreedingSource
  The probability that this BreedingSource will be chosen to breed over other BreedingSources.
probabilityOfPickingSizePlusOne - Variable in class ec.select.BestSelection
  Probablity of picking the size plus one.
probabilityOfPickingSizePlusOne - Variable in class ec.select.TournamentSelection
  Probablity of picking the size plus one
probabilityOfSelection - Variable in class ec.gp.GPNodeConstraints
  Probability of selection -- an auxillary measure mostly used by PTC1/PTC2 right now
probabilityOfSelection - Variable in class ec.parsimony.DoubleTournamentSelection
  What's our probability of selection? If 1.0, we always pick the "good" individual.
probabilityOfSelection2 - Variable in class ec.parsimony.DoubleTournamentSelection
problem - Variable in class ec.eval.MasterProblem
problem - Variable in class ec.gp.ge.GEProblem
Problem - Class in ec
  Problem is a prototype which defines the problem against which we will evaluate individuals in a population.
Problem() - Constructor for class ec.Problem
process(EvolutionState, int, String, int, Individual) - Method in class ec.Exchanger
  Typically called by preBreedingExchangePopulation prior to migrating an individual.
produce(int, int, int, int, Individual[], EvolutionState, int, HashMap<String, Object>) - Method in class ec.select.FirstSelection
produce(int, int, int, int, Individual[], EvolutionState, int, HashMap<String, Object>) - Method in class ec.select.RandomSelection
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.BufferedBreedingPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.CheckingPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.FirstCopyPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.ForceBreedingPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.GenerationSwitchPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.InitializationPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.MultiBreedingPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.RepeatPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.ReproductionPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.breed.UniquePipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.BreedingSource
  Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n.
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.InternalCrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.MutateAllNodesPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.MutateDemotePipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.MutateERCPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.MutateOneNodePipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.MutatePromotePipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.MutateSwapPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.RehangPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.breed.SizeFairCrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.koza.CrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.gp.koza.MutationPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.rule.breed.RuleCrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.rule.breed.RuleMutationPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.SelectionMethod
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.vector.breed.GeneDuplicationPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.vector.breed.ListCrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.vector.breed.MultipleVectorCrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.vector.breed.VectorCrossoverPipeline
produce(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.vector.breed.VectorMutationPipeline
produce(int, EvolutionState, int) - Method in class ec.es.ESSelection
produce(int, EvolutionState, int) - Method in class ec.parsimony.BucketTournamentSelection
produce(int, EvolutionState, int) - Method in class ec.parsimony.DoubleTournamentSelection
  Produces the index of a person selected from among several by a tournament.
produce(int, EvolutionState, int) - Method in class ec.parsimony.RatioBucketTournamentSelection
produce(int, EvolutionState, int) - Method in class ec.select.AnnealedSelection
produce(int, EvolutionState, int) - Method in class ec.select.BestSelection
produce(int, EvolutionState, int) - Method in class ec.select.FirstSelection
produce(int, EvolutionState, int) - Method in class ec.select.FitProportionateSelection
produce(int, EvolutionState, int) - Method in class ec.select.GreedyOverselection
produce(int, EvolutionState, int) - Method in class ec.select.LexicaseSelection
produce(int, EvolutionState, int) - Method in class ec.select.MultiSelection
produce(int, EvolutionState, int) - Method in class ec.select.RandomSelection
produce(int, EvolutionState, int) - Method in class ec.select.SUSSelection
produce(int, EvolutionState, int) - Method in class ec.select.TopSelection
produce(int, EvolutionState, int) - Method in class ec.select.TournamentSelection
produce(int, EvolutionState, int) - Method in class ec.SelectionMethod
  An alternative form of "produce" special to Selection Methods; selects an individual from the given subpopulation and returns its position in that subpopulation.
produce(SelectionMethod, int, int, EvolutionState, int) - Method in class ec.spatial.SpatialMultiPopCoevolutionaryEvaluator
produceCurrent(int, EvolutionState, int) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
  Selects one individual from the given subpopulation.
producePrevious(int, EvolutionState, int) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
  Selects one individual from the previous subpopulation.
produces(EvolutionState, Population, int, int) - Method in class ec.BreedingPipeline
produces(EvolutionState, Population, int, int) - Method in class ec.BreedingSource
  Returns true if this BreedingSource, when attached to the given subpopulation, will produce individuals of the subpopulation's species.
produces(EvolutionState, Population, int, int) - Method in class ec.gp.GPBreedingPipeline
  Returns true if s is a GPSpecies.
produces(EvolutionState, Population, int, int) - Method in class ec.select.MultiSelection
produces(EvolutionState, Population, int, int) - Method in class ec.SelectionMethod
  A default version of produces -- this method always returns true under the assumption that the selection method works with all Fitnesses.
produceWithoutCloning(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.es.ESSelection
produceWithoutCloning(int, int, int, ArrayList<Individual>, EvolutionState, int, HashMap<String, Object>) - Method in class ec.SelectionMethod
ProportionalTournamentSelection - Class in ec.parsimony
  This selection method adds parsimony pressure to the regular tournament selection.
ProportionalTournamentSelection() - Constructor for class ec.parsimony.ProportionalTournamentSelection
Prototype - Interface in ec
  Prototype classes typically have one or a few prototype instances created during the course of a run.
ps - Variable in class ec.eda.cmaes.CMAESSpecies
  The p_{\sigma} evolution path vector.
PS_NONE - Static variable in class ec.util.ParameterDatabase
PS_PRINT_PARAMS - Static variable in class ec.util.ParameterDatabase
PS_UNKNOWN - Static variable in class ec.util.ParameterDatabase
PSOBreeder - Class in ec.pso
  PSOBreeder is a simple single-threaded Breeder which performs Particle Swarm Optimization using the Particle class as individuals.
PSOBreeder() - Constructor for class ec.pso.PSOBreeder
PTC1 - Class in ec.gp.build
  PTC1 implements the "Strongly-typed Probabilistic Tree Creation 1 (PTC1)" algorithm described in
PTC1() - Constructor for class ec.gp.build.PTC1
PTC2 - Class in ec.gp.build
  PTC2 implements the "Strongly-typed Probabilistic Tree Creation 2 (PTC2)" algorithm described in
PTC2() - Constructor for class ec.gp.build.PTC2
PTCFunctionSet - Class in ec.gp.build
  PTCFunctionSet is a GPFunctionSet which adheres to PTCFunctionSetForm, and thus can be used with the PTC1 and PTC2 methods.
PTCFunctionSet() - Constructor for class ec.gp.build.PTCFunctionSet
PTCFunctionSetForm - Interface in ec.gp.build
  PTCFunctionSetForm defines the methods that the PTC1 and PTC2 tree-creation algorithms require of function sets.
push(int) - Method in class ec.util.IntBag
  Synonym for add(obj) -- try to use add instead unless you want to think of the IntBag as a stack.
push(ADFContext) - Method in class ec.gp.ADFStack
  Pushes an ADFContext onto the main stack.
push(String) - Method in class ec.util.Parameter
  Returns a new parameter with s added to the end of the current path items.
push(String[]) - Method in class ec.util.Parameter
  Returns a new parameter with the path items in s added to the end of the current path items.
PushBuilder - Class in ec.gp.push
  PushBuilder implements the Push-style tree building algorithm, which permits nonterminals of arbitrary arity.
PushBuilder() - Constructor for class ec.gp.push.PushBuilder
PushDefaults - Class in ec.gp.push
PushDefaults() - Constructor for class ec.gp.push.PushDefaults
PushInstruction - Class in ec.gp.push
  PushInstruction encapsulates a custom Push instruction.
PushInstruction() - Constructor for class ec.gp.push.PushInstruction
pushOntoFloatStack(Interpreter, float) - Method in class ec.gp.push.PushProblem
  Pushes a value onto the top of the float stack of the interpreter.
pushOntoIntStack(Interpreter, int) - Method in class ec.gp.push.PushProblem
  Pushes a value onto the top of the int stack of the interpreter.
PushProblem - Class in ec.gp.push
  A PushProblem contains useful methods to help you create an interpreter, write out the ECJ GP tree to a string, build a Push Program around this string, load the interpreter with all your custom instructions, and run the Push Program on the interpreter.
PushProblem() - Constructor for class ec.gp.push.PushProblem

## Q

q_ny - Variable in class ec.gp.build.PTCFunctionSet
  nonterminal probabilities[type][thenodes], in organized form
q_ty - Variable in class ec.gp.build.PTCFunctionSet
  terminal probabilities[type][thenodes], in organized form
qsort(byte[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(char[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(double[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(float[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(int[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(int[], SortComparatorL) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(long[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(long[], SortComparatorL) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(short[]) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
qsort(Object[], SortComparator) - Static method in class ec.util.QuickSort
  Non-Recursive QuickSort
QueueIndividual - Class in ec.steadystate
QueueIndividual(Individual, int) - Constructor for class ec.steadystate.QueueIndividual
QuickSort - Class in ec.util
  Implementations of various center-pivot QuickSort routines in Java, and (if you really want 'em) Insertion Sort routines as well.
QuickSort() - Constructor for class ec.util.QuickSort
quitOnRunComplete - Variable in class ec.EvolutionState
  Whether or not the system should prematurely quit when Evaluator returns true for runComplete(...) (that is, when the system found an ideal individual.

