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

## A

AbstractAlgorithm - Class in Algorithm
  An Abstract algorithm class that should be useful for most algorithms.
AbstractIndividual - Class in Individuals
  An Abstract individual.
AbstractRun - Class in Main
  AbstractRun class.
AbstractRun() - Constructor for class Main.AbstractRun
  Creates a new instance of AbstractRun
accept(File) - Method in class Util.FileNameExtensionFilter
accProbs - Variable in class Operator.Operations.RouletteWheel
actionPerformed(ActionEvent) - Method in class Fractal.Enlarged
actionPerformed(ActionEvent) - Method in class Fractal.FinalGuiComp
actionPerformed(ActionEvent) - Method in class Fractal.FinalProtoComp
actionPerformed(ActionEvent) - Method in class Fractal.GuiComp
add(Individual) - Method in interface Individuals.Populations.Population
  Add an individual to the population
add(Individual) - Method in class Individuals.Populations.SimplePopulation
add(int) - Method in interface Util.Structures.IntList
  Add an int
add(int) - Method in class Util.Structures.StaticIntList
  Add int to list.
add(TreeNode<E>) - Method in class Util.Structures.TreeNode
  Adds a child node to this node.
addAll(Collection<Individual>) - Method in interface Individuals.Populations.Population
  Add a collection of individuals to the population
addAll(Population) - Method in interface Individuals.Populations.Population
  Add an entire population to the population
addAll(Collection<Individual>) - Method in class Individuals.Populations.SimplePopulation
addAll(Population) - Method in class Individuals.Populations.SimplePopulation
addAwtPSFontMappingPropertiesFile(File) - Method in class com.rie.rieps.engine.Job
addChild(E) - Method in class Util.Structures.NimbleTree
  Add a child to the current node.
addLength(ArrayList<Integer>) - Method in class Util.Statistics.StatCatcher
  Add length data
addMappingFile(File) - Method in class com.rie.rieps.engine.fonts.PSFontFinder
  Load a properties file which contains awt description = psfont description
addMeanDerivationTreeDepth(Fitness[]) - Method in class Util.Statistics.StatCatcher
  Add mean depth of the derivation trees in the population
addMeanUsedGenes(Fitness[]) - Method in class Util.Statistics.StatCatcher
  Add mean used genes
addModule(Module) - Method in interface Algorithm.Pipeline
  Adds a module to the pipeline
addModule(Module) - Method in class Algorithm.SimplePipeline
  Add a module to the end of the pipeline
addPop(List<Individual>) - Method in class Util.Statistics.IndividualCatcher
  Add the population to a StringBuffer.
addPSFontFile(PSFontFile) - Method in class com.rie.rieps.engine.Job
addStats(Fitness[]) - Method in class Util.Statistics.StatCatcher
  Add stats.
addStatsPop(ArrayList<Individual>) - Method in class Util.Statistics.StatCatcher
  Add population to the statcatcher to work with.
addString(String) - Method in class Util.Statistics.IndividualCatcher
  Add a string to the string buffer
addTime(Long) - Method in class Util.Statistics.StatCatcher
  Add time
age - Variable in class Individuals.AbstractIndividual
Algorithm - package Algorithm
Algorithm - Interface in Algorithm
  Interface for Algorithms This simple interface defines three methods that an algorithm must implement init() - runs the initialisation pipline(s) of the algorithm.
algorithm - Variable in class Main.State
allFitness - Variable in class Util.Statistics.StatCatcher
allocationSize() - Method in class Util.Structures.StaticIntList
  Get the total
angle - Variable in class Fractal.LSystem2Config
  The phenotype of this LSystem's angle
ANT - Static variable in class FitnessEvaluation.SantaFeAntTrail.Trail
AskForUnknownFontPanel - Class in com.rie.rieps.engine.fonts
AskForUnknownFontPanel(JDialog, Font, String[]) - Constructor for class com.rie.rieps.engine.fonts.AskForUnknownFontPanel
  Creates new form AskForUnknownFontPanel
askForUnkownAWTFont() - Method in class com.rie.rieps.engine.fonts.PSFontFinder
askForUnkownAWTFont(boolean) - Method in class com.rie.rieps.engine.fonts.PSFontFinder
askForUnmappedAWTFont(boolean) - Method in class com.rie.rieps.engine.Job
askForUnmappedAWTFont() - Method in class com.rie.rieps.engine.Job
aveLength - Variable in class Util.Statistics.StatCatcher

## B

BadParameterException - Exception in Exceptions
  Thrown when the input parameters are exceptional
BadParameterException() - Constructor for exception Exceptions.BadParameterException
  Creates a new instance of BadParameterException
BadParameterException(String) - Constructor for exception Exceptions.BadParameterException
  Creates a new instance of BadParameterException
BadParameterException(String, String) - Constructor for exception Exceptions.BadParameterException
  Creates a new instance of BadParameterException
BasicFitness - Class in Individuals.FitnessPackage
  BasicFitness.
BasicFitness() - Constructor for class Individuals.FitnessPackage.BasicFitness
  Creates a new instance of BasicFitness
BasicFitness(double, Individual) - Constructor for class Individuals.FitnessPackage.BasicFitness
  Creates new instance of BasicFitness
BasicFitness(Individual) - Constructor for class Individuals.FitnessPackage.BasicFitness
  Creates new instance of BasicFitness
bestFitness - Variable in class Util.Statistics.StatCatcher
bestIndividualOfGeneration - Variable in class Util.Statistics.StatCatcher
BinaryNode<T> - Class in Util.Structures
BinaryNode(T) - Constructor for class Util.Structures.BinaryNode
BinaryNode() - Constructor for class Util.Structures.BinaryNode
BinomialBSF - Class in FitnessEvaluation.BinomialProblem
  Evaluates the fitness for the BinomialProblemExperiment class.
BinomialBSF() - Constructor for class FitnessEvaluation.BinomialProblem.BinomialBSF
  Creates a new instance of Binomial problem
BinomialFunkBSF - Class in FitnessEvaluation.BinomialProblem
  help class for SymbolicRegression.java
BinomialFunkBSF() - Constructor for class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Creates a new instance of BinomialFunkBSF
BinomialJScheme - Class in FitnessEvaluation.BinomialProblem
  Evaluates the fitness for the BinomialProblem class.
BinomialJScheme() - Constructor for class FitnessEvaluation.BinomialProblem.BinomialJScheme
  Creates a new instance of BinomialJScheme
BLACK - Static variable in class com.rie.rieps.engine.color.Gray
BooleanInterpreter - Class in FitnessEvaluation.ParityProblem
  Interpreter for parity problems.
BooleanInterpreter() - Constructor for class FitnessEvaluation.ParityProblem.BooleanInterpreter
BooleanInterpreter(Properties) - Constructor for class FitnessEvaluation.ParityProblem.BooleanInterpreter
BooleanInterpreter(int) - Constructor for class FitnessEvaluation.ParityProblem.BooleanInterpreter
BOX_COUNT_DIVISION - Static variable in class Util.Constants
buildDerivationTree() - Method in class Mapper.DerivationTree
  Build a derivation tree.
buildDerivationTree(Individual, DerivationNode) - Static method in class Util.GenotypeHelper
  Build a derivation tree rooted at the specified node for a given individual.
buildDerivationTree(Individual) - Static method in class Util.GenotypeHelper
  Build a derivation tree for a given individual
buildInvalidTree(Individual, DerivationNode) - Static method in class Util.GenotypeHelper
  Build derivation trees for invalid individuals for repair operators.
buildInvalidTree(Individual) - Static method in class Util.GenotypeHelper
  Build a derivation tree for a given individual
buildTreeFromPostfix() - Method in class Util.Structures.ReversePolish

## C

calcFractalDimension() - Method in interface Fractal.FractalDimension
calcFractalDimension() - Method in class Fractal.LSystem2FDBoxCounting
  Approximate the fractal dimension using box-counting.
calcNodeLength(DerivationNode) - Static method in class Util.GenotypeHelper
  Calculate how may codons are used to build a specified branch of a tree.
calculateAccumulatedFitnessProbabilities(List<Individual>) - Method in class Operator.Operations.ProportionalRouletteWheel
  Min fitness is the best fitness.
calculateAccumulatedFitnessProbabilities(List<Individual>) - Method in class Operator.Operations.RouletteWheel
calculateAccumulatedFitnessProbabilities(List<Individual>) - Method in class Operator.Operations.ScaledRouletteWheel
  Min fitness is the best fitness.
calculateFitness() - Method in class FitnessEvaluation.HelloWorld.WorldWriter
  Compare a string.
calculateFitnessSum(List<Individual>) - Method in class Operator.Operations.RouletteWheel
  Calculate the fitness sum.
calculateTarget(String) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
  Calcualte the value of the target function for each data point in the sample.
canCache() - Method in class FitnessEvaluation.Canvas.Paint
canCache() - Method in interface FitnessEvaluation.FitnessFunction
  Return true if it is ok to cache the results of the fitness function
canCache() - Method in class FitnessEvaluation.InterpretedFitnessEvaluation
canCache() - Method in class FitnessEvaluation.LSystem.LSystemDimension
canCache() - Method in class FitnessEvaluation.LSystem.LSystemInitialiser
canCache() - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
canCache() - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
canCache() - Method in class FitnessEvaluation.PatternMatch.WordMatch
canCache() - Method in class FitnessEvaluation.RoyalTree.RoyalTree
canCache() - Method in class FitnessEvaluation.SantaFeAntTrail.SantaFeAntTrailInterpreter
canCache() - Method in class FitnessEvaluation.Sudoku.SudokuFit
canCache() - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
checkBox(int[], int, int) - Method in class FitnessEvaluation.Sudoku.SudokuFit
checkGECodonValue(NimbleTree<Symbol>) - Method in class Operator.Operations.GrowInitialiser
  Check if it is a GECodonValue.
checkLine(int[], int, int) - Method in class FitnessEvaluation.Sudoku.SudokuFit
Chromosome - Interface in Individuals
  Interface for Chromosome
chromosome - Variable in class Operator.Operations.GrowInitialiser
clear() - Method in interface Individuals.Populations.Population
  Clear the population of all individuals
clear() - Method in class Individuals.Populations.SimplePopulation
clear() - Method in class Mapper.GEGrammar
  Clear the grammar
clear() - Method in class Mapper.Grammar
clear() - Method in interface Mapper.Mapper
  Clears the mapper by dereferencing the genotype and phenotype.
clear() - Method in class Mapper.Symbol
  Clears the string and type
clear() - Method in class Util.Statistics.IndividualCatcher
  Clear the stringbuffer
clear() - Method in class Util.Statistics.StatCatcher
  Clear the structures in the class
clear() - Method in interface Util.Structures.IntList
  Clear structure
clear() - Method in class Util.Structures.ReversePolish
clear() - Method in class Util.Structures.StaticIntList
  Clear list by setting current size to 0
clone() - Method in class Individuals.AbstractIndividual
clone() - Method in class Individuals.GEIndividual
  Clone this individual, invialidate and return the clone
clone() - Method in interface Individuals.Individual
  Clone the individual
clone() - Method in class Util.Random.MersenneTwisterFast
close() - Method in class com.rie.rieps.engine.Document
close() - Method in class com.rie.rieps.engine.Job
CODONS_USED_SENSITIVE - Static variable in class Util.Constants
  Only crossover in the codons used
codonsUsedSensitive - Variable in class Operator.Operations.SinglePointCrossover
collapse() - Method in class Util.Structures.TreeNode
  Collapse the node to a string
collector - Variable in class Main.AbstractRun
Collector - Class in Operator
  Collector is used as a base class for collecting data from a population, e.g for collecting statistics.
Collector(Operation) - Constructor for class Operator.Collector
  Creates a new instance of Collector
Color - Interface in com.rie.rieps.engine.color
com.rie.rieps.engine - package com.rie.rieps.engine
com.rie.rieps.engine.color - package com.rie.rieps.engine.color
com.rie.rieps.engine.factories - package com.rie.rieps.engine.factories
com.rie.rieps.engine.fonts - package com.rie.rieps.engine.fonts
com.rie.rieps.engine.image - package com.rie.rieps.engine.image
com.rie.rieps.exception - package com.rie.rieps.exception
com.rie.rieps.simpletest - package com.rie.rieps.simpletest
commandLineArgs(String[]) - Method in class Main.AbstractRun
  Read the commandline arguments.
compare(LSystem2Config, LSystem2Config) - Method in class Fractal.GuiComp
compareTo(Individual) - Method in class Individuals.AbstractIndividual
  Compare the indivdual
compareTo(Fitness) - Method in class Individuals.FitnessPackage.BasicFitness
  Compare the Fitness ascending
ConstantGenerator - Class in Util
  This class is used to generate constants for symbolic regression and the Binomial 3 problem.
ConstantGenerator() - Constructor for class Util.ConstantGenerator
Constants - Class in Util
  This class has all the constants.
contains(Individual) - Method in interface Individuals.Populations.Population
  Check if the individual is contained in the population
contains(AbstractIndividual) - Method in class Individuals.Populations.SimplePopulation
contains(Individual) - Method in class Individuals.Populations.SimplePopulation
containsKey(String) - Method in class Util.Structures.Operators
containsKey(E) - Method in class Util.Structures.Operators
ContextFreeGrammar - Class in Mapper
  Abstract ContextFreeGrammar
ContextualDerivationTree - Class in Mapper
  This class is used for building a genotype to phenotype mapping it also stores information on which codons affect structural or nodal grammar rules, for a more selective mutation
ContextualDerivationTree(GEGrammar, GEChromosome) - Constructor for class Mapper.ContextualDerivationTree
ContextualDerivationTree(ContextualDerivationTree) - Constructor for class Mapper.ContextualDerivationTree
  Copy Constructor
CONVERT_MODE_AVERAGE - Static variable in class com.rie.rieps.engine.image.SmallGrayImage
  to convert color image int o gray, this method is the most simplest.
CONVERT_MODE_CIE_601 - Static variable in class com.rie.rieps.engine.image.SmallGrayImage
  the 601 CIE (International Commission on Illumination), non-linear with gamma correction.
CONVERT_MODE_CIE_709 - Static variable in class com.rie.rieps.engine.image.SmallGrayImage
  The 709 CIE (International Commission on Illumination), true colors.
cos(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Trigonometric cosine function
cos(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Trigonometric cosine function
create(BufferedImage) - Method in class com.rie.rieps.engine.image.ImageFactory
createCode(Phenotype) - Method in class FitnessEvaluation.BinomialProblem.BinomialBSF
createCode(Phenotype) - Method in class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParityFitnessBSF
  Create a header and a tail for the input string.
createCode(Phenotype) - Method in class FitnessEvaluation.externalInterpreters.SantaFeAntTrail.SantaFeAntTrailBSF
  Create a header and a tail for the input string.
createCode(Phenotype) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionBSF
createCode(Phenotype) - Method in class FitnessEvaluation.HelloWorld.HelloWorldBSF
  Create a header and a tail for the input string.
createCode(Phenotype) - Method in class FitnessEvaluation.InterpretedFitnessEvaluationBSF
  Create code by adding header and tail to the evolved input
createDocument(int) - Method in class com.rie.rieps.engine.Job
createGrayColor(int, int, int) - Static method in class com.rie.rieps.engine.color.RGBToGray
createIndividual() - Method in interface Operator.Operations.CreationOperation
  Creates an individual
createIndividual() - Method in class Operator.Operations.GrowInitialiser
  Creates an Individuals
createIndividual() - Method in class Operator.Operations.RandomInitialiser
  Creates an Individual
createJob(OutputStream, Factory, float, float) - Static method in class com.rie.rieps.engine.Job
createPage() - Method in class com.rie.rieps.engine.Document
createPSTopLeftOriginJob(OutputStream, float, float) - Static method in class com.rie.rieps.engine.Job
  Change the origine of the postscript to upper left corner of the page.
createSmallGrayImageFactory(int) - Static method in class com.rie.rieps.engine.image.ImageFactory
CreationOperation - Interface in Operator.Operations
  Interface for creation of individuals
Creator - Interface in Operator
  Interface for modules that can create a population.
CROSSOVER_OPERATION - Static variable in class Util.Constants
  Class name of crossover operation.
CROSSOVER_PROBABILITY - Static variable in class Util.Constants
  Probability of crossing over inputs
CrossoverModule - Class in Operator
  CrossoverModule performs crossover on an entire population.
CrossoverModule(RandomNumberGenerator, CrossoverOperation) - Constructor for class Operator.CrossoverModule
  Creates a new instance of CrossoverModule
CrossoverOperation - Class in Operator.Operations
  Abstract class for CrossoverOperation
CrossoverOperation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.CrossoverOperation
  Creates a new instance of CrossoverOperation
CrossoverOperation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.CrossoverOperation
  New instance
currentCodonValue - Variable in class Mapper.DerivationTree
currentDepth - Variable in class Operator.RampedHalfAndHalfInitialiser
currentSize - Variable in class Util.Structures.StaticIntList
Cursor - Class in Fractal
  Logo Style cursor for use with 2-D L-Systems Applet
Cursor() - Constructor for class Fractal.Cursor
  Default Construtor
Cursor(Cursor) - Constructor for class Fractal.Cursor
  Copy Constructor

