org.jgap.gp.impl
Class GPConfiguration

java.lang.Object
  org.jgap.Configuration
      org.jgap.gp.impl.GPConfiguration

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable, Configurable, ICloneable

Direct Known Subclasses:

DrawingGPConfiguration

public class GPConfiguration
extends Configuration

Configuration for a GP.

Since:

3.0

See Also:

Serialized Form

Field Summary

Fields inherited from class org.jgap.Configuration

PROPERTY_BFITFNC_INST, PROPERTY_EVENT_MGR_INST, PROPERTY_FITEVAL_INST, PROPERTY_FITFUNC_INST, PROPERTY_JGAPFACTORY_CLASS, PROPERTY_SAMPLE_CHROM_INST, S_CHROMOSOME_SIZE, S_CONFIGURATION, S_CONFIGURATION_HANDLER, S_CONFIGURATION_NAME, S_EVENT_MANAGER, S_FITNESS_EVALUATOR, S_FITNESS_FUNCTION, S_GENETIC_OPERATORS, S_MINPOPSIZE, S_NATURAL_SELECTORS, S_NONE, S_POPULATION_SIZE, S_POST, S_PRE, S_RANDOM_GENERATOR, S_SAMPLE_CHROM, S_SIZE, S_TOSTRING

Constructor Summary

GPConfiguration()
Constructor utilizing the FitnessProportionateSelection.

GPConfiguration(INaturalGPSelector a_selectionMethod)
Constructor utilizing the FitnessProportionateSelection.

GPConfiguration(java.lang.String a_name)
Constructs a configuration with an informative name but without a unique ID.

GPConfiguration(java.lang.String a_id, java.lang.String a_name)