## R

R_FAILURE - Static variable in class ec.EvolutionState
  "The evolution run has quit, failing to find a perfect individual."
R_NOTDONE - Static variable in class ec.EvolutionState
  "The evolution run has not quit
R_SUCCESS - Static variable in class ec.EvolutionState
  "The evolution run has quit, finding a perfect individual."
Rand1EitherOrDEBreeder - Class in ec.de
  Rand1EitherOrDEBreeder is a differential evolution breeding operator.
Rand1EitherOrDEBreeder() - Constructor for class ec.de.Rand1EitherOrDEBreeder
random - Variable in class ec.EvolutionState
  An array of random number generators, indexed by the thread number you were given (or, if you're not in a multithreaded area, use 0).
RandomBranch - Class in ec.gp.build
  RandomBranch implements the `Random_Branch` tree generation method described in
RandomBranch() - Constructor for class ec.gp.build.RandomBranch
RandomChoice - Class in ec.util
  RandomChoice organizes arrays of floats into distributions which can be used to pick randomly from.
RandomChoice() - Constructor for class ec.util.RandomChoice
RandomChoiceChooser - Interface in ec.util
  Used by RandomChoice to pick objects by probability from a distribution.
RandomChoiceChooserD - Interface in ec.util
  Used by RandomChoice to pick objects by probability from a distribution.
randomizeOrder(EvolutionState, ArrayList<Individual>) - Method in class ec.coevolve.CompetitiveEvaluator
randomizeRulesOrder(EvolutionState, int) - Method in class ec.rule.RuleSet
  Randomizes the order of the rules in the rule set.
RandomRestarts - Class in ec.evolve
  A special Statistics class which performs random restarts on the population, effectively reininitializing the population and starting over again.
RandomRestarts() - Constructor for class ec.evolve.RandomRestarts
randomSeedOffset - Variable in class ec.EvolutionState
  An amount to add to each random number generator seed to "offset" it -- often this is simply the job number.
RandomSelection - Class in ec.select
  Picks a random individual in the subpopulation.
RandomSelection() - Constructor for class ec.select.RandomSelection
randomValueFromClosedInterval(byte, byte, MersenneTwisterFast) - Method in class ec.vector.ByteVectorIndividual
  Returns a random value from between min and max inclusive.
randomValueFromClosedInterval(int, int, MersenneTwisterFast) - Method in class ec.vector.IntegerVectorIndividual
  Returns a random value from between min and max inclusive.
randomValueFromClosedInterval(long, long, MersenneTwisterFast) - Method in class ec.vector.LongVectorIndividual
  Returns a random value from between min and max inclusive.
randomValueFromClosedInterval(short, short, MersenneTwisterFast) - Method in class ec.vector.LongVectorIndividual
  Returns a random value from between min and max inclusive.
randomValueFromClosedInterval(short, short, MersenneTwisterFast) - Method in class ec.vector.ShortVectorIndividual
  Returns a random value from between min and max inclusive.
randomWalkProbability - Variable in class ec.vector.FloatVectorSpecies
  The continuation probability for Integer Random Walk Mutation, per gene.
randomWalkProbability - Variable in class ec.vector.IntegerVectorSpecies
  The continuation probability for Integer Random Walk Mutation, per gene.
randomWalkProbability(int) - Method in class ec.vector.FloatVectorSpecies
randomWalkProbability(int) - Method in class ec.vector.IntegerVectorSpecies
RandTree - Class in ec.gp.build
RandTree() - Constructor for class ec.gp.build.RandTree
RandTree.ArityObject - Class in ec.gp.build
rank - Variable in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
  Pareto front rank measure (lower ranks are better)
ratio - Variable in class ec.parsimony.RatioBucketTournamentSelection
  The value of RATIO
RatioBucketTournamentSelection - Class in ec.parsimony
  Does a tournament selection, limited to the subpopulation it's working in at the time.
RatioBucketTournamentSelection() - Constructor for class ec.parsimony.RatioBucketTournamentSelection
rawFitness() - Method in class ec.gp.koza.KozaFitness
  Returns the raw fitness metric.
readBooleanWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a boolean value ("true" or "false") if there is one, and returns it.
readByteWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a byte if there is one, and returns it.
readCharacterWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a character if there is one, and returns it.
readDoubleWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a double if there is one, and returns it.
readFitness(EvolutionState, DataInput) - Method in class ec.Fitness
  Reads the binary form of an individual from a DataInput.
readFitness(EvolutionState, DataInput) - Method in class ec.gp.koza.KozaFitness
readFitness(EvolutionState, DataInput) - Method in class ec.multiobjective.MultiObjectiveFitness
readFitness(EvolutionState, DataInput) - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
readFitness(EvolutionState, DataInput) - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
readFitness(EvolutionState, DataInput) - Method in class ec.simple.SimpleFitness
readFitness(EvolutionState, LineNumberReader) - Method in class ec.Fitness
  Reads in the fitness from a form outputted by fitnessToString() and thus printFitnessForHumans(...).
readFitness(EvolutionState, LineNumberReader) - Method in class ec.gp.koza.KozaFitness
readFitness(EvolutionState, LineNumberReader) - Method in class ec.multiobjective.MultiObjectiveFitness
readFitness(EvolutionState, LineNumberReader) - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
readFitness(EvolutionState, LineNumberReader) - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
readFitness(EvolutionState, LineNumberReader) - Method in class ec.simple.SimpleFitness
  Presently does not decode the fact that the fitness is ideal or not
readFloatWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a float if there is one, and returns it.
readGene(EvolutionState, DataInput) - Method in class ec.vector.Gene
  Override this if you need to read rules in from a binary stream
readGene(EvolutionState, LineNumberReader) - Method in class ec.vector.Gene
  Reads a gene printed by printGene(...).
readGeneFromString(String, EvolutionState) - Method in class ec.neat.NEATGene
  This method is used to read a gene in start genome from file.
readGeneFromString(String, EvolutionState) - Method in class ec.vector.Gene
  Reads a gene from a string, which may contain a final '\n'.
readGenotype(EvolutionState, DataInput) - Method in class ec.gp.GPIndividual
  Overridden for the GPIndividual genotype.
readGenotype(EvolutionState, DataInput) - Method in class ec.Individual
  Reads in the genotypic information from a DataInput, erasing the previous genotype of this Individual.
readGenotype(EvolutionState, DataInput) - Method in class ec.rule.RuleIndividual
  Overridden for the RuleIndividual genotype.
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.BitVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.ByteVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.DoubleVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.FloatVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.GeneVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.IntegerVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.LongVectorIndividual
readGenotype(EvolutionState, DataInput) - Method in class ec.vector.ShortVectorIndividual
readIndividual(EvolutionState, DataInput) - Method in class ec.Individual
  Reads the binary form of an individual from a DataInput, erasing the previous information stored in this Individual.
readIndividual(EvolutionState, DataInput) - Method in class ec.pso.Particle
readIndividual(EvolutionState, LineNumberReader) - Method in class ec.Individual
  Reads in the individual from a form printed by printIndividual(), erasing the previous information stored in this Individual.
readIndividual(EvolutionState, LineNumberReader) - Method in class ec.pso.Particle
readIntegerWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in an integer if there is one, and returns it.
readLongWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a long if there is one, and returns it.
readNode(EvolutionState, DataInput) - Method in class ec.gp.ADF
readNode(EvolutionState, DataInput) - Method in class ec.gp.ADFArgument
readNode(EvolutionState, DataInput) - Method in class ec.gp.ERC
  To successfully read from a DataOutput, you must override this to read your specific ERC data in.
readNode(EvolutionState, DataInput) - Method in class ec.gp.GPNode
  Override this to read any additional node-specific information from dataInput besides: the number of arguments, the specific node class, the children, and the parent.
readNode(EvolutionState, LineNumberReader) - Method in class ec.neat.NEATNode
  Reads a Node printed by printNode(...).
readNode(DecodeReturn) - Method in class ec.gp.ERC
readNode(DecodeReturn) - Method in class ec.gp.GPNode
  Reads the node symbol, advancing the DecodeReturn to the first character in the string beyond the node symbol, and returns a new, empty GPNode of the appropriate class representing that symbol, else null if the node symbol is not of the correct type for your GPNode class.
readNodeFromString(String, EvolutionState) - Method in class ec.neat.NEATNode
  This method is used to read a node in start genome from file.
readPopulation(EvolutionState, DataInput) - Method in class ec.Population
  Reads a population in binary form, from the format generated by writePopulation(...).
readPopulation(EvolutionState, LineNumberReader) - Method in class ec.Population
  Reads a population from the format generated by printPopulation(....).
readRootedTree(int, DecodeReturn, GPType, GPFunctionSet, GPNodeParent, int, EvolutionState) - Static method in class ec.gp.GPNode
  Reads the node and its children from the form printed out by printRootedTree.
readRootedTree(EvolutionState, DataInput, GPType, GPFunctionSet, GPNodeParent, int) - Static method in class ec.gp.GPNode
readRule(EvolutionState, DataInput) - Method in class ec.rule.Rule
  Override this if you need to read rules in from a binary stream
readRule(EvolutionState, LineNumberReader) - Method in class ec.rule.Rule
  Reads a rule printed by printRule(...).
readRuleFromString(String, EvolutionState) - Method in class ec.rule.Rule
  Reads a rule from a string, which may contain a final '\n'.
readRuleSet(EvolutionState, DataInput) - Method in class ec.rule.RuleSet
  Reads RuleSets in from a binary stream
readRuleSet(EvolutionState, LineNumberReader) - Method in class ec.rule.RuleSet
  Reads the rule set
readShortWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a short if there is one, and returns it.
readState(DataInputStream) - Method in class ec.util.MersenneTwister
  Reads the entire state of the MersenneTwister RNG from the stream
readState(DataInputStream) - Method in class ec.util.MersenneTwisterFast
  Reads the entire state of the MersenneTwister RNG from the stream
readStringWithPreamble(String, EvolutionState, LineNumberReader) - Static method in class ec.util.Code
  Finds the next nonblank line, skips past an expected preamble, and reads in a string if there is one, and returns it.
readSubpopulation(EvolutionState, DataInput) - Method in class ec.Subpopulation
  Reads a subpopulation in binary form, from the format generated by writeSubpopulation(...).
readSubpopulation(EvolutionState, LineNumberReader) - Method in class ec.Subpopulation
  Reads a subpopulation from the format generated by printSubpopulation(....).
readTree(EvolutionState, DataInput) - Method in class ec.gp.GPTree
readTree(EvolutionState, LineNumberReader) - Method in class ec.gp.GPTree
  Reads in the tree from a form printed by printTree.
readTrials(EvolutionState, DataInput) - Method in class ec.Fitness
  Reads trials in from DataInput.
receiveAdditionalData(EvolutionState, DataInputStream) - Method in class ec.eval.MasterProblem
  This method is called on a MasterProblem by the Slave.
receiveAdditionalData(EvolutionState, DataInputStream) - Method in class ec.Problem
  This method is called on a Problem by the Slave.
recordObservation(EvolutionState, double) - Method in class ec.eda.dovs.DOVSFitness
  Record the result of the new simulation.
recurFlag - Variable in class ec.neat.NEATInnovation
  Is the link innovation a recurrent link.
recurOnlyProb - Variable in class ec.neat.NEATSpecies
  Probability of forcing selection of ONLY links that are naturally recurrent.
reevaluateElites - Variable in class ec.simple.SimpleBreeder
reevaluateIndividuals - Variable in class ec.eval.MetaProblem
  Whether to reevaluate individuals if and when they appear for evaluation in the future.
ReflectedObject - Class in ec.util
ReflectedObject(Object) - Constructor for class ec.util.ReflectedObject
ReflectedObject(Object, Class, String, Object) - Constructor for class ec.util.ReflectedObject
registerSlave(EvolutionState, Socket, Problem, boolean, int, int, int) - Method in class ec.eval.SlaveMonitor
  Registers a new slave with the monitor.
RehangPipeline - Class in ec.gp.breed
  RehangPipeline picks a nonterminal node other than the root and "rehangs" it as a new root.
RehangPipeline() - Constructor for class ec.gp.breed.RehangPipeline
reinitializeContacts(EvolutionState) - Method in class ec.eval.MasterProblem
  Reinitialize contacts with the slaves
reinitializeContacts(EvolutionState) - Method in class ec.Evaluator
  Called to reinitialize remote evaluation network contacts when the run is restarted from checkpoint.
reinitializeContacts(EvolutionState) - Method in class ec.exchange.InterPopulationExchange
  Initializes contacts with other processes, if that's what you're doing.
reinitializeContacts(EvolutionState) - Method in class ec.exchange.IslandExchange
  Initializes contacts with other processes, if that's what you're doing.
reinitializeContacts(EvolutionState) - Method in class ec.Exchanger
  Initializes contacts with other processes, if that's what you're doing.
reinitializeContacts(EvolutionState) - Method in class ec.gp.ge.GEProblem
reinitializeContacts(EvolutionState) - Method in class ec.Problem
  Called to reinitialize remote evaluation network contacts when the run is restarted from checkpoint.
reinitializeContacts(EvolutionState) - Method in class ec.simple.SimpleExchanger
  Doesn't do anything.
remove(int) - Method in class ec.util.IntBag
  Removes the int at the given index, moving the topmost int into its position.
remove(Parameter) - Method in class ec.util.ParameterDatabase
  Removes a parameter from the topmost database.
removeDeeply(Parameter) - Method in class ec.util.ParameterDatabase
