org.jgap.gp.impl

Class GPGenotype

java.lang.Object

org.jgap.gp.impl.GPGenotype

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, java.lang.Runnable

public class GPGenotype
extends java.lang.Object
implements java.lang.Runnable, java.io.Serializable, java.lang.Comparable

Genotype for GP Programs.

Since:

3.0

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
GPGenotype() Default constructor.
GPGenotype(GPConfiguration a_configuration, GPPopulation a_population, java.lang.Class[] a_types, java.lang.Class[][] a_argTypes, CommandGene[][] a_nodeSets, int[] a_minDepths, int[] a_maxDepths, int a_maxNodes) Preferred constructor to use, if not using the static method randomInitialGenotype.

Method Summary

Modifier and Type	Method and Description
void	addFittestProgram(IGPProgram a_toAdd) Adds a GP program to this Genotype.
void	calcFitness() Calculates the fitness value of all programs, of the best solution as well as the total fitness (sum of all fitness values).
static void	checkErroneousPop(GPPopulation pop, java.lang.String s)
static void	checkErroneousPop(GPPopulation a_pop, java.lang.String a_s, boolean a_clearFitness)
static void	checkErroneousPop(GPPopulation a_pop, java.lang.String a_s, boolean a_clearFitness, boolean a_active)
static void	checkErroneousProg(IGPProgram prog, java.lang.String s)
static void	checkErroneousProg(IGPProgram a_prog, java.lang.String a_s, boolean a_clearFitness)
static void	checkErroneousProg(IGPProgram a_prog, java.lang.String s, boolean a_clearFitness, boolean a_active)
int	compareTo(java.lang.Object a_other) Compares this Genotype against the specified object.
boolean	equals(java.lang.Object a_other) Compares this entity against the specified object.
void	evolve() Evolve the population by one generation.
void	evolve(int a_evolutions) Evolves the population n times.
void	fillPopulation(int a_num) Fills up the population with random programs if necessary.
IGPProgram	getAllTimeBest()
IGPProgram	getFittestProgram() Retrieves the GPProgram in the population with the highest fitness value.
IGPProgram	getFittestProgramComputed() Retrieves the GPProgram in the population with the highest fitness value.
GPConfiguration	getGPConfiguration()
GPPopulation	getGPPopulation()
static GPConfiguration	getStaticGPConfiguration()
double	getTotalFitness()
Variable	getVariable(java.lang.String a_varName)
int	hashCode() Hashcode function for the genotype, tries to create a unique hashcode for the chromosomes within the population.
void	outputSolution(IGPProgram a_best) Outputs the best solution until now.
void	putVariable(Variable a_var) Stores a Variable.
static GPGenotype	randomInitialGenotype(GPConfiguration a_conf, java.lang.Class[] a_types, java.lang.Class[][] a_argTypes, CommandGene[][] a_nodeSets, int[] a_minDepths, int[] a_maxDepths, int a_maxNodes, boolean a_verboseOutput) Creates a genotype with initial population for the world set.
static GPGenotype	randomInitialGenotype(GPConfiguration a_conf, java.lang.Class[] a_types, java.lang.Class[][] a_argTypes, CommandGene[][] a_nodeSets, int[] a_minDepths, int[] a_maxDepths, int a_maxNodes, boolean[] a_fullModeAllowed, boolean a_verboseOutput) Creates a genotype with a randomly created initial population.
static GPGenotype	randomInitialGenotype(GPConfiguration a_conf, java.lang.Class[] a_types, java.lang.Class[][] a_argTypes, CommandGene[][] a_nodeSets, int[] a_minDepths, int[] a_maxDepths, int a_maxNodes, boolean[] a_fullModeAllowed, boolean a_verboseOutput, IPopulationCreator a_popCreator) Allows to use a custom mechanism for population creation.
static GPGenotype	randomInitialGenotype(GPConfiguration a_conf, java.lang.Class[] a_types, java.lang.Class[][] a_argTypes, CommandGene[][] a_nodeSets, int a_maxNodes, boolean a_verboseOutput) Creates a genotype with initial population for the world set.
void	run() Default implementation of method to run GPGenotype as a thread.
void	setGPConfiguration(GPConfiguration a_configuration) Sets the configuration to use with the Genetic Algorithm.
static void	setStaticGPConfiguration(GPConfiguration a_configuration) Sets the static configuration to use with the Genetic Programming.
void	setVerboseOutput(boolean a_verbose)
static java.util.Map<java.lang.String,CommandGene>	verifyChildNodes(GPConfiguration a_conf, java.lang.Class[] a_types, CommandGene[][] a_nodeSets)
static java.util.Map<CommandGene,int[]>	verifyDepthsForNodes(GPConfiguration a_conf, java.lang.Class[] a_types, int[] a_minDepths, int[] a_maxDepths, int a_maxNodes, CommandGene[][] a_nodeSets)