Method Summary

void	addGeneticOperator(GeneticOperator a_operatorToAdd) Adds a genetic operator for use in this algorithm.
void	clearMemory() Clears the memory.
void	clearStack()
java.lang.Object	clone()
int	compareTo(java.lang.Object a_other) The compareTo-method.
void	createMatrix(java.lang.String a_name, int a_cols, int a_rows) Creates an instance of a matrix with a unique name.
boolean	equals(java.lang.Object a_other) Compares this entity against the specified object.
void	flagMaxNodeWarningPrinted() See ProgramChromosome.growOrFull(...) and GPGenotype.evolve().
CrossMethod	getCrossMethod()
double	getCrossoverProb()
double	getDynamizeArityProb()
double	getFunctionProb()
IGPFitnessEvaluator	getGPFitnessEvaluator()
GPFitnessFunction	getGPFitnessFunction()
IGPInitStrategy	getInitStrategy()
IJGAPFactory	getJGAPFactory()
char[][]	getMatrix(java.lang.String a_name) Retrieves a named matrix.
int	getMaxCrossoverDepth()
int	getMaxInitDepth()
int	getMemorySize()
int	getMinInitDepth()
double	getMutationProb()
double	getNewChromsPercent()
INodeValidator	getNodeValidator()
int	getProgramCreationMaxtries()
IGPProgram	getPrototypeProgram()
double	getReproductionProb()
INaturalGPSelector	getSelectionMethod()
Variable	getVariable(java.lang.String a_varName)
protected void	init(boolean a_fullInit) Helper for construction.
boolean	isMaxNodeWarningPrinted()
boolean	isNoCommandGeneCloning()
boolean	isStrictProgramCreation()
boolean	isUseProgramCache()
boolean	isVerifyPrograms()
GPConfiguration	newInstanceGP(java.lang.String a_id, java.lang.String a_name) Creates a new GPConfiguration instance by cloning.
java.lang.Object	peekStack()
java.lang.Object	popFromStack()
void	pushToStack(java.lang.Object a_value)
GPProgramInfo	putToProgramCache(GPProgram a_prog)
void	putVariable(Variable a_var) Stores a Variable.
java.lang.Object	readFromMemory(java.lang.String a_name) Reads a value from the internal memory.
java.lang.Object	readFromMemoryIfExists(java.lang.String a_name)
java.lang.Object	readIndexedMemory(int a_index) Reads a value from the internal indexed memory.
char	readMatrix(java.lang.String a_name, int a_col, int a_row) Reads a matrix cell and returns the value.
java.lang.Object	readMatrixMemory(int a_x, int a_y) Reads a value from the internal matrix memory.
GPProgramInfo	readProgramCache(GPProgram a_prog)
void	resetMatrix(java.lang.String a_name, char a_filler) Resets the matrix by filling it with a given character.
void	setCrossoverMethod(CrossMethod a_method) Sets the crossover method to use.
void	setCrossoverProb(float a_crossoverProb)
void	setDynamizeArityProb(float a_dynArityProb)
void	setFitnessEvaluator(IGPFitnessEvaluator a_fitnessEvaluator) Set the fitness evaluator (deciding if a given fitness value is better when it's higher or better when it's lower).
void	setFitnessFunction(GPFitnessFunction a_functionToSet) Sets the fitness function to be used for this genetic algorithm.
void	setFunctionProb(double a_functionProb)
void	setGPFitnessEvaluator(IGPFitnessEvaluator a_evaluator) Sets a GP fitness evaluator, such as org.jgap.gp.impl.DefaultGPFitnessEvaluator.
void	setInitStrategy(IGPInitStrategy a_strategy)
void	setMatrix(java.lang.String a_name, int a_col, int a_row, char a_value) Sets a matrix field with a value.
void	setMaxCrossoverDepth(int a_maxCrossoverDepth)
void	setMaxInitDepth(int a_maxDepth)
void	setMinInitDepth(int a_minDepth)
void	setMutationProb(float a_mutationProb)
void	setNewChromsPercent(double a_newChromsPercent)
void	setNoCommandGeneCloning(boolean a_noCommandGeneCloning) Decide whether to clone command genes when creating a new GP program in ProgramChromosome.
void	setNodeValidator(INodeValidator a_nodeValidator) Sets the node validator.
void	setProgramCreationMaxTries(int a_maxtries)
void	setPrototypeProgram(IGPProgram a_program)
void	setReproductionProb(float a_reproductionProb)
void	setSelectionMethod(INaturalGPSelector a_method) Sets the selection method to use.
void	setStrictProgramCreation(boolean a_strict)
void	setUseProgramCache(boolean a_useCache)
void	setVerifyPrograms(boolean a_verify)
int	stackSize()
CultureMemoryCell	storeIndexedMemory(int a_index, java.lang.Object a_value) Stores a value in the internal indexed memory.
void	storeInMemory(java.lang.String a_name, java.lang.Object a_value) Stores a value in the internal memory.
CultureMemoryCell	storeMatrixMemory(int a_x, int a_y, java.lang.Object a_value) Stores a value in the internal matrix memory.
boolean	validateNode(ProgramChromosome a_chrom, CommandGene a_node, CommandGene a_rootNode, int a_tries, int a_num, int a_recurseLevel, java.lang.Class a_type, CommandGene[] a_functionSet, int a_depth, boolean a_grow, int a_childIndex, boolean a_fullProgram) Validates a_node in the context of a_chrom.
void	verifyStateIsValid() Tests the state of this Configuration object to make sure it's valid.

Methods inherited from class org.jgap.Configuration

addNaturalSelector, checkProperty, doClone, getBreeder, getBulkFitnessFunction, getChromosomePool, getChromosomeSize, getConfigurationHandler, getEventManager, getFitnessEvaluator, getFitnessFunction, getGenerationNr, getGeneticOperators, getId, getMinimumPopSizePercent, getName, getNaturalSelector, getNaturalSelector, getNaturalSelectors, getNaturalSelectorsSize, getPopulationSize, getRandomGenerator, getSampleChromosome, getSelectFromPrevGen, getThreadKey, incrementGenerationNr, isAlwaysCalculateFitness, isKeepPopulationSizeConstant, isLocked, isPreserveFittestIndividual, lockSettings, makeKey, makeThreadKey, newInstance, removeNaturalSelectors, reset, reset, resetProperty, resetProperty, setAlwaysCaculateFitness, setBreeder, setBulkFitnessFunction, setChromosomePool, setEventManager, setFitnessEvaluator, setFitnessFunction, setId, setJGAPFactory, setKeepPopulationSizeConstant, setMinimumPopSizePercent, setName, setNaturalSelector, setPopulationSize, setPreservFittestIndividual, setRandomGenerator, setSampleChromosome, setSelectFromPrevGen, toString, verifyChangesAllowed

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GPConfiguration

public GPConfiguration()
                throws InvalidConfigurationException

Constructor utilizing the FitnessProportionateSelection.