removeLog(int) - Method in class ec.util.Output
  Removes the given log.
removeNondestructively(int) - Method in class ec.util.IntBag
  Removes the int at the given index, shifting the other ints down.
removePoorFitnessIndividuals() - Method in class ec.neat.NEATSubspecies
  Remove the individuals from current subspecies who have been mark as eliminate the remain individuals will be allow to reproduce
removeRandomRule(EvolutionState, int) - Method in class ec.rule.RuleSet
  Removes a randomly-chosen rule from the rule set and returns it.
removeRule(int) - Method in class ec.rule.RuleSet
  Removes a rule from the rule set and returns it.
removeTreeModelListener(TreeModelListener) - Method in class ec.util.ReflectedObject
reopen() - Method in class ec.util.Log
  Forces a file-based log to reopen, erasing its previous contents.
reopen(int) - Method in class ec.util.Output
  Forces a file-based log to reopen, erasing its previous contents.
reopen(int[]) - Method in class ec.util.Output
  Forces one or more file-based logs to reopen, erasing their previous contents.
reopen(Log) - Method in class ec.util.LogRestarter
RepeatPipeline - Class in ec.breed
  RepeatPipeline is a BreedingPipeline which, after prepareToProduce() is called, produces a single individual from its single source, then repeatedly clones that child to fulfill requests to produce().
RepeatPipeline() - Constructor for class ec.breed.RepeatPipeline
repetition - Variable in class ec.eda.dovs.DOVSSpecies
  This value will be updated at each generation to determine how many evaluation is needed for one individual.
replacementProbability - Variable in class ec.steadystate.SteadyStateEvolutionState
  When a new individual arrives, with what probability should it directly replace the existing "marked for death" individual, as opposed to only replacing it if it's superior?
replaceWith(GPNode) - Method in class ec.gp.GPNode
  Replaces the node with another node in its position in the tree.
repOK() - Method in class ec.util.IIntPoint
repostAnnouncementsOnRestart - Variable in class ec.util.Log
  Should the log repost all announcements on restart
reproduce(EvolutionState, int, int, ArrayList<NEATSubspecies>) - Method in class ec.neat.NEATSubspecies
  Where the actual reproduce is happening, it will grab the candidate parents, and calls the crossover or mutation method on these parents individuals.
ReproductionPipeline - Class in ec.breed
  ReproductionPipeline is a BreedingPipeline which simply makes a copy of the individuals it recieves from its source.
ReproductionPipeline() - Constructor for class ec.breed.ReproductionPipeline
reserve - Variable in class ec.gp.ADFStack
reset() - Method in class ec.eda.dovs.DOVSFitness
  Reset the fitness to initial status.
reset() - Method in class ec.gp.ADFStack
  Pops off all items on the stack and the substack.
reset() - Method in interface ec.gp.GPNodeSelector
  Resets the Node Selector before a new series of pickNode() if need be.
reset() - Method in class ec.gp.koza.KozaNodeSelector
reset() - Method in class ec.neat.NEATSubspecies
  Reset the status of the current subspecies.
reset() - Method in class ec.util.DataPipe
  Reset the buffer.
reset(double, int, int, boolean, int, double) - Method in class ec.neat.NEATGene
  Reset the gene with given parameters.
reset(int, int, boolean) - Method in class ec.neat.NEATInnovation
  When we have a new innovation, we clone an existing NEATInnovation instance, and change its information with this reset method.
reset(int, int, int) - Method in class ec.neat.NEATInnovation
  When we have a new innovation, we clone an existing NEATInnovation instance, and change its information with this reset method.
reset(int, int, int, double, boolean) - Method in class ec.neat.NEATInnovation
  When we have a new innovation, we clone an existing NEATInnovation instance, and change its information with this reset method.
reset(int, int, int, int, int, int) - Method in class ec.neat.NEATInnovation
  When we have a new innovation, we clone an existing NEATInnovation instance, and change its information with this reset method.
reset(EvolutionState, int) - Method in class ec.neat.NEATGene
reset(EvolutionState, int) - Method in class ec.neat.NEATIndividual
  Initializes an individual with minimal structure.
reset(EvolutionState, int) - Method in class ec.pso.Particle
reset(EvolutionState, int) - Method in class ec.rule.Rule
  The reset method randomly reinitializes the rule.
reset(EvolutionState, int) - Method in class ec.rule.RuleIndividual
reset(EvolutionState, int) - Method in class ec.rule.RuleSet
  A reset method for randomly reinitializing the RuleSet
reset(EvolutionState, int) - Method in class ec.vector.BitVectorIndividual
  Initializes the individual by randomly flipping the bits
reset(EvolutionState, int) - Method in class ec.vector.ByteVectorIndividual
  Initializes the individual by randomly choosing Integers uniformly from mingene to maxgene.
reset(EvolutionState, int) - Method in class ec.vector.DoubleVectorIndividual
  Initializes the individual by randomly choosing doubles uniformly from mingene to maxgene.
reset(EvolutionState, int) - Method in class ec.vector.FloatVectorIndividual
  Initializes the individual by randomly choosing floats uniformly from mingene to maxgene.
reset(EvolutionState, int) - Method in class ec.vector.Gene
  The reset method randomly reinitializes the gene.
reset(EvolutionState, int) - Method in class ec.vector.GeneVectorIndividual
  Initializes the individual by calling reset(...) on each gene.
reset(EvolutionState, int) - Method in class ec.vector.IntegerVectorIndividual
  Initializes the individual by randomly choosing Integers uniformly from mingene to maxgene.
reset(EvolutionState, int) - Method in class ec.vector.LongVectorIndividual
  Initializes the individual by randomly choosing Longs uniformly from mingene to maxgene.
reset(EvolutionState, int) - Method in class ec.vector.ShortVectorIndividual
  Initializes the individual by randomly choosing Integers uniformly from mingene to maxgene.
reset(EvolutionState, int) - Method in class ec.vector.VectorIndividual
  Initializes the individual.
reset(EvolutionState, int, int) - Method in class ec.vector.VectorIndividual
  Initializes the individual to a new size.
reset(NEATNode.NodeType, int, NEATNode.NodePlace) - Method in class ec.neat.NEATNode
  Reset the node to initial status.
reset(String) - Method in class ec.util.DecodeReturn
  Use this to reuse your DecodeReturn for another string
reset(String, int) - Method in class ec.util.DecodeReturn
  Use this to reuse your DecodeReturn for another string
reset(ArrayList<NEATNode>, ArrayList<Gene>) - Method in class ec.neat.NEATIndividual
  Reset the individual with given nodes and genome
resetEachGeneration - Variable in class ec.breed.UniquePipeline
resetFromCheckpoint() - Method in class ec.EvolutionState
  This method is called after a checkpoint is restored from but before the run starts up again.
resetInterpreter(Interpreter) - Method in class ec.gp.push.PushProblem
  Clears the Interpreter's stacks so it is ready to execute another program.
resetMaxSize - Variable in class ec.rule.RuleSetConstraints
resetMinSize - Variable in class ec.rule.RuleSetConstraints
resetNode(EvolutionState, int) - Method in class ec.gp.ERC
  Remember to override this to randomize your ERC after it has been cloned.
resetNode(EvolutionState, int) - Method in class ec.gp.GPNode
  Starts a node in a new life immediately after it has been cloned.
resetNode(EvolutionState, int) - Method in class ec.gp.push.Terminal
resize(int) - Method in class ec.util.IntBag
restart() - Method in class ec.util.Log
  Restarts a log after a system restart from checkpoint.
restart() - Method in class ec.util.Output
restart(Log) - Method in class ec.util.LogRestarter
restarter - Variable in class ec.util.Log
  The log's restarter
restoreFromCheckpoint(String) - Static method in class ec.util.Checkpoint
  Returns an EvolutionState object read from a checkpoint file whose filename is checkpoint
retries - Variable in class ec.de.DEBreeder
returntype - Variable in class ec.gp.GPNodeConstraints
  The return type for a GPNode
reverse() - Method in class ec.util.IntBag
  Reverses order of the elements in the IntBag
reverseMap(EvolutionState, GPIndividual, int) - Method in class ec.gp.ge.GESpecies
  Reverse of the original map() function, takes a GPIndividual and returns a corresponding GEIndividual; The GPIndividual may contain more than one trees, and such cases are handled accordingly, see the 3rd bullet below -- NOTE: This reverse mapping is only valid for S-expression trees ; This procedure supports ERC for the current population (not for population /subpopulation from other islands); However, that could be done by merging all ERCBanks from all the sub-populations but that is not done yet ; Support for the ADF's are done as follows -- suppose in one GPIndividual, there are N trees -- T1, T2, ,,, Tn and each of them follows n different grammars G1, G2, ,,, Gn respectively; now if they are reverse-mapped to int arrays, there will be n int arrays A1[], A2[], ,,, An[]; and suppose the i-th tree Ti is reverse mapped to int array Ai[] and morevoer Ai[] is the longest among all the arrays (Bj[]s); so Bi[] is sufficient to build all ADF trees Tjs.
ROOT_D - Variable in class ec.gp.build.Uniform
ROOT_D_ZERO - Variable in class ec.gp.build.Uniform
rootedTreeEquals(GPNode) - Method in class ec.gp.GPNode
  Returns true if the two rooted trees are "genetically" equal, though they may have different parents.
rootedTreeHashCode() - Method in class ec.gp.GPNode
  Returns a hashcode associated with all the nodes in the tree.
rootParent() - Method in class ec.gp.GPNode
  Returns the root ancestor of this node.
rootProbability - Variable in class ec.gp.koza.KozaNodeSelector
  The probability the root must be chosen
RPAREN - Static variable in class ec.gp.ge.GrammarParser
Rule - Class in ec.rule
  Rule is an abstract class for describing rules.
Rule() - Constructor for class ec.rule.Rule
RULE - Static variable in class ec.gp.ge.GrammarParser
ruleConstraintRepository - Variable in class ec.rule.RuleInitializer
ruleConstraints - Variable in class ec.rule.RuleInitializer
RuleConstraints - Class in ec.rule
  RuleConstraints is a class for constraints applicable to rules.
RuleConstraints() - Constructor for class ec.rule.RuleConstraints
RuleCrossoverPipeline - Class in ec.rule.breed
  RuleCrossoverPipeline is a BreedingPipeline which implements a simple default crossover for RuleIndividuals.
RuleCrossoverPipeline() - Constructor for class ec.rule.breed.RuleCrossoverPipeline
ruleCrossProbability - Variable in class ec.rule.breed.RuleCrossoverPipeline
  What is the probability of a rule migrating?
RuleDefaults - Class in ec.rule
  A static class that returns the base for "default values" which rule-style operators use, rather than making the user specify them all on a per- species basis.
RuleDefaults() - Constructor for class ec.rule.RuleDefaults
RuleIndividual - Class in ec.rule
  RuleIndividual is an Individual with an array of RuleSets, each of which is a set of Rules.
RuleIndividual() - Constructor for class ec.rule.RuleIndividual
RuleInitializer - Class in ec.rule
  A SimpleInitializer subclass designed to be used with rules.
RuleInitializer() - Constructor for class ec.rule.RuleInitializer
RuleMutationPipeline - Class in ec.rule.breed
  RuleMutationPipeline is a BreedingPipeline which implements a simple default Mutation for RuleIndividuals.
RuleMutationPipeline() - Constructor for class ec.rule.breed.RuleMutationPipeline
rulePrototype - Variable in class ec.rule.RuleSetConstraints
  The prototype of the Rule that will be used in the RuleSet (the RuleSet contains only rules with the specified prototype).
rules - Variable in class ec.rule.RuleSet
  The rules in the rule set
RuleSet - Class in ec.rule
  RuleSet is a set of Rules, implemented straightforwardly as an arbitrary-length array of Rules.
RuleSet() - Constructor for class ec.rule.RuleSet
ruleSetConstraintRepository - Variable in class ec.rule.RuleInitializer
ruleSetConstraints - Variable in class ec.rule.RuleInitializer
RuleSetConstraints - Class in ec.rule
  RuleSetConstraints is an basic class for constraints applicable to rulesets.
RuleSetConstraints() - Constructor for class ec.rule.RuleSetConstraints
rulesets - Variable in class ec.rule.RuleIndividual
  The individual's rulesets.
RuleSpecies - Class in ec.rule
  RuleSpecies is a simple individual which is suitable as a species for rule sets subpopulations.
RuleSpecies() - Constructor for class ec.rule.RuleSpecies
run(int) - Method in class ec.EvolutionState
  Starts the run.
runComplete - Variable in class ec.Evaluator
runComplete(EvolutionState) - Method in class ec.coevolve.CompetitiveEvaluator
runComplete(EvolutionState) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
runComplete(EvolutionState) - Method in class ec.Evaluator
  Returns non-NULL if the Evaluator believes that the run is finished: perhaps an ideal individual has been found or some other run result has shortcircuited the run so that it should end prematurely right now.
runComplete(EvolutionState) - Method in class ec.exchange.InterPopulationExchange
  Called after preBreedingExchangePopulation(...) to evaluate whether or not the exchanger wishes the run to shut down (with ec.EvolutionState.R_FAILURE).
runComplete(EvolutionState) - Method in class ec.exchange.IslandExchange
  Called after preBreedingExchangePopulation(...) to evaluate whether or not the exchanger wishes the run to shut down (with ec.EvolutionState.R_FAILURE).
runComplete(EvolutionState) - Method in class ec.Exchanger
  Called after preBreedingExchangePopulation(...) to evaluate whether or not the exchanger wishes the run to shut down (with ec.EvolutionState.R_FAILURE) -- returns a String (which will be printed out as a message) if the exchanger wants to shut down, else returns null if the exchanger does NOT want to shut down.
runComplete(EvolutionState) - Method in class ec.simple.SimpleEvaluator
  The SimpleEvaluator determines that a run is complete by asking each individual in each population if he's optimal; if he finds an individual somewhere that's optimal, he signals that the run is complete.
runComplete(EvolutionState) - Method in class ec.simple.SimpleExchanger
  Always returns null
runEvolve - Static variable in class ec.eval.Slave
runs - Variable in class ec.eval.MetaProblem
  The number of base-level evolutionary runs to perform to evaluate an individual.
runTime - Static variable in class ec.eval.Slave
runtimeArguments - Variable in class ec.EvolutionState
  The original runtime arguments passed to the Java process.

