Index of all Fields and Methods

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

Index of all Fields and Methods

A

addBest(GPPopulation). Method in class gpjpp.GPPopulation: Adds the best individual from this generation to the next.
AddBestToNewPopulation. Variable in class gpjpp.GPVariables: Determines whether the best individual is automatically added to the next generation, when SteadyState is false.
ADFNODESETID. Static variable in class gpjpp.GPObject: An ID code used to identify GPAdfNodeSet references in gpjpp streams.
adfNs. Variable in class gpjpp.GPPopulation: A reference to the functions and terminals for the run.
adfNs. Variable in class gpjpp.GPRun: The branch and node definitions for all the GPs used during the run.
adjFitness. Variable in class gpjpp.GP: The adjusted fitness of the GP.
adjustOverlaps(double[], double[], int). Method in class gpjpp.GPGenePrint: Adjusts the x coordinate of this node and its children whenever the node overlaps the region of the node to its left.
allNodes. Static variable in class gpjpp.GPGene: An array of all node types in all branches used temporarily while loading the array from a stream.
arcRadius. Static variable in class gpjpp.GPGenePrint: The pixel radius of the arc at each corner of a node rectangle.
arguments(). Method in class gpjpp.GPNode: Returns the number of arguments to the node.
as. Variable in class gpjpp.GPDrawing: The maximum ascent of any character in the current font.
assignContainer(GPContainer, int). Method in class gpjpp.GPGeneReference: Assigns a particular container and index to this gene reference.
assignRef(GPGeneReference). Method in class gpjpp.GPGeneReference: Assigns another gene reference to this one.
attemptedComplexCount. Variable in class gpjpp.GPPopulation: The number of individuals that were created for generation 0 but rejected because their complexity exceeded the global configuration variable MaximumComplexity.
attemptedDupCount. Variable in class gpjpp.GPPopulation: The number of duplicate individuals that were created in generation 0 but rejected.
avgDepth. Variable in class gpjpp.GPPopulation: Average tree depth of the entire population.
avgFitness. Variable in class gpjpp.GPPopulation: Average fitness of the entire population.
avgLength. Variable in class gpjpp.GPPopulation: Average complexity of the entire population.

B

baseName. Variable in class gpjpp.GPRun: The base name for all input and output files used in the run.
bestFitness. Variable in class gpjpp.GPPopulation: Best standardized fitness found in the entire population.
bestOfPopulation. Variable in class gpjpp.GPPopulation: The index of the individual with the best standardized fitness.
betterThan(GP). Method in class gpjpp.GP: Returns true if this GP is better than another specified non-null GP.
buildUniqueGPs(). Method in class gpjpp.GPPopulation: Clears the diversity table and calls updateUniqueGPs for each individual in the population.