Throws:

InvalidConfigurationException

Since:

3.0

GPConfiguration

public GPConfiguration(java.lang.String a_id,
                       java.lang.String a_name)
                throws InvalidConfigurationException

Throws:

InvalidConfigurationException

GPConfiguration

public GPConfiguration(java.lang.String a_name)
                throws InvalidConfigurationException

Constructs a configuration with an informative name but without a unique ID. This practically prevents more than one configurations to be instantiated within the same thread.

Parameters:

a_name - informative name of the configuration, may be null

Throws:

InvalidConfigurationException

GPConfiguration

public GPConfiguration(INaturalGPSelector a_selectionMethod)
                throws InvalidConfigurationException

Constructor utilizing the FitnessProportionateSelection.

Parameters:

a_selectionMethod - the selection method to use

Throws:

InvalidConfigurationException

Since:

3.1

Method Detail

setGPFitnessEvaluator

public void setGPFitnessEvaluator(IGPFitnessEvaluator a_evaluator)

Sets a GP fitness evaluator, such as org.jgap.gp.impl.DefaultGPFitnessEvaluator.

Parameters:

a_evaluator - the fitness evaluator to set

Since:

3.1

init

protected void init(boolean a_fullInit)
             throws InvalidConfigurationException

Helper for construction.

Parameters:

a_fullInit - true set event manager, random generator and fitness evaluator to defauklt

Throws:

InvalidConfigurationException

Since:

3.1

setSelectionMethod

public void setSelectionMethod(INaturalGPSelector a_method)

Sets the selection method to use.

Parameters:

a_method - the selection method to use

Since:

3.1

setCrossoverMethod

public void setCrossoverMethod(CrossMethod a_method)

Sets the crossover method to use.

Parameters:

a_method - the crossover method to use

Since:

3.1

verifyStateIsValid

public void verifyStateIsValid()
                        throws InvalidConfigurationException

Description copied from class: Configuration

Tests the state of this Configuration object to make sure it's valid. This generally consists of verifying that required settings have, in fact, been set. If this object is not in a valid state, then an exception will be thrown detailing the reason the state is not valid.

Overrides:

verifyStateIsValid in class Configuration

Throws:

InvalidConfigurationException - if the state of this Configuration is not valid. The error message in the exception will detail the reason for invalidity

addGeneticOperator

public void addGeneticOperator(GeneticOperator a_operatorToAdd)
                        throws InvalidConfigurationException

Description copied from class: Configuration

Adds a genetic operator for use in this algorithm. Genetic operators represent evolutionary steps that, when combined, make up the evolutionary process. Examples of genetic operators are reproduction, crossover, and mutation. During the evolution process, all of the genetic operators added via this method are invoked in the order they were added. At least one genetic operator must be provided.

Overrides:

addGeneticOperator in class Configuration

Parameters:

a_operatorToAdd - the genetic operator to add.

Throws:

InvalidConfigurationException - if the genetic operator is null or if this Configuration object is locked

getCrossoverProb

public double getCrossoverProb()

setCrossoverProb

public void setCrossoverProb(float a_crossoverProb)

getReproductionProb

public double getReproductionProb()

setReproductionProb

public void setReproductionProb(float a_reproductionProb)

getMutationProb

public double getMutationProb()

Returns:

probability for mutation of a node during growing a program

Since:

3.3.1

setMutationProb

public void setMutationProb(float a_mutationProb)

Parameters:

a_mutationProb - probability for mutation of a node during growing a program

Since:

3.3.1

getDynamizeArityProb

public double getDynamizeArityProb()

