org.jgap.gp.impl
Class ProgramChromosome

java.lang.Object
  org.jgap.gp.BaseGPChromosome
      org.jgap.gp.impl.ProgramChromosome

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable, IGPChromosome, IBusinessKey

public class ProgramChromosome
extends BaseGPChromosome
implements java.lang.Comparable, java.lang.Cloneable, IBusinessKey

Chromosome representing a single GP Program.

Since:

3.0

See Also:

Serialized Form

Constructor Summary

ProgramChromosome()
Default constructor.

ProgramChromosome(GPConfiguration a_conf)

ProgramChromosome(GPConfiguration a_conf, CommandGene[] a_initialGenes)

ProgramChromosome(GPConfiguration a_conf, int a_size)

ProgramChromosome(GPConfiguration a_conf, int a_size, CommandGene[] a_functionSet, java.lang.Class[] a_argTypes, IGPProgram a_ind)

ProgramChromosome(GPConfiguration a_conf, int a_size, IGPProgram a_ind)

Method Summary

void	cleanup() Clean up the chromosome.
java.lang.Object	clone()
int	compareTo(java.lang.Object a_other) Compares the given chromosome to this chromosome.
boolean	contains(CommandGene[] a_functionSet, java.lang.Class a_function) Checks if a function or terminal of the class of the given instance exists within a_functionSet
boolean	contains(CommandGene[] a_functionSet, CommandGene a_function) Checks if a function or terminal of the class of the given instance exists within a_functionSet
int	contains(CommandGene[] a_functionSet, CommandGene a_function, int a_limit) Checks if a function or terminal of the class of the given instance exists within a_functionSet at least a_limit times
protected CommandGene	createGene(java.lang.String a_geneClassName, java.lang.String a_persistentRepresentation) Creates a new instance of gene.
protected java.lang.String	decode(java.lang.String a_string)
protected java.lang.String	encode(java.lang.String a_string)
boolean	equals(java.lang.Object a_other) Compares this chromosome against the specified object.
boolean	execute_boolean(int n, int child, java.lang.Object[] args) Executes this node as a boolean.
boolean	execute_boolean(java.lang.Object[] args) Executes this node as a boolean.
double	execute_double(int n, int child, java.lang.Object[] args)
double	execute_double(java.lang.Object[] args) Executes this node as a double.
float	execute_float(int n, int child, java.lang.Object[] args)
float	execute_float(java.lang.Object[] args) Executes this node as a float.
int	execute_int(int n, int child, java.lang.Object[] args)
int	execute_int(java.lang.Object[] args) Executes this node as an integer.
long	execute_long(int n, int child, java.lang.Object[] args)
long	execute_long(java.lang.Object[] args) Executes this node as a long.
java.lang.Object	execute_object(int n, int child, java.lang.Object[] args)
java.lang.Object	execute_object(java.lang.Object[] args) Executes this node as an object.
void	execute_void(int n, int child, java.lang.Object[] args)
void	execute_void(java.lang.Object[] args) Executes this node, returning nothing.
java.lang.Object	execute(int n, int child, java.lang.Object[] args)
java.lang.Object	execute(java.lang.Object[] args) Executes this node without knowing its return type.
java.lang.Object	getApplicationData() Retrieves the application-specific data that is attached to this Chromosome.
java.lang.Class[]	getArgTypes()
int	getArity()
java.lang.String	getBusinessKey()
int	getChild(CommandGene a_node, int a_child)
int	getChild(int a_index, int a_child) Gets the a_child'th child of the a_index'th node in this chromosome.
int	getDepth(int a_index) Gets the depth of the branch starting at the a_index'th node.
CommandGene[]	getFunctions()
CommandGene[]	getFunctionSet()
CommandGene	getGene(int a_locus) Returns the Gene at the given index (locus) within the Chromosome.
CommandGene	getNode(java.lang.Class a_type, boolean a_exactMatch) Checks whether a node with a given type is contained in the program.
CommandGene	getNode(java.lang.Class a_type, boolean a_exactMatch, int a_startIndex)
int	getParentNode(int a_child) Gets the node which is the parent of the given node in this chromosome.
java.lang.String	getPersistentRepresentation()
int	getSize(int a_index) Gets the number of nodes in the branch starting at the a_index'th node.
void	growOrFull(int a_num, int a_depth, java.lang.Class a_type, java.lang.Class[] a_argTypes, CommandGene[] a_functionSet, boolean a_grow, int a_tries) Initialize this chromosome using the grow or the full method.
protected CommandGene[]	growOrFullNode(int a_num, int a_depth, java.lang.Class a_returnType, int a_subReturnType, CommandGene[] a_functionSet, CommandGene a_rootNode, int a_recurseLevel, boolean a_grow, int a_childNum, boolean a_validateNode) Create a tree of nodes using the grow or the full method.
boolean	isCompareApplicationData()
boolean	isPossible(java.lang.Class a_returnType, int a_subReturnType, CommandGene[] a_nodeSet, boolean a_function, boolean a_growing) Determines whether there exists a function or terminal in the given node set with the given return and sub return type.
void	redepth() Recalculate the depth of each node.
protected int	redepth(int a_index) Calculate the depth of the next node and the indices of the children of the current node.
protected CommandGene	selectNode(int a_chromIndex, java.lang.Class a_returnType, int a_subReturnType, CommandGene[] a_functionSet, boolean a_function, boolean a_growing) Randomly chooses a valid node from the functions set.
void	setArgTypes(java.lang.Class[] a_argTypes)
void	setCompareApplicationData(boolean a_doCompare) Should we also consider the application data when comparing?
void	setFunctions(CommandGene[] a_functions)
void	setFunctionSet(CommandGene[] a_functionSet)
void	setGene(int index, CommandGene a_gene)
void	setValueFromPersistentRepresentation(java.lang.String a_representation)
int	size()
protected static java.util.List	split(java.lang.String a_string) Splits a_string into individual gene representations.
java.lang.String	toString(int a_startNode) Output program in left-hand notion (e.g.: "+ X Y" for "X + Y").
java.lang.String	toStringDebug()
java.lang.String	toStringNorm(int a_startNode) Output program in "natural" notion (e.g.: "X + Y" for "X + Y").