C

calcAdjustedFitness(). Method in class gpjpp.GP: Calculates the adjusted fitness after evaluate() has computed the standardized fitness.
calcContainerCenter(). Method in class gpjpp.GPGenePrint: Returns the x coordinate of the horizontal center of the arguments to this node at their current positions.
calcCutoffFitness(GPPopulationRange). Method in class gpjpp.GPPopulation: Computes the adjusted fitness boundary that separates group I from group II individuals using Koza's form of greedy over-selection.
calcDepth(). Method in class gpjpp.GP: Calculates the depth of the GP by calling GPGene.depth() method for each of its branches.
calcGroupIFraction(int). Method in class gpjpp.GPPopulation: Calculates Koza's c constant for greedy over-selection.
calcLength(). Method in class gpjpp.GP: Calculates the complexity of the GP by calling GPGene.length() method for each of its branches.
calcMaxX(). Method in class gpjpp.GPGenePrint: Returns the largest x value anywhere in the tree.
calcMaxX(double). Method in class gpjpp.GPGenePrint: Returns the largest x value anywhere in the tree.
calcMinX(). Method in class gpjpp.GPGenePrint: Returns the smallest x value anywhere in the tree.
calcMinX(double). Method in class gpjpp.GPGenePrint: Returns the smallest x value anywhere in the tree.
calcPackedContainerWidth(). Method in class gpjpp.GPGenePrint: Returns the minimum width of the arguments to this node taking into account the node width of each argument and the minimum spacing between nodes, xSpacing.
calcPackedPos(double[], int). Method in class gpjpp.GPGenePrint: Calculates the x coordinates of all the nodes below this level assuming that all can be packed to minimum spacing and each container is centered under its parent.
calculateStatistics(). Method in class gpjpp.GPPopulation: Calculates statistics about a complete population, including the best, average, and worst fitness, complexity, and depth.
calcXPositions(). Method in class gpjpp.GPGenePrint: Calculates the x coordinates of all nodes so that none overlap, otherwise-unconstrained nodes are evenly spaced, and parent nodes are centered over their children as much as possible.
cfg. Variable in class gpjpp.GPPopulation: A reference to the global configuration variables for the run.
cfg. Variable in class gpjpp.GPRun: The configuration variables used for the run.
ch. Variable in class gpjpp.GPDrawing: The height of the current font.
checkChar(boolean). Method in class gpjpp.GPRun: Returns the symbols displayed in the statistical display when a checkpoint is finished or skipped.
checkForDiversity(GP). Method in class gpjpp.GPPopulation: Returns true if the specified GP is not already in the diversity table or if cfg.TestDiversity is false.
CheckpointGens. Variable in class gpjpp.GPVariables: The number of generations between checkpoints saved by GPRun.
chooseFunction(). Method in class gpjpp.GPNodeSet: Returns a random function node from this set.
chooseFunctionNode(GPGeneReference). Method in class gpjpp.GPGene: Finds a random function node within this gene, not considering this gene itself.
chooseFunctionOrTerminalNode(GPGeneReference). Method in class gpjpp.GPGene: Attempts to find a random function node within this gene, not considering this gene itself.
chooseNodeWithArgs(int). Method in class gpjpp.GPNodeSet: Returns a random node from this set with the specified number of arguments.
chooseTerminal(). Method in class gpjpp.GPNodeSet: Returns a random terminal node from this set.
clear(). Method in class gpjpp.GPContainer: Sets all container elements to null to ensure that no references remain to objects currently held by this container.
clearHeritage(). Method in class gpjpp.GP: Sets all of the heritage fields (dadIndex, dadCross, mumIndex, MumCross, crossTree, swapTree, swapPos, shrinkTree, shrinkPos) to -1 when a new GP is created or cloned.
clearUniqueGPs(). Method in class gpjpp.GPPopulation: Creates or clears the diversity table and the dupCount and attemptedDupCount fields.
clone(). Method in class gpjpp.GP: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPAdfNodeSet: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPContainer: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPGene: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPGenePrint: Disables the cloning operation inherited from GPGene, since GPGenePrint does not need to be cloned.
clone(). Method in class gpjpp.GPNode: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPNodeSet: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPObject: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPPopulation: Implements the Cloneable interface.
clone(). Method in class gpjpp.GPVariables: Implements the Cloneable interface.
cntGen. Variable in class gpjpp.GPRun: The number of generations until the next checkpoint will be stored.
ComplexityAffectsFitness. Variable in class gpjpp.GPVariables: A boolean that can be tested by the user evaluate() function to determine whether to incorporate complexity into the fitness calculation.
container. Variable in class gpjpp.GPContainer: An array that is allocated once during the lifetime of the container.
container. Variable in class gpjpp.GPGeneReference: The container that holds a particular gene.
CONTAINERID. Static variable in class gpjpp.GPObject: An ID code used to identify GPContainer references in gpjpp streams.
containerSize(). Method in class gpjpp.GPContainer: Returns the number of elements the container can hold.
count. Variable in class gpjpp.GPGeneReference: Used by a search function to count the number of genes to pass or the number that were passed.
countFunctions(). Method in class gpjpp.GPGene: Returns the total number of function genes included by this gene and all of its children.
create(). Method in class gpjpp.GPPopulation: Creates all of the individuals in an initial population.
create(int, int, int, GPAdfNodeSet). Method in class gpjpp.GP: Creates the branches of this GP and then creates the genes of each branch according to the limits and methods specified.
create(int, int, int, GPNodeSet). Method in class gpjpp.GPGene: Creates the arguments to this gene and recursively creates children according to the limits and methods specified.
createChild(GPNode). Method in class gpjpp.GPGene: Creates a child gene while new trees are being built.
createGene(GPNode). Method in class gpjpp.GP: Creates a root gene while a new branch is being built.
createGP(int). Method in class gpjpp.GPPopulation: Creates the GP used for a new individual.
createNodeIndex(GPAdfNodeSet). Static method in class gpjpp.GPGene: Must be called by the stream manager before saving and loading genes.
createNodeSet(GPVariables). Method in class gpjpp.GPRun: Returns a properly initialized instance of GPAdfNodeSet, containing the branch and node definitions for this problem.
createOrAppend(String, boolean). Method in class gpjpp.GPRun: Creates or appends to a specified file and returns a valid reference to a GPPrintStream for that file.
createPopulation(GPVariables, GPAdfNodeSet). Method in class gpjpp.GPRun: You must override this method to return a new instance of a user subclass of GPPopulation.
createRandomGenerator(). Method in class gpjpp.GPRun: Returns a valid instance of Random used to generate all random numbers throughout the package.
createRegisteredClassObject(byte). Static method in class gpjpp.GPObject: Creates an object of specified ID and returns it.
createVariables(). Method in class gpjpp.GPRun: Returns a valid instance of GPVariables.
CreationProbability. Variable in class gpjpp.GPVariables: Percent probability that a creation operation will occur while evolving a new generation.
CreationStr. Static variable in class gpjpp.GPVariables: An array of strings used to detect and print the creation type in configuration files and status reports.
CreationType. Variable in class gpjpp.GPVariables: The strategy used to create generation 0.
cross(GPContainer, int, int). Method in class gpjpp.GP: Performs crossover on two GPs.
CrossoverProbability. Variable in class gpjpp.GPVariables: Percent probability that a crossover operation will occur while evolving a new generation.
crossTree. Variable in class gpjpp.GP: The branch number of this GP's mum and dad when it was generated as a result of crossover.
curGen. Variable in class gpjpp.GPRun: The current generation number.
curRun. Variable in class gpjpp.GPRun: The current run number.
cutoffAdjFitness. Variable in class gpjpp.GPPopulation: The cutoff fitness for an individual to get into group I.
cvs. Variable in class gpjpp.GPDrawing: The canvas on which the image is drawn.
cw. Variable in class gpjpp.GPDrawing: The width of the widest character in the current font.