## S

s - Variable in class ec.util.DecodeReturn
  Stores strings, error messages
sbd - Variable in class ec.eda.cmaes.CMAESSpecies
  bd x sigma
scanAt(int) - Method in class ec.util.DecodeReturn
  Sets the DecodeReturn to begin scanning at _pos, which should be valid.
scheduleJobForEvaluation(EvolutionState, Job) - Method in class ec.eval.SlaveMonitor
  Schedules a job for execution on one of the available slaves.
SEED_INCREMENT - Static variable in class ec.eval.SlaveMonitor
SelectDefaults - Class in ec.select
SelectDefaults() - Constructor for class ec.select.SelectDefaults
selectForDiversity(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
SelectionMethod - Class in ec
  A SelectionMethod is a BreedingSource which provides direct IMMUTABLE pointers to original individuals in an old population, not fresh mutable copies.
SelectionMethod() - Constructor for class ec.SelectionMethod
selects - Variable in class ec.select.MultiSelection
  The MultiSelection's individuals
sendAdditionalData(EvolutionState, DataOutputStream) - Method in class ec.eval.MasterProblem
  This method is called from the SlaveMonitor's accept() thread to optionally send additional data to the Slave via the dataOut stream.
sendAdditionalData(EvolutionState, DataOutputStream) - Method in class ec.Problem
  This method is called from the SlaveMonitor's accept() thread to optionally send additional data to the Slave via the dataOut stream.
SENSOR - Enum constant in enum class ec.neat.NEATNode.NodeType
sensorLoad(double) - Method in class ec.neat.NEATNode
  If this node is a sensor node, load this node with the given input
sequentialBreeding - Variable in class ec.Breeder
  The flag to let the coevolutionary system know that we're doing sequential breeding.
seriesCollection - Variable in class ec.display.chart.XYSeriesChartStatistics
serverAddress - Variable in class ec.exchange.IslandExchange
  The address of the server
serverPort - Variable in class ec.exchange.IslandExchange
  The port of the server
serverThread - Variable in class ec.exchange.IslandExchange
  The thread of the server (is different than null only for the island with the server)
servSock - Variable in class ec.eval.SlaveMonitor
  The socket where slaves connect.
set - Variable in class ec.breed.UniquePipeline
set(int, int) - Method in class ec.util.IntBag
set(Parameter, String) - Method in class ec.util.ParameterDatabase
  Sets a parameter in the topmost database to a given value, trimmed of whitespace.
SET - Static variable in class ec.util.ParameterDatabaseEvent
setCheckpoint(EvolutionState) - Static method in class ec.util.Checkpoint
  Writes the evolution state out to a file.
setContext(Individual[]) - Method in class ec.Fitness
setContext(Individual[], int) - Method in class ec.Fitness
setFilePrefix(String) - Method in class ec.util.Output
setFitness(EvolutionState, double) - Method in class ec.gp.koza.KozaFitness
  Do not use this function.
setFitness(EvolutionState, double) - Method in class ec.simple.SimpleFitness
  Deprecated -- now redefined to set the fitness but ALWAYS say that it's not ideal.
setFitness(EvolutionState, double, boolean) - Method in class ec.simple.SimpleFitness
setFlush(boolean) - Method in class ec.util.Output
  Sets whether the Output flushes its announcements.
setGeneration(EvolutionState) - Method in class ec.neat.NEATIndividual
  Set the born generation of this individual.
setGenome(Object) - Method in class ec.pso.Particle
setGenome(Object) - Method in class ec.vector.BitVectorIndividual
setGenome(Object) - Method in class ec.vector.ByteVectorIndividual
setGenome(Object) - Method in class ec.vector.DoubleVectorIndividual
setGenome(Object) - Method in class ec.vector.FloatVectorIndividual
setGenome(Object) - Method in class ec.vector.GeneVectorIndividual
setGenome(Object) - Method in class ec.vector.IntegerVectorIndividual
setGenome(Object) - Method in class ec.vector.LongVectorIndividual
setGenome(Object) - Method in class ec.vector.ShortVectorIndividual
setGenome(Object) - Method in class ec.vector.VectorIndividual
  Sets the gene array.
setGenomeLength(int) - Method in class ec.pso.Particle
setGenomeLength(int) - Method in class ec.vector.BitVectorIndividual
setGenomeLength(int) - Method in class ec.vector.ByteVectorIndividual
setGenomeLength(int) - Method in class ec.vector.DoubleVectorIndividual
setGenomeLength(int) - Method in class ec.vector.FloatVectorIndividual
setGenomeLength(int) - Method in class ec.vector.GeneVectorIndividual
setGenomeLength(int) - Method in class ec.vector.IntegerVectorIndividual
setGenomeLength(int) - Method in class ec.vector.LongVectorIndividual
setGenomeLength(int) - Method in class ec.vector.ShortVectorIndividual
setGenomeLength(int) - Method in class ec.vector.VectorIndividual
  Sets the genome length.
setIndex(int, int) - Method in interface ec.spatial.Space
  Input: a threadnumber (either for evaluation or for breeding), and an index in a subpopulation (the index in the subpopulation is, of course, associated with a location in the space) Functionality: stores the index and the threadnumber for further accesses to the getIndexRandomNeighbor method.
setIndex(int, int) - Method in class ec.spatial.Spatial1DSubpopulation
setInnovationNumber(int) - Method in class ec.neat.NEATSpecies
setMinimumFitness(EvolutionState, int, Individual) - Method in class ec.parsimony.TarpeianStatistics
  Sets the fitness of an individual to the minimum fitness possible.
setObjectives(EvolutionState, double[]) - Method in class ec.multiobjective.MultiObjectiveFitness
setProbability(Object, double) - Method in class ec.BreedingSource
setProbability(Object, double) - Method in interface ec.util.RandomChoiceChooserD
  Sets obj's probability
setProbability(Object, float) - Method in interface ec.util.RandomChoiceChooser
  Sets obj's probability
setRunComplete(String) - Method in class ec.Evaluator
  Requests that the Evaluator quit soon for a user-defined reason provided in the message.
setSeed(int[]) - Method in class ec.util.MersenneTwister
  Sets the seed of the MersenneTwister using an array of integers.
setSeed(int[]) - Method in class ec.util.MersenneTwisterFast
  Sets the seed of the MersenneTwister using an array of integers.
setSeed(long) - Method in class ec.util.MersenneTwister
  Initalize the pseudo random number generator.
setSeed(long) - Method in class ec.util.MersenneTwisterFast
  Initalize the pseudo random number generator.
setSeed(String, int, int) - Method in class ec.display.ControlPanel
setStandardizedFitness(EvolutionState, double) - Method in class ec.gp.koza.KozaFitness
  Set the standardized fitness in the half-open interval [0.0,infinity) which is defined (NOTE: DIFFERENT FROM fitness()!!!) as 0.0 being the IDEAL and infinity being worse than the worst possible.
setStore(boolean) - Method in class ec.util.Output
  Sets whether the Output stores its announcements.
setThrowsErrors(boolean) - Method in class ec.util.Output
setToBestOf(EvolutionState, Fitness[]) - Method in class ec.Fitness
  Sets the fitness to be the same value as the best of the provided fitnesses.
setToBestOf(EvolutionState, Fitness[]) - Method in class ec.multiobjective.MultiObjectiveFitness
setToMeanOf(EvolutionState, Fitness[]) - Method in class ec.Fitness
  Sets the fitness to be the same value as the mean of the provided fitnesses.
setToMeanOf(EvolutionState, Fitness[]) - Method in class ec.gp.koza.KozaFitness
setToMeanOf(EvolutionState, Fitness[]) - Method in class ec.multiobjective.MultiObjectiveFitness
setToMeanOf(EvolutionState, Fitness[]) - Method in class ec.simple.SimpleFitness
setToMedianOf(EvolutionState, Fitness[]) - Method in class ec.Fitness
  Sets the fitness to be the median of the provided fitnesses.
setToMedianOf(EvolutionState, Fitness[]) - Method in class ec.multiobjective.MultiObjectiveFitness
setup(EvolutionState, Parameter) - Method in class ec.breed.BufferedBreedingPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.CheckingPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.FirstCopyPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.ForceBreedingPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.GenerationSwitchPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.InitializationPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.MultiBreedingPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.RepeatPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.ReproductionPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.StubPipeline
setup(EvolutionState, Parameter) - Method in class ec.breed.UniquePipeline
setup(EvolutionState, Parameter) - Method in class ec.BreedingPipeline
setup(EvolutionState, Parameter) - Method in class ec.BreedingSource
  Sets up the BreedingPipeline.
setup(EvolutionState, Parameter) - Method in class ec.coevolve.CompetitiveEvaluator
setup(EvolutionState, Parameter) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
setup(EvolutionState, Parameter) - Method in class ec.de.Best1BinDEBreeder
setup(EvolutionState, Parameter) - Method in class ec.de.DEBreeder
setup(EvolutionState, Parameter) - Method in class ec.de.Rand1EitherOrDEBreeder
setup(EvolutionState, Parameter) - Method in class ec.display.chart.BarChartStatistics
setup(EvolutionState, Parameter) - Method in class ec.display.chart.ChartableStatistics
setup(EvolutionState, Parameter) - Method in class ec.display.chart.PieChartStatistics
setup(EvolutionState, Parameter) - Method in class ec.display.chart.TimeSeriesStatistics
setup(EvolutionState, Parameter) - Method in class ec.display.chart.XYSeriesChartStatistics
setup(EvolutionState, Parameter) - Method in class ec.display.portrayal.SimpleIndividualPortrayal
setup(EvolutionState, Parameter) - Method in class ec.display.StatisticsChartPane
setup(EvolutionState, Parameter) - Method in class ec.display.SubpopulationPanel
setup(EvolutionState, Parameter) - Method in class ec.eda.amalgam.AMALGAMBreeder
setup(EvolutionState, Parameter) - Method in class ec.eda.amalgam.AMALGAMSpecies
setup(EvolutionState, Parameter) - Method in class ec.eda.cmaes.CMAESBreeder
setup(EvolutionState, Parameter) - Method in class ec.eda.cmaes.CMAESSpecies
setup(EvolutionState, Parameter) - Method in class ec.eda.dovs.DOVSBreeder
setup(EvolutionState, Parameter) - Method in class ec.eda.dovs.DOVSFitness
setup(EvolutionState, Parameter) - Method in class ec.eda.dovs.DOVSSpecies
setup(EvolutionState, Parameter) - Method in class ec.eda.dovs.HyperboxSpecies
setup(EvolutionState, Parameter) - Method in class ec.eda.pbil.PBILBreeder
setup(EvolutionState, Parameter) - Method in class ec.eda.pbil.PBILSpecies
setup(EvolutionState, Parameter) - Method in class ec.es.MuCommaLambdaBreeder
setup(EvolutionState, Parameter) - Method in class ec.eval.MasterProblem
setup(EvolutionState, Parameter) - Method in class ec.eval.MetaProblem
setup(EvolutionState, Parameter) - Method in class ec.Evaluator
setup(EvolutionState, Parameter) - Method in class ec.EvolutionState
  Unlike for other setup() methods, ignore the base; it will always be null.
setup(EvolutionState, Parameter) - Method in class ec.evolve.RandomRestarts
  Gets the clock ticking.
setup(EvolutionState, Parameter) - Method in class ec.exchange.InterPopulationExchange
setup(EvolutionState, Parameter) - Method in class ec.exchange.IslandExchange
setup(EvolutionState, Parameter) - Method in class ec.Fitness
setup(EvolutionState, Parameter) - Method in class ec.gp.ADF
setup(EvolutionState, Parameter) - Method in class ec.gp.ADFArgument
setup(EvolutionState, Parameter) - Method in class ec.gp.ADFContext
setup(EvolutionState, Parameter) - Method in class ec.gp.ADFStack
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.InternalCrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.MutateAllNodesPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.MutateDemotePipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.MutateERCPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.MutateOneNodePipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.MutatePromotePipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.MutateSwapPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.RehangPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.breed.SizeFairCrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.build.PTC1
setup(EvolutionState, Parameter) - Method in class ec.gp.build.PTC2
setup(EvolutionState, Parameter) - Method in class ec.gp.build.PTCFunctionSet
setup(EvolutionState, Parameter) - Method in class ec.gp.build.RandomBranch
setup(EvolutionState, Parameter) - Method in class ec.gp.build.RandTree
setup(EvolutionState, Parameter) - Method in class ec.gp.build.Uniform
setup(EvolutionState, Parameter) - Method in class ec.gp.ge.GEProblem
setup(EvolutionState, Parameter) - Method in class ec.gp.ge.GESpecies
setup(EvolutionState, Parameter) - Method in class ec.gp.ge.GrammarParser
setup(EvolutionState, Parameter) - Method in class ec.gp.GPData
setup(EvolutionState, Parameter) - Method in class ec.gp.GPFunctionSet
  Must be done after GPType and GPNodeConstraints have been set up
setup(EvolutionState, Parameter) - Method in class ec.gp.GPIndividual
  Sets up a prototypical GPIndividual with those features which it shares with other GPIndividuals in its species, and nothing more.
setup(EvolutionState, Parameter) - Method in class ec.gp.GPInitializer
setup(EvolutionState, Parameter) - Method in class ec.gp.GPNode
  Sets up a prototypical GPNode with those features all nodes of that prototype share, and nothing more.
setup(EvolutionState, Parameter) - Method in class ec.gp.GPNodeBuilder
setup(EvolutionState, Parameter) - Method in class ec.gp.GPNodeConstraints
  This must be called after the GPTypes have been set up.
setup(EvolutionState, Parameter) - Method in class ec.gp.GPProblem
setup(EvolutionState, Parameter) - Method in class ec.gp.GPSetType
setup(EvolutionState, Parameter) - Method in class ec.gp.GPSpecies
setup(EvolutionState, Parameter) - Method in class ec.gp.GPTree
  Sets up a prototypical GPTree with those features it shares with other GPTrees in its position in its GPIndividual, and nothhing more.
setup(EvolutionState, Parameter) - Method in class ec.gp.GPTreeConstraints
  This must be called after the GPTypes and GPFunctionSets have been set up.
setup(EvolutionState, Parameter) - Method in class ec.gp.GPType
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.CrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.HalfBuilder
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.KozaBuilder
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.KozaFitness
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.KozaNodeSelector
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.KozaShortStatistics
setup(EvolutionState, Parameter) - Method in class ec.gp.koza.MutationPipeline
setup(EvolutionState, Parameter) - Method in class ec.gp.push.PushBuilder
setup(EvolutionState, Parameter) - Method in class ec.gp.push.PushInstruction
setup(EvolutionState, Parameter) - Method in class ec.gp.push.Terminal
setup(EvolutionState, Parameter) - Method in class ec.Individual