Returns:

probability for dynamizing the arity of a node during growing a program

Since:

3.4

setDynamizeArityProb

public void setDynamizeArityProb(float a_dynArityProb)

Parameters:

a_dynArityProb - probability for dynamizing the arity of a node during growing a program

Since:

3.4

setFunctionProb

public void setFunctionProb(double a_functionProb)

Parameters:

a_functionProb - probability that a function instead of a terminal is chosen in crossing over (between 0 and 1)

Since:

3.2

getFunctionProb

public double getFunctionProb()

Returns:

probability that a function instead of a terminal is chosen in crossing over

Since:

3.2

setNewChromsPercent

public void setNewChromsPercent(double a_newChromsPercent)

getNewChromsPercent

public double getNewChromsPercent()

getMaxCrossoverDepth

public int getMaxCrossoverDepth()

setMaxCrossoverDepth

public void setMaxCrossoverDepth(int a_maxCrossoverDepth)

getSelectionMethod

public INaturalGPSelector getSelectionMethod()

getCrossMethod

public CrossMethod getCrossMethod()

getMaxInitDepth

public int getMaxInitDepth()

setMaxInitDepth

public void setMaxInitDepth(int a_maxDepth)

getMinInitDepth

public int getMinInitDepth()

setMinInitDepth

public void setMinInitDepth(int a_minDepth)

pushToStack

public void pushToStack(java.lang.Object a_value)

popFromStack

public java.lang.Object popFromStack()

peekStack

public java.lang.Object peekStack()

stackSize

public int stackSize()

clearStack

public void clearStack()

storeInMemory

public void storeInMemory(java.lang.String a_name,
                          java.lang.Object a_value)

Stores a value in the internal memory.

Parameters:

a_name - named index of the memory cell

a_value - the value to store

Since:

3.0

createMatrix

public void createMatrix(java.lang.String a_name,
                         int a_cols,
                         int a_rows)

Creates an instance of a matrix with a unique name.

Parameters:

a_name - the name of the matrix

a_cols - number of columns the matrix should have

a_rows - number of rows the matrix should have

Since:

3.4.3

setMatrix

public void setMatrix(java.lang.String a_name,
                      int a_col,
                      int a_row,
                      char a_value)

Sets a matrix field with a value.

Parameters:

a_name - the name of the matrix

a_col - column in the matrix

a_row - row in the matrix

a_value - the value to set in the matrix at given column and row

Since:

3.4.3

resetMatrix

public void resetMatrix(java.lang.String a_name,
                        char a_filler)

Resets the matrix by filling it with a given character.

Parameters:

a_name - the name of the matrix

a_filler - the character to fill the whole matrix with

Since:

3.4.3

readMatrix

public char readMatrix(java.lang.String a_name,
                       int a_col,
                       int a_row)

Reads a matrix cell and returns the value.

Parameters:

a_name - the name of the matrix

a_col - the column to read

a_row - the row to read

Returns:

the value in the matrix

Since:

3.4.3

getMatrix

public char[][] getMatrix(java.lang.String a_name)

Retrieves a named matrix.

Parameters:

a_name - the name of the matrix

Returns:

the matrix itself

Since:

3.4.3

storeMatrixMemory

public CultureMemoryCell storeMatrixMemory(int a_x,
                                           int a_y,
                                           java.lang.Object a_value)

Stores a value in the internal matrix memory.

Parameters:

a_x - the first coordinate of the matrix (width)

a_y - the second coordinate of the matrix (height)

a_value - the value to store

Returns:

created or used memory cell

Since:

3.2

readMatrixMemory

public java.lang.Object readMatrixMemory(int a_x,
                                         int a_y)

Reads a value from the internal matrix memory.

Parameters:

a_x - the first coordinate of the matrix (width)

a_y - the second coordinate of the matrix (height)

Returns:

read value

Since:

3.2

readFromMemory

public java.lang.Object readFromMemory(java.lang.String a_name)

Reads a value from the internal memory.