## D

data - Variable in class Util.Structures.StaticIntList
DEFAULT - Static variable in class com.rie.rieps.engine.fonts.PSFont
DEFAULT - Static variable in class com.rie.rieps.engine.LineFormat
DEFAULT_CHROMOSOME_SIZE - Static variable in class Util.Constants
  Default chromosome size
DEFAULT_FITNESS - Static variable in class Individuals.FitnessPackage.BasicFitness
DEFAULT_GEGRAMMAR - Static variable in class Util.Constants
  Defualt GEGrammar
DEFAULT_MAX_DERIVATION_TREE_DEPTH - Static variable in class Util.Constants
DEFAULT_PARAM_ROOT - Static variable in class Util.Constants
DEFAULT_POPULATION_SIZE - Static variable in class Util.Constants
  Default population size
DEFAULT_PRC_PRECISION - Static variable in class Util.Constants
DEFAULT_PRC_RANGE - Static variable in class Util.Constants
DEFAULT_PRC_SETSIZE - Static variable in class Util.Constants
DEFAULT_PROPERTIES - Static variable in class Util.Constants
  Path to default properties file
defaultSelect(List<Individual>) - Method in class Operator.Operations.UserSelect
depth - Variable in class Fractal.LSystem2Config
  The phenotype of this LSystem's depth
depthFirstTraversal(TreeNode<E>) - Method in class Util.Structures.NimbleTree
  Do a depth-first traversal of the tree starting at a given node.
depthInterval - Variable in class Operator.RampedHalfAndHalfInitialiser
dequeue() - Method in class Util.Structures.Queue
  Remove first element.
Derivation - Interface in Mapper
  Interface for derivation of the grammar
DERIVATION_TREE - Static variable in class Util.Constants
DerivationNode - Class in Mapper
DerivationNode() - Constructor for class Mapper.DerivationNode
DerivationNode(TreeNode<Symbol>) - Constructor for class Mapper.DerivationNode
DerivationNode(TreeNode<Symbol>, Symbol) - Constructor for class Mapper.DerivationNode
DerivationTree - Class in Mapper
  This class is used in the mapping from genotype to phenotype in GE.
DerivationTree(GEGrammar, GEChromosome) - Constructor for class Mapper.DerivationTree
  Create new Derivation Tree
DerivationTree(DerivationTree) - Constructor for class Mapper.DerivationTree
  Copy Constructor
derivationTreesEqual(DerivationTree, DerivationTree) - Static method in class Util.GenotypeHelper
  Compare the derivation trees for equality.
derive() - Method in interface Mapper.Derivation
derive() - Method in class Mapper.DerivationTree
destinationPopulation - Variable in class Operator.SplitOperator
DeviceParameter - Class in com.rie.rieps.engine
display(List<Individual>) - Method in class Operator.Operations.SimpleUserSelect
display(List<Individual>) - Method in class Operator.Operations.UserSelect
div(double, double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Protected division.
div(double, double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Protected division.
Document - Class in com.rie.rieps.engine
  A Document can generate the output postscript page per page.
doOperation(Individual) - Method in class Operator.Operations.ContextSensitiveOperations.NodalMutation
doOperation(List<Individual>) - Method in class Operator.Operations.ContextSensitiveOperations.NodalMutation
doOperation(Individual) - Method in class Operator.Operations.ContextSensitiveOperations.StructuralMutation
doOperation(List<Individual>) - Method in class Operator.Operations.ContextSensitiveOperations.StructuralMutation
doOperation(List<Individual>) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeCrossover
doOperation(Individual) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeCrossover
doOperation(Individual) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
doOperation(List<Individual>) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
doOperation(List<Individual>) - Method in class Operator.Operations.CrossoverOperation
doOperation(Individual) - Method in class Operator.Operations.EliteOperationSelection
doOperation(List<Individual>) - Method in class Operator.Operations.EliteOperationSelection
  Ranks the population.
doOperation(Individual) - Method in class Operator.Operations.EliteReplacementOperation
doOperation(List<Individual>) - Method in class Operator.Operations.EliteReplacementOperation
  Sort ascending and remove the worst individuals
doOperation(Individual) - Method in class Operator.Operations.FitnessEvaluationOperation
  Evaluates Individuals that are not alreadt evaluated.
doOperation(List<Individual>) - Method in class Operator.Operations.FitnessEvaluationOperation
doOperation(Individual) - Method in class Operator.Operations.GrowInitialiser
doOperation(List<Individual>) - Method in class Operator.Operations.GrowInitialiser
doOperation(List<Individual>) - Method in class Operator.Operations.IntFlipByteMutation
doOperation(Individual) - Method in class Operator.Operations.IntFlipByteMutation
  Calls doMutation(GEIndividual c) and then calls Individual.invalidate()
doOperation(List<Individual>) - Method in class Operator.Operations.IntFlipFitness
doOperation(Individual) - Method in class Operator.Operations.IntFlipFitness
  Calls doMutation(GEIndividual c) and then calls Individual.invalidate()
doOperation(List<Individual>) - Method in class Operator.Operations.IntFlipMutation
doOperation(Individual) - Method in class Operator.Operations.IntFlipMutation
  Calls doMutation(GEIndividual c) and then calls Individual.invalidate()
doOperation(Individual) - Method in class Operator.Operations.LSystemSelect
doOperation(List<Individual>) - Method in class Operator.Operations.LSystemSelect
doOperation(Individual) - Method in class Operator.Operations.MutationOperation
doOperation(List<Individual>) - Method in class Operator.Operations.MutationOperation
doOperation(List<Individual>) - Method in interface Operator.Operations.Operation
  Performs the operation on the list passed
doOperation(Individual) - Method in interface Operator.Operations.Operation
  Performs the operation on an operand
doOperation(Individual) - Method in class Operator.Operations.RandomInitialiser
  Set an integer chromsome of initChromSize filled with random integers in the incoming individual.
doOperation(List<Individual>) - Method in class Operator.Operations.RandomInitialiser
  Calls doOperation(Individual operand)
doOperation(Individual) - Method in class Operator.Operations.ReplacementOperation
doOperation(List<Individual>) - Method in class Operator.Operations.ReplacementOperation
  Sort ascending and remove the worst individuals
doOperation(List<Individual>, int) - Method in class Operator.Operations.ReplacementOperation
  Sort ascending and remove the size worst individuals
doOperation(Individual) - Method in class Operator.Operations.RouletteWheel
doOperation(List<Individual>) - Method in class Operator.Operations.RouletteWheel
doOperation(Individual) - Method in class Operator.Operations.SelectionOperation
doOperation(List<Individual>) - Method in class Operator.Operations.SelectionOperation
doOperation(List<Individual>) - Method in class Operator.Operations.ShapeGrammarSelect
doOperation(Individual) - Method in class Operator.Operations.ShapeGrammarSelect
doOperation(Individual) - Method in class Operator.Operations.SinglePointCrossover
doOperation(List<Individual>) - Method in class Operator.Operations.SinglePointCrossover
  Performes crossover on the 2 first individuals in the incoming list.
doOperation(Individual) - Method in class Operator.Operations.StatisticsCollectionOperation
doOperation(List<Individual>) - Method in class Operator.Operations.StatisticsCollectionOperation
  Store the time of the operation.
doOperation(Individual) - Method in class Operator.Operations.TournamentSelect
doOperation(List<Individual>) - Method in class Operator.Operations.TournamentSelect
  Individuals from operands will be added to the selected population if the win their tournament.
doOperation(Individual) - Method in class Operator.Operations.UserSelect
doOperation(List<Individual>) - Method in class Operator.Operations.UserSelect
DoubleFitness - Interface in Individuals.FitnessPackage
  Interface for DoubleFitness
doubleSize() - Method in class Individuals.GEChromosome
  Double the size of the data ????
DRAW_PHENOTYPE - Static variable in class Util.Constants
  boolean specifying whether or not phenotype should be drawn
drawCircle(float, float, float, boolean, boolean) - Method in class com.rie.rieps.engine.Page
drawEllipse(Page, float, float, float, float, float, boolean, boolean) - Method in interface com.rie.rieps.engine.factories.Factory
drawEllipse(Page, float, float, float, float, float, boolean, boolean) - Method in class com.rie.rieps.engine.factories.PSFactory
drawEllipse(float, float, float, float, float, boolean, boolean) - Method in class com.rie.rieps.engine.Page
drawFrame(Page, Frame) - Method in interface com.rie.rieps.engine.factories.Factory
drawFrame(Page, Frame) - Method in class com.rie.rieps.engine.factories.PSFactory
drawFrame(Frame) - Method in class com.rie.rieps.engine.Page
drawImage(Page, float, float, Image, float, float) - Method in interface com.rie.rieps.engine.factories.Factory
drawImage(Page, float, float, Image, float, float) - Method in class com.rie.rieps.engine.factories.PSFactory
drawImage(float, float, Image, float, float) - Method in class com.rie.rieps.engine.Page
drawLine(Page, float, float, float, float) - Method in interface com.rie.rieps.engine.factories.Factory
drawLine(Page, float, float, float, float) - Method in class com.rie.rieps.engine.factories.PSFactory
drawLine(float, float, float, float) - Method in class com.rie.rieps.engine.Page
drawLine(Object, int, int, int, int) - Method in class Fractal.LSystem2FDBoxCounting
drawLine(Object, int, int, int, int) - Method in class Fractal.LSystem2Renderer
drawLine(Object, int, int, int, int) - Method in class Fractal.PSLSystem2
  Execute the LSystem and write its movements to the PS file, scaled to fit the page
drawPath(String, double, Graphics) - Method in class Fractal.LargeLSystem
  draws the expanded LSystem string to the screen
drawPath(String, double, Graphics) - Method in class Fractal.LSystem
  draws the expanded LSystem string to the screen
drawRect(Page, float, float, float, float, float, float, boolean, boolean) - Method in interface com.rie.rieps.engine.factories.Factory
drawRect(Page, float, float, float, float, float, float, boolean, boolean) - Method in class com.rie.rieps.engine.factories.PSFactory
drawRect(float, float, float, float, float, float, boolean, boolean) - Method in class com.rie.rieps.engine.Page
DUPLEX - Static variable in class com.rie.rieps.engine.DeviceParameter
  Parameter to set duplex mode.
DUPLICATION_PROBABILITY - Static variable in class Util.Constants
  Probability of duplicating inputs

## E

echoFontMapping(boolean) - Method in class com.rie.rieps.engine.Job
ELITE_SIZE - Static variable in class Util.Constants
  Number of elites.
EliteOperationSelection - Class in Operator.Operations
  Class for selection of elites.
EliteOperationSelection(int) - Constructor for class Operator.Operations.EliteOperationSelection
  New instance
EliteOperationSelection(Properties) - Constructor for class Operator.Operations.EliteOperationSelection
  New instance
EliteReplacementOperation - Class in Operator.Operations
  EliteReplacementOperation removes the worst
EliteReplacementOperation(int) - Constructor for class Operator.Operations.EliteReplacementOperation
  Creates a new instance of ReplacementOperation
EliteReplacementOperation(Properties) - Constructor for class Operator.Operations.EliteReplacementOperation
  Creates a new instance of ReplacementOperation
EliteReplacementOperator - Class in Operator
  EliteReplacementOperator has a EliteReplacementOperation.
EliteReplacementOperator(RandomNumberGenerator, Population, EliteReplacementOperation) - Constructor for class Operator.EliteReplacementOperator
  Creates a new instance of EliteReplacementOperator
EMPTY - Static variable in class FitnessEvaluation.SantaFeAntTrail.Trail
enableDone(boolean) - Method in class Operator.Operations.UserSelect
Enlarged - Class in Fractal
Enlarged(String, int, float) - Constructor for class Fractal.Enlarged
enqueue(T) - Method in class Util.Structures.Queue
  add element to end of items
Enums - Class in Util
  Class for Enums
Enums() - Constructor for class Util.Enums
  Creates a new instance of Enums
Enums.SymbolType - Enum in Util
  Enum for SymbolType.
equals(Object) - Method in class Mapper.GEGrammar
equals(Symbol) - Method in class Mapper.Symbol
  Compare type and symbol string value
equals(String) - Method in class Mapper.Symbol
  Compares the symbol strings of this and the symbol passed as a parameter
evaluate(String) - Method in class FitnessEvaluation.RoyalTree.RoyalTree
  Given a string, calculate its fitness.
evaluate(int[]) - Method in class FitnessEvaluation.Sudoku.SudokuFit
EVALUATE_ELITES - Static variable in class Util.Constants
  If the elites should be evaluated each iteration
evaluated - Variable in class Individuals.AbstractIndividual
evaluateString(Phenotype) - Method in class FitnessEvaluation.PatternMatch.WordMatch
  Compare a string to the word.
evaluateString(Phenotype) - Method in class FitnessEvaluation.RoyalTree.RoyalTree
  The phenotype will be a tree in lisp-syntax.
EvenFiveParBSF - Class in FitnessEvaluation.externalInterpreters.ParityProblem
  Class implementing the functions called by the Even Five Parity problem
EvenFiveParBSF() - Constructor for class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParBSF
  Creates a new instance of EvenFiveParityHelpFile
EvenFiveParityFitnessBSF - Class in FitnessEvaluation.externalInterpreters.ParityProblem
  Evaluates the fitness for the EvenFiveParityExperiment.java.
EvenFiveParityFitnessBSF() - Constructor for class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParityFitnessBSF
  Creates a new instance of EvenFiveParityFitness
Exceptions - package Exceptions
exp(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Returns Euler's number e raised to the power of a double value.
exp(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Returns Euler's number e raised to the power of a double value.
expandPath(String, String, int) - Method in class Fractal.LargeLSystem
  expands an Lsystem grammar
expandPath(String, String, int) - Method in class Fractal.LSystem
  expands an Lsystem grammar
Experiment - Class in Main
  Wrapper class for loading different Main.Run files
Experiment() - Constructor for class Main.Experiment
experiment(String[]) - Method in class Main.Run
experiment(String[]) - Method in class Main.State
experiment(String[]) - Method in class Main.Tutorials.Tutorial4
experiment(String[]) - Method in class Main.Tutorials.Tutorial5
experiment(String[]) - Method in class Main.Tutorials.Tutorial6
experiment(String[]) - Method in class Main.Tutorials.Tutorial7
EXPERIMENT - Static variable in class Util.Constants
  Sets the run class to use
expr(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Expression to evaluate
expr(int, int, int, int, int) - Method in class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParBSF
  Abstract method to override for evaluating input expression.
expr(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Expression to evaluate
extendChromeAtRecursiveNode(Individual, GEChromosome, Symbol, int) - Static method in class Util.GenotypeHelper
extendRecursiveNode(int, Individual, Symbol) - Static method in class Util.GenotypeHelper
  This method takes the codon that's going to change and determines how it needs to change in order to map to the correct production.

## F

Factory - Interface in com.rie.rieps.engine.factories
  Little interface to add someother output than postscript.
FALSE - Static variable in class Util.Constants
fileList(String) - Static method in class Util.PathTools
  Build a file list of all the files in the specified directories matching the specified wildcard. pathList can contain several paths separated by a semi-colon (;) e.g.
fileName - Variable in class Operator.Operations.StatisticsCollectionOperation
FileNameExtensionFilter - Class in Util
  Implementation for 1.5 compatibility of the 1.6 Java class of the same name, which I didn't realise at the time of using, wasn't part of a 1.5
FileNameExtensionFilter(String, String...) - Constructor for class Util.FileNameExtensionFilter
FinalGuiComp - Class in Fractal
FinalGuiComp(String[], String[], String[], int) - Constructor for class Fractal.FinalGuiComp
FinalProtoComp - Class in Fractal
FinalProtoComp(String, int, float) - Constructor for class Fractal.FinalProtoComp
  Creates new form protoComp
findLastRecIndex(Individual) - Static method in class Util.GenotypeHelper
  This method takes and individual and returns the codon index of the last recurisve node in the derivation tree.
findLastRecIndex(DerivationNode, GEGrammar) - Static method in class Util.GenotypeHelper
  This method takes a derivation node and a grammar and returns the codon index of the last recurisve node in the derivation tree.
findNodeFromCodonIndex(DerivationTree, int) - Static method in class Util.GenotypeHelper
  Given a derivation tree and a codon index, return the tree node that makes use of the codon at that index. e.g., if codonIndex was 0, the root branch decides which production is picked based on the value of the codon at index 0, so the root is returned in this case
findNodeFromCodonIndex(DerivationTree, int, int) - Static method in class Util.GenotypeHelper
findRule(Symbol) - Method in class Mapper.ContextFreeGrammar
  Find a rule given a symbol.
findRule(String) - Method in class Mapper.ContextFreeGrammar
  Find a rule given a string.
fitness - Variable in class Fractal.LSystem2Config
  The fitness of this LSystem, multiplied by .99 each time it is selected in LSystemSelect
fitness - Variable in class Individuals.AbstractIndividual
Fitness - Interface in Individuals.FitnessPackage
  Interface for Fitness.
FITNESS_FUNCTION - Static variable in class Util.Constants
  Class name of fitness function.
fitnessA - Variable in class Operator.Operations.ReplacementOperation
FitnessEvaluation - package FitnessEvaluation
FitnessEvaluation.BinomialProblem - package FitnessEvaluation.BinomialProblem
FitnessEvaluation.Canvas - package FitnessEvaluation.Canvas
FitnessEvaluation.externalInterpreters.ParityProblem - package FitnessEvaluation.externalInterpreters.ParityProblem
FitnessEvaluation.externalInterpreters.SantaFeAntTrail - package FitnessEvaluation.externalInterpreters.SantaFeAntTrail
FitnessEvaluation.externalInterpreters.SymbolicRegression - package FitnessEvaluation.externalInterpreters.SymbolicRegression
FitnessEvaluation.HelloWorld - package FitnessEvaluation.HelloWorld
FitnessEvaluation.LSystem - package FitnessEvaluation.LSystem
FitnessEvaluation.MaxProblem - package FitnessEvaluation.MaxProblem
FitnessEvaluation.ParityProblem - package FitnessEvaluation.ParityProblem
FitnessEvaluation.PatternMatch - package FitnessEvaluation.PatternMatch
FitnessEvaluation.RoyalTree - package FitnessEvaluation.RoyalTree
FitnessEvaluation.SantaFeAntTrail - package FitnessEvaluation.SantaFeAntTrail
FitnessEvaluation.Sudoku - package FitnessEvaluation.Sudoku
FitnessEvaluation.SymbolicRegression - package FitnessEvaluation.SymbolicRegression
FitnessEvaluation.util - package FitnessEvaluation.util
FitnessEvaluationOperation - Class in Operator.Operations
  Operation for evaluating the fitness.
FitnessEvaluationOperation(FitnessFunction) - Constructor for class Operator.Operations.FitnessEvaluationOperation
  Creates a new instance of FitnessEvaluationOperation
FitnessEvaluator - Class in Operator
  FitnessEvaluator is a module that is used to evaluate an entire populations fitness.
FitnessEvaluator(RandomNumberGenerator, FitnessEvaluationOperation) - Constructor for class Operator.FitnessEvaluator
  Creates a new instance of FitnessEvaluator
FitnessFunction - Interface in FitnessEvaluation
  A simple interface to be implemented by any fitness evaluator makes making fitness evaluation classes pluggable.
fitnessFunction - Variable in class Operator.Operations.MutationOperation
FIXED_POINT_CROSSOVER - Static variable in class Util.Constants
  If the crossover point is fixed
fixedCrossoverPoint - Variable in class Operator.Operations.SinglePointCrossover
FOOD - Static variable in class FitnessEvaluation.SantaFeAntTrail.Trail
food - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
food_ahead() - Method in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
  Check if there is food in the square ahead. 0 is false, 1 is true.
food_ahead() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Check if there is food in the square ahead. 0 is false, 1 is true.
foundOptimum(boolean, StatCatcher) - Method in class Main.AbstractRun
  Check if the global optimum value has been found
Fractal - package Fractal
FractalDimension - Interface in Fractal
Frame - Class in com.rie.rieps.engine
Frame(float, float, float, float, float, float, float, float, LineFormat, LineFormat, LineFormat, LineFormat, boolean, Color, float, String, PSFont, TextParameter) - Constructor for class com.rie.rieps.engine.Frame
  Creates a new instance of Frame
FullInitialiser - Class in Operator.Operations
  Create a genotype by growing a tree to maxDepth for all leaves
FullInitialiser(RandomNumberGenerator, GEGrammar, int) - Constructor for class Operator.Operations.FullInitialiser
  New instance
FullInitialiser(RandomNumberGenerator, GEGrammar, Properties) - Constructor for class Operator.Operations.FullInitialiser
  New instance
fun(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Hardcoded binomial target function
fun(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Hardcoded quadratic target function