D

dadCross. Variable in class gpjpp.GP: The s-expression index of this GP's "dad" when it was generated as a result of crossover.
dadIndex. Variable in class gpjpp.GP: The population index of this GP's "dad" when it was generated as a result of crossover or reproduction.
defFontSize. Static variable in class gpjpp.GPDrawing: The default font size used for the font.
DemeSize. Variable in class gpjpp.GPVariables: The number of individuals in each demetic group, if DemeticGrouping is true.
DemeticGrouping. Variable in class gpjpp.GPVariables: Determines whether demetic migration is performed.
DemeticMigProbability. Variable in class gpjpp.GPVariables: Percent probability that demetic migration will occur for each demetic group, if DemeticGrouping is true.
demeticMigration(). Method in class gpjpp.GPPopulation: Based on the configuration variable DemeticMigProbability, fitness-selects a good individual from each deme and exchanges it with a good individual from the next deme.
depth(). Method in class gpjpp.GP: Returns the maximum depth of the GP.
depth(). Method in class gpjpp.GPGene: Returns the largest depth of the tree attached to this gene.
depth(int). Method in class gpjpp.GPGene: Called internally by depth() to compute the tree depth.
dout. Variable in class gpjpp.GPRun: The PrintStream used for the detailed population output file.
drawGifNode(GPDrawing, int). Method in class gpjpp.GPGenePrint: Draws all the nodes recursively starting with this one, including each node's text, a rounded rectangle surrounding it, and connectors to all of its children.
drawOn(GPDrawing, String, GPVariables). Method in class gpjpp.GP: Writes a GP in graphic gif file format.
drawOn(GPDrawing, String, String, GPVariables). Method in class gpjpp.GPGene: Writes a GPGene in graphic gif file format.
drawOn(GPDrawing, String, String, GPVariables). Method in class gpjpp.GPGenePrint: Computes the x coordinates for all nodes in this gene tree and writes the tree in gif format to the specified file.
dupCount. Variable in class gpjpp.GPPopulation: The number of duplicate individuals in the current generation.

E

echoPrint(String). Method in class gpjpp.GPRun: Prints a string to System.out and also to sout.
equals(Object). Method in class gpjpp.GP: Determines whether this GP equals another object.
equals(Object). Method in class gpjpp.GPAdfNodeSet: Determines whether this GPAdfNodeSet equals another object.
equals(Object). Method in class gpjpp.GPGene: Determines whether this GPGene equals another object.
equals(Object). Method in class gpjpp.GPNode: Determines whether this GPNode equals another object.
equals(Object). Method in class gpjpp.GPNodeSet: Determines whether this GPNodeSet equals another object.
equals(Object). Method in class gpjpp.GPVariables: Determines whether this set of variables equals another object.
evaluate(GPVariables). Method in class gpjpp.GP: The user must override this method to evaluate and return the standardized fitness of the GP.
evolve(GPPopulationRange). Method in class gpjpp.GPPopulation: Based on the configuration variables CrossoverProbability and CreationProbability, creates two individuals using crossover or one new individual using creation (a brand-new GP) or reproduction (a fitness-selected copy of an existing individual).

F

findNthNode(GPGeneReference, boolean). Method in class gpjpp.GPGene: Returns true if a gene of specified position and type can be found within this gene.
findRegisteredClass(byte). Static method in class gpjpp.GPObject: Returns index of existing registered class, -1 if not found.
flip(double). Static method in class gpjpp.GPRandom: Returns true if a random real in the range from 0.0 to 100.0 is less than the specified percent.
fm. Variable in class gpjpp.GPDrawing: Font metrics for the active font.
fnt. Variable in class gpjpp.GPDrawing: The active font for the image.
fontName. Static variable in class gpjpp.GPDrawing: The typeface used to display text in genetic trees.
fontSize. Variable in class gpjpp.GPDrawing: The current font size.
formatDouble(double, int, int). Static method in class gpjpp.GPPopulation: Converts a double to a string right justified in a field of specified width.
formatInt(int, int). Static method in class gpjpp.GPPopulation: Converts an integer to a string right-justified in a field of specified width.
formatParentage(int, int, int, int). Method in class gpjpp.GPPopulation: Formats a string that shows the heritage of a crossover, reproduction, or mutation operation.
functions(). Method in class gpjpp.GPNodeSet: Returns the number of functions in this node set.