Parameters:

a_name - named index of the memory cell to read out

Returns:

read value

Since:

3.0

readFromMemoryIfExists

public java.lang.Object readFromMemoryIfExists(java.lang.String a_name)

Parameters:

a_name - the name of the cell to evaluate

Returns:

the value of a memory cell, if it exsists. Otherwise returns null.

Since:

3.2

storeIndexedMemory

public CultureMemoryCell storeIndexedMemory(int a_index,
                                            java.lang.Object a_value)

Stores a value in the internal indexed memory.

Parameters:

a_index - index of the cell

a_value - the value to store

Returns:

created or used memory cell

Since:

3.2

readIndexedMemory

public java.lang.Object readIndexedMemory(int a_index)

Reads a value from the internal indexed memory.

Parameters:

a_index - index of the cell

Returns:

read value (maybe null )

Since:

3.2

clearMemory

public void clearMemory()

Clears the memory.

Since:

3.0

getGPFitnessFunction

public GPFitnessFunction getGPFitnessFunction()

setFitnessEvaluator

public void setFitnessEvaluator(IGPFitnessEvaluator a_fitnessEvaluator)

Set the fitness evaluator (deciding if a given fitness value is better when it's higher or better when it's lower).

Parameters:

a_fitnessEvaluator - the FitnessEvaluator to be used

Since:

3.3.3

setFitnessFunction

public void setFitnessFunction(GPFitnessFunction a_functionToSet)
                        throws InvalidConfigurationException

Sets the fitness function to be used for this genetic algorithm. The fitness function is responsible for evaluating a given Chromosome and returning a positive integer that represents its worth as a candidate solution. These values are used as a guide by the natural to determine which Chromosome instances will be allowed to move on to the next round of evolution, and which will instead be eliminated.

Parameters:

a_functionToSet - fitness function to be used

Throws:

InvalidConfigurationException - if the fitness function is null, or if this Configuration object is locked.

Since:

1.1

isStrictProgramCreation

public boolean isStrictProgramCreation()

Returns:

true: throw an error during evolution in case a situation is detected where no function or terminal of a required type is declared in the GPConfiguration; false: don't throw an error but try a completely different combination of functions and terminals

setStrictProgramCreation

public void setStrictProgramCreation(boolean a_strict)

Parameters:

a_strict - true: throw an error during evolution in case a situation is detected where no function or terminal of a required type is declared in the GPConfiguration; false: don't throw an error but try a completely different combination of functions and terminals

getProgramCreationMaxtries

public int getProgramCreationMaxtries()

setProgramCreationMaxTries

public void setProgramCreationMaxTries(int a_maxtries)

getGPFitnessEvaluator

public IGPFitnessEvaluator getGPFitnessEvaluator()

Returns:

the fitness evaluator set

Since:

3.0

validateNode

public boolean validateNode(ProgramChromosome a_chrom,
                            CommandGene a_node,
                            CommandGene a_rootNode,
                            int a_tries,
                            int a_num,
                            int a_recurseLevel,
                            java.lang.Class a_type,
                            CommandGene[] a_functionSet,
                            int a_depth,
                            boolean a_grow,
                            int a_childIndex,
                            boolean a_fullProgram)

Validates a_node in the context of a_chrom. Considers the recursion level (a_recursLevel), the type needed (a_type) for the node, the functions available (a_functionSet) and the depth of the whole chromosome needed (a_depth), and whether grow mode is used (a_grow is true) or not.

Parameters:

a_chrom - the chromosome that will contain the node, if valid

a_node - the node selected and to be validated

a_rootNode - root node of the node to be validated (may be null)

a_tries - number of times the validator has been called, useful for stopping by returning true if the number exceeds a limit

a_num - the chromosome's index in the individual of this chromosome

a_recurseLevel - level of recursion

a_type - the return type of the node needed

a_functionSet - the array of available functions

a_depth - the needed depth of the program chromosome

a_grow - true: use grow mode, false: use full mode

a_childIndex - index of the child in the parent node to which it belongs (-1 if node is root node)

a_fullProgram - true: whole program is available in a_chrom

Returns:

true: node is valid; false: node is invalid

Since:

3.0

setNodeValidator

public void setNodeValidator(INodeValidator a_nodeValidator)

Sets the node validator. Also see method validateNode.