## G

GE_CODON_VALUE - Static variable in class Util.Constants
  Signature of a GE Codon.
GE_CODON_VALUE_PARSING - Static variable in class Util.Constants
  Identifying a GE codon when parsing
GEChromosome - Class in Individuals
  Fixed length linear integer chromosome.
GEChromosome() - Constructor for class Individuals.GEChromosome
GEChromosome(int) - Constructor for class Individuals.GEChromosome
GEChromosome(int, int[]) - Constructor for class Individuals.GEChromosome
GEChromosome(GEChromosome) - Constructor for class Individuals.GEChromosome
  Copy constructor
GEGrammar - Class in Mapper
  Class for GEGrammar.
GEGrammar() - Constructor for class Mapper.GEGrammar
  Creates a new instance of GEGrammar
GEGrammar(String) - Constructor for class Mapper.GEGrammar
  New instance
GEGrammar(Properties) - Constructor for class Mapper.GEGrammar
  New instance
GEGrammar(GEGrammar) - Constructor for class Mapper.GEGrammar
  Copy constructor.
GEGRAMMAR - Static variable in class Util.Constants
  GEGrammar to use
GEIndividual - Class in Individuals
  GEIndividual.
GEIndividual() - Constructor for class Individuals.GEIndividual
  Creates a new instance of GEIndividual
GEIndividual(GEGrammar, Phenotype, Genotype, Fitness) - Constructor for class Individuals.GEIndividual
  Create new GEindividual instance
geneCnt - Variable in class Mapper.DerivationTree
generatePRC() - Method in class Mapper.GEGrammar
  Replaces constants in the grammar with an array of randomly generated constants
GENERATION - Static variable in class Util.Constants
  Number of iterations of algorithm
GENERATION_GAP - Static variable in class Util.Constants
  Porportion of new solutions (population) that will be inserted among the old solutions (population)
GENERATIONAL - Static variable in class Util.Constants
  Sets generation gap to population size.
genIter - Variable in class Mapper.DerivationTree
genny - Variable in class Mapper.DerivationTree
Genotype - Class in Individuals
  Genotype is an ArryaList.
Genotype() - Constructor for class Individuals.Genotype
  Creates a new instance of Genotype
Genotype(int) - Constructor for class Individuals.Genotype
Genotype(Genotype) - Constructor for class Individuals.Genotype
  Copy constructor
Genotype(int, Chromosome) - Constructor for class Individuals.Genotype
genotype - Variable in class Operator.Operations.GrowInitialiser
genotype2Phenotype() - Method in class Mapper.ContextFreeGrammar
genotype2Phenotype() - Method in class Mapper.GEGrammar
  Map input to output
genotype2Phenotype(boolean) - Method in class Mapper.GEGrammar
  Instanciates a derivation tree and calls buildDerivationTree() if b is true else sets valid map to true
genotype2Phenotype() - Method in class Mapper.Grammar
genotype2Phenotype() - Method in interface Mapper.Mapper
  Maps from a input(genotype) to an output (phenotype)
GenotypeHelper - Class in Util
  A collection of useful functions for manipulating genotype and such
GenPSFile - Class in com.rie.rieps.simpletest
GenPSFile() - Constructor for class com.rie.rieps.simpletest.GenPSFile
get(int) - Method in interface Individuals.Populations.Population
  Get an individual from the specified index
get(int) - Method in class Individuals.Populations.SimplePopulation
get(int) - Method in interface Util.Structures.IntList
  Get int at index position
get(int) - Method in class Util.Structures.StaticIntList
  Get element at index
get_Energy() - Method in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
get_Energy() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Get the energy
get_Energy_Left() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Get energy left
get_Picked_Up() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  get food picked up
getAbsolutePath(String) - Static method in class Util.PathTools
  Turn a relative path or filename into an absolute one
getAbsolutePath(String, String) - Static method in class Util.PathTools
  Turn a relative path or filename into an absolute one, relative to a directory other than the current directory
getAbsolutePath(String, boolean) - Static method in class Util.PathTools
  Turn a relative path or filename into an absolute one
getAbsolutePath(String, String, boolean) - Static method in class Util.PathTools
  Turn a relative path or filename into an absolute one, relative to a directory other than the current directory
getAge() - Method in class Individuals.AbstractIndividual
getAge() - Method in interface Individuals.Individual
  The age of the individual, counted as how many iterations it has survived.
getAlgorithm() - Method in class Main.State
getAll() - Method in interface Individuals.Populations.Population
  Get a list of all the individuals
getAll() - Method in class Individuals.Populations.SimplePopulation
getAllFitness() - Method in class Util.Statistics.StatCatcher
  Get all fitness stored
getAncestorChain(TreeNode<E>, int) - Method in class Util.Structures.NimbleTree
  Starting at a given node, get a chain of ancestors of length n or less.
getAncestorChains(int) - Method in class Util.Structures.NimbleTree
  Get all the chains of ancestors of length n in this tree.
getAngle() - Method in class Fractal.LSystem2
  Get the angle this LSystem turns by for each + - input
getAngle() - Method in class Fractal.LSystem2State
  Get the angle of the state in radians.
getAveLength() - Method in class Util.Statistics.StatCatcher
  Get the average length
getAWTID() - Method in class com.rie.rieps.engine.fonts.AskForUnknownFontPanel
  Return the ID of the linked AWT Font.
getAwtPSMapping() - Method in class com.rie.rieps.engine.fonts.PSFontFinder
  Clone the AWT->PSFont mapping and return it.
getBeginJob(int, float, float) - Method in interface com.rie.rieps.engine.factories.Factory
getBeginJob(int, float, float) - Method in class com.rie.rieps.engine.factories.PSFactory
getBest() - Method in class Operator.Collector
  Call the getBest(list operands) in the operation.
getBest(List<Individual>) - Method in interface Operator.Operations.OutputI
getBest(List<Individual>) - Method in class Operator.Operations.StatisticsCollectionOperation
  Return the best individual in the group
getBestFitness() - Method in class Util.Statistics.StatCatcher
  Get best fitness
getBestIndiv() - Method in class Main.AbstractRun
getBestIndividualOfGeneration() - Method in class Util.Statistics.StatCatcher
  Get best individual of generation
getBestIndividualOfGenerations() - Method in class Util.Statistics.StatCatcher
  Get best individuals of all generations
getBottomPadding() - Method in class com.rie.rieps.engine.Frame
getBranchLengths() - Method in class Util.Structures.NimbleTree
  Do a depth first traversal and return the list of branch depths
getBranchLengths(TreeNode<E>) - Method in class Util.Structures.NimbleTree
getCapacity() - Method in class Util.Statistics.IndividualCatcher
  Get the capacity of the stringbuffer
getCatchInterval() - Method in class Util.Statistics.IndividualCatcher
  Get catch intervall
getCodonIndex() - Method in class Mapper.DerivationNode
  Get the index of the codon used to choose the child (production) of this tree node. -1 is returned if no codon was used (e.g., if production was choosen because it was the only one to pick)
getCodonPick() - Method in class Mapper.DerivationNode
  Get the production picked by the codon. -1 is returned if no codon was used (e.g., if production was choosen because it was the only one to pick)
getCodonSize() - Method in class Individuals.GEChromosome
getCodonSizeBits() - Method in class Individuals.GEChromosome
getCollector() - Method in class Main.AbstractRun
  helper method for getting the StatisticsCollectionOperation
getColor() - Method in class com.rie.rieps.engine.LineFormat
getColor() - Method in class com.rie.rieps.engine.TextParameter
getComposite() - Method in interface com.rie.rieps.engine.color.Color
getComposite() - Method in class com.rie.rieps.engine.color.Gray
getComposite() - Method in class com.rie.rieps.engine.color.RGBToGray
getConstant() - Method in class Util.ConstantGenerator
  This generates a float constant value
getCrossoverOperation(RandomNumberGenerator, Properties) - Method in class Main.AbstractRun
getCrossoverPoints() - Method in class Individuals.GEIndividual
getCurrentBestFitness() - Method in class Util.Statistics.StatCatcher
  Get the best fitness for the latest generation
getCurrentFillColor() - Method in class com.rie.rieps.engine.Page
getCurrentFont() - Method in class com.rie.rieps.engine.Page
getCurrentLevel() - Method in class Util.Structures.NimbleTree
  Get current level
getCurrentLineFormat() - Method in class com.rie.rieps.engine.Page
getCurrentMean() - Method in class Util.Statistics.StatCatcher
  Get mean for the latest generation
getCurrentMeanUsedGenes() - Method in class Util.Statistics.StatCatcher
  Get the mean used genes for the latest generation
getCurrentNode() - Method in class Util.Structures.NimbleTree
  Get current node
getDashOffset() - Method in class com.rie.rieps.engine.LineFormat
getDashPattern() - Method in class com.rie.rieps.engine.LineFormat
getData() - Method in class Util.Structures.TreeNode
  Get data in node
getDecimalPlaces() - Static method in class Util.ConstantGenerator
  This displays the current decimal places (default is 2);
getDefaultFitness() - Method in class Individuals.FitnessPackage.BasicFitness
getDefaultLength() - Static method in class Individuals.GEChromosome
  get the default length
getDepth() - Method in class Mapper.DerivationNode
getDepth() - Method in class Util.Structures.NimbleTree
  Get maximum depth of tree
getDepth() - Method in class Util.Structures.TreeNode
  Get depth of this node in the tree
getDepthInterval(int) - Method in class Operator.RampedHalfAndHalfInitialiser
  Calculates how the population should be partitioned between the different initialisation depths
getDerivationString() - Method in class Mapper.GEGrammar
getDerivationString() - Method in class Mapper.Grammar
getDerivationTree() - Method in class Mapper.GEGrammar
getDerivationTree(GEGrammar) - Static method in class Mapper.TreeMill
getDerivationTreeIndeces(DerivationTree) - Static method in class Util.GenotypeHelper
getDerivedGrammar() - Method in class Fractal.LSystem2
  Get the grammar expanded to the specified depth
getDerivedGrammar() - Method in class Fractal.LSystem2Panel
getDerivedGrammar() - Method in class Fractal.LSystem2Renderer
  Get the grammar expanded to the specified depth
getDescription() - Method in class Util.FileNameExtensionFilter
getDeviceParameters() - Method in class com.rie.rieps.engine.Page
getDimensions() - Method in class FitnessEvaluation.BinomialProblem.Range
getDimensions() - Method in class FitnessEvaluation.util.Range
getDistance(DoubleFitness) - Method in class Individuals.FitnessPackage.BasicFitness
getDistance(DoubleFitness) - Method in interface Individuals.FitnessPackage.DoubleFitness
  Get the distance
getDistance(IntFitness) - Method in interface Individuals.FitnessPackage.IntFitness
getDouble() - Method in class Individuals.FitnessPackage.BasicFitness
getDouble() - Method in interface Individuals.FitnessPackage.Fitness
getDTNodeCount() - Method in class Mapper.GEGrammar
getEliteSize() - Method in class Operator.Operations.EliteReplacementOperation
getEnd() - Method in class Util.Structures.TreeNode
  Get the last node
getEndJob() - Method in interface com.rie.rieps.engine.factories.Factory
getEndJob() - Method in class com.rie.rieps.engine.factories.PSFactory
getExtensions() - Method in class Util.FileNameExtensionFilter
getFillColor() - Method in class com.rie.rieps.engine.Frame
getFitness() - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Calculating the fitness as the sum of errors.
getFitness(Individual) - Method in class FitnessEvaluation.Canvas.Paint
getFitness() - Method in class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParBSF
  Calculates the fitness by comparing the input expression to all possible cases.
getFitness() - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Calculating the fitness as the sum of errors.
getFitness(Individual) - Method in interface FitnessEvaluation.FitnessFunction
  Creates a new instance of FitnessEvaluator
getFitness(Individual) - Method in class FitnessEvaluation.InterpretedFitnessEvaluation
  Evaluate an individual and set the fitness
getFitness(Individual) - Method in class FitnessEvaluation.LSystem.LSystemDimension
getFitness(Individual) - Method in class FitnessEvaluation.LSystem.LSystemInitialiser
getFitness(Individual) - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
  Split the phenotype of the individual.
getFitness(Individual) - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
  Split the phenotype of the individual.
getFitness(Individual) - Method in class FitnessEvaluation.PatternMatch.WordMatch
getFitness(Individual) - Method in class FitnessEvaluation.RoyalTree.RoyalTree
getFitness(Individual) - Method in class FitnessEvaluation.SantaFeAntTrail.SantaFeAntTrailInterpreter
  Calculate the fitness for the individual by interpreting the the phenotype
getFitness() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Get fitness.
getFitness(Individual) - Method in class FitnessEvaluation.Sudoku.SudokuFit
getFitness(Individual) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
  Split the phenotype of the individual.
getFitness() - Method in class Individuals.AbstractIndividual
getFitness() - Method in interface Individuals.Individual
  Get fitness of individuals
getFitnessFunction(Properties) - Method in class Main.AbstractRun
  Load the fitness class according to the parameters
getFitnessFunction() - Method in class Operator.Operations.FitnessEvaluationOperation
  Get the fitness function
getFood() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Get food
getGECodonValue(String, int) - Method in class Mapper.DerivationTree
  Extract range for value from non-terminal specification, where specification is in the format (set-mode) or (range-mode -- range can be open, closed, or half-open).
getGEGrammar(Properties) - Method in class Main.AbstractRun
  Load a GEGrammar.
getGELSYSFitness() - Method in class Fractal.GuiComp
getGeneCnt() - Method in class Mapper.DerivationTree
  Get the input used, called genes
getGenotype() - Method in class Individuals.AbstractIndividual
getGenotype() - Method in class Individuals.GEIndividual
getGenotype() - Method in interface Individuals.Individual
  Get the genotype
getGenotype() - Method in class Mapper.GEGrammar
getGenotype() - Method in interface Mapper.Mapper
  Returns the mappers input (genotype)
getGenotype(int) - Method in class Operator.Operations.GrowInitialiser
  Creates a genotype by building a tree to the most maxDepth for one branch.
getGrammar(GEGrammar) - Static method in class Mapper.GEGrammar
  Get a grammar of the right type
getHeight() - Method in class com.rie.rieps.engine.Frame
getHorizontal() - Method in class com.rie.rieps.engine.TextParameter
getID() - Method in class Util.Structures.TreeNode
getIncomingPopulation() - Method in class Operator.JoinOperator
  Get the population coming in
getIndividual() - Method in class Individuals.FitnessPackage.BasicFitness
getIndividual() - Method in interface Individuals.FitnessPackage.Fitness
  Get the individual that is refered to by the fitness
getIndividual(GEGrammar, Phenotype, Genotype, Fitness) - Static method in class Individuals.GEIndividual
  Factory method for creating GEIndivdual with different grammars
getIndividualCatcher() - Method in class Operator.Operations.StatisticsCollectionOperation
  Return IndividualCatcher for information retival.
getInfo() - Method in class Util.Structures.TreeNode
getInitialiser(GEGrammar, RandomNumberGenerator, Properties) - Method in class Main.AbstractRun
  Load and initialise the initialiser class according to the parameters Defualt initialiser is the RandomInitialiser.
getInitialiser(GEGrammar, RandomNumberGenerator, Properties) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
  Load and initialise the initialiser class according to the parameters Defualt initialiser is the RandomInitialiser.
getInitPipeline() - Method in class Algorithm.AbstractAlgorithm
getInt() - Method in class Individuals.FitnessPackage.BasicFitness
getInt() - Method in interface Individuals.FitnessPackage.Fitness
getInt() - Method in interface Individuals.FitnessPackage.IntFitness
getInvalids() - Method in class Util.Statistics.StatCatcher
  Get number of invalid individuals
getJoinOperator(Properties, RandomNumberGenerator, Population, ReplacementOperation) - Method in class Main.AbstractRun
  Load the fitness class according to the parameters
getLeft() - Method in class com.rie.rieps.engine.Frame
getLeft() - Method in class Util.Structures.BinaryNode
getLeftPadding() - Method in class com.rie.rieps.engine.Frame
getLength() - Method in interface Individuals.Chromosome
  Get length of the chromosome
getLength() - Method in class Individuals.GEChromosome
  Returns the length of the genotype.
getLfBottom() - Method in class com.rie.rieps.engine.Frame
getLfLeft() - Method in class com.rie.rieps.engine.Frame
getLfRight() - Method in class com.rie.rieps.engine.Frame
getLfTop() - Method in class com.rie.rieps.engine.Frame
getLHS() - Method in class Mapper.Rule
  Get the left hand symbol of the rule
getLoopPipeline() - Method in class Algorithm.AbstractAlgorithm
getMapper() - Method in class Individuals.AbstractIndividual
getMapper() - Method in class Individuals.GEIndividual
getMapper() - Method in interface Individuals.Individual
  Get the map use to map input and output
getMatrix_a() - Method in class com.rie.rieps.engine.fonts.PSFont
getMatrix_b() - Method in class com.rie.rieps.engine.fonts.PSFont
getMatrix_c() - Method in class com.rie.rieps.engine.fonts.PSFont
getMatrix_d() - Method in class com.rie.rieps.engine.fonts.PSFont
getMatrix_e() - Method in class com.rie.rieps.engine.fonts.PSFont
getMatrix_f() - Method in class com.rie.rieps.engine.fonts.PSFont
getMaxChromosomeLength() - Method in class Individuals.GEChromosome
getMaxChromosomeLengthByDepth() - Method in class Mapper.GEGrammar
  This method calculates an upper bound for the number of inputs needed to build a derivation tree according to the specified maxDerivationTreeDepth and the max number of non terminals in a production of the grammars rules.
getMaxCodonValue() - Method in class Individuals.GEChromosome
  Maximum value of a codon
getMaxCurrentTreeDepth() - Method in class Mapper.GEGrammar
  Get the max depth of the derivation tree built by the grammar
getMaxDepth() - Method in class Operator.Operations.GrowInitialiser
  Get max depth of tree
getMaxDepth() - Method in class Util.Structures.TreeNode
getMaxDerivationTreeDepth() - Method in class Mapper.GEGrammar
getMaxDoubleFitness() - Method in class Individuals.FitnessPackage.BasicFitness
getMaxDoubleFitness() - Method in interface Individuals.FitnessPackage.Fitness
getMaxDTIndex(DerivationTree) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
getMaxDTIndex(DerivationTree) - Static method in class Util.GenotypeHelper
  Method to return the maximum codon index value in a derivation tree
getMaxIntFitness() - Method in class Individuals.FitnessPackage.BasicFitness
getMaxIntFitness() - Method in interface Individuals.FitnessPackage.Fitness
getMaxLength() - Method in class Util.Statistics.StatCatcher
  Get max length
getMaxSize() - Method in class Util.Structures.StaticIntList
  Get max size
getMaxStackSize() - Method in class Util.Structures.NimbleTree
  Get max stack size
getMaxValue() - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
getMaxWraps() - Method in class Mapper.GEGrammar
  Get max wraps allowed
getMaxXOPoint(GEIndividual) - Method in class Operator.Operations.SinglePointCrossover
  Get xover max point based on used codons.
getMeanDerivationTreeDepth() - Method in class Util.Statistics.StatCatcher
  Get the mean max depth of the derivation trees in the population
getMeanFitness() - Method in class Util.Statistics.StatCatcher
  Get mean fitness of the population
getMeanUsedGenes() - Method in class Util.Statistics.StatCatcher
  Get mean used genes
getMinDepth() - Method in class Operator.Operations.GrowInitialiser
  Get minimum depth of tree
getMinDoubleFitness() - Method in class Individuals.FitnessPackage.BasicFitness
getMinDoubleFitness() - Method in interface Individuals.FitnessPackage.Fitness
getMinimumDepth() - Method in class Mapper.Production
  Return the minimum mapping depth of this production.
getMinimumDepth() - Method in class Mapper.Rule
  Return the minimum mapping depth of this rule.
getMinIntFitness() - Method in class Individuals.FitnessPackage.BasicFitness
getMinIntFitness() - Method in interface Individuals.FitnessPackage.Fitness
getMinLength() - Method in class Util.Statistics.StatCatcher
  Get min length
getMod() - Static method in class Util.ConstantGenerator
  This displays the current set modulo value (default is 1000);
getModule(int) - Method in interface Algorithm.Pipeline
  Gets module number i from the pipeline
getModule(int) - Method in class Algorithm.SimplePipeline
  Return element specified by i
getModules() - Method in interface Algorithm.Pipeline
  Gets a Collection from the pipeline
getModules() - Method in class Algorithm.SimplePipeline
  Return the entire collection of modules
getMutationOperation(RandomNumberGenerator, Properties) - Method in class Main.AbstractRun
getMutationPoints() - Method in class Individuals.GEIndividual
getName() - Method in class com.rie.rieps.engine.fonts.PSFont
getName() - Method in class Mapper.GEGrammar
getNodeCodonList() - Method in class Mapper.ContextualDerivationTree
  this vector contains the index of every nodal codon.
getNodeCount() - Method in class Util.Structures.NimbleTree
  Get node count
getNodePhenotype(DerivationNode) - Static method in class Util.GenotypeHelper
getNonTerminalRules() - Method in class Mapper.ContextFreeGrammar
  This method returns a vector of the rules with exclusively terminal productions
getNTSymbols() - Method in class Mapper.Production
  Return the number of NTSymbols in the production JByrne also added GE_CODONS to the terminal list.
getOperation() - Method in class Operator.Collector
getOperation() - Method in class Operator.CrossoverModule
getOperation() - Method in class Operator.EliteReplacementOperator
getOperation() - Method in class Operator.FitnessEvaluator
getOperation() - Method in class Operator.Initialiser
getOperation() - Method in class Operator.MeritReplacementStrategy
getOperation() - Method in class Operator.MutationOperator
getOperation() - Method in interface Operator.Operator
  Get operation that operator performs
getOperation() - Method in class Operator.SelectionScheme
getOperation() - Method in class Operator.SimpleReplacementStrategy
getOperation() - Method in class Operator.SplitOperator
getOriginalPopulationSize() - Method in class Operator.Operations.FitnessEvaluationOperation
getOutputCharset() - Method in class com.rie.rieps.engine.Job
getOwnerDocument() - Method in class com.rie.rieps.engine.Page
getOwnerJob() - Method in class com.rie.rieps.engine.Document
getPageStringBuffer() - Method in class com.rie.rieps.engine.Page
getPanel() - Method in class Operator.Operations.UserSelect
getParent() - Method in class Util.Structures.TreeNode
  Get parent node
getParents() - Method in class Individuals.GEIndividual
getParentUIDs() - Method in class Individuals.AbstractIndividual
  Get the parentUIDs
getPhenotype() - Method in class Individuals.AbstractIndividual
getPhenotype() - Method in class Individuals.GEIndividual
getPhenotype() - Method in interface Individuals.Individual
  Get phenotype
getPhenotype() - Method in class Mapper.GEGrammar
getPhenotype() - Method in interface Mapper.Mapper
  Returns the mappers output (phenotype)
getPhenotypeString(int) - Method in class Individuals.AbstractIndividual
getPhenotypeString(int) - Method in class Individuals.GEIndividual
getPhenotypeString(int) - Method in interface Individuals.Individual
  Get a String representation of the output(Phenotype)
getPopulation() - Method in interface Operator.Creator
  Returns a reference to the population
getPopulation() - Method in class Operator.Initialiser
getPopulation() - Method in class Operator.SelectionScheme
  Returns the selected population.
getPopulation() - Method in class Operator.SourceModule
getPopulation() - Method in class Operator.SplitOperator
getPopulationSize() - Method in class Operator.Operations.FitnessEvaluationOperation
getPossibleRules(NimbleTree<Symbol>, Rule) - Method in class Operator.Operations.FullInitialiser
getPossibleRules(NimbleTree<Symbol>, Rule) - Method in class Operator.Operations.GrowInitialiser
getPostfix() - Method in class Util.Structures.ReversePolish
getPreviouslyUsedCodons() - Method in class Individuals.GEIndividual
  Get number of codons used for mapping previoulsy.
getProductionCount() - Method in class Mapper.Grammar
  Get the number of productions in the grammar
getPSCommande() - Method in interface com.rie.rieps.engine.color.Color
getPSCommande() - Method in class com.rie.rieps.engine.color.Gray
getPSCommande() - Method in class com.rie.rieps.engine.color.RGBToGray
getPSDesc() - Method in class com.rie.rieps.engine.fonts.PSFont
  Return the postscript font description linked to the awt one.
getPsfnt() - Method in class com.rie.rieps.engine.Frame
getPSFont() - Method in class com.rie.rieps.engine.fonts.AskForUnknownFontPanel
getPSFontFromAWT(Font) - Method in class com.rie.rieps.engine.Job
getPSImage() - Method in interface com.rie.rieps.engine.image.Image
getPSImage() - Method in class com.rie.rieps.engine.image.SmallGrayImage
getRange() - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
getRecursive() - Method in class Mapper.Production
  Return the recursive nature of this production.
getRecursive() - Method in class Mapper.Rule
  Return the recursive nature of this rule.
getRecursiveNodeIndeces(DerivationTree, GEGrammar) - Static method in class Util.GenotypeHelper
  Return an array with all the indeces of recursive derivation tree nodes.
getRelativePath(String) - Static method in class Util.PathTools
  Get relative path of absolutePath from the current directory.
getRelativePath(String, boolean) - Static method in class Util.PathTools
  Get relative path of absolutePath from the current directory, optionally appending the result with a path separator
getRelativePath(String, String) - Static method in class Util.PathTools
  Get relative path of absolutePath from the current directory.
getRelativePath(String, String, boolean) - Static method in class Util.PathTools
  Get relative path of absolutePath from workingPath, optionally appending the result with a path separator
getReplacementSize() - Method in class Operator.Operations.ReplacementOperation
  Get replacement size
getRight() - Method in class Util.Structures.BinaryNode
getRightPadding() - Method in class com.rie.rieps.engine.Frame
getRNG() - Method in class FitnessEvaluation.BinomialProblem.BinomialJScheme
getRNG() - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionJScheme
getRNG() - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
getRNG() - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
getRNG() - Method in class Operator.Operations.CrossoverOperation
getRNG() - Method in class Operator.Operations.GrowInitialiser
getRNG() - Method in class Operator.Operations.LSystemSelect
getRNG() - Method in class Operator.Operations.MutationOperation
getRNG() - Method in class Operator.Operations.RandomInitialiser
getRNG() - Method in class Operator.Operations.RouletteWheel
getRNG() - Method in class Operator.Operations.TournamentSelect
getRNG() - Method in class Operator.OperatorModule
  Get the randomnumbergenerator
getRNG() - Method in interface Util.Random.Stochastic
  Get the number generator
getRoot() - Method in class Util.Structures.NimbleTree
  Get root of tree
getRoot() - Method in class Util.Structures.ReversePolish
getRootToLeafPaths() - Method in class Util.Structures.NimbleTree
  Find all the paths from root to leaves.
getRotate() - Method in class com.rie.rieps.engine.fonts.PSFont
getRotate() - Method in class com.rie.rieps.engine.Frame
getRotate() - Method in class com.rie.rieps.engine.TextParameter
getRules() - Method in class Mapper.Grammar
  Get the rules in the grammar
getSafePath(String) - Static method in class Util.PathTools
  Ensure a path ends with a '/'
getSamples() - Method in class FitnessEvaluation.util.Range
  Get samples from the range.
getScale(String, double) - Method in class Fractal.LargeLSystem
  sets the scale so that the applet shows the whole Lsystem graphic
getScale(String, double) - Method in class Fractal.LSystem
  sets the scale so that the applet shows the whole Lsystem graphic
getSelectedPopulation() - Method in class Operator.Operations.SelectionOperation
  Returns the selected population.
getSelectionOperation(Properties, RandomNumberGenerator) - Method in class Main.AbstractRun
  Load the fitness class according to the parameters
getSize() - Method in class com.rie.rieps.engine.fonts.PSFont
getSize() - Method in class Operator.Operations.SelectionOperation
  Size of the population to be selecetd
getStart(int) - Method in class FitnessEvaluation.BinomialProblem.Range
getStart(int) - Method in class FitnessEvaluation.util.Range
getStart() - Method in class FitnessEvaluation.util.Range
getStartRule() - Method in class Mapper.Grammar
  Return pointer to current start rule.
getStartSymbol() - Method in class Mapper.Grammar
  Get the start symbol of the grammar If there are no rules null is returned
getStats() - Method in class Operator.Operations.StatisticsCollectionOperation
  Return StatCatcher for information retival.
getStep(int) - Method in class FitnessEvaluation.BinomialProblem.Range
getStep(int) - Method in class FitnessEvaluation.util.Range
getStep() - Method in class FitnessEvaluation.util.Range
getStop(int) - Method in class FitnessEvaluation.BinomialProblem.Range
getStop(int) - Method in class FitnessEvaluation.util.Range
getStop() - Method in class FitnessEvaluation.util.Range
getString() - Method in class Individuals.Phenotype
  Get a string reperesentation of the output(Phenotype)
getStringConstant() - Method in class Util.ConstantGenerator
  This generates a float constant value in a string format
getStringNoSpace() - Method in class Individuals.Phenotype
  Get string representaiton without added whitespace
getStructCodonList() - Method in class Mapper.ContextualDerivationTree
  this vector contains the index of every structural codon.
getSymbolString() - Method in class Mapper.Symbol
  Get the symbol string
getTerminalRules() - Method in class Mapper.ContextFreeGrammar
  This method returns a vector of the rules with exclusively terminal productions
getTerminals() - Method in class Mapper.Grammar
  Get a list of all the symbols which are terminals, ie the alphabet over which this grammar's language is defined.
getTerminalStrings() - Method in class Mapper.Grammar
  Get a list of all the terminal strings for this grammar.
getText() - Method in class com.rie.rieps.engine.Frame
getTextParameter() - Method in class com.rie.rieps.engine.Frame
getTime() - Method in class Util.Statistics.StatCatcher
  Get the time for execution of a generation
getTokens() - Method in class Util.Structures.ReversePolish
getTop() - Method in class com.rie.rieps.engine.Frame
getTopPadding() - Method in class com.rie.rieps.engine.Frame
getTotalSamples(int) - Method in class FitnessEvaluation.util.Range
  Total samples for the dimension.
getTour(List<Individual>) - Method in class Operator.Operations.TournamentSelect
  Adds individual to the tournament by randomly selecting from the operands untill the tounramentSize is reached.
getTrail(int) - Method in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
  Get the trail.
getType() - Method in class Mapper.Symbol
  Return the type of the symbol
getUID() - Method in class Individuals.AbstractIndividual
  Use: @{inheritDoc}
getUsedCodons() - Method in class Individuals.GEIndividual
  Get number of codons used for mapping
getUsedCodons() - Method in class Mapper.ContextFreeGrammar
getUsedCodons() - Method in class Mapper.GEGrammar
  Get used inputs (codons in the genotype)
getUsedGenes() - Method in class Individuals.GEChromosome
  Get how many genes where used when mapping
getUsedWraps() - Method in class Individuals.GEChromosome
  Get how many wraps were used
getUsedWraps() - Method in class Individuals.GEIndividual
  Get number of wraps used for mapping
getUsedWraps() - Method in class Mapper.ContextFreeGrammar
getUsedWraps() - Method in class Mapper.GEGrammar
  Get used wraps (Number of times the input was reread from the start)
getValid() - Method in class Individuals.GEChromosome
  Returns the current valid field.
getValue() - Method in class Util.Structures.BinaryNode
getVarFitness() - Method in class Util.Statistics.StatCatcher
  Get variance of the fitness in the population
getVarLength() - Method in class Util.Statistics.StatCatcher
  Get variance of the lengths in the population
getVertical() - Method in class com.rie.rieps.engine.TextParameter
getWidth() - Method in class com.rie.rieps.engine.Frame
getWidth() - Method in class com.rie.rieps.engine.LineFormat
getWrapCount() - Method in class Mapper.DerivationTree
  Get the number of wraps used
getX() - Method in class Fractal.LSystem2State
  Get the x co-ordinate value of the state
getXCoord(double) - Method in class Fractal.LargeLSystem
  maps an LSystem x value to a screen x-coordinate
getXCoord(double) - Method in class Fractal.LSystem
  maps an LSystem x value to a screen x-coordinate
getXoverPoint(int, int) - Method in class Operator.Operations.SinglePointCrossover
  Get the crossover point within the shortest of the incoming chromosomes
getY() - Method in class Fractal.LSystem2State
  Get the y co-ordinate value of the state
getYCoord(double) - Method in class Fractal.LargeLSystem
  maps an LSystem y value to a screen y-coordinate
getYCoord(double) - Method in class Fractal.LSystem
  maps an LSystem y value to a screen y-coordinate
GEVAHelper - Class in Util
  Some helpful methods for repeated tasks across several classes
grammar - Variable in class Fractal.LSystem2Config
  The phenotype of this LSystem's grammar
Grammar - Class in Mapper
  Abstract class for mapping using a Grammar
grammar - Variable in class Operator.Operations.GrowInitialiser
grammar - Variable in class Operator.Operations.RandomInitialiser
GRAMMAR_FILE - Static variable in class Util.Constants
  Path to grammar file *.bnf
grammy - Variable in class Mapper.DerivationTree
Gray - Class in com.rie.rieps.engine.color
Gray(float) - Constructor for class com.rie.rieps.engine.color.Gray
  Creates a new instance of Gray
GRID_HEIGHT - Static variable in class FitnessEvaluation.SantaFeAntTrail.LosAltosTrail
GRID_HEIGHT - Static variable in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
GRID_HEIGHT - Static variable in class FitnessEvaluation.SantaFeAntTrail.Trail
GRID_WIDTH - Static variable in class FitnessEvaluation.SantaFeAntTrail.LosAltosTrail
GRID_WIDTH - Static variable in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
GRID_WIDTH - Static variable in class FitnessEvaluation.SantaFeAntTrail.Trail
gridAdd(Container, Container, int, int, double) - Static method in class Operator.Operations.UserSelect
  gridAdd(Container, Container, int, int, int, int, double, double) overload.
gridAdd(Container, Container, int, int, int, int, double, double) - Static method in class Operator.Operations.UserSelect
  Helper for adding a control to a GridBagLayout control
gridAdd(Container, Container, int, int, double) - Static method in class Util.GEVAHelper
  gridAdd(Container, Container, int, int, int, int, double, double) overload.
gridAdd(Container, Container, int, int, int, int, double, double) - Static method in class Util.GEVAHelper
  Helper for adding a control to a GridBagLayout control
grow(NimbleTree<Symbol>) - Method in class Operator.Operations.GrowInitialiser
  Recursively builds a tree.
GROW_PROBABILITY - Static variable in class Util.Constants
  Probability of choosing a to grow a full depth tree when rampde full grow initialisation is used.
growInitialisation - Variable in class Operator.RampedHalfAndHalfInitialiser
GrowInitialiser - Class in Operator.Operations
  Class for growing individuals to the maximum derrivationTree size of maxDepth
GrowInitialiser(RandomNumberGenerator, GEGrammar, int) - Constructor for class Operator.Operations.GrowInitialiser
  New instance
GrowInitialiser(RandomNumberGenerator, GEGrammar, Properties) - Constructor for class Operator.Operations.GrowInitialiser
  New instance
growNode(DerivationNode) - Method in class Mapper.ContextualDerivationTree
  Grows the nodes of the tree in a recursive procedure.
growNode(DerivationNode) - Method in class Mapper.DerivationTree
  Grows the nodes of the tree in a recursive procedure.
growProb - Variable in class Operator.RampedHalfAndHalfInitialiser
GuiComp - Class in Fractal
GuiComp(String[], String[], String[], double[], int, int, int) - Constructor for class Fractal.GuiComp