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GPGenotype

public GPGenotype()
           throws InvalidConfigurationException

Default constructor. Ony use with dynamic instantiation.

Throws:

InvalidConfigurationException

Since:

3.0

GPGenotype

public GPGenotype(GPConfiguration a_configuration,
                  GPPopulation a_population,
                  java.lang.Class[] a_types,
                  java.lang.Class[][] a_argTypes,
                  CommandGene[][] a_nodeSets,
                  int[] a_minDepths,
                  int[] a_maxDepths,
                  int a_maxNodes)
           throws InvalidConfigurationException

Preferred constructor to use, if not using the static method randomInitialGenotype.

Parameters:

a_configuration - the configuration to use

a_population - the initialized population to use

a_types - the type for each chromosome, the length of the array represents the number of chromosomes

a_argTypes - the types of the arguments to each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of arguments to the chromosome

a_nodeSets - the nodes which are allowed to be used by each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of nodes

a_minDepths - contains the minimum depth allowed for each chromosome

a_maxDepths - contains the maximum depth allowed for each chromosome

a_maxNodes - reserve space for a_maxNodes number of nodes

Throws:

InvalidConfigurationException

Since:

3.0

Method Detail

randomInitialGenotype

public static GPGenotype randomInitialGenotype(GPConfiguration a_conf,
                                               java.lang.Class[] a_types,
                                               java.lang.Class[][] a_argTypes,
                                               CommandGene[][] a_nodeSets,
                                               int a_maxNodes,
                                               boolean a_verboseOutput)
                                        throws InvalidConfigurationException

Creates a genotype with initial population for the world set.

Parameters:

a_conf - the configuration to use

a_types - the type of each chromosome, the length is the number of chromosomes

a_argTypes - the types of the arguments to each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of arguments to the chromosome

a_nodeSets - the nodes which are allowed to be used by each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of nodes. Note that it is not necessary to include the arguments of a chromosome as terminals in the chromosome's node set. This is done automatically

a_maxNodes - reserve space for a_maxNodes number of nodes

a_verboseOutput - true: output status information to console

Returns:

created genotype with initialized population

Throws:

InvalidConfigurationException

Since:

3.0

randomInitialGenotype

public static GPGenotype randomInitialGenotype(GPConfiguration a_conf,
                                               java.lang.Class[] a_types,
                                               java.lang.Class[][] a_argTypes,
                                               CommandGene[][] a_nodeSets,
                                               int[] a_minDepths,
                                               int[] a_maxDepths,
                                               int a_maxNodes,
                                               boolean a_verboseOutput)
                                        throws InvalidConfigurationException

Creates a genotype with initial population for the world set.

Parameters:

a_conf - the configuration to use

a_types - the type of each chromosome, the length is the number of chromosomes

a_argTypes - the types of the arguments to each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of arguments to the chromosome

a_nodeSets - the nodes which are allowed to be used by each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of nodes. Note that it is not necessary to include the arguments of a chromosome as terminals in the chromosome's node set. This is done automatically

a_minDepths - array of minimum depths to use: for each chromosome one entry

a_maxDepths - array of maximum depths to use: for each chromosome one entry

a_maxNodes - reserve space for a_maxNodes number of nodes

a_verboseOutput - true: output status information to console

Returns:

created genotype with initialized population

Throws:

InvalidConfigurationException

Since:

3.0

randomInitialGenotype

public static GPGenotype randomInitialGenotype(GPConfiguration a_conf,
                                               java.lang.Class[] a_types,
                                               java.lang.Class[][] a_argTypes,
                                               CommandGene[][] a_nodeSets,
                                               int[] a_minDepths,
                                               int[] a_maxDepths,
                                               int a_maxNodes,
                                               boolean[] a_fullModeAllowed,
                                               boolean a_verboseOutput)
                                        throws InvalidConfigurationException

Creates a genotype with a randomly created initial population.