  This should be used to set up only those things which you share in common with all other individuals in your species; individual-specific items which make you you should be filled in by Species.newIndividual(...), and modified by breeders.
setup(EvolutionState, Parameter) - Method in class ec.multiobjective.HypervolumeStatistics
setup(EvolutionState, Parameter) - Method in class ec.multiobjective.MultiObjectiveFitness
  Sets up.
setup(EvolutionState, Parameter) - Method in class ec.multiobjective.MultiObjectiveStatistics
setup(EvolutionState, Parameter) - Method in class ec.multiobjective.nsga2.NSGA2Breeder
setup(EvolutionState, Parameter) - Method in class ec.multiobjective.spea2.SPEA2Breeder
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATBreeder
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATGene
  The setup method initializes a "meaningless" gene that does not specify any connection.
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATIndividual
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATInnovation
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATNetwork
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATNode
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATSpecies
setup(EvolutionState, Parameter) - Method in class ec.neat.NEATSubspecies
setup(EvolutionState, Parameter) - Method in class ec.parsimony.BucketTournamentSelection
setup(EvolutionState, Parameter) - Method in class ec.parsimony.DoubleTournamentSelection
setup(EvolutionState, Parameter) - Method in class ec.parsimony.ProportionalTournamentSelection
setup(EvolutionState, Parameter) - Method in class ec.parsimony.RatioBucketTournamentSelection
setup(EvolutionState, Parameter) - Method in class ec.parsimony.TarpeianStatistics
setup(EvolutionState, Parameter) - Method in class ec.Population
setup(EvolutionState, Parameter) - Method in class ec.Problem
setup(EvolutionState, Parameter) - Method in interface ec.Prototype
  Sets up the object by reading it from the parameters stored in state, built off of the parameter base base.
setup(EvolutionState, Parameter) - Method in class ec.pso.Particle
setup(EvolutionState, Parameter) - Method in class ec.pso.PSOBreeder
setup(EvolutionState, Parameter) - Method in class ec.rule.breed.RuleCrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.rule.Rule
setup(EvolutionState, Parameter) - Method in class ec.rule.RuleConstraints
setup(EvolutionState, Parameter) - Method in class ec.rule.RuleIndividual
setup(EvolutionState, Parameter) - Method in class ec.rule.RuleInitializer
  Sets up the RuleConstraints and RuleSetConstraints cliques.
setup(EvolutionState, Parameter) - Method in class ec.rule.RuleSet
setup(EvolutionState, Parameter) - Method in class ec.rule.RuleSetConstraints
setup(EvolutionState, Parameter) - Method in class ec.rule.RuleSpecies
setup(EvolutionState, Parameter) - Method in class ec.select.AnnealedSelection
setup(EvolutionState, Parameter) - Method in class ec.select.BestSelection
setup(EvolutionState, Parameter) - Method in class ec.select.BoltzmannSelection
setup(EvolutionState, Parameter) - Method in class ec.select.GreedyOverselection
setup(EvolutionState, Parameter) - Method in class ec.select.MultiSelection
setup(EvolutionState, Parameter) - Method in class ec.select.SigmaScalingSelection
setup(EvolutionState, Parameter) - Method in class ec.select.SUSSelection
setup(EvolutionState, Parameter) - Method in class ec.select.TopSelection
setup(EvolutionState, Parameter) - Method in class ec.select.TournamentSelection
setup(EvolutionState, Parameter) - Method in interface ec.Setup
  Sets up the object by reading it from the parameters stored in state, built off of the parameter base base.
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleBreeder
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleEvaluator
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleExchanger
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleFinisher
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleFitness
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleInitializer
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleShortStatistics
setup(EvolutionState, Parameter) - Method in class ec.simple.SimpleStatistics
setup(EvolutionState, Parameter) - Method in class ec.spatial.Spatial1DSubpopulation
  Read additional parameters for the spatially-embedded subpopulation.
setup(EvolutionState, Parameter) - Method in class ec.spatial.SpatialBreeder
setup(EvolutionState, Parameter) - Method in class ec.spatial.SpatialTournamentSelection
setup(EvolutionState, Parameter) - Method in class ec.Species
  The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities.
setup(EvolutionState, Parameter) - Method in class ec.Statistics
setup(EvolutionState, Parameter) - Method in class ec.steadystate.SteadyStateBreeder
setup(EvolutionState, Parameter) - Method in class ec.steadystate.SteadyStateEvaluator
setup(EvolutionState, Parameter) - Method in class ec.steadystate.SteadyStateEvolutionState
setup(EvolutionState, Parameter) - Method in class ec.Subpopulation
setup(EvolutionState, Parameter) - Method in class ec.vector.BitVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.BitVectorSpecies
setup(EvolutionState, Parameter) - Method in class ec.vector.breed.ListCrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.vector.breed.MultipleVectorCrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.vector.breed.VectorCrossoverPipeline
setup(EvolutionState, Parameter) - Method in class ec.vector.ByteVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.DoubleVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.FloatVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.FloatVectorSpecies
setup(EvolutionState, Parameter) - Method in class ec.vector.Gene
setup(EvolutionState, Parameter) - Method in class ec.vector.GeneVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.GeneVectorSpecies
setup(EvolutionState, Parameter) - Method in class ec.vector.IntegerVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.IntegerVectorSpecies
setup(EvolutionState, Parameter) - Method in class ec.vector.LongVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.ShortVectorIndividual
setup(EvolutionState, Parameter) - Method in class ec.vector.VectorSpecies
Setup - Interface in ec
  Setup classes are classes which get set up once from user-supplied parameters prior to being used.
setupArities(EvolutionState, GPFunctionSet) - Method in class ec.gp.build.RandTree
setupConstraints(EvolutionState, Parameter) - Method in class ec.rule.RuleInitializer
  Sets up all the RuleConstraints, loading them from the parameter file.
setupFunctionSets(EvolutionState, Parameter) - Method in class ec.gp.GPInitializer
setupGenome(EvolutionState, Parameter) - Method in class ec.vector.VectorSpecies
setupNodeConstraints(EvolutionState, Parameter) - Method in class ec.gp.GPInitializer
  Sets up all the GPNodeConstraints, loading them from the parameter file.
setupPopulation(EvolutionState, int) - Method in class ec.eda.cmaes.CMAESInitializer
setupPopulation(EvolutionState, int) - Method in class ec.Initializer
  Loads a Population from the parameter file, sets it up, and returns it.
setupPopulation(EvolutionState, int) - Method in class ec.simple.SimpleInitializer
setupProbabilities(BreedingSource[]) - Static method in class ec.BreedingSource
  Normalizes and arranges the probabilities in sources so that they are usable by pickRandom(...).
setupRuleSetConstraints(EvolutionState, Parameter) - Method in class ec.rule.RuleInitializer
setupTreeConstraints(EvolutionState, Parameter) - Method in class ec.gp.GPInitializer
  Sets up all the GPTreeConstraints, loading them from the parameter file.
setupTypes(EvolutionState, Parameter) - Method in class ec.gp.GPInitializer
  Sets up all the types, loading them from the parameter file.
setValue(int, Object) - Method in interface ec.util.Indexed
  Throws an IndexOutOfBoundsException if index is inappropriate, and IllegalArgumentException if the value is inappropriate.
setValue(int, Object) - Method in class ec.util.IntBag
setVerbosity(int) - Method in class ec.util.Output
  Sets the Output object's general verbosity to v.
setVisibleLeaves(boolean) - Method in class ec.util.ParameterDatabaseTreeModel
shiftIndividual(EvolutionState, DoubleVectorIndividual) - Method in class ec.eda.amalgam.AMALGAMSpecies
ShortVectorIndividual - Class in ec.vector
  ShortVectorIndividual is a VectorIndividual whose genome is an array of shorts.
ShortVectorIndividual() - Constructor for class ec.vector.ShortVectorIndividual
shouldBreedSubpop(EvolutionState, int, int) - Method in class ec.Breeder
  Returns true if we're doing sequential breeding and it's the subpopulation's turn (round robin, one subpopulation per generation).
shouldBreedSubpop(EvolutionState, int, int) - Method in class ec.simple.SimpleBreeder
  Returns true if we're doing sequential breeding and it's the subpopulation's turn (round robin, one subpopulation per generation).
shouldEvaluateSubpop(EvolutionState, int, int) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
  Returns true if the subpopulation should be evaluated.
shrink(int) - Method in class ec.util.IntBag
  Resizes the objs array to max(numObjs, desiredLength), unless that value is greater than or equal to objs.length, in which case no resizing is done (this operation only shrinks -- use resize() instead).
shuffle - Variable in class ec.select.SUSSelection
  Should we shuffle first?
shuffle(EvolutionState, int[]) - Method in class ec.coevolve.MultiPopCoevolutionaryEvaluator
shuffle(GPNode[], EvolutionState, int) - Method in class ec.gp.push.PushBuilder
shuffle(MersenneTwisterFast) - Method in class ec.util.IntBag
  Shuffles (randomizes the order of) the IntBag
shuffle(Random) - Method in class ec.util.IntBag
  Shuffles (randomizes the order of) the IntBag
shutdown() - Method in class ec.eval.SlaveMonitor
  Shuts down the slave monitor (also shuts down all slaves).
sigma - Variable in class ec.eda.cmaes.CMAESSpecies
  The "sigma" scaling factor for the covariance matrix.
SigmaScalingSelection - Class in ec.select
  Similar to FitProportionateSelection, but with adjustments to scale up/exaggerate differences in fitness for selection when true fitness values are very close to eachother across the population.
SigmaScalingSelection() - Constructor for class ec.select.SigmaScalingSelection
sigmoid(double) - Method in class ec.neat.NEATNode
  The Sigmoid function.
SIGMOID - Enum constant in enum class ec.neat.NEATNode.FunctionType
SIGMOID_SLOPE - Static variable in class ec.neat.NEATNetwork
  constant used for the sigmoid function
silent - Variable in class ec.util.Log
  Should we write to this log at all?
silentFile - Variable in class ec.Statistics
silentFront - Variable in class ec.multiobjective.MultiObjectiveStatistics
silentPrint - Variable in class ec.Statistics
SimpleBreeder - Class in ec.simple
  Breeds each subpopulation separately, with no inter-population exchange, and using a generational approach.
SimpleBreeder() - Constructor for class ec.simple.SimpleBreeder
SimpleDefaults - Class in ec.simple
SimpleDefaults() - Constructor for class ec.simple.SimpleDefaults
SimpleEvaluator - Class in ec.simple
  The SimpleEvaluator is a simple, non-coevolved generational evaluator which evaluates every single member of every subpopulation individually in its own problem space.
SimpleEvaluator() - Constructor for class ec.simple.SimpleEvaluator
SimpleEvolutionState - Class in ec.simple
  A SimpleEvolutionState is an EvolutionState which implements a simple form of generational evolution.
SimpleEvolutionState() - Constructor for class ec.simple.SimpleEvolutionState
SimpleExchanger - Class in ec.simple
  A SimpleExchanger is a default Exchanger which, well, doesn't do anything.
SimpleExchanger() - Constructor for class ec.simple.SimpleExchanger
SimpleFinisher - Class in ec.simple
  SimpleFinisher is a default Finisher which doesn't do anything.
SimpleFinisher() - Constructor for class ec.simple.SimpleFinisher
SimpleFitness - Class in ec.simple
  A simple default fitness, consisting of a double floating-point value where fitness A is superior to fitness B if and only if A > B.
SimpleFitness() - Constructor for class ec.simple.SimpleFitness
SimpleGroupedEvaluator - Class in ec.simple
SimpleGroupedEvaluator() - Constructor for class ec.simple.SimpleGroupedEvaluator
SimpleIndividualPortrayal - Class in ec.display.portrayal
  This portrayal uses a text pane to display the results of `printIndividualForHumans()`.
SimpleIndividualPortrayal() - Constructor for class ec.display.portrayal.SimpleIndividualPortrayal
SimpleInitializer - Class in ec.simple
  SimpleInitializer is a default Initializer which initializes a Population by calling the Population's populate(...) method.
SimpleInitializer() - Constructor for class ec.simple.SimpleInitializer
SimpleProblemForm - Interface in ec.simple
  SimpleProblemForm is an interface which defines methods for Problems to implement simple, single-individual (non-coevolutionary) evaluation.
SimpleShortStatistics - Class in ec.simple
  A Simple-style statistics generator, intended to be easily parseable with awk or other Unix tools.
SimpleShortStatistics() - Constructor for class ec.simple.SimpleShortStatistics
SimpleStatistics - Class in ec.simple
  A basic Statistics class suitable for simple problem applications.
SimpleStatistics() - Constructor for class ec.simple.SimpleStatistics
simulatedBinaryCrossover(MersenneTwisterFast, DoubleVectorIndividual, double) - Method in class ec.vector.DoubleVectorIndividual
simulatedBinaryCrossover(MersenneTwisterFast, FloatVectorIndividual, float) - Method in class ec.vector.FloatVectorIndividual
Singleton - Interface in ec
  A Singleton is a class for which there will be only one instance in the entire course of a run, and which will exist for pretty much the entire run.
size - Variable in class ec.exchange.IslandExchange
  how many individuals to send each time
size - Variable in class ec.parsimony.BucketTournamentSelection
  Size of the tournament
size - Variable in class ec.parsimony.DoubleTournamentSelection
  Size of the tournament
size - Variable in class ec.parsimony.RatioBucketTournamentSelection
  Size of the tournament
size - Variable in class ec.select.BestSelection
  Base size of the tournament; this may change.
size - Variable in class ec.select.TournamentSelection
  Base size of the tournament; this may change.
size() - Method in class ec.gp.GPIndividual
  Returns the "size" of the individual, namely, the number of nodes in all of its subtrees.
size() - Method in class ec.Individual
  Returns the "size" of the individual.
size() - Method in class ec.rule.RuleIndividual
size() - Method in class ec.util.DataPipe
  Returns the total size of the buffer.
size() - Method in interface ec.util.Indexed
size() - Method in class ec.util.IntBag
size() - Method in class ec.vector.VectorIndividual
SIZE_OF_BYTE - Static variable in class ec.gp.GPInitializer
SIZE_OF_BYTE - Static variable in class ec.gp.GPNodeConstraints
SIZE_OF_BYTE - Static variable in class ec.gp.GPTreeConstraints
SIZE_OF_BYTE - Static variable in class ec.rule.RuleInitializer
size2 - Variable in class ec.parsimony.DoubleTournamentSelection