## H

hashCode() - Method in class Mapper.GEGrammar
hasNext() - Method in interface Util.Structures.IntIterator
  Check if there are more elements
hasNext() - Method in class Util.Structures.StaticIntIterator
HelloWorldBSF - Class in FitnessEvaluation.HelloWorld
  Class for executing the HelloWorld example using BSF.
HelloWorldBSF() - Constructor for class FitnessEvaluation.HelloWorld.HelloWorldBSF
  Creates a new instance of HelloWorldBSF
HELP_FLAG - Static variable in class Util.Constants
HZ_CENTER - Static variable in class com.rie.rieps.engine.TextParameter
HZ_JUSTIFY - Static variable in class com.rie.rieps.engine.TextParameter
HZ_LEFT - Static variable in class com.rie.rieps.engine.TextParameter
HZ_RIGHT - Static variable in class com.rie.rieps.engine.TextParameter

## I

Image - Interface in com.rie.rieps.engine.image
ImageFactory - Class in com.rie.rieps.engine.image
incomingPopulation - Variable in class Operator.JoinOperator
increaseAge(List<Individual>) - Method in class Operator.JoinOperator
  Increase the age of the operands by 1
increaseUIDCounter() - Method in class Individuals.AbstractIndividual
  Increase the unique id counter and return the new counter value
indCatch - Variable in class Operator.Operations.StatisticsCollectionOperation
indexes - Variable in class Fractal.LSystem2Config
  Because all LSystems are coalesced before display, when the user selects one, it must relate back to all the orignal LSystems that were coalsesced.
Individual - Interface in Individuals
  This interface defines the methods for individual objects.
INDIVIDUAL_CATCH_INTERVAL - Static variable in class Util.Constants
  Interval between saved individuals in the population
IndividualCatcher - Class in Util.Statistics
  Stores Individuals
IndividualCatcher() - Constructor for class Util.Statistics.IndividualCatcher
  Creates a new instance of StatCatcher
IndividualCatcher(Properties) - Constructor for class Util.Statistics.IndividualCatcher
  New instance
Individuals - package Individuals
Individuals.FitnessPackage - package Individuals.FitnessPackage
Individuals.Populations - package Individuals.Populations
INFIX_GRAMMAR - Static variable in class Util.Constants
  Specifying if an infix grammar
init() - Method in class Algorithm.AbstractAlgorithm
init() - Method in interface Algorithm.Algorithm
  Initializing the algorithm
init() - Method in class Algorithm.MyFirstSearchEngine
  Step the init pipeline
init(String[], int[], float[]) - Method in class Fractal.FinalGuiComp
  Initializes the applet prototype
init(int, int) - Method in class Fractal.GuiComp
  Initializes the applet prototype
init() - Method in class Fractal.LargeLSystem
  Initializes the components of the applet
init(int) - Method in class Fractal.LSystem
  Initializes the components of the applet
init() - Method in class Main.AbstractRun
  Runs the init pipeline.
init() - Method in interface Operator.Creator
  Initialise the module;
init() - Method in class Operator.Initialiser
  Creates the population and the individuals
initChromSize - Variable in class Operator.Operations.GrowInitialiser
initChromSize - Variable in class Operator.Operations.RandomInitialiser
INITIAL_CHROMOSOME_SIZE - Static variable in class Util.Constants
  Length of input for random initialisation
initialiser - Variable in class Main.AbstractRun
Initialiser - Class in Operator
  Initialiser has a CreationOperation and is used to create a population.
Initialiser(RandomNumberGenerator, int, CreationOperation) - Constructor for class Operator.Initialiser
  Initialiser creates the population
Initialiser(RandomNumberGenerator, CreationOperation, Properties) - Constructor for class Operator.Initialiser
  Initialiser creates the population
Initialiser() - Constructor for class Operator.Initialiser
  Creat ne instance
initialiser - Variable in class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
INITIALISER - Static variable in class Util.Constants
  Class name of initialiser operation.
InitializationException - Exception in Exceptions
  Thrown when the initialization of an Individual is exceptional
InitializationException() - Constructor for exception Exceptions.InitializationException
  Creates a new instance of InitializationException
InitializationException(String) - Constructor for exception Exceptions.InitializationException
  Constructor
initialSize - Variable in class Util.Structures.StaticIntList
INTERACT_GENS - Static variable in class Util.Constants
  After how many generations should the user be prompted for interaction
INTERACTIVE_GE - Static variable in class Util.Constants
  Sets interactive fitness GE on or off
InterpretedFitnessEvaluation - Class in FitnessEvaluation
  Abstract class for interpreting generated code, instead of compiling
InterpretedFitnessEvaluation() - Constructor for class FitnessEvaluation.InterpretedFitnessEvaluation
  Creates a new instance of InterpretedFitnessEvaluation
InterpretedFitnessEvaluationBSF - Class in FitnessEvaluation
  Interprets code using the BSF framework (http://jakarta.apache.org/bsf/)
InterpretedFitnessEvaluationBSF() - Constructor for class FitnessEvaluation.InterpretedFitnessEvaluationBSF
  Creates a new instance of InterpretedFitnessEvaluationGr
InterpretedJScheme - Class in FitnessEvaluation
  Interpret code using JScheme
InterpretedJScheme() - Constructor for class FitnessEvaluation.InterpretedJScheme
  Creates a new instance of InterpretedJScheme
IntFitness - Interface in Individuals.FitnessPackage
  Interface for an Integer fitness
IntFlipByteMutation - Class in Operator.Operations
  IntFlipMutation does integer mutation.
IntFlipByteMutation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.IntFlipByteMutation
  Creates a new instance of IntFlipMutation
IntFlipByteMutation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.IntFlipByteMutation
  New instance
IntFlipFitness - Class in Operator.Operations
  IntFlipMutation does integer mutation.
IntFlipFitness(double, RandomNumberGenerator) - Constructor for class Operator.Operations.IntFlipFitness
  Creates a new instance of IntFlipMutation
IntFlipFitness(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.IntFlipFitness
  New instance
IntFlipMutation - Class in Operator.Operations
  IntFlipMutation does integer mutation
IntFlipMutation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.IntFlipMutation
  Creates a new instance of IntFlipMutation
IntFlipMutation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.IntFlipMutation
  New instance
IntIterator - Interface in Util.Structures
  Interface for an iterator objects that uses int primitaves instead of using the boxed Integer vesion.
IntList - Interface in Util.Structures
  Interface for a list structure that stores ints
inv(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Method for inverting x.
inv(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Method for inverting x.
invalidate() - Method in class Individuals.GEIndividual
  Invalidate the individual.
invalids - Variable in class Util.Statistics.StatCatcher
isClip() - Method in class com.rie.rieps.engine.TextParameter
isClosed() - Method in class com.rie.rieps.engine.Document
isEchoMapping() - Method in class com.rie.rieps.engine.fonts.PSFontFinder
isEmpty() - Method in class Util.Structures.Queue
  Check if queue is empty
isEvaluated() - Method in class Individuals.AbstractIndividual
isEvaluated() - Method in interface Individuals.Individual
  Has the individual been evaluated
isEvaluateElites() - Method in class Operator.Operations.EliteOperationSelection
isFill() - Method in class com.rie.rieps.engine.Frame
isFixedCrossoverPoint() - Method in class Operator.Operations.SinglePointCrossover
  Chech is the crossover point is fixed
isLinked() - Method in class com.rie.rieps.engine.fonts.AskForUnknownFontPanel
isMapped() - Method in class Individuals.GEIndividual
  Is the individual mapped
isOpenned() - Method in class com.rie.rieps.engine.Document
isRandom() - Method in class FitnessEvaluation.BinomialProblem.Range
isRandom() - Method in class FitnessEvaluation.util.Range
isRandom(int) - Method in class FitnessEvaluation.util.Range
isUnary(String) - Method in class Util.Structures.Operators
isUnary(E) - Method in class Util.Structures.Operators
isValid() - Method in class Individuals.GEIndividual
isValid() - Method in interface Individuals.Individual
  Get the validity of the individual
iterator() - Method in interface Individuals.Populations.Population
  Get an iterator over the population
iterator() - Method in class Individuals.Populations.SimplePopulation
iterator() - Method in interface Util.Structures.IntList
  Get an iterator
iterator() - Method in class Util.Structures.StaticIntList
  Create iterator over list