G

GENEID. Static variable in class gpjpp.GPObject: An ID code used to identify GPGene references in gpjpp streams.
geneNode(). Method in class gpjpp.GPGene: Returns the node reference of this gene.
GENEPRINTID. Static variable in class gpjpp.GPObject: An ID code used to identify GPGenePrint references in gpjpp streams.
generate(GPPopulation). Method in class gpjpp.GPPopulation: Generates the next generation of individuals using genetic processes.
geneRep(). Method in class gpjpp.GPGene: Returns the string representation of this gene as given by its node type.
get(int). Method in class gpjpp.GPContainer: Returns the object reference from the specified location in the container.
getAdjFitness(). Method in class gpjpp.GP: Returns the already-calculated adjusted fitness.
getBoolean(Properties, String, boolean). Method in class gpjpp.GPVariables: An internal routine used to convert a property string to a boolean.
getCheckpointFile(). Method in class gpjpp.GPRun: Returns an instantiated File of the stream file if checkpointing is enabled and the stream file exists.
getCheckpointName(). Method in class gpjpp.GPRun: Returns the checkpoint file name, baseName+".stm" by default.
getCreationType(Properties, String, int). Method in class gpjpp.GPVariables: An internal routine that calls getEnumerated type to convert a property string to the int value for a creation type.
getDetailName(). Method in class gpjpp.GPRun: Returns the detail file name, baseName+".det" by default.
getDouble(Properties, String, double). Method in class gpjpp.GPVariables: An internal routine used to convert a property string to a double.
getEnumeratedType(Properties, String[], String, int). Method in class gpjpp.GPVariables: An internal routine used to convert a property string to an enumerated type with int values.
getFitness(). Method in class gpjpp.GP: Returns the already-calculated standard fitness.
getGene(). Method in class gpjpp.GPGeneReference: Returns the gene referenced by this class.
getGra(). Method in class gpjpp.GPDrawing: Returns the graphics context on which drawing is done.
getIndex(). Method in class gpjpp.GPNode: Returns the node index used for streaming.
getInt(Properties, String, int). Method in class gpjpp.GPVariables: An internal routine used to convert a property string to an int.
getNodeRight(). Method in class gpjpp.GPGenePrint: Returns the x coordinate of the right edge of the node text in characters.
getNodeWidth(). Method in class gpjpp.GPGenePrint: Returns the length of the node representation string in characters.
getProperty(String). Method in class gpjpp.GPProperties: Looks up a property value based on a key.
getSelectionType(Properties, String, int). Method in class gpjpp.GPVariables: An internal routine that calls getEnumerated type to convert a property string to the int value for a selection type.
getStatisticsName(). Method in class gpjpp.GPRun: Returns the statistics file name, baseName+".stc" by default.
getUniqueGPsSize(). Method in class gpjpp.GPPopulation: Computes the size of the hash table used for diversity checking.
goodRuns. Variable in class gpjpp.GPRun: The number of good runs found so far.
GoodRuns. Variable in class gpjpp.GPVariables: GPRun does multiple runs until this many of them terminate with the best individual's fitness below TerminationFitness.
GP(). Constructor for class gpjpp.GP: Public null constructor used during stream loading only.
GP(GP). Constructor for class gpjpp.GP: A constructor that is called to clone a GP.
GP(int). Constructor for class gpjpp.GP: Constructor used when GPs are first created.
GPAdfNodeSet(). Constructor for class gpjpp.GPAdfNodeSet: Public null constructor used during stream loading only.
GPAdfNodeSet(GPAdfNodeSet). Constructor for class gpjpp.GPAdfNodeSet: A constructor that can be called to clone a GPAdfNodeSet.
GPAdfNodeSet(int). Constructor for class gpjpp.GPAdfNodeSet: The constructor called by user code to reserve space for the branches in each GP.
GPContainer(). Constructor for class gpjpp.GPContainer: Public null constructor used during stream loading only.
GPContainer(GPContainer). Constructor for class gpjpp.GPContainer: Constructor called to clone a deep copy of another container.
GPContainer(int). Constructor for class gpjpp.GPContainer: The constructor called by many GPContainer subclasses to allocate a container of specified size.
gpDepth. Variable in class gpjpp.GP: The maximum depth of any branch of the GP.
GPDrawing(). Constructor for class gpjpp.GPDrawing: Public null constructor for this class.
GPGene(). Constructor for class gpjpp.GPGene: Public null constructor used during stream loading only.
GPGene(GPGene). Constructor for class gpjpp.GPGene: A constructor that is called to clone a GPGene.
GPGene(GPNode). Constructor for class gpjpp.GPGene: Constructor used when trees are first created with random node types.
GPGeneReference(). Constructor for class gpjpp.GPGeneReference: Instantiates a gene reference for later use.
GPGeneReference(GPContainer, int). Constructor for class gpjpp.GPGeneReference: Instantiates a gene reference with a known container and index.
GPGeneReference(GPGeneReference). Constructor for class gpjpp.GPGeneReference: Clones another gene reference.
GPGREEDYSELECTION. Static variable in class gpjpp.GPVariables: A fitness-based selection type that uses greedy over-selection.
GPGROW. Static variable in class gpjpp.GPVariables: A tree creation type that makes every node but those on the bottom level a function and that builds every tree to MaximumDepthForCreation.
GPID. Static variable in class gpjpp.GPObject: An ID code used to identify GP references in gpjpp streams.
gpLength. Variable in class gpjpp.GP: The complexity, or length, of the GP.
GPNode(). Constructor for class gpjpp.GPNode: Public null constructor used during stream loading only.
GPNode(GPNode). Constructor for class gpjpp.GPNode: A constructor that can be called to clone a GPNode.
GPNode(int, String). Constructor for class gpjpp.GPNode: The constructor called by user code to describe the terminals for the genetic programming problem.
GPNode(int, String, int). Constructor for class gpjpp.GPNode: The constructor called by user code to describe the functions for the genetic programming problem.
GPNodeSet(). Constructor for class gpjpp.GPNodeSet: Public null constructor used during stream loading only.
GPNodeSet(GPNodeSet). Constructor for class gpjpp.GPNodeSet: A constructor that can be called to clone a GPNodeSet.
GPNodeSet(int). Constructor for class gpjpp.GPNodeSet: The constructor called by user code to reserve space for the functions and terminals allowed in this branch.
GPObject(). Constructor for class gpjpp.GPObject: This do-nothing constructor gets called implicitly by subclasses of GPObject.
GPPopulation(). Constructor for class gpjpp.GPPopulation: Public null constructor used during stream loading only.
GPPopulation(GPPopulation). Constructor for class gpjpp.GPPopulation: A constructor that can be called to clone a population.
GPPopulation(GPVariables, GPAdfNodeSet). Constructor for class gpjpp.GPPopulation: Constructor used when populations are first created.
GPPrintStream(OutputStream). Constructor for class gpjpp.GPPrintStream: Creates a GPPrintStream filter over an OutputStream.
GPPrintStream(OutputStream, boolean). Constructor for class gpjpp.GPPrintStream: Creates a GPPrintStream filter over an OutputStream.
GPPROBABILISTICSELECTION. Static variable in class gpjpp.GPVariables: A fitness-based selection type that uses a roulette algorithm.
GPProperties(). Constructor for class gpjpp.GPProperties: Creates an empty property set.
GPProperties(Properties). Constructor for class gpjpp.GPProperties: Creates an empty property set with specified default values.
GPRAMPEDGROW. Static variable in class gpjpp.GPVariables: A tree creation type that is like GPGROW but starts with a tree depth of two and increases the depth by one for each tree until it reaches MaximumDepthForCreation, at which point it cycles back to two.
GPRAMPEDHALF. Static variable in class gpjpp.GPVariables: A tree creation type that builds alternating trees using the GPRAMPEDVARIABLE and GPRAMPEDGROW methods.
GPRAMPEDVARIABLE. Static variable in class gpjpp.GPVariables: A tree creation type that is like GPVARIABLE but starts with a tree depth of two and increases the depth by one for each tree until it reaches MaximumDepthForCreation, at which point it cycles back to two.
GPRun(String, boolean). Constructor for class gpjpp.GPRun: This constructor allocates the basic data structures and prepares for a run.
GPTOURNAMENTSELECTION. Static variable in class gpjpp.GPVariables: A fitness-based selection type that uses a tournament algorithm.
GPVARIABLE. Static variable in class gpjpp.GPVariables: A tree creation type that selects each non-root node with a 50:50 chance of becoming a function or terminal and that continues building every tree to MaximumDepthForCreation.
GPVariables(). Constructor for class gpjpp.GPVariables: Public null constructor used to create a set of variables with default values and also during stream loading.
GPVariables(GPVariables). Constructor for class gpjpp.GPVariables: A constructor that can be called to clone GPVariables.
gra. Variable in class gpjpp.GPDrawing: A graphics context whose methods are called to produce the off-screen image.
greedySelection(int[], int, boolean, GPPopulationRange). Method in class gpjpp.GPPopulation: Selects one or more individuals from the specified range of the population by using Koza's "greedy over-selection".