Parameters:

a_nodeValidator - sic

Since:

3.0

getNodeValidator

public INodeValidator getNodeValidator()

Returns:

the node validator set

Since:

3.0

equals

public boolean equals(java.lang.Object a_other)

Compares this entity against the specified object.

Overrides:

equals in class Configuration

Parameters:

a_other - the object to compare against

Returns:

true: if the objects are the same, false otherwise

Since:

3.1

compareTo

public int compareTo(java.lang.Object a_other)

Description copied from class: Configuration

The compareTo-method.

Specified by:

compareTo in interface java.lang.Comparable

Overrides:

compareTo in class Configuration

Parameters:

a_other - the other object to compare

Returns:

-1, 0, 1

isMaxNodeWarningPrinted

public boolean isMaxNodeWarningPrinted()

Returns:

see ProgramChromosome.growOrFull(...) and GPGenotype.evolve()

Since:

3.2

flagMaxNodeWarningPrinted

public void flagMaxNodeWarningPrinted()

See ProgramChromosome.growOrFull(...) and GPGenotype.evolve().

Since:

3.2

setPrototypeProgram

public void setPrototypeProgram(IGPProgram a_program)

Parameters:

a_program - IGPProgram

Since:

3.2

getPrototypeProgram

public IGPProgram getPrototypeProgram()

Returns:

prototype program set (maybe null if not setted previously)

Since:

3.2

getMemorySize

public int getMemorySize()

Returns:

capacity of the memory in cells

Since:

3.2

readProgramCache

public GPProgramInfo readProgramCache(GPProgram a_prog)

putToProgramCache

public GPProgramInfo putToProgramCache(GPProgram a_prog)

isUseProgramCache

public boolean isUseProgramCache()

setUseProgramCache

public void setUseProgramCache(boolean a_useCache)

putVariable

public void putVariable(Variable a_var)

Stores a Variable.

Parameters:

a_var - the Variable to store

Since:

3.2

getVariable

public Variable getVariable(java.lang.String a_varName)

Parameters:

a_varName - name of variable to retriebe

Returns:

Variable instance or null, if not found

Since:

3.2

clone

public java.lang.Object clone()

Specified by:

clone in interface ICloneable

Overrides:

clone in class Configuration

Returns:

deep clone of this instance

Since:

3.2

newInstanceGP

public GPConfiguration newInstanceGP(java.lang.String a_id,
                                     java.lang.String a_name)

Creates a new GPConfiguration instance by cloning. Allows to preset the ID and the name.

Parameters:

a_id - new ID for clone

a_name - new name for clone

Returns:

deep clone of this instance

Since:

3.2

getJGAPFactory

public IJGAPFactory getJGAPFactory()

Overrides:

getJGAPFactory in class Configuration

Returns:

the JGAP factory registered

Since:

3.2

setInitStrategy

public void setInitStrategy(IGPInitStrategy a_strategy)

Parameters:

a_strategy - IGPInitStrategy

Since:

3.2.2

getInitStrategy

public IGPInitStrategy getInitStrategy()

Returns:

IGPInitStrategy

Since:

3.2.2

setVerifyPrograms

public void setVerifyPrograms(boolean a_verify)

Parameters:

a_verify - true: verify GP programs for correctness (i.e. is fitness computation possible without exception?)

Since:

3.3.4

isVerifyPrograms

public boolean isVerifyPrograms()

Returns:

true: verify GP programs for correctness (i.e. is fitness computation possible without exception?)

Since:

3.3.4

setNoCommandGeneCloning

public void setNoCommandGeneCloning(boolean a_noCommandGeneCloning)

Decide whether to clone command genes when creating a new GP program in ProgramChromosome.

Parameters:

a_noCommandGeneCloning - boolean

Since:

3.4.3

isNoCommandGeneCloning

public boolean isNoCommandGeneCloning()

Returns:

true: do not clone command genes when creating a new GP program in ProgramChromosome

Since:

3.4.3