Methods inherited from class org.jgap.gp.BaseGPChromosome

getAssignableFromClass, getCommandOfClass, getFunction, getFunction, getGPConfiguration, getIndividual, getNode, getTerminal, getTerminal, getVariableWithReturnType, numFunctions, numFunctions, numTerminals, numTerminals, setIndividual

Methods inherited from class java.lang.Object

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

Constructor Detail

ProgramChromosome

public ProgramChromosome(GPConfiguration a_conf,
                         int a_size)
                  throws InvalidConfigurationException

Throws:

InvalidConfigurationException

ProgramChromosome

public ProgramChromosome(GPConfiguration a_conf,
                         int a_size,
                         IGPProgram a_ind)
                  throws InvalidConfigurationException

Throws:

InvalidConfigurationException

ProgramChromosome

public ProgramChromosome(GPConfiguration a_conf,
                         int a_size,
                         CommandGene[] a_functionSet,
                         java.lang.Class[] a_argTypes,
                         IGPProgram a_ind)
                  throws InvalidConfigurationException

Throws:

InvalidConfigurationException

ProgramChromosome

public ProgramChromosome(GPConfiguration a_conf,
                         CommandGene[] a_initialGenes)
                  throws InvalidConfigurationException

Throws:

InvalidConfigurationException

ProgramChromosome

public ProgramChromosome(GPConfiguration a_conf)
                  throws InvalidConfigurationException

Throws:

InvalidConfigurationException

ProgramChromosome

public ProgramChromosome()
                  throws InvalidConfigurationException

Default constructor. Only use for dynamic instantiation.

Throws:

InvalidConfigurationException

Since:

3.0

Method Detail

setArgTypes

public void setArgTypes(java.lang.Class[] a_argTypes)

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

cleanup

public void cleanup()

Clean up the chromosome.

Specified by:

cleanup in interface IGPChromosome

Since:

3.0

growOrFull

public void growOrFull(int a_num,
                       int a_depth,
                       java.lang.Class a_type,
                       java.lang.Class[] a_argTypes,
                       CommandGene[] a_functionSet,
                       boolean a_grow,
                       int a_tries)

Initialize this chromosome using the grow or the full method.