Parameters:

a_conf - the configuration to use

a_types - the type of each chromosome, the length is the number of chromosomes

a_argTypes - the types of the arguments to each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of arguments to the chromosome

a_nodeSets - the nodes which are allowed to be used by each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of nodes. Note that it is not necessary to include the arguments of a chromosome as terminals in the chromosome's node set. This is done automatically

a_minDepths - array of minimum depths to use: for each chromosome one entry

a_maxDepths - array of maximum depths to use: for each chromosome one entry

a_maxNodes - reserve space for a_maxNodes number of nodes

a_fullModeAllowed - array of boolean values. For each chromosome there is one value indicating whether the full mode for creating chromosome generations during evolution is allowed (true) or not (false)

a_verboseOutput - true: output status information to console

Returns:

created genotype with initialized population

Throws:

InvalidConfigurationException

Since:

3.0

randomInitialGenotype

public static GPGenotype randomInitialGenotype(GPConfiguration a_conf,
                                               java.lang.Class[] a_types,
                                               java.lang.Class[][] a_argTypes,
                                               CommandGene[][] a_nodeSets,
                                               int[] a_minDepths,
                                               int[] a_maxDepths,
                                               int a_maxNodes,
                                               boolean[] a_fullModeAllowed,
                                               boolean a_verboseOutput,
                                               IPopulationCreator a_popCreator)
                                        throws InvalidConfigurationException

Allows to use a custom mechanism for population creation.

Parameters:

a_conf - the configuration to use

a_types - the type of each chromosome, the length is the number of chromosomes

a_argTypes - the types of the arguments to each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of arguments to the chromosome

a_nodeSets - the nodes which are allowed to be used by each chromosome, must be an array of arrays, the first dimension of which is the number of chromosomes and the second dimension of which is the number of nodes. Note that it is not necessary to include the arguments of a chromosome as terminals in the chromosome's node set. This is done automatically

a_minDepths - array of minimum depths to use: for each chromosome one entry

a_maxDepths - array of maximum depths to use: for each chromosome one entry

a_maxNodes - reserve space for a_maxNodes number of nodes

a_fullModeAllowed - array of boolean values. For each chromosome there is one value indicating whether the full mode for creating chromosome generations during evolution is allowed (true) or not (false)

a_verboseOutput - true: output status information to console

a_popCreator - mechanism fior creating the population

Returns:

GPGenotype

Throws:

InvalidConfigurationException

Since:

3.2.2

getGPConfiguration

public GPConfiguration getGPConfiguration()

getStaticGPConfiguration

public static GPConfiguration getStaticGPConfiguration()

Returns:

the static configuration to use with Genetic Programming

Since:

3.2

setStaticGPConfiguration

public static void setStaticGPConfiguration(GPConfiguration a_configuration)

Sets the static configuration to use with the Genetic Programming.

Parameters:

a_configuration - the static configuration to use

Since:

3.2

evolve

public void evolve(int a_evolutions)

Evolves the population n times.

Parameters:

a_evolutions - number of evolution

Since:

3.0

calcFitness

public void calcFitness()

Calculates the fitness value of all programs, of the best solution as well as the total fitness (sum of all fitness values).

Since:

3.0

getAllTimeBest

public IGPProgram getAllTimeBest()

Returns:

the all-time best solution found

Since:

3.0

outputSolution

public void outputSolution(IGPProgram a_best)

Outputs the best solution until now.

Parameters:

a_best - the fittest ProgramChromosome

Since:

3.0

evolve

public void evolve()

Evolve the population by one generation. Probabilistically reproduces and crosses individuals into a new population which then overwrites the original population.

Since:

3.0

getGPPopulation

public GPPopulation getGPPopulation()

getTotalFitness

public double getTotalFitness()

Returns:

the total fitness, that is the fitness over all chromosomes

Since:

3.0

run

public void run()

Default implementation of method to run GPGenotype as a thread.

Specified by:

run in interface java.lang.Runnable

Since:

3.0

getFittestProgram

public IGPProgram getFittestProgram()

Retrieves the GPProgram in the population with the highest fitness value.