H

hashCode(). Method in class gpjpp.GP: Returns an integer hashcode for this GP.
hBox(GPDrawing). Method in class gpjpp.GPGenePrint: Computes the pixel height of the node rectangle.

I

img. Variable in class gpjpp.GPDrawing: An off-screen image associated with the canvas on which the drawing is created.
index. Variable in class gpjpp.GPGeneReference: The index of a particular gene within its container.
isA(). Method in class gpjpp.GP: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPAdfNodeSet: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPContainer: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPGene: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPGenePrint: Returns a code identifying the class.
isA(). Method in class gpjpp.GPNode: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPNodeSet: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPObject: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPPopulation: Returns a code identifying the class in a stream file.
isA(). Method in class gpjpp.GPVariables: Returns a code identifying the class in a stream file.
isFunction(). Method in class gpjpp.GPGene: Returns true if this gene represents a function.
isFunction(). Method in class gpjpp.GPNode: Returns true if the node is a function, that is, has more than zero arguments.
isTerminal(). Method in class gpjpp.GPGene: Returns true if this gene represents a terminal.
isTerminal(). Method in class gpjpp.GPNode: Returns true if the node is a terminal, that is, has zero arguments.

L

length(). Method in class gpjpp.GP: Returns the complexity (length, or number of nodes) of the GP.
length(). Method in class gpjpp.GPGene: Returns the number of genes attached to this one, including itself.
lineSeparator. Variable in class gpjpp.GPPrintStream: The line separator string obtained by calling System.getProperty("line.separator").
load(DataInputStream). Method in class gpjpp.GP: Loads a GP from the specified stream.
load(DataInputStream). Method in class gpjpp.GPContainer: Loads a GPContainer from the specified stream.
load(DataInputStream). Method in class gpjpp.GPGene: Loads a GPGene from the specified stream.
load(DataInputStream). Method in class gpjpp.GPGenePrint: Disables the load operation inherited from GPGene, since GPGenePrint does not need to be streamed.
load(DataInputStream). Method in class gpjpp.GPNode: Loads a GPNode from the specified stream.
load(DataInputStream). Method in class gpjpp.GPNodeSet: Loads a GPNodeSet from the specified stream.
load(DataInputStream). Method in class gpjpp.GPObject: Loads a GPObject subclass from the specified stream.
load(DataInputStream). Method in class gpjpp.GPPopulation: Loads a GPPopulation from the specified stream.
load(DataInputStream). Method in class gpjpp.GPRun: Loads a checkpoint file from the specified stream.
load(DataInputStream). Method in class gpjpp.GPVariables: Loads the GPVariables from the specified stream.
load(InputStream). Method in class gpjpp.GPProperties: Loads a property set from an InputStream.
load(Properties). Method in class gpjpp.GPVariables: Loads the values from a Properties container (read from a configuration file) into the GPVariables fields.
loadCheckpoint(). Method in class gpjpp.GPRun: Loads a checkpoint if cfg.CheckpointGens is greater than zero and the checkpoint file is found.
longestLength. Variable in class gpjpp.GPPopulation: The highest complexity found anywhere in the population.

M

MaximumComplexity. Variable in class gpjpp.GPVariables: The largest complexity (number of nodes) allowed in any individual GP, including the main branch and all ADFs.
MaximumDepthForCreation. Variable in class gpjpp.GPVariables: The largest depth allowed for newly created trees.
MaximumDepthForCrossover. Variable in class gpjpp.GPVariables: The largest depth allowed for trees after crossover.
minTreeDepth. Static variable in class gpjpp.GPPopulation: Specifies the minimum tree depth for newly created individuals.
mumCross. Variable in class gpjpp.GP: The s-expression index of this GP's "mum" when it was generated as a result of crossover.
mumIndex. Variable in class gpjpp.GP: The population index of this GP's "mum" when it was generated as a result of crossover.
mutate(GPVariables, GPAdfNodeSet). Method in class gpjpp.GP: Uses the configuration probabilities SwapMutationProbability and ShrinkMutationProbability to determine whether to apply either or both forms of mutation to this GP.