Parameters:

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

a_depth - the maximum depth of the chromosome to create

a_type - the type of the chromosome to create

a_argTypes - the array of argument types for this chromosome

a_functionSet - the set of nodes valid to pick from

a_grow - true: use grow method; false: use full method

a_tries - maximum number of tries for creating a valid program

Since:

3.0

toString

public java.lang.String toString(int a_startNode)

Output program in left-hand notion (e.g.: "+ X Y" for "X + Y").

Parameters:

a_startNode - node to start with

Returns:

output in left-hand notion

Since:

3.0

toStringNorm

public java.lang.String toStringNorm(int a_startNode)

Output program in "natural" notion (e.g.: "X + Y" for "X + Y").

Specified by:

toStringNorm in interface IGPChromosome

Parameters:

a_startNode - the node to start with, e.g. 0 for a complete dump of the program

Returns:

output in normalized notion

Since:

3.0

getBusinessKey

public java.lang.String getBusinessKey()

Specified by:

getBusinessKey in interface IBusinessKey

Returns:

business key of the chromosome

Since:

3.4

toStringDebug

public java.lang.String toStringDebug()

Returns:

debug representation of progrm chromosome, containing class names of all children

Since:

3.4

isPossible

public boolean isPossible(java.lang.Class a_returnType,
                          int a_subReturnType,
                          CommandGene[] a_nodeSet,
                          boolean a_function,
                          boolean a_growing)

Determines whether there exists a function or terminal in the given node set with the given return and sub return type.

Parameters:

a_returnType - the return type to look for

a_subReturnType - the sub return type to look for

a_nodeSet - the array of nodes to look through

a_function - true to look for a function, false to look for a terminal

a_growing - true: grow mode, false: full mode

Returns:

true if such a node exists, false otherwise

Since:

3.0

selectNode

protected CommandGene selectNode(int a_chromIndex,
                                 java.lang.Class a_returnType,
                                 int a_subReturnType,
                                 CommandGene[] a_functionSet,
                                 boolean a_function,
                                 boolean a_growing)

Randomly chooses a valid node from the functions set.

Parameters:

a_chromIndex - index of the chromosome in the individual (0..n-1)

a_returnType - the return type of node to choose

a_subReturnType - the sub return type to look for

a_functionSet - the functions to use

a_function - true to choose a function, false to choose a terminal

a_growing - true to ignore the function parameter, false otherwise

Returns:

the node chosen

Since:

3.0

growOrFullNode

protected CommandGene[] growOrFullNode(int a_num,
                                       int a_depth,
                                       java.lang.Class a_returnType,
                                       int a_subReturnType,
                                       CommandGene[] a_functionSet,
                                       CommandGene a_rootNode,
                                       int a_recurseLevel,
                                       boolean a_grow,
                                       int a_childNum,
                                       boolean a_validateNode)

Create a tree of nodes using the grow or the full method.

Parameters:

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

a_depth - the maximum depth of the tree to create

a_returnType - the return type the lastly evaluated node must have

a_subReturnType - the sub return type to look for

a_functionSet - the set of function valid to pick from

a_rootNode - null, or parent node of the node to develop

a_recurseLevel - 0 for first call

a_grow - true: use grow method; false: use full method

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

a_validateNode - true: check if node selected is valid (when called recursively a_validateNode is set to true)

Returns:

possible modified set of functions (e.g. to avoid having a unique command more than once)

Since:

3.0

redepth

public void redepth()

Recalculate the depth of each node.

Specified by:

redepth in interface IGPChromosome

Since:

3.0

redepth

protected int redepth(int a_index)

Calculate the depth of the next node and the indices of the children of the current node. The depth of the next node is just one plus the depth of the current node. The index of the first child is always the next node. The index of the second child is found by recursively calling this method on the tree starting with the first child.

Parameters:

a_index - the index of the reference depth

Returns:

the index of the next node of the same depth as the current node (i.e. the next sibling node)

Since:

3.0

getChild

public int getChild(int a_index,
                    int a_child)

Gets the a_child'th child of the a_index'th node in this chromosome. This is the same as the a_child'th node whose depth is one more than the depth of the a_index'th node.