sizeDistribution - Variable in class ec.gp.GPNodeBuilder
  the maximum possible size -- if unused, it's 0
sizeDistribution - Variable in class ec.rule.RuleSetConstraints
SizeFairCrossoverPipeline - Class in ec.gp.breed
  SizeFairCrossover works similarly to one written in the paper "Size Fair and Homologous Tree Genetic Programming Crossovers" by Langdon (1998).
SizeFairCrossoverPipeline() - Constructor for class ec.gp.breed.SizeFairCrossoverPipeline
Slave - Class in ec.eval
  Slave.java
Slave() - Constructor for class ec.eval.Slave
SlaveMonitor - Class in ec.eval
  SlaveMonitor.java
SlaveMonitor(EvolutionState, boolean, MasterProblem) - Constructor for class ec.eval.SlaveMonitor
  Simple constructor that initializes the data structures for keeping track of the state of each slave.
slaveNum - Static variable in class ec.eval.Slave
  My unique slave number.
SLEEP_TIME - Static variable in class ec.eval.Slave
  How long we sleep in between attempts to connect to the master (in milliseconds).
SLEEP_TIME - Static variable in class ec.exchange.IslandExchange
  How long we sleep in between attempts to connect or look for signals
smaller(CornerMap.Pair) - Method in class ec.eda.dovs.CornerMap
  Get a greatest key value pair from this CornerMap who is the immediate previous element of pair
sort() - Method in class ec.util.IntBag
  Sorts the ints into ascending numerical order.
sort(Object, Comparator) - Method in class ec.util.ParameterDatabaseTreeModel
SortComparator - Interface in ec.util
  The interface for passing objects to ec.util.QuickSort
SortComparatorL - Interface in ec.util
  The interface for passing objects to ec.util.QuickSort
sortedFitOver - Variable in class ec.select.GreedyOverselection
sortedFitUnder - Variable in class ec.select.GreedyOverselection
sortedPop - Variable in class ec.select.BestSelection
  Sorted, normalized, totalized fitnesses for the population
sortedPop - Variable in class ec.select.GreedyOverselection
  Sorted population -- since I *have* to use an int-sized individual (short gives me only 16K), I might as well just have pointers to the population itself.
sortIndividuals() - Method in class ec.neat.NEATSubspecies
  Sort the individuals in this subspecies, the one with highest fitness comes first.
sources - Variable in class ec.BreedingPipeline
  Array of sources feeding the pipeline
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.BreedingPipeline
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.parsimony.BucketTournamentSelection
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.parsimony.DoubleTournamentSelection
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.parsimony.RatioBucketTournamentSelection
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.select.FirstSelection
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.select.RandomSelection
sourcesAreProperForm(SteadyStateEvolutionState) - Method in class ec.select.TournamentSelection
sourcesAreProperForm(SteadyStateEvolutionState) - Method in interface ec.steadystate.SteadyStateBSourceForm
  Issue an error (not a fatal -- we guarantee that callers of this method will also call exitIfErrors) if any of your sources, or their sources, etc., are not of SteadyStateBSourceForm.
sourcesAreProperForm(SteadyStateEvolutionState, BreedingSource[]) - Method in class ec.steadystate.SteadyStateBreeder
  Called to check to see if the breeding sources are correct -- if you use this method, you must call state.output.exitIfErrors() immediately afterwards.
Space - Interface in ec.spatial
  In a spatially-embedded EA, the subpopulations of individuals are assumed to be spatially distributed in some sort of space, be it one-dimmensional, two- dimmensional, or whatever else.
sparsity - Variable in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
  Sparsity along front rank measure (higher sparsity is better)
Spatial1DSubpopulation - Class in ec.spatial
  A Spatial1DSubpopulation is an EC subpopulation that is additionally embedded into a one-dimmensional space.
Spatial1DSubpopulation() - Constructor for class ec.spatial.Spatial1DSubpopulation
SpatialBreeder - Class in ec.spatial
  A slight modification of the simple breeder for spatially-embedded EAs.
SpatialBreeder() - Constructor for class ec.spatial.SpatialBreeder
SpatialDefaults - Class in ec.spatial
SpatialDefaults() - Constructor for class ec.spatial.SpatialDefaults
SpatialMultiPopCoevolutionaryEvaluator - Class in ec.spatial
  SpatialMultiPopCoevolutionaryEvaluator implements a coevolutionary evaluator involving multiple spatially-embedded subpopulations.
SpatialMultiPopCoevolutionaryEvaluator() - Constructor for class ec.spatial.SpatialMultiPopCoevolutionaryEvaluator
SpatialTournamentSelection - Class in ec.spatial
  A slight modification of the tournament selection procedure for use with spatially-embedded EAs.
SpatialTournamentSelection() - Constructor for class ec.spatial.SpatialTournamentSelection
spawnWithTemplate(EvolutionState, NEATSpecies, int, NEATIndividual) - Method in class ec.neat.NEATSpecies
  Spawn a new individual with given individual as template.
SPEA2_DISTANCE_PREAMBLE - Static variable in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
SPEA2_FITNESS_PREAMBLE - Static variable in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
SPEA2_STRENGTH_PREAMBLE - Static variable in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
SPEA2Breeder - Class in ec.multiobjective.spea2
  This subclass of SimpleBreeder overrides the loadElites method to build an archive in the top elites[subpopnum] of each subpopulation.
SPEA2Breeder() - Constructor for class ec.multiobjective.spea2.SPEA2Breeder
SPEA2Breeder.BreedingState - Enum Class in ec.multiobjective.spea2
  We use a state variable to make sure that the archive isn't built twice in a row.
SPEA2MultiObjectiveFitness - Class in ec.multiobjective.spea2
  SPEA2MultiObjectiveFitness is a subclass of MultiObjectiveFitness which adds three auxiliary fitness measures used in SPEA2: strength S(i), kthNNDistance D(i), and a final fitness value R(i) + D(i).
SPEA2MultiObjectiveFitness() - Constructor for class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
speciate(EvolutionState, Individual) - Method in class ec.neat.NEATSpecies
  Assign the individual into a species, if not found, create a new one
species - Variable in class ec.Individual
  The species of the Individual.
species - Variable in class ec.Subpopulation
  The species for individuals in this subpopulation.
Species - Class in ec
  Species is a prototype which defines the features for a set of individuals in the population.
Species() - Constructor for class ec.Species
split(int[], RuleSet[]) - Method in class ec.rule.RuleSet
  Splits the rule set into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.BitVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.ByteVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.DoubleVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.FloatVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.GeneVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.IntegerVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.LongVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.ShortVectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(int[], Object[]) - Method in class ec.vector.VectorIndividual
  Splits the genome into n pieces, according to points, which *must* be sorted.
split(EvolutionState, int, RuleSet[]) - Method in class ec.rule.RuleSet
  Splits the rule set into a number of disjoint rule sets, copying the rules and adding them to the sets as appropriate.
splitIntoTwo(EvolutionState, int, RuleSet[], double) - Method in class ec.rule.RuleSet
  Splits the rule set into a two disjoint rule sets, copying the rules and adding them to the sets as appropriate.
stack - Variable in class ec.gp.ADFStack
stack - Variable in class ec.gp.GPProblem
  The GPProblem's stack
standardizedFitness - Variable in class ec.gp.koza.KozaFitness
  This ranges from 0 (best) to infinity (worst).
standardizedFitness() - Method in class ec.gp.koza.KozaFitness
  Returns the standardized fitness metric.
start - Variable in class ec.evolve.RandomRestarts
start(Runnable) - Method in class ec.util.ThreadPool
  Start a thread on the given Runnable and returns it.
start(Runnable, int) - Method in class ec.util.ThreadPool
  Start a thread on the given Runnable and returns it.
start(Runnable, int, String) - Method in class ec.util.ThreadPool
  Start a thread on the given Runnable with a given thread name (for debugging purposes) and returns it.
start(Runnable, String) - Method in class ec.util.ThreadPool
  Start a thread on the given Runnable with a given thread name (for debugging purposes).
startFresh() - Method in class ec.EvolutionState
startFresh() - Method in class ec.exchange.IslandExchange
startFresh() - Method in class ec.simple.SimpleEvolutionState
startFresh() - Method in class ec.steadystate.SteadyStateEvolutionState
startFromCheckpoint() - Method in class ec.EvolutionState
startFromCheckpoint() - Method in class ec.exchange.IslandExchange
state - Variable in class ec.eval.SlaveMonitor
stateEquals(MersenneTwister) - Method in class ec.util.MersenneTwister
  Returns true if the MersenneTwister's current internal state is equal to another MersenneTwister.
stateEquals(MersenneTwisterFast) - Method in class ec.util.MersenneTwisterFast
  Returns true if the MersenneTwisterFast's current internal state is equal to another MersenneTwisterFast.
statistics - Variable in class ec.EvolutionState
  The population statistics, a singleton object.
Statistics - Class in ec
  Statistics and its subclasses are Cliques which generate statistics during the run.
Statistics() - Constructor for class ec.Statistics
StatisticsChartPane - Class in ec.display
StatisticsChartPane() - Constructor for class ec.display.StatisticsChartPane
StatisticsChartPane(int) - Constructor for class ec.display.StatisticsChartPane
StatisticsChartPane(int, int) - Constructor for class ec.display.StatisticsChartPane
StatisticsChartPaneTab - Class in ec.display.chart
StatisticsChartPaneTab(ChartPanel) - Constructor for class ec.display.chart.StatisticsChartPaneTab
StatisticsChartPaneTab(ChartPanel, boolean) - Constructor for class ec.display.chart.StatisticsChartPaneTab
statisticslog - Variable in class ec.simple.SimpleShortStatistics
statisticslog - Variable in class ec.simple.SimpleStatistics
  The Statistics' log
stDevRatioThresh - Variable in class ec.eda.amalgam.AMALGAMSpecies
SteadyStateBreeder - Class in ec.steadystate
  This subclass of Breeder performs the evaluation portion of Steady-State Evolution and (in distributed form) Asynchronous Evolution.
SteadyStateBreeder() - Constructor for class ec.steadystate.SteadyStateBreeder
  Do we allow duplicates?
SteadyStateBSourceForm - Interface in ec.steadystate
SteadyStateDefaults - Class in ec.steadystate
SteadyStateDefaults() - Constructor for class ec.steadystate.SteadyStateDefaults
SteadyStateEvaluator - Class in ec.steadystate
  This subclass of Evaluator performs the evaluation portion of Steady-State Evolution and (in distributed form) Asynchronous Evolution.
SteadyStateEvaluator() - Constructor for class ec.steadystate.SteadyStateEvaluator
SteadyStateEvolutionState - Class in ec.steadystate
  This subclass of EvolutionState implements basic Steady-State Evolution and (in distributed form) Asynchronous Evolution.
SteadyStateEvolutionState() - Constructor for class ec.steadystate.SteadyStateEvolutionState
SteadyStateExchangerForm - Interface in ec.steadystate
  The SteadyStateExchangerForm is a badge which Exchanger subclasses may wear if they work properly with the SteadyStateEvolutionState mechanism.
SteadyStateStatisticsForm - Interface in ec.steadystate
  This interface defines the hooks for SteadyStateEvolutionState objects to update themselves on.
stealBabies(EvolutionState, int, int, ArrayList<NEATSubspecies>) - Method in class ec.neat.NEATSpecies
  Steal the babies from champion subspecies.
steps - Variable in class ec.select.SUSSelection
  How many samples have been done?
stochastic - Variable in class ec.eda.dovs.DOVSSpecies
  Is the problem a stochastic problem.
strength - Variable in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
  SPEA2 strength (# of nodes it dominates)
STRING_CONSTANT - Static variable in class ec.gp.ge.GrammarParser
stubPipeline - Variable in class ec.breed.StubPipeline
StubPipeline - Class in ec.breed
  StubPipeline is a BreedingPipeline subclass which, during fillStubs(), fills all the stubs with its own stub pipeline.
StubPipeline() - Constructor for class ec.breed.StubPipeline
style - Variable in class ec.coevolve.CompetitiveEvaluator
STYLE_N_RANDOM_COMPETITORS_ONEWAY - Static variable in class ec.coevolve.CompetitiveEvaluator
STYLE_N_RANDOM_COMPETITORS_TWOWAY - Static variable in class ec.coevolve.CompetitiveEvaluator
STYLE_ROUND_ROBIN - Static variable in class ec.coevolve.CompetitiveEvaluator
STYLE_SINGLE_ELIMINATION - Static variable in class ec.coevolve.CompetitiveEvaluator
subpop - Variable in class ec.steadystate.QueueIndividual
SUBPOP_INDEX_PREAMBLE - Static variable in class ec.Population
subpops - Variable in class ec.Population
Subpopulation - Class in ec
  Subpopulation is a group which is basically an array of Individuals.
Subpopulation() - Constructor for class ec.Subpopulation
SubpopulationPanel - Class in ec.display
SubpopulationPanel(Console, int) - Constructor for class ec.display.SubpopulationPanel
SubpopulationPanel(Console, int, boolean) - Constructor for class ec.display.SubpopulationPanel
subspecies - Variable in class ec.neat.NEATIndividual
  The individual's subpecies
subspecies - Variable in class ec.neat.NEATSpecies
  A list of the all the subspecies.
subspeciesPrototype - Variable in class ec.neat.NEATSpecies
  The prototypical subspecies for individuals in this species.
substack - Variable in class ec.gp.ADFStack
sum - Variable in class ec.eda.dovs.DOVSFitness
  Sum of the all the fitness value with all the evaluation.
sumSquared - Variable in class ec.eda.dovs.DOVSFitness
  Sum of the all the squared fitness value with all the evaluation.
sumSquaredObjectiveDistance(MultiObjectiveFitness, boolean) - Method in class ec.multiobjective.MultiObjectiveFitness
  Returns the sum of the squared difference between two Fitnesses in Objective space.
superChampionOffspring - Variable in class ec.neat.NEATIndividual
  Number of reserved offspring for a population leader.
survivalThreshold - Variable in class ec.neat.NEATSpecies
  Percent of ave fitness for survival.
SUSSelection - Class in ec.select
  Picks individuals in a population using the Stochastic Universal Selection (SUS) process, using fitnesses as returned by their fitness() methods.
SUSSelection() - Constructor for class ec.select.SUSSelection
swapCompatibleWith(GPInitializer, GPNode) - Method in class ec.gp.GPNode
  Returns true if I can swap into node's position.
SYNC - Static variable in class ec.exchange.IslandExchange
  Synchronize signal
synchronous - Variable in class ec.exchange.IslandExchange
  synchronous or asynchronous communication
systemMessage(String) - Method in class ec.util.Output
  Posts a system message.