N

newPop. Variable in class gpjpp.GPRun: The secondary population.
nextDouble(). Static method in class gpjpp.GPRandom: Returns a random double uniformly distributed in the range 0.0 to 1.0.
nextInt(int). Static method in class gpjpp.GPRandom: Returns a random integer uniformly distributed in the range 0 to limit-1.
node. Variable in class gpjpp.GPGene: A reference to the node type for this gene.
NODEID. Static variable in class gpjpp.GPObject: An ID code used to identify GPNode references in gpjpp streams.
nodeIndex. Variable in class gpjpp.GPNode: A unique index value used to stream genes efficiently.
NODESETID. Static variable in class gpjpp.GPObject: An ID code used to identify GPNodeSet references in gpjpp streams.
nodeValue. Variable in class gpjpp.GPNode: Indicates a node's purpose to a user fitness evaluation method.
NULLID. Static variable in class gpjpp.GPObject: An ID code used to identify null object references in gpjpp streams.
NumberOfGenerations. Variable in class gpjpp.GPVariables: The maximum number of generations in a run.
numFunctions. Variable in class gpjpp.GPNodeSet: The number of function node types supported by this branch.
numOfArgs. Variable in class gpjpp.GPNode: The number of arguments used by the node, 0 if the node is a terminal instead of a function.
numTerminals. Variable in class gpjpp.GPNodeSet: The number of terminal node types supported by this branch.

O

OBJECTID. Static variable in class gpjpp.GPObject: An ID code used to identify GPObject references in gpjpp streams.
outBufSize. Static variable in class gpjpp.GPRun: The size in bytes of the output buffer used for PrintStreams.
overflow(int). Static method in class gpjpp.GPPopulation: Returns a string of asterisks with specified width.

P

peer. Variable in class gpjpp.GPGenePrint: A reference to the original gene of which the GPGenePrint object is an extended copy.
pop. Variable in class gpjpp.GPRun: The main population, instantiated in GPRun() and reused repeatedly in run().
POPULATIONID. Static variable in class gpjpp.GPObject: An ID code used to identify GPPopulation references in gpjpp streams.
PopulationSize. Variable in class gpjpp.GPVariables: The number of individuals (GP instances) in a population.
prepImage(int, int). Method in class gpjpp.GPDrawing: Prepares an off-screen drawing image of the specified pixel width and height.
prepImage(int, int, int). Method in class gpjpp.GPDrawing: Sets a new font size and prepares an off-screen drawing image.
printConnectors(PrintStream, int, int, double[]). Method in class gpjpp.GPGenePrint: Prints pseudo-graphic connectors between nodes at level depToPrint and nodes at level depToPrint+1.
PrintDetails. Variable in class gpjpp.GPVariables: Determines whether a detail file is generated by GPRun.
printDetails(int, boolean, boolean, boolean, boolean, boolean, PrintStream). Method in class gpjpp.GPPopulation: Prints details about some or all of the population.
PrintExpression. Variable in class gpjpp.GPVariables: Determines whether the detail file shows the s-expression for each selected individual after each generation.
printIndividual(GP, int, boolean, boolean, PrintStream). Method in class gpjpp.GPPopulation: Prints details about a particular individual to the specified PrintStream.
printLevel(PrintStream, int, int, double[]). Method in class gpjpp.GPGenePrint: Prints all nodes at level depToPrint in left-to-right order.
printOn(PrintStream, GPVariables). Method in class gpjpp.GP: Writes a GP in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPAdfNodeSet: Writes a GPAdfNodeSet in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPContainer: Writes a GPContainer in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPGene: Writes a GPGene in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPGenePrint: Computes the x coordinates for all nodes in this gene tree and writes the tree in pseudo-graphic format to the specified PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPNode: Writes a GPNode in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPNodeSet: Writes a GPNodeSet in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPObject: Writes a GPObject subclass in text format to a PrintStream.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPPopulation: Writes every GP in text format to a PrintStream by simply calling GP.printOn() for every individual in the population.
printOn(PrintStream, GPVariables). Method in class gpjpp.GPVariables: Writes the GPVariables fields in the format of a Properties text file.
PrintPopulation. Variable in class gpjpp.GPVariables: Determines whether the detail file includes every individual in the population (PrintPopulation = true) or just the best and worst individuals in the population (PrintPopulation = false).
printStatistics(int, char, PrintStream). Method in class gpjpp.GPPopulation: Prints one generation's statistics to the specified PrintStream.
printStatisticsLegend(PrintStream). Method in class gpjpp.GPPopulation: Prints a legend line for the standard statistics report to the specified PrintStream.
PrintTree. Variable in class gpjpp.GPVariables: Determines whether the statistics file shows a pseudo-graphic tree for the best individual of each run.
printTree(PrintStream, GPVariables). Method in class gpjpp.GP: Writes a GP in text tree format to a PrintStream.
printTree(PrintStream, GPVariables). Method in class gpjpp.GPGene: Writes a GPGene in text tree format to a PrintStream.
probabilisticSelection(int[], int, boolean, GPPopulationRange). Method in class gpjpp.GPPopulation: Selects one or more individuals from the specified range of the population by using a roulette algorithm.
put(int, GPObject). Method in class gpjpp.GPContainer: Stores an object reference at the specified location in the container.
putGene(GPGene). Method in class gpjpp.GPGeneReference: Puts a different gene into the place of this class.
putNode(GPNode). Method in class gpjpp.GPNodeSet: Adds a function or terminal node to a GPNodeSet.