Specified by:

getChild in interface IGPChromosome

Parameters:

a_index - the node number of the parent

a_child - the child number (starting from 0) of the parent

Returns:

the node number of the child, or -1 if not found

Since:

3.01

getChild

public int getChild(CommandGene a_node,
                    int a_child)

getFunctionSet

public CommandGene[] getFunctionSet()

Specified by:

getFunctionSet in interface IGPChromosome

Returns:

set of CommandGene instances allowed

setFunctionSet

public void setFunctionSet(CommandGene[] a_functionSet)

getFunctions

public CommandGene[] getFunctions()

Specified by:

getFunctions in interface IGPChromosome

setFunctions

public void setFunctions(CommandGene[] a_functions)
                  throws InvalidConfigurationException

Throws:

InvalidConfigurationException

getSize

public int getSize(int a_index)

Gets the number of nodes in the branch starting at the a_index'th node.

Parameters:

a_index - the index of the node at which to start counting

Returns:

the number of nodes in the branch starting at the a_index'th node

Since:

3.0

getDepth

public int getDepth(int a_index)

Gets the depth of the branch starting at the a_index'th node.

Parameters:

a_index - the index of the node at which to check the depth

Returns:

the depth of the branch starting at the a_index'th node

Since:

3.0

getParentNode

public int getParentNode(int a_child)

Gets the node which is the parent of the given node in this chromosome. If the child is at depth d then the parent is the first function at depth d-1 when iterating backwards through the function list starting from the child.

Parameters:

a_child - the child node

Returns:

the parent node, or null if the child is the root node

Since:

3.0

getNode

public CommandGene getNode(java.lang.Class a_type,
                           boolean a_exactMatch)

Checks whether a node with a given type is contained in the program.

Parameters:

a_type - the type to look for

a_exactMatch - true: look for exactly the given type: false: also look for sub types

Returns:

true specific node found

Since:

3.2.1

getNode

public CommandGene getNode(java.lang.Class a_type,
                           boolean a_exactMatch,
                           int a_startIndex)

execute_boolean

public boolean execute_boolean(java.lang.Object[] args)

Executes this node as a boolean.

Parameters:

args - the arguments for execution

Returns:

the boolean return value of this node

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not boolean

Since:

3.0

execute_boolean

public boolean execute_boolean(int n,
                               int child,
                               java.lang.Object[] args)

Executes this node as a boolean.

Parameters:

n - the index of the parent node

child - the child number of the node to execute

args - the arguments for execution

Returns:

the boolean return value of this node

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not boolean

Since:

3.0

execute_void

public void execute_void(java.lang.Object[] args)

Executes this node, returning nothing.

Parameters:

args - the arguments for execution

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not void

Since:

3.0

execute_void

public void execute_void(int n,
                         int child,
                         java.lang.Object[] args)

execute_int

public int execute_int(java.lang.Object[] args)

Executes this node as an integer.

Parameters:

args - the arguments for execution

Returns:

the integer return value of this node

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not integer

Since:

3.0

execute_int

public int execute_int(int n,
                       int child,
                       java.lang.Object[] args)

execute_long

public long execute_long(java.lang.Object[] args)

Executes this node as a long.

Parameters:

args - the arguments for execution

Returns:

the long return value of this node

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not long

Since:

3.0

execute_long

public long execute_long(int n,
                         int child,
                         java.lang.Object[] args)

execute_float

public float execute_float(java.lang.Object[] args)

Executes this node as a float.

Parameters:

args - the arguments for execution

Returns:

the float return value of this node

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not float

Since:

3.0

execute_float

public float execute_float(int n,
                           int child,
                           java.lang.Object[] args)

execute_double

public double execute_double(java.lang.Object[] args)

Executes this node as a double.

Parameters:

args - the arguments for execution

Returns:

the double return value of this node

Throws:

java.lang.UnsupportedOperationException - if this node's type is not double

Since:

3.0

execute_double

public double execute_double(int n,
                             int child,
                             java.lang.Object[] args)

execute_object

public java.lang.Object execute_object(java.lang.Object[] args)

Executes this node as an object.

Parameters:

args - the arguments for execution

Returns:

the object return value of this node

Throws:

java.lang.UnsupportedOperationException - if the type of this node is not of type Object

Since:

3.0

execute_object

public java.lang.Object execute_object(int n,
                                       int child,
                                       java.lang.Object[] args)

execute

public java.lang.Object execute(java.lang.Object[] args)

Executes this node without knowing its return type.