## J

Job - Class in com.rie.rieps.engine
  Todo open a dictionnary at the beginning of the job and close it when close method is called Todo the page size must be given !
JoinOperator - Class in Operator
  Abstract class for joining two populations.
JoinOperator(RandomNumberGenerator, Population) - Constructor for class Operator.JoinOperator
  Constructor
JoinOperator() - Constructor for class Operator.JoinOperator
  Create new instance
js - Variable in class FitnessEvaluation.InterpretedJScheme

## L

LargeLSystem - Class in Fractal
  2-D L-System Applet LSystem.java
LargeLSystem(String, int, float) - Constructor for class Fractal.LargeLSystem
left() - Method in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
left() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Turn the ant left
LF_FIT - Static variable in class Fractal.GuiComp
  Was picked as a fit individual
LF_NOFIT - Static variable in class Fractal.GuiComp
  Was not picked as a fit individual
LF_UNFIT - Static variable in class Fractal.GuiComp
  Was picked as an unfit individual - to be purged
LineFormat - Class in com.rie.rieps.engine
LineFormat() - Constructor for class com.rie.rieps.engine.LineFormat
LineFormat(LineFormat) - Constructor for class com.rie.rieps.engine.LineFormat
LineFormat(float, int, Color) - Constructor for class com.rie.rieps.engine.LineFormat
LineFormat(float, int[], int, Color) - Constructor for class com.rie.rieps.engine.LineFormat
LineFormat(float, Color) - Constructor for class com.rie.rieps.engine.LineFormat
load(BufferedImage) - Method in interface com.rie.rieps.engine.image.Image
load(BufferedImage) - Method in class com.rie.rieps.engine.image.SmallGrayImage
load(String) - Method in class Main.State
  Load a State
log(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Natural logarithm
log(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Natural logarithm
LosAltosTrail - Class in FitnessEvaluation.SantaFeAntTrail
  Taken from lib GE and refactored to java
LosAltosTrail() - Constructor for class FitnessEvaluation.SantaFeAntTrail.LosAltosTrail
  Creates a new instance of Trail.
LosAltosTrail(int) - Constructor for class FitnessEvaluation.SantaFeAntTrail.LosAltosTrail
  Create new instance
LSystem - Class in Fractal
  2-D L-System Applet LSystem.java
LSystem(String, int, float, int, double) - Constructor for class Fractal.LSystem
LSystem2 - Class in Fractal
  LSystem algorithm.
LSystem2(String, int, float) - Constructor for class Fractal.LSystem2
  Create a new LSystem and compile the grammar (recurse 'grammar', 'depth' times) with axiom of l-value of grammar or 'F'
LSystem2(String, String, int, float) - Constructor for class Fractal.LSystem2
  Create a new LSystem and compile the grammar (recurse 'grammar', 'depth' times)
LSystem2Config - Class in Fractal
  Track information about each LSystem displayed to the user in guiComp
LSystem2Config(int, String, int, float, double) - Constructor for class Fractal.LSystem2Config
LSystem2Config.Indexes - Class in Fractal
LSystem2Config.Indexes() - Constructor for class Fractal.LSystem2Config.Indexes
LSystem2Config.SelectAction - Interface in Fractal
LSystem2Control - Class in Fractal
  View LSystems with input controls for modifying the LSystem
LSystem2Control(String, int, float, Component) - Constructor for class Fractal.LSystem2Control
LSystem2Control(String, String, int, float, Component) - Constructor for class Fractal.LSystem2Control
LSystem2FDBoxCounting - Class in Fractal
  Extended LSystem renderer with box-counting fractal dimension calculating
LSystem2FDBoxCounting(String, String, int, float, int) - Constructor for class Fractal.LSystem2FDBoxCounting
LSystem2Panel - Class in Fractal
  View LSystems in a JPanel
LSystem2Panel(String, int, float) - Constructor for class Fractal.LSystem2Panel
LSystem2Panel(String, String, int, float) - Constructor for class Fractal.LSystem2Panel
LSystem2PanelSelect - Class in Fractal
LSystem2PanelSelect(String, String, int, float, double) - Constructor for class Fractal.LSystem2PanelSelect
LSystem2PanelSelect(String, int, float, double) - Constructor for class Fractal.LSystem2PanelSelect
LSystem2Renderer - Class in Fractal
  Base class for rendering an LSystem.
LSystem2Renderer(String, String, int, float) - Constructor for class Fractal.LSystem2Renderer
  Create a new renderable LSystem
LSystem2State - Class in Fractal
  Track and update the state of the LSystem.
LSystem2State() - Constructor for class Fractal.LSystem2State
  Create a new state at position (0, 0) and at angle 270 degrees, or pointing vertically up, in screen co-ordinates, i.e. calling move would move up the screen
LSystem2State(LSystem2State) - Constructor for class Fractal.LSystem2State
  Create a new state cloned from another
LSystemDimension - Class in FitnessEvaluation.LSystem
  A fitness which tends towards a specified fractal dimension
LSystemDimension() - Constructor for class FitnessEvaluation.LSystem.LSystemDimension
LSystemInitialiser - Class in FitnessEvaluation.LSystem
LSystemInitialiser() - Constructor for class FitnessEvaluation.LSystem.LSystemInitialiser
LSystemSelect - Class in Operator.Operations
LSystemSelect() - Constructor for class Operator.Operations.LSystemSelect
LSystemSelect(int) - Constructor for class Operator.Operations.LSystemSelect
LSystemViewer - Class in UI
  View LSystems in a stand-alone project
LSystemViewer(String, int, float) - Constructor for class UI.LSystemViewer

## M

m - Variable in class Util.ConstantGenerator
Main - package Main
main(String[]) - Static method in class com.rie.rieps.engine.fonts.PSFontFinder
main(String[]) - Static method in class com.rie.rieps.simpletest.GenPSFile
main(String[]) - Static method in class com.rie.rieps.simpletest.VerySimpleExample
main(String[]) - Static method in class FitnessEvaluation.BinomialProblem.Range
main(String[]) - Static method in class FitnessEvaluation.RoyalTree.RoyalTree
main(String[]) - Static method in class Main.Experiment
  Create a new Experiment instance and call the getMain function
main(String[]) - Static method in class Main.Run
  Run
main(String[]) - Static method in class Main.Tutorials.Tutorial4
  Run the state
main(String[]) - Static method in class Main.Tutorials.Tutorial5
  Run the state
main(String[]) - Static method in class Main.Tutorials.Tutorial6
  Run the state
main(String[]) - Static method in class Main.Tutorials.Tutorial7
  Run the state
main(String[]) - Static method in class Operator.Operations.ProportionalRouletteWheel
main(String[]) - Static method in class Operator.Operations.ScaledRouletteWheel
main(String[]) - Static method in class Operator.Operations.SinglePointCrossover
main(String[]) - Static method in class Operator.SelectionScheme
main(String[]) - Static method in class Util.ConstantGenerator
main(String[]) - Static method in class Util.Random.MersenneTwisterFast
  Tests the code.
main(String[]) - Static method in class Util.Structures.StaticIntIterator
main(String[]) - Static method in class Util.Structures.StaticIntList
main(String[]) - Static method in class Util.Structures.TreeNode
Main.Tutorials - package Main.Tutorials
mainWindow - Static variable in class Util.GEVAHelper
  When showing error messages in classes that don't have direct access to a parent window, this allows them to set the parent to be the application window.
makeNewChromosome(GEChromosome, GEChromosome, int, int) - Method in class Operator.Operations.SinglePointCrossover
  Creates the new chromsome, with fixed crossver point or not, and returns the crossover points on the individuals.
makeNewChromosome(Individual, int, int, Individual, int, int) - Static method in class Util.GenotypeHelper
  Given two individuals, whoses chromosomes are split into three codon groups running from [0..point1), [point1..point1+length), and [point1+length..usedGenes), named head, body, and tail respectively, return a chromosome with a head and tail made up of individual-one's chromosome, and individual-two's body, i.e., head(i1)+body(i2)+tail(i1).
makeNewChromosome(Individual, int, int, Individual, int, int, DerivationTree) - Static method in class Util.GenotypeHelper
makeNewChromosome(Individual, int, int, Individual, DerivationTree) - Static method in class Util.GenotypeHelper
  Given two individuals, whose chromosomes are split into three codon groups running from [0..point1), [point1..point1+length), and [point1+length..usedGenes), named head, body, and tail respectively, return a chromosome with a head and tail made up of individual-one's chromosome, and all of individual-two, i.e., head(i1)+all(i2)+tail(i1).
makeTreeOverStringFromSExpression(String) - Static method in class Util.Structures.NimbleTree
  A static constructor (is this the right term?)
MalformedGrammarException - Exception in Exceptions
  Thrown if the Grammar file fails to parse.
MalformedGrammarException() - Constructor for exception Exceptions.MalformedGrammarException
  Creates a new instance of MalformedGrammarException
MalformedGrammarException(String) - Constructor for exception Exceptions.MalformedGrammarException
  Creates a new instance of MalformedGrammarException
map(int) - Method in class Individuals.AbstractIndividual
map(int) - Method in class Individuals.GEIndividual
  Setting these both here so as to negate the need for multiple copies of the Mapper.
map(int) - Method in interface Individuals.Individual
  Map the input(Genotype) to output(Phenotype) using a grammar as a map
Mapper - package Mapper
Mapper - Interface in Mapper
  Interface for mapping input (genotype) to output (phenotype).
MAX_DEPTH - Static variable in class Util.Constants
  Max depth of tree growth for full and grow initialisation
MAX_DERIVATION_TREE_DEPTH - Static variable in class Util.Constants
MAX_WRAPS - Static variable in class Util.Constants
  Number of times the input is reread from start.
maxDepth - Variable in class Operator.Operations.GrowInitialiser
maxDepth - Variable in class Operator.RampedHalfAndHalfInitialiser
maxLength - Variable in class Util.Statistics.StatCatcher
MAXPROBLEM_DEPTH - Static variable in class Util.Constants
  Methods for selecting max tree depth for max problem
MaxProblemInterpreter - Class in FitnessEvaluation.MaxProblem
  This problem tries to generate the largest number possible from with a given terminal and functional set and with a depth limit.
MaxProblemInterpreter() - Constructor for class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
maxSize - Static variable in class Util.Structures.StaticIntList
meanDerivationTreeDepth - Variable in class Util.Statistics.StatCatcher
meanFitness - Variable in class Util.Statistics.StatCatcher
meanUsedGenes - Variable in class Util.Statistics.StatCatcher
MEDIA_TYPE - Static variable in class com.rie.rieps.engine.DeviceParameter
  Parameter to set the media type of pages.
MeritReplacementStrategy - Class in Operator
  MeritReplacementStrategy joins to populations.
MeritReplacementStrategy(RandomNumberGenerator, Population, ReplacementOperation) - Constructor for class Operator.MeritReplacementStrategy
  Creates a new instance of MeritReplacementStrategy
MeritReplacementStrategy() - Constructor for class Operator.MeritReplacementStrategy
  New instance
MersenneTwisterFast - Class in Util.Random
  MersenneTwister and MersenneTwisterFast Version 13, based on version MT199937(99/10/29) of the Mersenne Twister algorithm found at The Mersenne Twister Home Page, with the initialization improved using the new 2002/1/26 initialization algorithm By Sean Luke, October 2004.
MersenneTwisterFast() - Constructor for class Util.Random.MersenneTwisterFast
  Constructor using the default seed.
MersenneTwisterFast(long) - Constructor for class Util.Random.MersenneTwisterFast
  Constructor using a given seed.
MersenneTwisterFast(int[]) - Constructor for class Util.Random.MersenneTwisterFast
  Constructor using an array of integers as seed.
minDepth - Variable in class Operator.Operations.GrowInitialiser
minFit - Variable in class Operator.Operations.RouletteWheel
minLength - Variable in class Util.Statistics.StatCatcher
mngr - Variable in class FitnessEvaluation.InterpretedFitnessEvaluationBSF
Module - Interface in Operator
  Interface for modules.
move - Variable in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
move() - Method in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
  Move the ant forward Death on the electric fence
move() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Move the ant forward
MUTATION_OPERATION - Static variable in class Util.Constants
  Class name of mutation operation.
MUTATION_PROBABILITY - Static variable in class Util.Constants
  Probability of mutating an input
MutationOperation - Class in Operator.Operations
  Abstract class for mutaion operation.
MutationOperation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.MutationOperation
  Creates a new instance of MutationOperation
MutationOperation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.MutationOperation
  Creates a new instance of MutationOperation
MutationOperator - Class in Operator
  MutationOperator has a MutationOperation.
MutationOperator(RandomNumberGenerator, MutationOperation) - Constructor for class Operator.MutationOperator
  Creates a new instance of MutationOperator
MyFirstSearchEngine - Class in Algorithm
  Contains the module pipelines used to perform the algorithm.
MyFirstSearchEngine() - Constructor for class Algorithm.MyFirstSearchEngine
  Constructor

## N

newNode() - Method in class Mapper.DerivationTree
newNode() - Method in class Util.Structures.NimbleTree
next() - Method in interface Util.Structures.IntIterator
  Get next int
next() - Method in class Util.Structures.StaticIntIterator
nextBoolean() - Method in class Util.Random.MersenneTwisterFast
nextBoolean(float) - Method in class Util.Random.MersenneTwisterFast
  This generates a coin flip with a probability `probability` of returning true, else returning false.
nextBoolean(double) - Method in class Util.Random.MersenneTwisterFast
  This generates a coin flip with a probability `probability` of returning true, else returning false.
nextBoolean() - Method in interface Util.Random.RandomNumberGenerator
  Get the next boolean
nextBoolean(double) - Method in interface Util.Random.RandomNumberGenerator
  Get the next boolean with probability of true defined by d 0<=d<=1
nextByte() - Method in class Util.Random.MersenneTwisterFast
nextBytes(byte[]) - Method in class Util.Random.MersenneTwisterFast
nextChar() - Method in class Util.Random.MersenneTwisterFast
nextChar() - Method in interface Util.Random.RandomNumberGenerator
  Get the next char
nextDouble() - Method in class Util.Random.MersenneTwisterFast
  Returns a random double in the half-open range from [0.0,1.0).
nextDouble() - Method in interface Util.Random.RandomNumberGenerator
  Get the next double 0<=x<1
nextFloat() - Method in class Util.Random.MersenneTwisterFast
  Returns a random float in the half-open range from [0.0f,1.0f).
nextGaussian() - Method in class Util.Random.MersenneTwisterFast
nextInt() - Method in class Util.Random.MersenneTwisterFast
nextInt(int) - Method in class Util.Random.MersenneTwisterFast
  Returns an integer drawn uniformly from 0 to n-1.
nextInt(int) - Method in interface Util.Random.RandomNumberGenerator
  Get the next int, where n is max
nextInt() - Method in interface Util.Random.RandomNumberGenerator
  Get the next int
nextLong() - Method in class Util.Random.MersenneTwisterFast
nextLong(long) - Method in class Util.Random.MersenneTwisterFast
  Returns a long drawn uniformly from 0 to n-1.
nextShort() - Method in class Util.Random.MersenneTwisterFast
nextShort() - Method in interface Util.Random.RandomNumberGenerator
  Get the next short
NimbleTree<E> - Class in Util.Structures
  Lightweight tree n-arity structure
NimbleTree() - Constructor for class Util.Structures.NimbleTree
  Creates a new instance of NimbleTree
NimbleTree(E) - Constructor for class Util.Structures.NimbleTree
  Creates a new Tree with `data` as the root nodes data
NimbleTree(NimbleTree<E>) - Constructor for class Util.Structures.NimbleTree
  Copy constructor
NodalMutation - Class in Operator.Operations.ContextSensitiveOperations
  This will find if the chromosome contains a expandable leaf node and will mutate it depending on the mutation probability
NodalMutation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.ContextSensitiveOperations.NodalMutation
NodalMutation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.ContextSensitiveOperations.NodalMutation
nodesDifferentAtIndex(DerivationNode, DerivationNode) - Static method in class Util.GenotypeHelper
  This method is used to compare two different derivation nodes to see at which index in the tree, they differ.
noOfMutationCalls - Variable in class Operator.Operations.MutationOperation
not(int) - Method in class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParBSF
  Negates the input, 1 becomes 0, 0 becomes 1
numRecNodes(DerivationTree, GEGrammar) - Static method in class Util.GenotypeHelper
  This method takes a derivation tree and a grammar and returns the number of recursive nodes in that derivation tree.