## T

T_BOOLEAN - Static variable in class ec.util.DecodeReturn
T_BYTE - Static variable in class ec.util.DecodeReturn
T_CHAR - Static variable in class ec.util.DecodeReturn
T_CHARACTER - Static variable in class ec.util.DecodeReturn
  Same as T_CHAR
T_DOUBLE - Static variable in class ec.util.DecodeReturn
T_ERROR - Static variable in class ec.util.DecodeReturn
  The actual error is stored in the String slot
T_FLOAT - Static variable in class ec.util.DecodeReturn
T_INT - Static variable in class ec.util.DecodeReturn
T_INTEGER - Static variable in class ec.util.DecodeReturn
  Same as T_INT
T_LONG - Static variable in class ec.util.DecodeReturn
T_SHORT - Static variable in class ec.util.DecodeReturn
T_STRING - Static variable in class ec.util.DecodeReturn
TarpeianStatistics - Class in ec.parsimony
  This Statistics subclass implements Poli's "Tarpeian" method of parsimony control, whereby some kill-proportion of above-average-sized individuals in each subpopulation have their fitnesses set to a very bad value, and marks them as already evaluated (so the Evaluator can skip them).
TarpeianStatistics() - Constructor for class ec.parsimony.TarpeianStatistics
tau - Variable in class ec.eda.amalgam.AMALGAMSpecies
temp - Variable in class ec.eda.amalgam.AMALGAMSpecies
temp2 - Variable in class ec.eda.amalgam.AMALGAMSpecies
temp3 - Variable in class ec.eda.amalgam.AMALGAMSpecies
tempMatrix - Variable in class ec.eda.amalgam.AMALGAMSpecies
Terminal - Class in ec.gp.push
  Terminal is the leaf node in Push trees and is used to represent Push instructions of all types.
Terminal() - Constructor for class ec.gp.push.Terminal
terminalProbabilities(int) - Method in class ec.gp.build.PTCFunctionSet
terminalProbabilities(int) - Method in interface ec.gp.build.PTCFunctionSetForm
  Returns an organized distribution (see ec.util.RandomChoice) of likelihoods that various terminals in the function set will be chosen over other terminals with the same return type.
terminalProbability - Variable in class ec.gp.koza.KozaNodeSelector
  The probability a terminal must be chosen
terminals - Variable in class ec.gp.GPFunctionSet
  The terminals our GPTree can use: terminals[type][thenodes].
terminals - Variable in class ec.gp.koza.KozaNodeSelector
  The number of terminals in the tree, -1 if unknown.
terminals_h - Variable in class ec.gp.GPFunctionSet
  The terminals our GPTree can use: arrays of terminals hashed by type.
test(GPNode) - Method in class ec.gp.GPNodeGatherer
  Returns true if thisNode is the kind of node to be considered in the gather count for nodeInPosition(...) and GPNode.numNodes(GPNodeGatherer).
ThreadPool - Class in ec.util
  ThreadPool.java A simple, lightweight thread pool, for those who cannot or will not use Java's baroque java.util.concurrent package.
ThreadPool() - Constructor for class ec.util.ThreadPool
ThreadPool.Worker - Interface in ec.util
  A Worker is a special kind of object which represents an underlying Worker thread usable in the ThreadPool.
timeAlive - Variable in class ec.neat.NEATIndividual
  When playing in real-time allows knowing the maturity of an individual
timeCollection - Variable in class ec.display.chart.TimeSeriesStatistics
timeDelay - Variable in class ec.neat.NEATGene
  Time delay of the link, used in network activation.
TimeSeriesStatistics - Class in ec.display.chart
TimeSeriesStatistics() - Constructor for class ec.display.chart.TimeSeriesStatistics
timeSinceLastImproved() - Method in class ec.neat.NEATSubspecies
  Compute generations gap since last improvement
title - Variable in class ec.display.chart.ChartableStatistics
toArray() - Method in class ec.util.IntBag
toDoubleArray() - Method in class ec.util.IntBag
toIntArray() - Method in class ec.util.IIntPoint
toIntegerArray() - Method in class ec.util.IntBag
toLongArray() - Method in class ec.util.IntBag
toNewGeneration() - Method in class ec.neat.NEATSubspecies
  After we finish the reproduce, the newGenIndividual list has the all the individuals that is ready for evalution in next generation.
top() - Method in class ec.util.IntBag
  Returns 0 if the IntBag is empty, else returns the topmost int.
top() - Method in class ec.util.Parameter
  Returns the path item at the far end of the parameter.
top(int) - Method in class ec.gp.ADFStack
  Returns the nth item in the stack (0-indexed), or null if this goes to the bottom of the stack.
top_n_percent - Variable in class ec.select.GreedyOverselection
topOfFloatStack(Interpreter) - Method in class ec.gp.push.PushProblem
  Returns the top of the interpreter's float stack.
topOfIntStack(Interpreter) - Method in class ec.gp.push.PushProblem
  Returns the top of the interpreter's int stack.
TopSelection - Class in ec.select
  Returns the single fittest individual in the population, breaking ties randomly.
TopSelection() - Constructor for class ec.select.TopSelection
toroidal - Variable in class ec.spatial.Spatial1DSubpopulation
tossSecondParent - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  Should the pipeline discard the second parent after crossing over?
tossSecondParent - Variable in class ec.gp.koza.CrossoverPipeline
  Should the pipeline discard the second parent after crossing over?
tossSecondParent - Variable in class ec.rule.breed.RuleCrossoverPipeline
  Should the pipeline discard the second parent after crossing over?
tossSecondParent - Variable in class ec.vector.breed.ListCrossoverPipeline
tossSecondParent - Variable in class ec.vector.breed.VectorCrossoverPipeline
  Should the pipeline discard the second parent after crossing over?
toString() - Method in class ec.display.ParameterValue
toString() - Method in class ec.gp.ADF
toString() - Method in class ec.gp.ADFArgument
toString() - Method in class ec.gp.ERC
  This defaults to simply name() + "[" + encode() + "]".
toString() - Method in class ec.gp.ge.GrammarFunctionNode
  A better toString() function -- khaled
toString() - Method in class ec.gp.ge.GrammarNode
toString() - Method in class ec.gp.ge.GrammarParser
toString() - Method in class ec.gp.ge.GrammarRuleNode
  A better toString() function -- khaled
toString() - Method in class ec.gp.GPFunctionSet
  Returns the name.
toString() - Method in class ec.gp.GPNode
  Returns a Lisp-like atom for the node which can be read in again by computer.
toString() - Method in class ec.gp.GPNodeConstraints
toString() - Method in class ec.gp.GPTreeConstraints
toString() - Method in class ec.gp.GPType
  Returns the type's name
toString() - Method in class ec.gp.push.Nonterminal
toString() - Method in class ec.Individual
  Overridden here because hashCode() is not expected to return the pointer to the object.
toString() - Method in class ec.neat.NEATGene
  This method convert the gene in to human readable format.
toString() - Method in class ec.neat.NEATIndividual
  This method convert the individual in to human readable format.
toString() - Method in class ec.neat.NEATNode
  This method convert the gene in to human readable format.
toString() - Method in class ec.rule.RuleConstraints
  Converting the rule to a string ( the name )
toString() - Method in class ec.rule.RuleSetConstraints
  Converting the rule to a string ( the name )
toString() - Method in class ec.util.DataPipe
toString() - Method in class ec.util.IIntPoint
toString() - Method in class ec.util.Parameter
toString() - Method in class ec.util.ParameterDatabase
toString() - Method in class ec.util.ReflectedObject
toStringForError() - Method in class ec.gp.GPNode
  Returns a description of the node that can make it easy to identify in error messages (by default, at least its name and the tree it's found in).
toStringForHumans() - Method in class ec.gp.ERC
  You might want to override this to return a special human-readable version of the erc value; otherwise this defaults to toString(); This should be something that resembles a LISP atom.
toStringForHumans() - Method in class ec.gp.GPNode
  Returns a Lisp-like atom for the node which is intended for human consumption, and not to be read in again.
toStringForHumans() - Method in class ec.gp.push.Nonterminal
toStringForHumans() - Method in class ec.gp.push.Terminal
totalFitnessThisGen - Variable in class ec.simple.SimpleShortStatistics
totalIndsSoFar - Variable in class ec.simple.SimpleShortStatistics
totalIndsThisGen - Variable in class ec.simple.SimpleShortStatistics
totalSizeSoFar - Variable in class ec.simple.SimpleShortStatistics
totalSizeThisGen - Variable in class ec.simple.SimpleShortStatistics
TournamentSelection - Class in ec.select
  Does a simple tournament selection, limited to the subpopulation it's working in at the time.
TournamentSelection() - Constructor for class ec.select.TournamentSelection
transferAdditionalData(EvolutionState) - Method in class ec.eval.MasterProblem
  This method is called by a Slave to transfer data previously loaded via receiveAdditionalData() to a running EvolutionState at the beginning of evolution.
transferAdditionalData(EvolutionState) - Method in class ec.Problem
  This method is called by a Slave to transfer data previously loaded via receiveAdditionalData() to a running EvolutionState at the beginning of evolution.
traverseTreeForDepth(GPNode, ArrayList, HashMap) - Method in class ec.gp.breed.SizeFairCrossoverPipeline
  Recursively travel the tree so that depth and subtree below are computed only once and can be reused later.
TREE_UNFIXED - Static variable in class ec.gp.GPBreedingPipeline
  Standard value for an unfixed tree
tree1 - Variable in class ec.gp.breed.InternalCrossoverPipeline
  Is the first tree fixed? If not, this is -1
tree1 - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  Is the first tree fixed? If not, this is -1
tree1 - Variable in class ec.gp.koza.CrossoverPipeline
  Is the first tree fixed? If not, this is -1
tree2 - Variable in class ec.gp.breed.InternalCrossoverPipeline
  Is the second tree fixed? If not, this is -1
tree2 - Variable in class ec.gp.breed.SizeFairCrossoverPipeline
  Is the second tree fixed? If not, this is -1
tree2 - Variable in class ec.gp.koza.CrossoverPipeline
  Is the second tree fixed? If not, this is -1
treeConstraintRepository - Variable in class ec.gp.GPInitializer
treeConstraints - Variable in class ec.gp.GPInitializer
treeEquals(GPTree) - Method in class ec.gp.GPTree
  Returns true if I am "genetically" the same as tree, though we may have different owners.
treeHashCode() - Method in class ec.gp.GPTree
  Returns a hash code for comparing different GPTrees.
treeNumber() - Method in class ec.gp.GPTree
  An expensive function which determines my tree number -- only use for errors, etc.
trees - Variable in class ec.gp.GPIndividual
treetype - Variable in class ec.gp.GPTreeConstraints
  The type of the root of the tree
trials - Variable in class ec.Fitness
  Auxiliary variable, used by coevolutionary processes, to compute the number of trials used to compute this Fitness value.
truesizes - Variable in class ec.gp.build.Uniform
truncate(int) - Method in class ec.Subpopulation
  Truncates the Subpopulation to a new size.
TRUNCATE - Static variable in class ec.Subpopulation
tweak(EvolutionState, double[], double, double, double, double, int) - Method in class ec.pso.Particle
type - Variable in class ec.gp.GPType
  The preassigned integer value for the type
type - Variable in class ec.neat.NEATNode
  Distinguish the Sensor node or other neuron node.
type - Variable in class ec.util.DecodeReturn
  The DecodeReturn type
TYPE_RANDOM_WALK - Static variable in class ec.spatial.SpatialTournamentSelection
TYPE_UNIFORM - Static variable in class ec.spatial.SpatialTournamentSelection
typeFor(String, EvolutionState) - Static method in class ec.gp.GPType
  Returns a type for a given name.
typeRepository - Variable in class ec.gp.GPInitializer
  TODO Comment these members.
types - Variable in class ec.gp.GPInitializer
types_h - Variable in class ec.gp.GPSetType
  The hashtable of types in the set
types_packed - Variable in class ec.gp.GPSetType
  A packed, sorted array of atomic types in the set
types_sparse - Variable in class ec.gp.GPSetType
  A sparse array of atomic types in the set
typicalIndsProduced() - Method in class ec.breed.BufferedBreedingPipeline
typicalIndsProduced() - Method in class ec.breed.ForceBreedingPipeline
  Returns the max of typicalIndsProduced() of all its children
typicalIndsProduced() - Method in class ec.breed.GenerationSwitchPipeline
  Returns the max of typicalIndsProduced() of all its children
typicalIndsProduced() - Method in class ec.breed.MultiBreedingPipeline
  Returns the max of typicalIndsProduced() of all its children
typicalIndsProduced() - Method in class ec.BreedingPipeline
  Returns the "typical" number of individuals produced -- by default this is the minimum typical number of individuals produced by any children sources of the pipeline.
typicalIndsProduced() - Method in class ec.BreedingSource
  Returns the "typical" number of individuals generated with one call of produce(...).
typicalIndsProduced() - Method in class ec.gp.breed.SizeFairCrossoverPipeline
  Returns 2 * minimum number of typical individuals produced by any sources, else 1* minimum number if tossSecondParent is true.
typicalIndsProduced() - Method in class ec.gp.koza.CrossoverPipeline
  Returns 2 * minimum number of typical individuals produced by any sources, else 1* minimum number if tossSecondParent is true.
typicalIndsProduced() - Method in class ec.rule.breed.RuleCrossoverPipeline
  Returns 2 (unless tossing the second sibling, in which case it returns 1)
typicalIndsProduced() - Method in class ec.rule.breed.RuleMutationPipeline
  Returns 1
typicalIndsProduced() - Method in class ec.SelectionMethod
  Returns 1 (the typical default value)
typicalIndsProduced() - Method in class ec.vector.breed.ListCrossoverPipeline
typicalIndsProduced() - Method in class ec.vector.breed.MultipleVectorCrossoverPipeline
  Returns the minimum number of children that are produced per crossover
typicalIndsProduced() - Method in class ec.vector.breed.VectorCrossoverPipeline
  Returns 2 * minimum number of typical individuals produced by any sources, else 1* minimum number if tossSecondParent is true.

## U

UNDEFINED - Static variable in class ec.EvolutionState
Uniform - Class in ec.gp.build
  Uniform implements the algorithm described in
Uniform() - Constructor for class ec.gp.build.Uniform
UniquePipeline - Class in ec.breed
  UniquePipeline is a BreedingPipeline which tries very hard to guarantee that all the individuals it produces are unique from members of the original subpopulation.
UniquePipeline() - Constructor for class ec.breed.UniquePipeline
uniqueSamples(EvolutionState, ArrayList<Individual>) - Method in class ec.eda.dovs.DOVSSpecies
  This method will take a candidate list and identify is there is redundant individual in it.
UNKNOWN_VALUE - Static variable in class ec.util.ParameterDatabase
unmarkElitesEvaluated(EvolutionState, Population) - Method in class ec.simple.SimpleBreeder
unregisterSlave(SlaveConnection) - Method in class ec.eval.SlaveMonitor
  Unregisters a dead slave from the monitor.
update(EvolutionState, int, int, int) - Method in class ec.pso.Particle
updateDistribution(EvolutionState, Subpopulation) - Method in class ec.eda.amalgam.AMALGAMSpecies
updateDistribution(EvolutionState, Subpopulation) - Method in class ec.eda.cmaes.CMAESSpecies
  Revises the CMA-ES distribution to reflect the current fitness results in the provided subpopulation.
updateDistribution(EvolutionState, Subpopulation) - Method in class ec.eda.pbil.PBILSpecies
  Revises the PBIL distribution to reflect the current fitness results in the provided subpopulation.
updateIndividual(EvolutionState, Individual) - Method in class ec.Species
  A hook for code that is run on every individual as soon as it is evaluated.
updateMostPromisingArea(EvolutionState) - Method in class ec.eda.dovs.DOVSSpecies
  Define a most promising area for search of next genertion of individuals.
updateMostPromisingArea(EvolutionState) - Method in class ec.eda.dovs.HyperboxSpecies
  Constructing a hyperbox, which defines the next search area.
updateSubpopulation(EvolutionState, Subpopulation) - Method in class ec.Species
  A hook for code that is run on the entire subpopulation as soon as it has been evaluated.
updateSubspeciesMaxFitness() - Method in class ec.neat.NEATSubspecies
  Update the maxFitnessEver variable.
UPPER_BOUND - Static variable in class ec.eda.dovs.HyperboxSpecies
upperbound - Variable in class ec.evolve.RandomRestarts
upperBound(int) - Method in class ec.eda.dovs.CornerMap
  This method returns the smallest element whose key is bigger than (excluding equal to) "key",
useAltGenerator - Variable in class ec.eda.cmaes.CMAESSpecies
  If, after trying altGeneratorTries to build an indiviual, we are still building one which violates min/max gene constraints, should we instead fill those violated genes with uniformly-selected values between the min and max?
useAltTermination - Variable in class ec.eda.amalgam.AMALGAMSpecies
useAltTermination - Variable in class ec.eda.cmaes.CMAESSpecies
  Should we terminate when the eigenvalues get too small? If we don't, they might go negative and the eigendecomposition will fail.
useCompression - Variable in class ec.eval.SlaveMonitor
  Indicates whether compression is used over the socket IO streams.
userAlphaAMS - Variable in class ec.eda.amalgam.AMALGAMSpecies
userEtaP - Variable in class ec.eda.amalgam.AMALGAMSpecies
userEtaS - Variable in class ec.eda.amalgam.AMALGAMSpecies
useTrueDistribution - Variable in class ec.gp.build.Uniform
usingElitism(int) - Method in class ec.simple.SimpleBreeder