Returns:

the GPProgram with the highest fitness value, or null if there are no programs in this Genotype

Since:

3.0

getFittestProgramComputed

public IGPProgram getFittestProgramComputed()

Retrieves the GPProgram in the population with the highest fitness value. Only considers programs for which the fitness value has already been computed.

Returns:

the GPProgram with the highest fitness value, or null if there are no programs with known fitness value in this Genotype

Since:

3.2

setGPConfiguration

public void setGPConfiguration(GPConfiguration a_configuration)

Sets the configuration to use with the Genetic Algorithm.

Parameters:

a_configuration - the configuration to use

Since:

3.0

equals

public boolean equals(java.lang.Object a_other)

Compares this entity against the specified object.

Overrides:

equals in class java.lang.Object

Parameters:

a_other - the object to compare against

Returns:

true: if the objects are the same, false otherwise

Since:

3.0

compareTo

public int compareTo(java.lang.Object a_other)

Compares this Genotype against the specified object. The result is true if the argument is an instance of the Genotype class, has exactly the same number of programs as the given Genotype, and, for each GPProgram in this Genotype, there is an equal program in the given Genotype. The programs do not need to appear in the same order within the populations.

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

a_other - the object to compare against

Returns:

a negative number if this genotype is "less than" the given genotype, zero if they are equal to each other, and a positive number if this genotype is "greater than" the given genotype

Since:

3.0

hashCode

public int hashCode()

Hashcode function for the genotype, tries to create a unique hashcode for the chromosomes within the population. The logic for the hashcode is Step Result ---- ------ 1 31*0 + hashcode_0 = y(1) 2 31*y(1) + hashcode_1 = y(2) 3 31*y(2) + hashcode_2 = y(3) n 31*y(n-1) + hashcode_n-1 = y(n) Each hashcode is a number and the binary equivalent is computed and returned.

Overrides:

hashCode in class java.lang.Object

Returns:

the computed hashcode

Since:

3.0

setVerboseOutput

public void setVerboseOutput(boolean a_verbose)

Parameters:

a_verbose - true: output status information to console

Since:

3.0

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

addFittestProgram

public void addFittestProgram(IGPProgram a_toAdd)

Adds a GP program to this Genotype. Does nothing when given null. The injection is actually executed in method create(..) of GPPopulation.

Parameters:

a_toAdd - the program to add

Since:

3.2

fillPopulation

public void fillPopulation(int a_num)
                    throws InvalidConfigurationException

Fills up the population with random programs if necessary.

Parameters:

a_num - the number of programs to add

Throws:

InvalidConfigurationException

Since:

3.2

checkErroneousPop

public static void checkErroneousPop(GPPopulation pop,
                                     java.lang.String s)

checkErroneousPop

public static void checkErroneousPop(GPPopulation a_pop,
                                     java.lang.String a_s,
                                     boolean a_clearFitness)

checkErroneousPop

public static void checkErroneousPop(GPPopulation a_pop,
                                     java.lang.String a_s,
                                     boolean a_clearFitness,
                                     boolean a_active)

checkErroneousProg

public static void checkErroneousProg(IGPProgram prog,
                                      java.lang.String s)

checkErroneousProg

public static void checkErroneousProg(IGPProgram a_prog,
                                      java.lang.String a_s,
                                      boolean a_clearFitness)

checkErroneousProg

public static void checkErroneousProg(IGPProgram a_prog,
                                      java.lang.String s,
                                      boolean a_clearFitness,
                                      boolean a_active)

verifyChildNodes

public static java.util.Map<java.lang.String,CommandGene> verifyChildNodes(GPConfiguration a_conf,
                                                                           java.lang.Class[] a_types,
                                                                           CommandGene[][] a_nodeSets)

Parameters:

a_conf - GPConfiguration

a_types - Class[]

a_nodeSets - CommandGene[][]

Returns:

Map

Since:

3.4.4

verifyDepthsForNodes

public static java.util.Map<CommandGene,int[]> verifyDepthsForNodes(GPConfiguration a_conf,
                                                                    java.lang.Class[] a_types,
                                                                    int[] a_minDepths,
                                                                    int[] a_maxDepths,
                                                                    int a_maxNodes,
                                                                    CommandGene[][] a_nodeSets)