## O

ODE_DAMAGE_WALL_HEIGHT - Static variable in class Util.Constants
  Sets wall height in blocks in ode DamageCalc
ODE_DAMAGE_WALL_WIDTH - Static variable in class Util.Constants
  Sets wall width in blocks in ode DamageCalc
ODE_INTERACTIONS - Static variable in class Util.Constants
  Sets number of step interactions to perform (higher is more accurate)
ODE_STEPS - Static variable in class Util.Constants
  Sets number of simulation seconds to run for
ODE_STEPSIZE - Static variable in class Util.Constants
  Sets size of a single step (number of seconds of action per step, lower is more accurate)
open() - Method in class com.rie.rieps.engine.Document
open() - Method in class com.rie.rieps.engine.Job
operation - Variable in class Operator.Initialiser
operation - Variable in class Operator.MutationOperator
Operation - Interface in Operator.Operations
  Operation performs actions on a List or a single Individual
operation - Variable in class Operator.SplitOperator
Operator - package Operator
Operator - Interface in Operator
  Interface for Operator.
Operator.Operations - package Operator.Operations
Operator.Operations.ContextSensitiveOperations - package Operator.Operations.ContextSensitiveOperations
OperatorModule - Class in Operator
  Abstract class for Modules with operations.
OperatorModule(RandomNumberGenerator) - Constructor for class Operator.OperatorModule
  Creates a new instance of OperatorModule
OperatorModule() - Constructor for class Operator.OperatorModule
  Creates a new instance of OperatorModule
Operators<E> - Class in Util.Structures
  FIXME Make singelton
Operators() - Constructor for class Util.Structures.Operators
OUTPUT - Static variable in class Util.Constants
  Path for output file.
OutputI - Interface in Operator.Operations
  Interface for printing

## P

Page - Class in com.rie.rieps.engine
PAGE_SIZE - Static variable in class com.rie.rieps.engine.DeviceParameter
  Parameter to set the page size.
Paint - Class in FitnessEvaluation.Canvas
Paint() - Constructor for class FitnessEvaluation.Canvas.Paint
paint(Graphics) - Method in class Fractal.LargeLSystem
  repaints the main window
paint(Graphics) - Method in class Fractal.LSystem
  repaints the main window
paint(Graphics) - Method in class Fractal.LSystem2Panel
paint(Graphics) - Method in class Fractal.LSystem2PanelSelect
Parameter - package Parameter
ParameterI - Interface in Parameter
  Interface used for setting properties
parentUIDs - Variable in class Individuals.AbstractIndividual
PARITY_DEGREE - Static variable in class Util.Constants
  Specifying the parity degree
parseDouble(String) - Static method in class Util.GEVAHelper
  Parse a string containing a double with locale specific formatting e.g. 1.000,00 is formatted to 1000.00 and then parsed to double
parseFloat(String) - Static method in class Util.GEVAHelper
  Parse a string containing a float with locale specific formatting e.g. 1.000,00 is formatted to 1000.00 and then parsed to float
parseInt(String) - Static method in class Util.GEVAHelper
  Parse a string containing an integer with locale specific formatting.
parsePhen(String) - Method in class FitnessEvaluation.Sudoku.SudokuFit
PathTools - Class in Util
  Collection of file path related stuff
perform() - Method in class Operator.Collector
perform() - Method in class Operator.CrossoverModule
  Crossover is performed on in pairs.
perform() - Method in class Operator.EliteReplacementOperator
  Remove worst individuals form the elite population.
perform() - Method in class Operator.FitnessEvaluator
  Calls doOperation(List operands) in the FitnessEvaluationOperation.
perform() - Method in class Operator.Initialiser
  Calls the operation to add codons to the individuals in the population
perform() - Method in class Operator.JoinOperator
perform() - Method in class Operator.MeritReplacementStrategy
  A ReplacementOperation is performed after the populations are joined.
perform() - Method in interface Operator.Module
  Performs the operation on the population
perform() - Method in class Operator.MutationOperator
perform() - Method in class Operator.OperatorModule
perform() - Method in class Operator.RampedHalfAndHalfInitialiser
  The population is divided(ramped) between minimum depth(shortest possible depth of a derivationTree) and maximum depth(Maximum allowed depth of a derivationTree).
perform() - Method in class Operator.SelectionScheme
perform() - Method in class Operator.SimpleReplacementStrategy
  A ReplacementOperation is performed on the original population before the incomigPopulation is joined.
perform() - Method in class Operator.SplitOperator
performCrossover(GEIndividual, GEIndividual, GEChromosome, GEChromosome, int, int) - Method in class Operator.Operations.SinglePointCrossover
  This method actually performs the crossover and returns an int array with the crossover points.
Phenotype - Class in Individuals
  Phenotype extends ArrayList Phenotype holds the result of mapping from a genotype through a mapper.
Phenotype() - Constructor for class Individuals.Phenotype
Phenotype(Phenotype) - Constructor for class Individuals.Phenotype
  Copy constructor
phenotype2Genotype() - Method in class Mapper.ContextFreeGrammar
phenotype2Genotype() - Method in class Mapper.GEGrammar
  Map output to input
phenotype2Genotype() - Method in class Mapper.Grammar
phenotype2Genotype() - Method in interface Mapper.Mapper
  Not yet implemented!
Pipeline - Interface in Algorithm
  Interface for a pipline.
populateStack() - Method in class Util.Structures.NimbleTree
  Create nodes and push to the stack
Population - Interface in Individuals.Populations
  Interface for a population.
population - Variable in class Operator.OperatorModule
POPULATION_SIZE - Static variable in class Util.Constants
  Size of individual solutions
pow(double, double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Method for x to the power of y
pow(double, double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Method for x to the power of y
PRC_PRECISION - Static variable in class Util.Constants
  this is the decimal precision of the constants that are generated the number specifies how many decimal places there should be
PRC_RANGE - Static variable in class Util.Constants
  this is the range that the constants will be generated within
PRC_SETSIZE - Static variable in class Util.Constants
  this is the number of elements is the set
pressureModifier - Variable in class Operator.Operations.TournamentSelect
print(boolean) - Method in class Operator.Collector
  Call the print(list operands, boolean b) in the operation.
print(List<Individual>, boolean) - Method in interface Operator.Operations.OutputI
  Print information about operands.
print(List<Individual>, boolean) - Method in class Operator.Operations.StatisticsCollectionOperation
  Print the statistics to file.
printHeader() - Method in class Operator.Operations.StatisticsCollectionOperation
  Prints the header for statistics output
printHelp(Fitness[]) - Method in class Operator.Operations.EliteReplacementOperation
printStatistics(long) - Method in class Operator.Operations.StatisticsCollectionOperation
  Print stats for the current generation
printStats() - Method in class Operator.Operations.StatisticsCollectionOperation
  Print the StatCatcher to file
printStuff() - Method in class Main.AbstractRun
  Prints the collected statistics
priority(String) - Method in class Util.Structures.Operators
priority(E) - Method in class Util.Structures.Operators
probability - Variable in class Operator.Operations.CrossoverOperation
probability - Variable in class Operator.Operations.MutationOperation
Production - Class in Mapper
  Production extends an ArrayList.
Production(int) - Constructor for class Mapper.Production
  Creates a new Production with newLength elements.
Production() - Constructor for class Mapper.Production
  Creates a new Production
Production(Production) - Constructor for class Mapper.Production
  Copy constructor; copy all symbols.
properties - Variable in class Main.AbstractRun
PROPERTIES_FILE - Static variable in class Util.Constants
  Path to properties file
propertiesFilePath - Variable in class Main.AbstractRun
ProportionalRouletteWheel - Class in Operator.Operations
  Roulette wheel selection based on fitness proprtional selection.
ProportionalRouletteWheel(int, RandomNumberGenerator) - Constructor for class Operator.Operations.ProportionalRouletteWheel
  New instance
ProportionalRouletteWheel() - Constructor for class Operator.Operations.ProportionalRouletteWheel
  New instance
ProtoComp - Class in Fractal
ProtoComp(LSystem2Config.SelectAction, LSystem2Config, int) - Constructor for class Fractal.ProtoComp
  Creates new form protoComp
prune(String[]) - Static method in class Util.GEVAHelper
  Trim an array of strings so that all white-space padding is removed and any strings that contained just white-space and removed completely from the array. e.g. {" a ", " ", "b"} -> {"a", "b"}
PSFactory - Class in com.rie.rieps.engine.factories
  Todocd compact postscript command : /mt {moveto} def, for example Todo verify if I need/when I need to use 'newpath'
PSFactory() - Constructor for class com.rie.rieps.engine.factories.PSFactory
PSFont - Class in com.rie.rieps.engine.fonts
PSFont() - Constructor for class com.rie.rieps.engine.fonts.PSFont
  Creates a new instance of PSFont
PSFont(String, float) - Constructor for class com.rie.rieps.engine.fonts.PSFont
PSFont(String, float, float) - Constructor for class com.rie.rieps.engine.fonts.PSFont
PSFont(String, String, String, String, String, String, String) - Constructor for class com.rie.rieps.engine.fonts.PSFont
PSFont(PSFont) - Constructor for class com.rie.rieps.engine.fonts.PSFont
PSFont(String) - Constructor for class com.rie.rieps.engine.fonts.PSFont
PSFontFile - Class in com.rie.rieps.engine.fonts
PSFontFile() - Constructor for class com.rie.rieps.engine.fonts.PSFontFile
  Creates a new instance of PSFontFile
PSFontFinder - Class in com.rie.rieps.engine.fonts
PSFontFinder() - Constructor for class com.rie.rieps.engine.fonts.PSFontFinder
  Creates a new instance of PSFontFinder
PSLSystem2 - Class in Fractal
  Write an LSystem grammar to a PostScript file
PSLSystem2(String, int, float) - Constructor for class Fractal.PSLSystem2
  Create a new LSystem that can be written to a PS file with axiom 'F'
PSLSystem2(String, String, int, float) - Constructor for class Fractal.PSLSystem2
  Create a new LSystem that can be written to a PS file
purge - Variable in class Fractal.LSystem2Config
  Set to true if this LSystem has been selected to die

## Q

Queue<T> - Class in Util.Structures
  A FIFO queue implementation containting a linked list
Queue() - Constructor for class Util.Structures.Queue
  Create queue
quote(String) - Static method in class Util.GEVAHelper
  Given a string, wrap it in quotes (") if that string contains spaces

## R

RampedHalfAndHalfInitialiser - Class in Operator
  Class for performing ramped full and grow initialization.
RampedHalfAndHalfInitialiser(RandomNumberGenerator, int, CreationOperation, CreationOperation, double, int) - Constructor for class Operator.RampedHalfAndHalfInitialiser
  New instance
RampedHalfAndHalfInitialiser() - Constructor for class Operator.RampedHalfAndHalfInitialiser
  New instance
rand - Variable in class Operator.Operations.CrossoverOperation
RandomInitialiser - Class in Operator.Operations
  Create an Individual with a randomly generated chromosome
RandomInitialiser(RandomNumberGenerator, GEGrammar, int) - Constructor for class Operator.Operations.RandomInitialiser
  New instance
RandomInitialiser(RandomNumberGenerator, GEGrammar, Properties) - Constructor for class Operator.Operations.RandomInitialiser
  New instance
RandomNumberGenerator - Interface in Util.Random
  Interface for number generators
Range - Class in FitnessEvaluation.BinomialProblem
Range(String) - Constructor for class FitnessEvaluation.BinomialProblem.Range
Range - Class in FitnessEvaluation.util
  Parses an input string to a range of doubles, either random or fixed FIXME allow samples from each dimension to be of different sizes
Range(String) - Constructor for class FitnessEvaluation.util.Range
Range(String, RandomNumberGenerator) - Constructor for class FitnessEvaluation.util.Range
rankPopulation(List<Individual>) - Method in class Operator.Operations.RouletteWheel
  Rank the population
readBNFFile(String) - Method in class Mapper.ContextFreeGrammar
  Read a BNF file to a string and call readBNFString to parse the grammar string.
readProperties(String[]) - Method in class Main.AbstractRun
  Read the default properties.
readState(DataInputStream) - Method in class Util.Random.MersenneTwisterFast
  Reads the entire state of the MersenneTwister RNG from the stream
remove(Individual) - Method in interface Individuals.Populations.Population
  Remove individual from population
remove(Individual) - Method in class Individuals.Populations.SimplePopulation
render(Object) - Method in class Fractal.LSystem2Renderer
  Render the LSystem, calls on drawLine to do actual drawing
repaint() - Method in class Fractal.LargeLSystem
repaint() - Method in class Fractal.LSystem
REPLACEMENT_OPERATOR - Static variable in class Util.Constants
  Class name of replacement operator.
REPLACEMENT_TYPE - Static variable in class Util.Constants
  Generational or steady state replacment.
replacementOperation - Variable in class Operator.MeritReplacementStrategy
ReplacementOperation - Class in Operator.Operations
  ReplacementOperation removes replacementSize Individuals from the population
ReplacementOperation(int) - Constructor for class Operator.Operations.ReplacementOperation
  Creates a new instance of ReplacementOperation
ReplacementOperation(Properties) - Constructor for class Operator.Operations.ReplacementOperation
  Creates a new instance of ReplacementOperation
replacementOperation - Variable in class Operator.SimpleReplacementStrategy
replacementSize - Variable in class Operator.Operations.ReplacementOperation
resetMatch() - Method in class FitnessEvaluation.Sudoku.SudokuFit
revalidate(GEIndividual) - Method in class Individuals.GEIndividual
  Sets the values reset by invalidate to the values from the individual passed in.
ReversePolish - Class in Util.Structures
ReversePolish() - Constructor for class Util.Structures.ReversePolish
ReversePolish(String) - Constructor for class Util.Structures.ReversePolish
RGBToGray - Class in com.rie.rieps.engine.color
RiepsException - Exception in com.rie.rieps.exception
RiepsException(String) - Constructor for exception com.rie.rieps.exception.RiepsException
  Creates a new instance of RiepsException
right() - Method in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
right() - Method in class FitnessEvaluation.SantaFeAntTrail.Trail
  Turn the ant right
rng - Variable in class Main.State
rng - Variable in class Operator.Operations.GrowInitialiser
rng - Variable in class Operator.Operations.LSystemSelect
rng - Variable in class Operator.Operations.MutationOperation
rng - Variable in class Operator.Operations.RandomInitialiser
rng - Variable in class Operator.Operations.RouletteWheel
rng - Variable in class Operator.Operations.ShapeGrammarSelect
rng - Variable in class Operator.Operations.TournamentSelect
rng - Variable in class Operator.OperatorModule
RNG_SEED - Static variable in class Util.Constants
  The seed for the random number generator.
RouletteWheel - Class in Operator.Operations
  This is an abstract class for creating Roulette wheel selection methods with different distributions
RouletteWheel(int, RandomNumberGenerator) - Constructor for class Operator.Operations.RouletteWheel
RouletteWheel() - Constructor for class Operator.Operations.RouletteWheel
  New instance
RoyalTree - Class in FitnessEvaluation.RoyalTree
RoyalTree() - Constructor for class FitnessEvaluation.RoyalTree.RoyalTree
  Creates a new instance of RoyalTree
Rule - Class in Mapper
  Rule extends Arraylist.
Rule(int) - Constructor for class Mapper.Rule
  Creates a new rule with newLength elements.
Rule() - Constructor for class Mapper.Rule
  Creates a new rule
Rule(Rule) - Constructor for class Mapper.Rule
  Copy constructor.
run(int) - Method in class Algorithm.AbstractAlgorithm
run(int) - Method in interface Algorithm.Algorithm
  Run for the specified number of steps
run(int) - Method in class Algorithm.MyFirstSearchEngine
  Iterate `step()`
run() - Method in class Main.AbstractRun
  Run the loop pipeline.
Run - Class in Main
  Run main class.
Run() - Constructor for class Main.Run
  Creates a new instance of Run
runFile(Phenotype) - Method in class FitnessEvaluation.BinomialProblem.BinomialJScheme
runFile(Phenotype) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionJScheme
runFile(Phenotype) - Method in class FitnessEvaluation.InterpretedFitnessEvaluation
  Run the phenotype and return the fitness
runFile(Phenotype) - Method in class FitnessEvaluation.InterpretedFitnessEvaluationBSF
  Create a header and a tail for the input string.