## V

V_ALIAS - Static variable in class ec.util.ParameterDatabase
V_ANY_POINT - Static variable in class ec.vector.VectorSpecies
V_AUTO - Static variable in class ec.simple.SimpleEvaluator
V_BEST - Static variable in class ec.simple.SimpleEvaluator
V_BOOLEAN - Static variable in class ec.eval.MetaProblem
V_C - Static variable in class ec.gp.GPTree
V_CENTER - Static variable in class ec.eda.cmaes.CMAESSpecies
V_CUTDOWN - Static variable in class ec.select.AnnealedSelection
V_DEFAULT - Static variable in class ec.util.ParameterDatabase
V_DOT - Static variable in class ec.gp.GPTree
V_EVALUATEGROUPED - Static variable in class ec.eval.Slave
V_EVALUATESIMPLE - Static variable in class ec.eval.Slave
V_FILL - Static variable in class ec.Subpopulation
V_FITNESS - Static variable in class ec.eval.Slave
V_FLIP_MUTATION - Static variable in class ec.vector.BitVectorSpecies
V_FLOAT - Static variable in class ec.eval.MetaProblem
V_GAUSS_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
V_GEOMETRIC - Static variable in class ec.vector.VectorSpecies
V_IDENTITY - Static variable in class ec.eda.cmaes.CMAESSpecies
V_INDIVIDUAL - Static variable in class ec.eval.Slave
V_INTEGER - Static variable in class ec.eval.MetaProblem
V_INTEGER_RANDOM_WALK_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
V_INTEGER_RESET_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
V_INTERMED_RECOMB - Static variable in class ec.vector.VectorSpecies
V_LATEX - Static variable in class ec.gp.GPTree
V_LINE_RECOMB - Static variable in class ec.vector.VectorSpecies
V_LISP - Static variable in class ec.gp.GPTree
V_MEAN - Static variable in class ec.simple.SimpleEvaluator
V_MEDIAN - Static variable in class ec.simple.SimpleEvaluator
V_NEIGHBORHOOD_RANDOM - Static variable in class ec.pso.PSOBreeder
V_NEIGHBORHOOD_RANDOM_EACH_TIME - Static variable in class ec.pso.PSOBreeder
V_NEIGHBORHOOD_TOROIDAL - Static variable in class ec.pso.PSOBreeder
V_NO_ERRORS - Static variable in class ec.util.Output
  Don't print warnings, messages, or simple errors
V_NO_GENERAL - Static variable in class ec.util.Output
  The standard verbosity to use if you don't want common reporting (like statistics)
V_NO_MESSAGES - Static variable in class ec.util.Output
  Don't print messages
V_NO_WARNINGS - Static variable in class ec.util.Output
  Don't print warnings or messages
V_NOTHING - Static variable in class ec.eval.Slave
V_ONE_POINT - Static variable in class ec.vector.VectorSpecies
V_ONE_POINT_NO_NOP - Static variable in class ec.vector.VectorSpecies
V_POLYNOMIAL_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
V_RANDOM - Static variable in class ec.eda.cmaes.CMAESSpecies
V_RANDOM_WALK - Static variable in class ec.spatial.SpatialTournamentSelection
V_RANDOM_WALK_MUTATION - Static variable in class ec.vector.IntegerVectorSpecies
V_RESET_MUTATION - Static variable in class ec.vector.BitVectorSpecies
V_RESET_MUTATION - Static variable in class ec.vector.FloatVectorSpecies
V_RESET_MUTATION - Static variable in class ec.vector.IntegerVectorSpecies
V_SAME - Static variable in class ec.BreedingPipeline
  Indicates that a source is the exact same source as the previous source.
V_SCALED - Static variable in class ec.eda.cmaes.CMAESSpecies
V_SEED_TIME - Static variable in class ec.Evolve
  'time' seed parameter value
V_SHUTDOWN - Static variable in class ec.eval.Slave
V_SIMULATED_BINARY - Static variable in class ec.vector.VectorSpecies
V_STUB - Static variable in class ec.BreedingPipeline
  Indicates that the source will be filled later via a call to setStubs().
V_THREADS_AUTO - Static variable in class ec.Evolve
  'auto' thread parameter value
V_TOTALLY_SILENT - Static variable in class ec.util.Output
  No verbosity at all, not even system messages or fatal errors
V_TRUNCATE - Static variable in class ec.Subpopulation
V_TWO_POINT - Static variable in class ec.vector.VectorSpecies
V_TWO_POINT_NO_NOP - Static variable in class ec.vector.VectorSpecies
V_UNIFORM - Static variable in class ec.spatial.SpatialTournamentSelection
V_UNIFORM - Static variable in class ec.vector.VectorSpecies
V_VERBOSE - Static variable in class ec.util.Output
  Total verbosity
V_WRAP - Static variable in class ec.Subpopulation
V_ZERO - Static variable in class ec.eda.cmaes.CMAESSpecies
valid(DoubleVectorIndividual) - Method in class ec.de.DEBreeder
  Tests the Individual to see if its values are in range.
validateRules() - Method in class ec.gp.ge.GrammarParser
  Checks that all grammar rules in ruleshashmap have at least one possible production
value - Variable in class ec.eda.dovs.CornerMap.Pair
valueForPathChanged(TreePath, Object) - Method in class ec.util.ReflectedObject
valueOf(String) - Static method in enum class ec.multiobjective.nsga2.NSGA2Breeder.BreedingState
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ec.multiobjective.spea2.SPEA2Breeder.BreedingState
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ec.neat.NEATNode.FunctionType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ec.neat.NEATNode.NodePlace
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ec.neat.NEATNode.NodeType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ec.neat.NEATSpecies.MutationType
  Returns the enum constant of this class with the specified name.
values() - Static method in enum class ec.multiobjective.nsga2.NSGA2Breeder.BreedingState
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ec.multiobjective.spea2.SPEA2Breeder.BreedingState
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ec.neat.NEATNode.FunctionType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ec.neat.NEATNode.NodePlace
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ec.neat.NEATNode.NodeType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ec.neat.NEATSpecies.MutationType
  Returns an array containing the constants of this enum class, in the order they are declared.
variance - Variable in class ec.eda.dovs.DOVSFitness
  Variance of the fitness value of the current individual.
VectorCrossoverPipeline - Class in ec.vector.breed
  VectorCrossoverPipeline is a BreedingPipeline which implements a simple default crossover for VectorIndividuals.
VectorCrossoverPipeline() - Constructor for class ec.vector.breed.VectorCrossoverPipeline
VectorDefaults - Class in ec.vector
  Vector defaults is the basic defaults class for the Vector package.
VectorDefaults() - Constructor for class ec.vector.VectorDefaults
VectorIndividual - Class in ec.vector
  VectorIndividual is the abstract superclass of simple individual representations which consist of vectors of values (booleans, integers, floating-point, etc.)
VectorIndividual() - Constructor for class ec.vector.VectorIndividual
VectorMutationPipeline - Class in ec.vector.breed
  VectorMutationPipeline is a BreedingPipeline which implements a simple default Mutation for VectorIndividuals.
VectorMutationPipeline() - Constructor for class ec.vector.breed.VectorMutationPipeline
VectorSpecies - Class in ec.vector
  VectorSpecies is a species which can create VectorIndividuals.
VectorSpecies() - Constructor for class ec.vector.VectorSpecies
velCoeff - Variable in class ec.pso.PSOBreeder
velocity - Variable in class ec.pso.Particle
verify(EvolutionState) - Method in class ec.gp.GPIndividual
  Verification of validity of the GPIndividual -- strictly for debugging purposes only
verify(EvolutionState) - Method in class ec.gp.GPTree
  Verification of validity of the tree -- strictly for debugging purposes only
verifyPoints(GPInitializer, GPNode, GPNode) - Method in class ec.gp.breed.SizeFairCrossoverPipeline
  Returns true if inner1 can feasibly be swapped into inner2's position.
verifyPoints(GPInitializer, GPNode, GPNode) - Method in class ec.gp.koza.CrossoverPipeline
  Returns true if inner1 can feasibly be swapped into inner2's position.
verifyPoints(GPNode, GPNode) - Method in class ec.gp.koza.MutationPipeline
  Returns true if inner1 can feasibly be swapped into inner2's position
version - Static variable in class ec.util.Version
Version - Class in ec.util
  Version is a static class which stores version information for this evolutionary computation system.
Version() - Constructor for class ec.util.Version
visited - Variable in class ec.eda.dovs.DOVSSpecies
  This list contains all the sample we have visited during current algorithm run.
visitedIndexMap - Variable in class ec.eda.dovs.DOVSSpecies
  Given a individual, return the index of this individual in ArrayList visited

## W

waitForAllSlavesToFinishEvaluating(EvolutionState) - Method in class ec.eval.SlaveMonitor
  This method returns only when all slaves have finished the jobs that they were assigned.
waitForIndividual() - Method in class ec.eval.SlaveMonitor
  Blocks until an individual comes available
waitOnMonitor(Object) - Method in class ec.eval.SlaveMonitor
warmUp - Variable in class ec.eda.dovs.DOVSSpecies
  warm up period for RMD sampling.
warnAboutNonterminal(boolean, GPType, boolean, EvolutionState) - Method in class ec.gp.GPNodeBuilder
  If the given test is true, issues a warning that no terminal was found with a return type of the given type, and that an algorithm had requested one.
warnAboutNonTerminalWithType(GPType, boolean, EvolutionState) - Method in class ec.gp.GPNodeBuilder
  Issues a warning that no nonterminal was found with a return type of the given type, and that an algorithm had requested one.
warnAboutNoTerminalWithType(GPType, boolean, EvolutionState) - Method in class ec.gp.GPNodeBuilder
  Issues a warning that no terminal was found with a return type of the given type, and that an algorithm had requested one.
warning(String) - Method in class ec.util.Output
  Posts a warning.
warning(String, Parameter) - Method in class ec.util.Output
  Posts a warning.
warning(String, Parameter, Parameter) - Method in class ec.util.Output
  Posts a warning.
warnOnce(String) - Method in class ec.util.Output
  Posts a warning one time only.
warnOnce(String, Parameter) - Method in class ec.util.Output
warnOnce(String, Parameter, Parameter) - Method in class ec.util.Output
weight - Variable in class ec.neat.NEATGene
  The weight of link this gene is represent.
weightMutationPower - Variable in class ec.neat.NEATSpecies
  The Mutation power of the link's weights.
weights - Variable in class ec.eda.cmaes.CMAESSpecies
  The ranked fitness weights for the mu individuals.
WRAP - Static variable in class ec.Subpopulation
writeFitness(EvolutionState, DataOutput) - Method in class ec.Fitness
  Writes the binary form of an individual out to a DataOutput.
writeFitness(EvolutionState, DataOutput) - Method in class ec.gp.koza.KozaFitness
writeFitness(EvolutionState, DataOutput) - Method in class ec.multiobjective.MultiObjectiveFitness
writeFitness(EvolutionState, DataOutput) - Method in class ec.multiobjective.nsga2.NSGA2MultiObjectiveFitness
writeFitness(EvolutionState, DataOutput) - Method in class ec.multiobjective.spea2.SPEA2MultiObjectiveFitness
writeFitness(EvolutionState, DataOutput) - Method in class ec.simple.SimpleFitness
writeGene(EvolutionState, DataOutput) - Method in class ec.vector.Gene
  Override this if you need to write rules out to a binary stream
writeGenotype(EvolutionState, DataOutput) - Method in class ec.gp.GPIndividual
  Overridden for the GPIndividual genotype.
writeGenotype(EvolutionState, DataOutput) - Method in class ec.Individual
  Writes the genotypic information to a DataOutput.
writeGenotype(EvolutionState, DataOutput) - Method in class ec.rule.RuleIndividual
  Overridden for the RuleIndividual genotype, writing each ruleset in turn.
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.BitVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.ByteVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.DoubleVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.FloatVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.GeneVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.IntegerVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.LongVectorIndividual
writeGenotype(EvolutionState, DataOutput) - Method in class ec.vector.ShortVectorIndividual
writeIndividual(EvolutionState, DataOutput) - Method in class ec.Individual
  Writes the binary form of an individual out to a DataOutput.
writeIndividual(EvolutionState, DataOutput) - Method in class ec.pso.Particle
writeNode(EvolutionState, DataOutput) - Method in class ec.gp.ADF
writeNode(EvolutionState, DataOutput) - Method in class ec.gp.ADFArgument
writeNode(EvolutionState, DataOutput) - Method in class ec.gp.ERC
  To successfully write to a DataOutput, you must override this to write your specific ERC data out.
writeNode(EvolutionState, DataOutput) - Method in class ec.gp.GPNode
  Override this to write any additional node-specific information to dataOutput besides: the number of arguments, the specific node class, the children, and the parent.
writePopulation(EvolutionState, DataOutput) - Method in class ec.Population
  Writes a population in binary form, in a format readable by readPopulation(EvolutionState, DataInput).
writer - Variable in class ec.util.Log
  The log's writer
writeRootedTree(EvolutionState, GPType, GPFunctionSet, DataOutput) - Method in class ec.gp.GPNode
writeRule(EvolutionState, DataOutput) - Method in class ec.rule.Rule
  Override this if you need to write rules out to a binary stream
writeRuleSet(EvolutionState, DataOutput) - Method in class ec.rule.RuleSet
  Writes RuleSets out to a binary stream
writeState(DataOutputStream) - Method in class ec.util.MersenneTwister
  Writes the entire state of the MersenneTwister RNG to the stream
writeState(DataOutputStream) - Method in class ec.util.MersenneTwisterFast
  Writes the entire state of the MersenneTwister RNG to the stream
writeSubpopulation(EvolutionState, DataOutput) - Method in class ec.Subpopulation
  Writes a subpopulation in binary form, in a format readable by readSubpopulation(EvolutionState, DataInput).
writeTree(EvolutionState, DataOutput) - Method in class ec.gp.GPTree
writeTrials(EvolutionState, DataOutput) - Method in class ec.Fitness
  Writes trials out to DataOutput

## X

x - Variable in class ec.util.IIntPoint
xAvgImp - Variable in class ec.eda.amalgam.AMALGAMSpecies
xlabel - Variable in class ec.display.chart.ChartableStatistics
xmean - Variable in class ec.eda.cmaes.CMAESSpecies
  The mean of the distribution.
XYSeriesChartStatistics - Class in ec.display.chart
XYSeriesChartStatistics() - Constructor for class ec.display.chart.XYSeriesChartStatistics

## Y

y - Variable in class ec.util.IIntPoint
ylabel - Variable in class ec.display.chart.ChartableStatistics

## Z

zeroChildren - Variable in class ec.gp.GPNodeConstraints
  A little memory optimization: if GPNodes have no children, they are welcome to use share this zero-sized array as their children array.

## _

_functionsets - Variable in class ec.gp.build.Uniform
_truesizes - Variable in class ec.gp.build.Uniform

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