R

r. Static variable in class gpjpp.GPRandom: A static instance of a Random that is used throughout the gpjpp package.
readIni(String, boolean). Method in class gpjpp.GPRun: Reads the specified file to get run configuration variables.
rectMargin. Static variable in class gpjpp.GPGenePrint: The number of pixels separating the node rectangle from the node text that it surrounds in a graphic tree.
registerAllClasses(). Method in class gpjpp.GPRun: Registers with the GPObject stream manager all classes needed for checkpointing.
registerClass(byte, Class). Static method in class gpjpp.GPObject: Registers a single class.
registerClass(GPObject). Static method in class gpjpp.GPObject: Registers the class of the specified object and all of its non-abstract superclasses up to but not including GPObject.
rep(). Method in class gpjpp.GPNode: Returns the string representation of the node.
representation. Variable in class gpjpp.GPNode: The string usually printed by printOn when displaying s-expressions and when drawing graphic tree images.
reserveSpace(int). Method in class gpjpp.GPContainer: Reserves space for the specified number of object references.
rowsPerNode. Static variable in class gpjpp.GPGenePrint: The number of character heights per node level in a graphic tree.
run(). Method in class gpjpp.GPRun: The main method of GPRun creates and evolves populations, writes reports, loads and saves checkpoint files, and does multiple runs until a configurable number of good ones is found.
RUNENDID. Static variable in class gpjpp.GPRun: An ID code written at the end of checkpoint streams.

S

save(DataOutputStream). Method in class gpjpp.GP: Saves a GP to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPContainer: Saves a GPContainer to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPGene: Saves a GPGene to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPGenePrint: Disables the save operation inherited from GPGene, since GPGenePrint does not need to be streamed.
save(DataOutputStream). Method in class gpjpp.GPNode: Saves a GPNode to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPNodeSet: Saves a GPNodeSet to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPObject: Saves a GPObject subclass to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPRun: Saves a checkpoint to the specified stream.
save(DataOutputStream). Method in class gpjpp.GPVariables: Writes the GPVariables to the specified stream.
saveCheckpoint(). Method in class gpjpp.GPRun: Saves a checkpoint to disk if cfg.CheckpointGens is greater than zero and that many generations has passed since the last checkpoint.
searchForNode(int). Method in class gpjpp.GPNodeSet: Returns the GPNode in this set that has the specified node value, or null if none is found.
select(int, GPPopulationRange). Method in class gpjpp.GPPopulation: Returns one or more individuals from the specified range of this population using a fitness-based selection method.
selectIndices(int[], int, boolean, GPPopulationRange). Method in class gpjpp.GPPopulation: Calls one of the available selection methods based on the configuration variable SelectionType.
SelectionStr. Static variable in class gpjpp.GPVariables: An array of strings used to detect and print the selection type in configuration files and status reports.
SelectionType. Variable in class gpjpp.GPVariables: The strategy used to select individuals with a probability related to their fitness.
selectParents(GPPopulationRange). Method in class gpjpp.GPPopulation: Calls select() to select exactly two parents for use in crossover.
setFontSize(int). Method in class gpjpp.GPDrawing: Changes the font size.
setGenerator(Random). Static method in class gpjpp.GPRandom: Sets the static field r to an instance of Random.
setIndex(byte). Method in class gpjpp.GPNode: Sets the node index used for streaming.
shiftX(double). Method in class gpjpp.GPGenePrint: Shifts the x coordinates of all nodes by subtracting dx.
show(). Method in class gpjpp.GPProperties: Writes the contents of the properties to System.out.
showConfiguration(). Method in class gpjpp.GPRun: Prints the configuration variables and the node definitions to sout.
showCreation(boolean). Method in class gpjpp.GPRun: Prints a status message to System.out while the initial population is being created.
showFinalGeneration(int, boolean). Method in class gpjpp.GPRun: Prints information about the final generation of a run.
showGeneration(boolean, int, boolean). Method in class gpjpp.GPRun: Prints information to System.out and to sout about the generation just completed.
showRunNumber(int, int). Method in class gpjpp.GPRun: Prints the current run number and number of good runs so far to System.out, sout, and dout.
showTiming(double, double). Method in class gpjpp.GPRun: Print to System.out and to sout the total elapsed seconds for a run and also the number of seconds to process each generation.
shrinkMutation(). Method in class gpjpp.GP: Mutates this GP by finding a random function gene in a random branch and then replacing that gene by one of its immediate children.
ShrinkMutationProbability. Variable in class gpjpp.GPVariables: Percent probability that shrink mutation will occur for each individual added to a new generation.
shrinkPos. Variable in class gpjpp.GP: The s-expression index used to apply shrink mutation.
shrinkTree. Variable in class gpjpp.GP: The branch number used in shrink mutation when this GP was generated.
sout. Variable in class gpjpp.GPRun: The PrintStream used for statistics and summary reporting.
spaceTo(PrintStream, int, double[], double). Method in class gpjpp.GPGenePrint: Prints spaces until curX[curDepth] equals or exceeds rx.
spreadTerminals(). Method in class gpjpp.GPGenePrint: Spreads terminal nodes so that they are equally spaced within the boundaries of the container.
stdFitness. Variable in class gpjpp.GP: The standardized fitness of the GP.
SteadyState. Variable in class gpjpp.GPVariables: Determines whether each new generation is created in isolation from the previous generation (SteadyState = false) or is created by replacing the weaker individuals one by one (SteadyState = true).
stmBufSize. Static variable in class gpjpp.GPRun: The size in bytes of the input or output buffer used for a DataInputStream or a DataOutputStream during checkpoint loading or saving.
stringWidth(String). Method in class gpjpp.GPDrawing: Returns the pixel width of a text string when displayed in the default font.
sumAdjFitness. Variable in class gpjpp.GPPopulation: The sum of the adjusted fitness over an entire range.
sumFitness. Variable in class gpjpp.GPPopulation: The sum of the standardized fitness over an entire range.
sumFitnessRange(GPPopulationRange). Method in class gpjpp.GPPopulation: Sums the standardized and adjusted fitnesses over a specified range and stores the results in the fields sumFitness and sumAdjFitness.
sumG1AdjFitness. Variable in class gpjpp.GPPopulation: The sum of the adjusted fitness for group I individuals.
sumG2AdjFitness. Variable in class gpjpp.GPPopulation: The sum of the adjusted fitness for group II individuals.
swapMutation(GPAdfNodeSet). Method in class gpjpp.GP: Mutates this GP by finding a random function gene in a random branch and changing the node type of that gene.
SwapMutationProbability. Variable in class gpjpp.GPVariables: Percent probability that swap mutation will occur for each individual added to a new generation.
swapPos. Variable in class gpjpp.GP: The s-expression index used to apply swap mutation.
swapTree. Variable in class gpjpp.GP: The branch number used in swap mutation when this GP was generated.