## S

s - Static variable in class FitnessEvaluation.HelloWorld.WorldWriter
SanMateoTrail - Class in FitnessEvaluation.SantaFeAntTrail
  Taken from lib GE and refactored to java
SanMateoTrail() - Constructor for class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
  Creates a new instance of Trail.
SanMateoTrail(int) - Constructor for class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
  Create new instance
SantaFeAntTrailBSF - Class in FitnessEvaluation.externalInterpreters.SantaFeAntTrail
  Class for running Santa Fe ant trail interpreted via BSF
SantaFeAntTrailBSF() - Constructor for class FitnessEvaluation.externalInterpreters.SantaFeAntTrail.SantaFeAntTrailBSF
  Creates a new instance of SantaFeAntTrailBSF
SantaFeAntTrailInterpreter - Class in FitnessEvaluation.SantaFeAntTrail
  Too run the interpreter the -trail_type needs to be provided FIXME parse the phenotype to a tree instead of using lookahead
SantaFeAntTrailInterpreter() - Constructor for class FitnessEvaluation.SantaFeAntTrail.SantaFeAntTrailInterpreter
save(String) - Method in class Fractal.PSLSystem2
  Save the LSystem to the named file at dimensions (500, 500)
save(String, float, float) - Method in class Fractal.PSLSystem2
  Save the LSystem to the named file at the specified dimensions
save() - Method in class Main.State
  Save the State
savePostScript() - Method in class Fractal.Enlarged
ScaledRouletteWheel - Class in Operator.Operations
  Scaled Roulette wheel selection based on weighted selection, The likelyhood of an individual getting picked is: total sum of the fitness - fitness of the individual
ScaledRouletteWheel(int, RandomNumberGenerator) - Constructor for class Operator.Operations.ScaledRouletteWheel
  New instance
ScaledRouletteWheel() - Constructor for class Operator.Operations.ScaledRouletteWheel
  New instance
searchPSFont(Font) - Method in class com.rie.rieps.engine.fonts.PSFontFinder
  Gives a PSfont from a awt one.
select - Variable in class Fractal.LSystem2Config
  Set to true if this LSystem is picked as a parent in guiComp
select(List<Individual>) - Method in class Operator.Operations.SimpleUserSelect
select(List<Individual>) - Method in class Operator.Operations.UserSelect
selectedPopulation - Variable in class Operator.Operations.SelectionOperation
selectFromTour() - Method in class Operator.Operations.TournamentSelect
  Select a winner from the tournament and add to the selected population.
SELECTION_OPERATION - Static variable in class Util.Constants
  Class name of selection operation.
SELECTION_SIZE - Static variable in class Util.Constants
  Selection size proportion of population used selected.
SelectionOperation - Class in Operator.Operations
  Abstract SelectionOperation class.
SelectionOperation(int) - Constructor for class Operator.Operations.SelectionOperation
  New instance
SelectionOperation(Properties) - Constructor for class Operator.Operations.SelectionOperation
  New instance
SelectionOperation() - Constructor for class Operator.Operations.SelectionOperation
  New instance
SelectionScheme - Class in Operator
  SelectionScheme has a SelectionOperation This opertor is used for selecting from the population
SelectionScheme(RandomNumberGenerator, int, Operation) - Constructor for class Operator.SelectionScheme
  Creates a new instance of SelectionScheme
SelectionScheme(RandomNumberGenerator, Operation) - Constructor for class Operator.SelectionScheme
  Creates a new instance of SelectionScheme
selectPerformed() - Method in class Fractal.GuiComp
selectPerformed() - Method in interface Fractal.LSystem2Config.SelectAction
set(int, Individual) - Method in class Individuals.Populations.SimplePopulation
set(int, int) - Method in interface Util.Structures.IntList
  Set item at index
set(int, int) - Method in class Util.Structures.StaticIntList
  Set element at index
setAge(int) - Method in class Individuals.AbstractIndividual
setAge(int) - Method in interface Individuals.Individual
  Age is how long the individual has existed
setAll(int[]) - Method in class Util.Structures.StaticIntList
  Set all the elements to data
setAngle(float) - Method in class Fractal.LSystem2Panel
setAvailableDeviceFont(String[]) - Method in class com.rie.rieps.engine.fonts.PSFontFinder
setAvailableDeviceFont(String[]) - Method in class com.rie.rieps.engine.Job
setAWTFont(Font) - Method in class com.rie.rieps.engine.Page
setAxiom(String) - Method in class Fractal.LSystem2Panel
setBottomPadding(float) - Method in class com.rie.rieps.engine.Frame
setBoxSize(int) - Method in class Fractal.LSystem2FDBoxCounting
  Change the box-size.
setCatchInterval(int) - Method in class Util.Statistics.IndividualCatcher
  Individuals in the population are stored according to this interval.
setClip(boolean) - Method in class com.rie.rieps.engine.TextParameter
setCodonIndex(int, int, int) - Method in class Mapper.DerivationNode
setColor(Color) - Method in class com.rie.rieps.engine.LineFormat
setColor(Color) - Method in class com.rie.rieps.engine.Page
setColor(Color) - Method in class com.rie.rieps.engine.TextParameter
setCreationOperation(CreationOperation) - Method in class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
setCrossoverPoints(int[]) - Method in class Individuals.GEIndividual
setCurrentLevel(int) - Method in class Util.Structures.NimbleTree
  Set current level
setCurrentNode(TreeNode<E>) - Method in class Util.Structures.NimbleTree
  Set current node
setDash(int) - Method in class com.rie.rieps.engine.LineFormat
setDash(int[], int) - Method in class com.rie.rieps.engine.LineFormat
setData(E) - Method in class Util.Structures.TreeNode
  Set data in node
setDecimalPlaces(int) - Static method in class Util.ConstantGenerator
  This sets the number of decimal places
setDefault() - Method in class Individuals.FitnessPackage.BasicFitness
setDefault() - Method in interface Individuals.FitnessPackage.Fitness
  Set the default value of fitness.
setDefaultLength(int) - Static method in class Individuals.GEChromosome
  Set the default length
setDepth(int) - Method in class Fractal.LSystem2Panel
setDepth(int) - Method in class Mapper.DerivationNode
setDepth(int) - Method in class Util.Structures.NimbleTree
  Set depth of tree
setDepth(int) - Method in class Util.Structures.TreeNode
  Set depth of this node and it's children
setDerivationTree(DerivationTree) - Method in class Mapper.GEGrammar
  Set the derivation tree
setDerivationTreeType(String) - Method in class Mapper.GEGrammar
setDeviceParameter(DeviceParameter, Object) - Method in class com.rie.rieps.engine.Document
setDeviceParameter(DeviceParameter, Object) - Method in class com.rie.rieps.engine.Page
setDeviceParameter(Map) - Method in class com.rie.rieps.engine.Page
setDimension(float, float) - Method in class Fractal.LSystem2Renderer
  Set the width and hight to scale the render to.
setDouble(double) - Method in class Individuals.FitnessPackage.BasicFitness
setDouble(double) - Method in interface Individuals.FitnessPackage.Fitness
setEchoMapping(boolean) - Method in class com.rie.rieps.engine.fonts.PSFontFinder
setEvaluate_elites(boolean) - Method in class Operator.Operations.EliteOperationSelection
setEvaluated(boolean) - Method in class Individuals.AbstractIndividual
setEvaluated(boolean) - Method in interface Individuals.Individual
  Indicate if the individual should be evaluated or not
setFill(boolean) - Method in class com.rie.rieps.engine.Frame
setFillColor(Color) - Method in class com.rie.rieps.engine.Frame
setFitness(Fitness) - Method in class Individuals.AbstractIndividual
setFitness(Fitness) - Method in interface Individuals.Individual
  Set fitness
setFitnessFunction(FitnessFunction) - Method in class Operator.Operations.MutationOperation
setFixedCrossoverPoint(boolean) - Method in class Operator.Operations.SinglePointCrossover
  Set crossover point to be fixed (same on both chromsomes) or not fixed
setGenotype(Genotype) - Method in class Individuals.AbstractIndividual
setGenotype(Genotype) - Method in class Individuals.GEIndividual
  Invalidates the individual because a change has been made to the genotype.
setGenotype(Genotype) - Method in interface Individuals.Individual
  Set genotype
setGenotype(GEChromosome) - Method in class Mapper.GEGrammar
  Set input
setGenotype(Object) - Method in class Mapper.GEGrammar
setGenotype(Object) - Method in interface Mapper.Mapper
  Sets the input (genotype)
setGrammar(String) - Method in class Fractal.LSystem2Panel
setHead(Range) - Method in class FitnessEvaluation.BinomialProblem.BinomialJScheme
setHead(Range) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionJScheme
setHeight(float) - Method in class com.rie.rieps.engine.Frame
setHorizontal(int) - Method in class com.rie.rieps.engine.TextParameter
setIContinue() - Static method in class Fractal.FinalGuiComp
setID(int) - Method in class Util.Structures.TreeNode
setIncomingPopulation(Population) - Method in class Operator.JoinOperator
  Set the incomming population
setIndividual(Individual) - Method in class Individuals.FitnessPackage.BasicFitness
setIndividual(Individual) - Method in interface Individuals.FitnessPackage.Fitness
  Set individual to which the fitness belongs
setInfix(boolean) - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
setInfo(int) - Method in class Util.Structures.TreeNode
setInitPipeline(Pipeline) - Method in class Algorithm.AbstractAlgorithm
setInt(int) - Method in class Individuals.FitnessPackage.BasicFitness
setInt(int) - Method in interface Individuals.FitnessPackage.Fitness
setInt(int) - Method in interface Individuals.FitnessPackage.IntFitness
setLeft(float) - Method in class com.rie.rieps.engine.Frame
setLeft(BinaryNode<T>) - Method in class Util.Structures.BinaryNode
setLeftPadding(float) - Method in class com.rie.rieps.engine.Frame
setLfBottom(LineFormat) - Method in class com.rie.rieps.engine.Frame
setLfLeft(LineFormat) - Method in class com.rie.rieps.engine.Frame
setLfRight(LineFormat) - Method in class com.rie.rieps.engine.Frame
setLfTop(LineFormat) - Method in class com.rie.rieps.engine.Frame
setLHS(Symbol) - Method in class Mapper.Rule
  Set the left hand side symbol of the rule Must be a Non Terminal symbol.
setLineFormat(LineFormat) - Method in class com.rie.rieps.engine.Page
setLoopPipeline(Pipeline) - Method in class Algorithm.AbstractAlgorithm
setMapped(boolean) - Method in class Individuals.GEIndividual
  Set the mapped status of the individual
setMapper(Mapper) - Method in class Individuals.AbstractIndividual
setMapper(Mapper) - Method in class Individuals.GEIndividual
setMapper(Mapper) - Method in interface Individuals.Individual
  Set mapper
setMatrix(String, String, String, String, String, String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMatrix_a(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMatrix_b(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMatrix_c(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMatrix_d(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMatrix_e(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMatrix_f(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setMaxChromosomeLength(int) - Method in class Individuals.GEChromosome
setMaxCodonValue(int) - Method in class Individuals.GEChromosome
  Set maximum codon value.
setMaxCurrentTreeDepth(int) - Method in class Mapper.GEGrammar
  Set the max depth of the derriation tree that was built by this grammar
setMaxDepth(int) - Method in class Operator.Operations.GrowInitialiser
  Set maximum depth of tree
setMaxDerivationTreeDepth(int) - Method in class Mapper.GEGrammar
setMaxProblemDepth(int) - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
setMaxSize(int) - Method in class Util.Structures.StaticIntList
  Set max size
setMaxStackSize(int) - Method in class Util.Structures.NimbleTree
  Set max stack size
setMaxValue() - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
setMaxWraps(int) - Method in class Mapper.GEGrammar
  Set max wraps
setMinDepth(int) - Method in class Operator.Operations.GrowInitialiser
  Set minimum depth
setMinimumDepth(int) - Method in class Mapper.Production
  Update the minimum mapping depth of this production.
setMinimumDepth(int) - Method in class Mapper.Rule
  Update the minimum mapping depth of this Rule.
setMod(int) - Static method in class Util.ConstantGenerator
  This sets the modulo value to limit the range
setMutationPoints(int[]) - Method in class Individuals.GEIndividual
setName(String) - Method in class com.rie.rieps.engine.fonts.PSFont
setNodeCount(int) - Method in class Util.Structures.NimbleTree
  Set node count
setOperation(Operation) - Method in class Operator.Collector
setOperation(Operation) - Method in class Operator.CrossoverModule
setOperation(Operation) - Method in class Operator.EliteReplacementOperator
setOperation(Operation) - Method in class Operator.FitnessEvaluator
setOperation(Operation) - Method in class Operator.Initialiser
setOperation(Operation) - Method in class Operator.JoinOperator
setOperation(Operation) - Method in class Operator.MeritReplacementStrategy
setOperation(Operation) - Method in class Operator.MutationOperator
setOperation(Operation) - Method in interface Operator.Operator
  Set operation that operator performs
setOperation(Operation) - Method in class Operator.SelectionScheme
setOperation(Operation) - Method in class Operator.SimpleReplacementStrategy
setOperation(Operation) - Method in class Operator.SplitOperator
setOperations(List<CreationOperation>) - Method in class Operator.RampedHalfAndHalfInitialiser
  First item in collection is set as fullInitalion.
setOutput() - Method in class Main.AbstractRun
setOutputCharset(String) - Method in class com.rie.rieps.engine.Job
setParent(TreeNode<E>) - Method in class Util.Structures.TreeNode
  Set parent node
setParents(ArrayList<Fitness>) - Method in class Individuals.GEIndividual
setParentUIDs(List<Integer>) - Method in class Individuals.AbstractIndividual
  Set the parentUIDs
setParities(int) - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
setParitiesValues(int) - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
setPhenotype(Phenotype) - Method in class Individuals.AbstractIndividual
setPhenotype(Phenotype) - Method in class Individuals.GEIndividual
setPhenotype(Phenotype) - Method in interface Individuals.Individual
  Set phenotype
setPhenotype(Phenotype) - Method in class Mapper.GEGrammar
  Set output
setPhenotype(Object) - Method in class Mapper.GEGrammar
setPhenotype(Object) - Method in interface Mapper.Mapper
  Sets the output(phenotype)
setPopulation(Population) - Method in class Operator.Collector
setPopulation(Population) - Method in interface Operator.Module
  Set the population on which the module will perform its operations
setPopulation(Population) - Method in class Operator.OperatorModule
  Set the population that the module will operate on
setPopulationSize(int) - Method in class Operator.Operations.FitnessEvaluationOperation
setPreviouslyUsedCodons(int) - Method in class Individuals.GEIndividual
setProperties(Properties) - Method in class FitnessEvaluation.BinomialProblem.BinomialBSF
setProperties(Properties) - Method in class FitnessEvaluation.BinomialProblem.BinomialJScheme
setProperties(Properties) - Method in class FitnessEvaluation.Canvas.Paint
setProperties(Properties) - Method in class FitnessEvaluation.externalInterpreters.ParityProblem.EvenFiveParityFitnessBSF
  Set properties
setProperties(Properties) - Method in class FitnessEvaluation.externalInterpreters.SantaFeAntTrail.SantaFeAntTrailBSF
setProperties(Properties) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionBSF
setProperties(Properties) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionJScheme
setProperties(Properties) - Method in class FitnessEvaluation.HelloWorld.HelloWorldBSF
  Set properties
setProperties(Properties) - Method in class FitnessEvaluation.LSystem.LSystemDimension
setProperties(Properties) - Method in class FitnessEvaluation.LSystem.LSystemInitialiser
setProperties(Properties) - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
setProperties(Properties) - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
setProperties(Properties) - Method in class FitnessEvaluation.PatternMatch.WordMatch
setProperties(Properties) - Method in class FitnessEvaluation.RoyalTree.RoyalTree
setProperties(Properties) - Method in class FitnessEvaluation.SantaFeAntTrail.SantaFeAntTrailInterpreter
setProperties(Properties) - Method in class FitnessEvaluation.Sudoku.SudokuFit
setProperties(Properties) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
setProperties(Properties) - Method in class Mapper.GEGrammar
  Set properties
setProperties(Properties) - Method in class Operator.Initialiser
setProperties(Properties) - Method in class Operator.Operations.CrossoverOperation
  Set properties
setProperties(Properties) - Method in class Operator.Operations.EliteOperationSelection
setProperties(Properties) - Method in class Operator.Operations.EliteReplacementOperation
  Set properties
setProperties(Properties) - Method in class Operator.Operations.FitnessEvaluationOperation
  Get the size of the population, and use this to determine the size of the cache.
setProperties(Properties) - Method in class Operator.Operations.GrowInitialiser
setProperties(Properties) - Method in class Operator.Operations.LSystemSelect
setProperties(Properties) - Method in class Operator.Operations.MutationOperation
  Set properties
setProperties(Properties) - Method in class Operator.Operations.RandomInitialiser
setProperties(Properties) - Method in class Operator.Operations.ReplacementOperation
  Set properties
setProperties(Properties) - Method in class Operator.Operations.RouletteWheel
setProperties(Properties) - Method in class Operator.Operations.SelectionOperation
  Set properties
setProperties(Properties) - Method in class Operator.Operations.ShapeGrammarSelect
setProperties(Properties) - Method in class Operator.Operations.SinglePointCrossover
  Set properties
setProperties(Properties) - Method in class Operator.Operations.StatisticsCollectionOperation
  Set properties
setProperties(Properties) - Method in class Operator.Operations.TournamentSelect
setProperties(Properties) - Method in class Operator.Operations.UserSelect
setProperties(Properties) - Method in class Operator.RampedHalfAndHalfInitialiser
setProperties(Properties) - Method in class Operator.SelectionScheme
  Set properties
setProperties(Properties) - Method in interface Parameter.ParameterI
  Set properties
setProperties(Properties) - Method in class Util.Statistics.IndividualCatcher
setPsfnt(PSFont) - Method in class com.rie.rieps.engine.Frame
setPSFont(PSFont) - Method in class com.rie.rieps.engine.Page
setRandom(boolean) - Method in class FitnessEvaluation.BinomialProblem.Range
setRandom(boolean) - Method in class FitnessEvaluation.util.Range
setRandom(boolean, int) - Method in class FitnessEvaluation.util.Range
setRange(Range) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
setRecursive(boolean) - Method in class Mapper.Production
  Update the recursive nature of this production.
setRecursive(boolean) - Method in class Mapper.Rule
  Update the recursive nature of this rule.
setReplacementSize(int) - Method in class Operator.Operations.ReplacementOperation
  Set replacement size
setRevesePolish(ReversePolish) - Method in class FitnessEvaluation.ParityProblem.BooleanInterpreter
setRight(BinaryNode<T>) - Method in class Util.Structures.BinaryNode
setRightPadding(float) - Method in class com.rie.rieps.engine.Frame
setRNG(RandomNumberGenerator) - Method in class FitnessEvaluation.BinomialProblem.BinomialJScheme
setRNG(RandomNumberGenerator) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionJScheme
setRNG(RandomNumberGenerator) - Method in class FitnessEvaluation.MaxProblem.MaxProblemInterpreter
setRNG(RandomNumberGenerator) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.CrossoverOperation
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.GrowInitialiser
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.LSystemSelect
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.MutationOperation
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.RandomInitialiser
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.RouletteWheel
setRNG(RandomNumberGenerator) - Method in class Operator.Operations.TournamentSelect
setRNG(RandomNumberGenerator) - Method in class Operator.OperatorModule
  Set the RandomNumberGenerator
setRNG(RandomNumberGenerator) - Method in interface Util.Random.Stochastic
  Set the number generator
setRoot(TreeNode<E>) - Method in class Util.Structures.NimbleTree
  Set tree root
setRotate(float) - Method in class com.rie.rieps.engine.fonts.PSFont
setRotate(float) - Method in class com.rie.rieps.engine.Frame
setRotate(float) - Method in class com.rie.rieps.engine.TextParameter
setRules(ArrayList<Rule>) - Method in class Mapper.Grammar
  Set rules in grammar
setSamples(double[][]) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
setScale(float) - Method in class Fractal.LSystem2Panel
setSeed(long) - Method in class Util.Random.MersenneTwisterFast
  Initalize the pseudo random number generator.
setSeed(int[]) - Method in class Util.Random.MersenneTwisterFast
  Sets the seed of the MersenneTwister using an array of integers.
setSeed(long) - Method in interface Util.Random.RandomNumberGenerator
  Set the seed
setSeed(int[]) - Method in interface Util.Random.RandomNumberGenerator
  Set the seed
setSize(float) - Method in class com.rie.rieps.engine.fonts.PSFont
setSize(int) - Method in interface Operator.Creator
  Sets the size of the desired population
setSize(int) - Method in class Operator.SourceModule
  Set the size
setStartSymbol(Symbol) - Method in class Mapper.Grammar
  Change start symbol by symbol.
setStartSymbol(String) - Method in class Mapper.Grammar
  Change start symbol by string.
setSymbolString(String) - Method in class Mapper.Symbol
  Set the string of the symbol
setText(String) - Method in class com.rie.rieps.engine.Frame
setTextParameter(TextParameter) - Method in class com.rie.rieps.engine.Frame
setTokens(String) - Method in class Util.Structures.ReversePolish
setTokens(ArrayList<Symbol>) - Method in class Util.Structures.ReversePolish
setTop(float) - Method in class com.rie.rieps.engine.Frame
setTopPadding(float) - Method in class com.rie.rieps.engine.Frame
setTrail_type(String) - Method in class FitnessEvaluation.SantaFeAntTrail.SantaFeAntTrailInterpreter
setType(Enums.SymbolType) - Method in class Mapper.Symbol
  Set the type of the symbol
setup(String[]) - Method in class Main.AbstractRun
  Setup the algorithm.
setup(String[]) - Method in class Main.Run
  Setup the algorithm.
setup(String[]) - Method in class Main.State
setup() - Method in class Main.Tutorials.Tutorial4
setup(String[]) - Method in class Main.Tutorials.Tutorial4
  Setup the algorithm.
setup() - Method in class Main.Tutorials.Tutorial5
setup(String[]) - Method in class Main.Tutorials.Tutorial5
  Setup the algorithm.
setup() - Method in class Main.Tutorials.Tutorial6
setup(String[]) - Method in class Main.Tutorials.Tutorial6
  Setup the algorithm.
setup() - Method in class Main.Tutorials.Tutorial7
setup(String[]) - Method in class Main.Tutorials.Tutorial7
  Setup the algorithm.
setUsedCodons(int) - Method in class Individuals.GEIndividual
  Set how many codons were used
setUsedGenes(int) - Method in class Individuals.GEChromosome
  Set how many genes where used during mapping
setUsedWraps(int) - Method in class Individuals.GEChromosome
  Set how many wraps that where used
setUsedWraps(int) - Method in class Individuals.GEIndividual
  Set how many wraps were used
setValid(boolean) - Method in class Individuals.GEChromosome
  Set a new value for the valid field.
setValid(boolean) - Method in class Individuals.GEIndividual
setValid(boolean) - Method in interface Individuals.Individual
  Set the validity of the individual
setValue(T) - Method in class Util.Structures.BinaryNode
setVertical(int) - Method in class com.rie.rieps.engine.TextParameter
setWidth(float) - Method in class com.rie.rieps.engine.Frame
setWidth(float) - Method in class com.rie.rieps.engine.LineFormat
setWrapCount(int) - Method in class Mapper.DerivationTree
  Set the number of wraps used
setX(double[]) - Method in class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
ShapeGrammarSelect - Class in Operator.Operations
ShapeGrammarSelect() - Constructor for class Operator.Operations.ShapeGrammarSelect
shouldContinue() - Static method in class Fractal.FinalGuiComp
showPage(Page) - Method in class com.rie.rieps.engine.Document
  Send a complete page to the outputStream.
showPage(Page, int, int) - Method in interface com.rie.rieps.engine.factories.Factory
showPage(Page, int, int) - Method in class com.rie.rieps.engine.factories.PSFactory
showPage() - Method in class com.rie.rieps.engine.Page
showText(Page, float, float, float, float, String, TextParameter) - Method in interface com.rie.rieps.engine.factories.Factory
showText(Page, float, float, float, float, String, TextParameter) - Method in class com.rie.rieps.engine.factories.PSFactory
showText(float, float, float, float, String, TextParameter) - Method in class com.rie.rieps.engine.Page
SimplePipeline - Class in Algorithm
  A pipeline containing modules.
SimplePipeline(int) - Constructor for class Algorithm.SimplePipeline
  Constructor for a pipeline of set initial size
SimplePipeline() - Constructor for class Algorithm.SimplePipeline
  Constructor
SimplePopulation - Class in Individuals.Populations
  Population using an array list structure for storing the individuals.
SimplePopulation() - Constructor for class Individuals.Populations.SimplePopulation
  Creates a new instance of SimplePopulation
SimplePopulation(int) - Constructor for class Individuals.Populations.SimplePopulation
SimpleReplacementStrategy - Class in Operator
  SimpleReplacementStrategy joins two populations.
SimpleReplacementStrategy(RandomNumberGenerator, Population, ReplacementOperation) - Constructor for class Operator.SimpleReplacementStrategy
  Creates a new instance of SimpleReplacementStrategy
SimpleReplacementStrategy() - Constructor for class Operator.SimpleReplacementStrategy
  New instance
SimpleUserSelect - Class in Operator.Operations
SimpleUserSelect() - Constructor for class Operator.Operations.SimpleUserSelect
sin(double) - Method in class FitnessEvaluation.BinomialProblem.BinomialFunkBSF
  Trigonometric sine function
sin(double) - Method in class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Trigonometric sine function
SinglePointCrossover - Class in Operator.Operations
  Single point crossover.
SinglePointCrossover(RandomNumberGenerator, double) - Constructor for class Operator.Operations.SinglePointCrossover
  Creates a new instance of SinglePointCrossover
SinglePointCrossover(double, RandomNumberGenerator) - Constructor for class Operator.Operations.SinglePointCrossover
  Creates a new instance of SinglePointCrossover
SinglePointCrossover(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.SinglePointCrossover
  New instance
size() - Method in interface Individuals.Populations.Population
  The number of individuals in the population
size() - Method in class Individuals.Populations.SimplePopulation
size - Variable in class Operator.Operations.SelectionOperation
size - Variable in class Operator.SourceModule
size() - Method in interface Util.Structures.IntList
  Size of structure
size() - Method in class Util.Structures.StaticIntList
  Get current size of the list
SM_FITNESS - Static variable in class Fractal.GuiComp
SM_FRACTALDIMENSION - Static variable in class Fractal.GuiComp
SM_PHENOTYPE - Static variable in class Fractal.GuiComp
smallFit - Variable in class Operator.Operations.RouletteWheel
SmallGrayImage - Class in com.rie.rieps.engine.image
  This class generate Black and White image from a file.
SmallGrayImage(int) - Constructor for class com.rie.rieps.engine.image.SmallGrayImage
  If convert_mode is unknown value, it uses @see{CONVERT_MODE_AVERAGE}.
sort() - Method in interface Individuals.Populations.Population
  Sort the individuals in the population
sort() - Method in class Individuals.Populations.SimplePopulation
sortMethod - Static variable in class Fractal.GuiComp
SourceModule - Class in Operator
  Abstract class used for a source module.
SourceModule(RandomNumberGenerator, int) - Constructor for class Operator.SourceModule
  Creates a new instance of SourceModule
SourceModule() - Constructor for class Operator.SourceModule
  Creates a new instance of SourceModule
SourceModule(RandomNumberGenerator, Properties) - Constructor for class Operator.SourceModule
  Creates a new instance of SourceModule
spinRoulette(List<Individual>) - Method in class Operator.Operations.RouletteWheel
  Selects Indivudals from operand and adds to the selected population until the selected population is full.
SplitOperator - Class in Operator
  Abstract class for splitting a population.
SplitOperator(RandomNumberGenerator, int, Operation) - Constructor for class Operator.SplitOperator
  New instance
SplitOperator(RandomNumberGenerator, Operation, Properties) - Constructor for class Operator.SplitOperator
  New instance
SR_RANGE - Static variable in class Util.Constants
  Specifies the range to test the fitness for symbolic regression.The format is sr_range= x eq [start; stepSize; stop]; and multiple ranges can be specified eg sr_range = x0 eq [0:.5:2]; x1 eq [2:.1:5].
SR_TARGET - Static variable in class Util.Constants
  the phenotypic target for symbolic regression
StatCatcher - Class in Util.Statistics
  Stores statistics from the population;
StatCatcher() - Constructor for class Util.Statistics.StatCatcher
  Creates a new instance of StatCatcher
StatCatcher(int) - Constructor for class Util.Statistics.StatCatcher
  New instance
State - Class in Main
  State allows loading, saving, and setup of the algorithm's state.
State() - Constructor for class Main.State
stateEquals(Object) - Method in class Util.Random.MersenneTwisterFast
StaticIntIterator - Class in Util.Structures
StaticIntIterator(int[], int) - Constructor for class Util.Structures.StaticIntIterator
  Create instance
StaticIntList - Class in Util.Structures
  This is a simple implementation of a wrapper for a dynamically sized static array to hold ints.
StaticIntList(int) - Constructor for class Util.Structures.StaticIntList
  Creates a new instance of StaticIntList
StaticIntList(StaticIntList) - Constructor for class Util.Structures.StaticIntList
  Copy constructor
StatisticsCollectionOperation - Class in Operator.Operations
  Operation that collects statistics from the algorithm.
StatisticsCollectionOperation(StatCatcher, IndividualCatcher) - Constructor for class Operator.Operations.StatisticsCollectionOperation
  Creates a new instance of StatisticsCollectionOperation
StatisticsCollectionOperation(StatCatcher, IndividualCatcher, Properties) - Constructor for class Operator.Operations.StatisticsCollectionOperation
  Creates a new instance of StatisticsCollectionOperation
stats - Variable in class Operator.Operations.StatisticsCollectionOperation
stdErr - Variable in class Main.AbstractRun
STDERR - Static variable in class Util.Constants
  Used for redirecting stdErr
stdOut - Variable in class Main.AbstractRun
STDOUT - Static variable in class Util.Constants
  Used for redirecting stdOut
STEADY_STATE - Static variable in class Util.Constants
  Sets generation gap to 1/population size.
step() - Method in class Algorithm.AbstractAlgorithm
step() - Method in interface Algorithm.Algorithm
  Step the algorithm once
step() - Method in class Algorithm.MyFirstSearchEngine
  Step the loop pipeline.
step() - Method in interface Algorithm.Pipeline
  Step through all the modules in the pipeline once
step() - Method in class Algorithm.SimplePipeline
  Iterate over the modules in the pipeline
stillRunning() - Method in class Fractal.GuiComp
Stochastic - Interface in Util.Random
  Interface to be used to declare that a class is in some way stochastic and therefore needs a Random number generator
STOP_WHEN_SOLVED - Static variable in class Util.Constants
  Stop algorithm if global optimum is found before max iterations
stringToRange(String) - Method in class FitnessEvaluation.BinomialProblem.Range
  String as x = [start:step:stop]; or x = rnd(start, cases ,stop)
stringToRange(String) - Method in class FitnessEvaluation.util.Range
  For a fixed range input string as x eq [start:step:stop]; e.g inputs 0,0.1,0.2,...,1 for x0 and x1 is x0 eq [0:0.1:1]; x1 eq [0:0.1:1] For random numbers from a range or x eq rnd(start, cases ,stop); e.g random inputs rom range 0 to 1 for x0 and x1 is x0 eq rnd(0,10,1); x1 eq rnd(0,10,1)
StructuralMutation - Class in Operator.Operations.ContextSensitiveOperations
  This will find if the chromosome contains a expandable structural node and will mutate it depending on the mutation probability
StructuralMutation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.ContextSensitiveOperations.StructuralMutation
StructuralMutation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.ContextSensitiveOperations.StructuralMutation
SubtreeCrossover - Class in Operator.Operations.ContextSensitiveOperations
  Preform a crossover where the branch of one tree crosses with the branch of another.
SubtreeCrossover(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.ContextSensitiveOperations.SubtreeCrossover
SubtreeCrossover(double, RandomNumberGenerator) - Constructor for class Operator.Operations.ContextSensitiveOperations.SubtreeCrossover
SubtreeMutation - Class in Operator.Operations.ContextSensitiveOperations
  Pick a single point to mutate, but having mutated, remove all the codons that used to define the old branch, and then follow the new branch, randomly generating values to pick productions, until a complete branch is built or the maximum depth is reached.
SubtreeMutation(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
SubtreeMutation(double, RandomNumberGenerator) - Constructor for class Operator.Operations.ContextSensitiveOperations.SubtreeMutation
SudokuFit - Class in FitnessEvaluation.Sudoku
SudokuFit() - Constructor for class FitnessEvaluation.Sudoku.SudokuFit
  Creates a new instance of SudokuFit
sumFit - Variable in class Operator.Operations.RouletteWheel
Symbol - Class in Mapper
  This class implements a symbol of a grammar, be it a non-terminal or terminal symbol.
Symbol() - Constructor for class Mapper.Symbol
  Default constructor, creates a symbol with an empty string.
Symbol(String, Enums.SymbolType) - Constructor for class Mapper.Symbol
  Creates a symbol of type symbolType and with the string
Symbol(Symbol) - Constructor for class Mapper.Symbol
  Copy constructor
SymbolicRegressionBSF - Class in FitnessEvaluation.externalInterpreters.SymbolicRegression
  Evaluates the fitness for the SymbolicRegressionExperiment class.
SymbolicRegressionBSF() - Constructor for class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionBSF
  Creates a new instance of SymbolicRegression
SymbolicRegressionInterpreter - Class in FitnessEvaluation.SymbolicRegression
  Interpreter for symbolic regression.
SymbolicRegressionInterpreter() - Constructor for class FitnessEvaluation.SymbolicRegression.SymbolicRegressionInterpreter
SymbolicRegressionJScheme - Class in FitnessEvaluation.externalInterpreters.SymbolicRegression
  Evaluates the fitness for the SymbolicRegressionExperiment class.
SymbolicRegressionJScheme() - Constructor for class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymbolicRegressionJScheme
  Creates a new instance of SymbolicRegressionJScheme
SymRegFunkBSF - Class in FitnessEvaluation.externalInterpreters.SymbolicRegression
  help class for SymbolicRegression.java
SymRegFunkBSF() - Constructor for class FitnessEvaluation.externalInterpreters.SymbolicRegression.SymRegFunkBSF
  Creates a new instance of SymRegFunkBSF