Parameters:

args - the arguments for execution

Returns:

the Object which wraps the return value of this node, or null if the return type is null or unknown

Since:

3.0

execute

public java.lang.Object execute(int n,
                                int child,
                                java.lang.Object[] args)

setGene

public void setGene(int index,
                    CommandGene a_gene)

getArgTypes

public java.lang.Class[] getArgTypes()

getArity

public int getArity()

size

public int size()

Returns:

number of functions and terminals present

Since:

3.0

compareTo

public int compareTo(java.lang.Object a_other)

Compares the given chromosome to this chromosome. This chromosome is considered to be "less than" the given chromosome if it has a fewer number of genes or if any of its gene values (alleles) are less than their corresponding gene values in the other chromosome.

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

a_other - the chromosome against which to compare this chromosome

Returns:

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

Since:

3.0

equals

public boolean equals(java.lang.Object a_other)

Compares this chromosome 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

setCompareApplicationData

public void setCompareApplicationData(boolean a_doCompare)

Should we also consider the application data when comparing? Default is "false" as "true" means a Chromosome is losing its identity when application data is set differently!

Parameters:

a_doCompare - true: consider application data in method compareTo

Since:

3.0

isCompareApplicationData

public boolean isCompareApplicationData()

getApplicationData

public java.lang.Object getApplicationData()

Retrieves the application-specific data that is attached to this Chromosome. Attaching application-specific data may be useful for some applications when it comes time to evaluate this Chromosome in the fitness function. JGAP ignores this data functionally.

Returns:

the application-specific data previously attached to this Chromosome, or null if there is no data attached

Since:

3.0

getGene

public CommandGene getGene(int a_locus)

Returns the Gene at the given index (locus) within the Chromosome. The first gene is at index zero and the last gene is at the index equal to the size of this Chromosome - 1.

Parameters:

a_locus - index of the gene value to be returned

Returns:

Gene at the given index

Since:

3.0

encode

protected java.lang.String encode(java.lang.String a_string)

decode

protected java.lang.String decode(java.lang.String a_string)

getPersistentRepresentation

public java.lang.String getPersistentRepresentation()

Specified by:

getPersistentRepresentation in interface IGPChromosome

Returns:

the persistent representation of the chromosome, including all genes

Since:

3.3

setValueFromPersistentRepresentation

public void setValueFromPersistentRepresentation(java.lang.String a_representation)
                                          throws UnsupportedRepresentationException

Parameters:

a_representation - String

Throws:

UnsupportedRepresentationException

Since:

3.3

createGene

protected CommandGene createGene(java.lang.String a_geneClassName,
                                 java.lang.String a_persistentRepresentation)
                          throws java.lang.Exception

Creates a new instance of gene.

Parameters:

a_geneClassName - name of the gene class

a_persistentRepresentation - persistent representation of the gene to create (could be obtained via getPersistentRepresentation)

Returns:

newly created gene

Throws:

java.lang.Exception

Since:

3.3

split

protected static final java.util.List split(java.lang.String a_string)
                                     throws UnsupportedRepresentationException

Splits a_string into individual gene representations.

Parameters:

a_string - the string to split

Returns:

the elements of the returned array are the persistent representation strings of the gene's components

Throws:

UnsupportedRepresentationException

Since:

3.3

contains

public boolean contains(CommandGene[] a_functionSet,
                        CommandGene a_function)

Checks if a function or terminal of the class of the given instance exists within a_functionSet

Parameters:

a_functionSet - the set of functions to check

a_function - the commandgene to check for via its class

Returns:

true if a_function's class exists within a_functionSet

Since:

3.6

contains

public boolean contains(CommandGene[] a_functionSet,
                        java.lang.Class a_function)

Checks if a function or terminal of the class of the given instance exists within a_functionSet

Parameters:

a_functionSet - the set of functions to check

a_function - the commandgene to check for via its class

Returns:

true if a_function's class exists within a_functionSet

Since:

3.6

contains

public int contains(CommandGene[] a_functionSet,
                    CommandGene a_function,
                    int a_limit)

Checks if a function or terminal of the class of the given instance exists within a_functionSet at least a_limit times

Parameters:

a_functionSet - the set of functions to check

a_function - the commandgene to check for via its class

a_limit - if a_limit occurrences of a_function were detected, exit

Returns:

true if a_function's class exists at least a_limit times within a_functionSet

Since:

3.6