T

terminals(). Method in class gpjpp.GPNodeSet: Returns the number of terminals in this node set.
TerminationFitness. Variable in class gpjpp.GPVariables: A run terminates if the best individual in any generation has standardized fitness below this level.
TestDiversity. Variable in class gpjpp.GPVariables: Determines whether gpjpp tests the diversity of genetic populations.
testNull(). Method in class gpjpp.GP: A debugging/testing method used to ensure that no null node or gene references are found in this GP.
testNull(). Method in class gpjpp.GPGene: A debugging/testing method to ensure that no null node or gene references are found in this gene or any of its children.
tournamentSelection(int[], int, boolean, GPPopulationRange). Method in class gpjpp.GPPopulation: Selects one or two individuals from the specified range of the population by using a tournament algorithm.
TournamentSize. Variable in class gpjpp.GPVariables: Number of randomly selected individuals forming a "tournament" when SelectionType is GPTOURNAMENTSELECTION.
TreeFontSize. Variable in class gpjpp.GPVariables: The font size in points used to draw the text in graphic trees enabled by PrintTree.
trimFormatDouble(double, int, int). Static method in class gpjpp.GPPopulation: Calls formatDouble to create a formatted string and then strips any leading blanks.

U

uniqueGPs. Variable in class gpjpp.GPPopulation: A table of the unique GPs found in the population.
updateUniqueGPs(GP). Method in class gpjpp.GPPopulation: Adds the specified GP to the diversity table, or increments its count if already in the table.
UseADFs. Variable in class gpjpp.GPVariables: A boolean that can be tested by user functions to determine whether to add ADFs to the branch definition and whether to evaluate them in fitness functions.
USERGENEID. Static variable in class gpjpp.GPObject: An ID code normally used to identify the user subclass of GPGene.
USERGPID. Static variable in class gpjpp.GPObject: An ID code normally used to identify the user subclass of GP.
USERPOPULATIONID. Static variable in class gpjpp.GPObject: An ID code normally used to identify the user subclass of GPPopulation.
USERVARIABLESID. Static variable in class gpjpp.GPObject: An ID code normally used to identify the user subclass of GPVariables.

V

value(). Method in class gpjpp.GPNode: Returns the integer node value.
VARIABLESID. Static variable in class gpjpp.GPObject: An ID code used to identify GPVariables references in gpjpp streams.

W

wBox(GPDrawing, String). Method in class gpjpp.GPGenePrint: Computes the pixel width of the node rectangle given the string to appear within the rectangle.
worstFitness. Variable in class gpjpp.GPPopulation: Worst standardized fitness found in the entire population.
worstOfPopulation. Variable in class gpjpp.GPPopulation: The index of the individual with the worst standardized fitness.
write(int). Method in class gpjpp.GPPrintStream: Detects '\n' and expands it to a full line separator string.
writeEol(). Method in class gpjpp.GPPrintStream: Writes the line separator string to the PrintStream.
writeGif(String). Method in class gpjpp.GPDrawing: Writes the current off-screen image to a gif file.

X

x. Variable in class gpjpp.GPGenePrint: The computed x position of this node, in character units.
xBox(GPDrawing, double). Method in class gpjpp.GPGenePrint: Converts the x coordinate of a node to the corresponding x pixel position for the left edge of the surrounding node rectangle.
xMargin. Static variable in class gpjpp.GPGenePrint: The number of blank columns printed at the left edge of the tree by printOn().
xSpacing. Static variable in class gpjpp.GPGenePrint: The minimum number of columns (character widths) that separate adjacent nodes.
xText(GPDrawing, double). Method in class gpjpp.GPGenePrint: Converts the x coordinate of a node to the corresponding x pixel position for the start of the node text.

Y

yBox(GPDrawing, int). Method in class gpjpp.GPGenePrint: Converts the depth of a node to the corresponding y pixel position for the top edge of the surrounding node rectangle.
yText(GPDrawing, int). Method in class gpjpp.GPGenePrint: Converts the depth of a node to the corresponding y pixel position for the node text.