## T

TAIL_PERCENTAGE - Static variable in class Util.Constants
  Reletive percentage of chromosome tail
TARGET_FRACTAL_DIMENSION - Static variable in class Util.Constants
TARGET_IMAGE - Static variable in class Util.Constants
  This specifies the file location for the target picture
TARGET_PHENOTYPE - Static variable in class Util.Constants
  This specifies a phenotype string for the target picture
TextParameter - Class in com.rie.rieps.engine
TextParameter(int, int, Color, float, boolean) - Constructor for class com.rie.rieps.engine.TextParameter
time - Variable in class Util.Statistics.StatCatcher
toArray() - Method in interface Util.Structures.IntList
  Make an array view
toArray() - Method in class Util.Structures.StaticIntList
  To array
toPrefixPhenotype(Phenotype) - Method in class Util.Structures.ReversePolish
toPrefixString(BinaryNode<Symbol>) - Method in class Util.Structures.ReversePolish
  Traverses a binary tree depth first
toReversePolish() - Method in class Util.Structures.ReversePolish
  The method toReversePolish converts the infix expression into a reverse Polish string.
toString() - Method in class FitnessEvaluation.BinomialProblem.Range
toString() - Method in class FitnessEvaluation.util.Range
toString() - Method in class Individuals.GEChromosome
toString() - Method in class Individuals.GEIndividual
toString() - Method in class Individuals.Phenotype
toString() - Method in class Individuals.Populations.SimplePopulation
toString() - Method in class Mapper.DerivationNode
  Build the string using a textural tree-view
toString() - Method in class Mapper.Production
toString() - Method in class Mapper.Rule
toString() - Method in class Mapper.Symbol
toString() - Method in class Util.FileNameExtensionFilter
toString() - Method in class Util.Statistics.IndividualCatcher
toString() - Method in class Util.Structures.NimbleTree
toString() - Method in class Util.Structures.TreeNode
  Build the string using a textural tree-view
tour - Variable in class Operator.Operations.TournamentSelect
TOURNAMENT_SIZE - Static variable in class Util.Constants
  Size of tournament for tournament selection
TournamentSelect - Class in Operator.Operations
  The operation of this class is tournament selection.
TournamentSelect(int, int, RandomNumberGenerator) - Constructor for class Operator.Operations.TournamentSelect
  Creates a new instance of TournamentSelect
TournamentSelect(RandomNumberGenerator, Properties) - Constructor for class Operator.Operations.TournamentSelect
  Creates a new instance of TournamentSelect
TournamentSelect() - Constructor for class Operator.Operations.TournamentSelect
  New instantion
tournamentSize - Variable in class Operator.Operations.TournamentSelect
Trail - Class in FitnessEvaluation.SantaFeAntTrail
  Taken from lib GE and refactored to java
Trail() - Constructor for class FitnessEvaluation.SantaFeAntTrail.Trail
  Creates a new instance of Trail.
Trail(int) - Constructor for class FitnessEvaluation.SantaFeAntTrail.Trail
  Create new instance
trailCnt - Variable in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
trails - Static variable in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
treeFromPostfix() - Method in class Util.Structures.ReversePolish
TreeMill - Class in Mapper
TreeMill() - Constructor for class Mapper.TreeMill
TreeNode<E> - Class in Util.Structures
  Node for use in the nimble tree structure.
TreeNode() - Constructor for class Util.Structures.TreeNode
  Creates a new instance of TreeNode
TreeNode(TreeNode<E>, E) - Constructor for class Util.Structures.TreeNode
  Create node with parent and data
TreeNode(TreeNode<E>) - Constructor for class Util.Structures.TreeNode
  Copy constructor
TreeNode(TreeNode<E>, TreeNode<E>) - Constructor for class Util.Structures.TreeNode
trim(String[]) - Static method in class Util.GEVAHelper
  Trim an array of strings so that all padding white-space is removed, e.g. {" a ", " ", "b"} -> {"a", "", "b"}
TRUE - Static variable in class Util.Constants
TUMBLE - Static variable in class com.rie.rieps.engine.DeviceParameter
  Parameter to rotate 180 degrees the page. the value must be a boolean.
turn - Variable in class FitnessEvaluation.SantaFeAntTrail.SanMateoTrail
Tutorial4 - Class in Main.Tutorials
  Tutorial4 main class.
Tutorial4() - Constructor for class Main.Tutorials.Tutorial4
  Creates a new instance of Tutorial4
Tutorial5 - Class in Main.Tutorials
  Tutorial5 main class.
Tutorial5() - Constructor for class Main.Tutorials.Tutorial5
  Creates a new instance of Tutorial5
Tutorial6 - Class in Main.Tutorials
  Tutorial6 main class.
Tutorial6() - Constructor for class Main.Tutorials.Tutorial6
  Creates a new instance of Tutorial6
Tutorial7 - Class in Main.Tutorials
  Tutorial7 main class.
Tutorial7() - Constructor for class Main.Tutorials.Tutorial7
  Creates a new instance of Tutorial7

## U

UI - package UI
update(Graphics) - Method in class Fractal.LargeLSystem
update(Graphics) - Method in class Fractal.LSystem
userPick(List<Individual>) - Method in class Operator.Operations.SimpleUserSelect
userPick(List<Individual>) - Method in class Operator.Operations.UserSelect
USERPICK_SIZE - Static variable in class Util.Constants
  Size of population for user selection
UserSelect - Class in Operator.Operations
  The top N individuals are visually offered to the user and the user picks who should win.
UserSelect(int, int) - Constructor for class Operator.Operations.UserSelect
  Creates a new instance of TournamentSelect
UserSelect() - Constructor for class Operator.Operations.UserSelect
  New instantion
Util - package Util
Util.Random - package Util.Random
Util.Statistics - package Util.Statistics
Util.Structures - package Util.Structures

## V

valueOf(String) - Static method in enum Util.Enums.SymbolType
  Returns the enum constant of this type with the specified name.
values() - Static method in enum Util.Enums.SymbolType
  Returns an array containing the constants of this enum type, in the order they are declared.
varFitness - Variable in class Util.Statistics.StatCatcher
varLength - Variable in class Util.Statistics.StatCatcher
VERSION_FLAG - Static variable in class Util.Constants
VERT_BOTTOM - Static variable in class com.rie.rieps.engine.TextParameter
VERT_MIDDLE - Static variable in class com.rie.rieps.engine.TextParameter
VERT_TOP - Static variable in class com.rie.rieps.engine.TextParameter
VerySimpleExample - Class in com.rie.rieps.simpletest
  This is a minimal example of how to use RiePS.
VerySimpleExample() - Constructor for class com.rie.rieps.simpletest.VerySimpleExample

## W

wasPreviouslyValid() - Method in class Individuals.GEIndividual
  Find out whether individual was *previously* valid.
WHITE - Static variable in class com.rie.rieps.engine.color.Gray
WordMatch - Class in FitnessEvaluation.PatternMatch
  Matches strings
WordMatch() - Constructor for class FitnessEvaluation.PatternMatch.WordMatch
  Creates a new instance of WordMatch
WordMatch(String) - Constructor for class FitnessEvaluation.PatternMatch.WordMatch
  Creates a new instance of WordMatch
WORDMATCH_WORD - Static variable in class Util.Constants
  Word to match when using the wordmatch fitness function
WorldWriter - Class in FitnessEvaluation.HelloWorld
  Class to be extended by HelloWorldBSF Contains methods for appending, printing and calculating the fitness compared to "geva"
WorldWriter() - Constructor for class FitnessEvaluation.HelloWorld.WorldWriter
  Create an instance
wrapCount - Variable in class Mapper.DerivationTree
writeChar(char) - Method in class FitnessEvaluation.HelloWorld.WorldWriter
  Append a char to the string
writeChar(String) - Method in class FitnessEvaluation.HelloWorld.WorldWriter
writeChar(HashMap) - Method in class FitnessEvaluation.HelloWorld.WorldWriter
  Append a char to the string from a hashmap
writeState(DataOutputStream) - Method in class Util.Random.MersenneTwisterFast
  Writes the entire state of the MersenneTwister RNG to the stream

## _

_current_X - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_current_Y - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_energy - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_facing_current_X - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_facing_current_Y - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_picked_up - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_trail - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail
_trail_la - Variable in class FitnessEvaluation.SantaFeAntTrail.LosAltosTrail
_working_trail - Variable in class FitnessEvaluation.SantaFeAntTrail.Trail

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

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