GEP::Chromosome< ChromosomeType > Class Template Reference

Karva chromosome template. Implemented as a vector<unsigned short> holding indexes of elements in _oneArgFunction, _twoArgFunction and _terminals vectors. More...

#include <Chromosome.h>

Inheritance diagram for GEP::Chromosome< ChromosomeType >:

[legend]

List of all members.

Public Types
typedef ChromosomeType	CType
Public Member Functions
	Chromosome ()
	Chromosome (const Chromosome &)
virtual	~Chromosome ()
	Chromosome (const std::vector< CElement > &chromo)
u_short	evaluateTreeDepth (const u_short &idx) const
ChromosomeType	evaluateGeneTree (const u_short &idx) const
virtual ChromosomeType	calculateValue ()
void	calculateSubValues (std::vector< std::pair< bool, ChromosomeType > > &vals)
void	terminalsUsed (const u_short &idx, std::vector< short > &ref, const bool &append=false) const
void	terminalsUsed (std::vector< short > &ref) const
CElement &	operator[] (const u_short &idx)
CElement	operator[] (const u_short &idx) const
CElement	getElement (const u_short &gidx, const u_short &idx) const
CElement	getElement (const u_short &gidx, const u_short &idx)
std::vector< CElement > &	getChromosome ()
const std::vector< CElement > &	getChromosome () const
std::vector< u_short > &	getLinks ()
const std::vector< u_short > &	getLinks () const
twoArg< ChromosomeType > *	getLink (const u_short &idx)
twoArg< ChromosomeType > *	getLink (const u_short &idx) const
std::vector< double > &	getRandomConstants ()
const std::vector< double > &	getRandomConstants () const
bool	isViable () const
void	setElement (const u_short &gidx, const u_short &idx, const CElement &element)
void	insertHeadElement (const u_short &gidx, const u_short &idx, const CElement &element)
void	setEmpty ()
void	setChromosome (const std::vector< CElement > &fchromo)
void	setLinks (const std::vector< u_short > &links)
void	setLink (const u_short &link, const size_t &pos)
void	setViable (const bool &b)
void	setRandomConstants (const std::vector< double > &rcs)
void	kill ()
std::string	geneToString (const u_short &numGene) const
virtual std::string	toString () const
Static Public Member Functions
static void	readConfig (const std::string &path)
static void	readConfig (const ConfigArgs &cfg)
static std::string	symbolic (const CElement &a)
static std::string	terminalToLetter (const u_short &a)
static CElement	getCombinedIndex (const std::string &name)
static u_short	getRcLength ()
static u_short	getTermLength ()
static u_short	getHeadLength ()
static u_short	getTailLength ()
static u_short	getGeneLength ()
static u_short	getChromosomeLength ()
static u_short	getNumGenes ()
static std::vector< twoArg < ChromosomeType > * >	getLinkPool ()
static std::vector< oneArg < ChromosomeType > * >	getOneArgFunctions ()
static std::vector< oneArg < ChromosomeType > * > &	getROneArgFunctions ()
static std::vector< twoArg < ChromosomeType > * >	getTwoArgFunctions ()
static std::vector< twoArg < ChromosomeType > * > &	getRTwoArgFunctions ()
static std::vector < ChromosomeType >	getTerminals ()
static std::vector < ChromosomeType > &	getRTerminals ()
static void	setHeadLength (const u_short &fhead)
static void	setLinkPool (const std::string &easy)
static void	setOneArgFunctions (const std::string &easyones)
static void	setTwoArgFunctions (const std::string &easytwos)
static void	assignValues (const std::vector< ChromosomeType > &vals, const size_t pop_age=0)
static void	clearFunctionPointers ()
static void	setNumGenes (const u_short &fgenes)
static void	setOneArgFunctions (const std::vector< oneArg< ChromosomeType > * > &ones)
static void	setTwoArgFunctions (const std::vector< twoArg< ChromosomeType > * > &twos)
static void	setLinkPool (const std::vector< twoArg< ChromosomeType > * > &pool)
static void	setLinkPool (const twoArg< ChromosomeType > *&pool)
static void	setTerminals (const std::vector< ChromosomeType > &terms)
static void	setTerminals (const u_short &tSize)
static void	setTerminal (const ChromosomeType &term, const size_t &idx)
static void	setRcLength (const u_short &length)
Protected Attributes
std::vector< CElement >	_chromosome
std::vector< u_short >	_links
std::vector< double >	_rconstants
bool	_viable
Static Protected Attributes
static std::vector< twoArg < ChromosomeType > * >	_linkPool = std::vector< twoArg<ChromosomeType>* >()
static std::vector< oneArg < ChromosomeType > * >	_oneArgFunctions = std::vector< oneArg<ChromosomeType>* >()
static std::vector< twoArg < ChromosomeType > * >	_twoArgFunctions = std::vector< twoArg<ChromosomeType>* >()
static std::vector < ChromosomeType >	_terminals = std::vector<ChromosomeType>()
static std::vector < ChromosomeType >	_results = std::vector<ChromosomeType>()
static u_short	_termLength = 0
static u_short	_rcLength = 0
static u_short	_numGenes = 3
static u_short	_headLength = 10
static u_short	_tailLength = (_headLength + 1)
static u_short	_geneLength = Chromosome<ChromosomeType>::_headLength + Chromosome<ChromosomeType>::_tailLength
Friends
template<class T2 >
std::ostream &	operator<< (std::ostream &os, const Chromosome< T2 > &a)

Detailed Description

template<class ChromosomeType = double>
class GEP::Chromosome< ChromosomeType >

Karva chromosome template. Implemented as a vector<unsigned short> holding indexes of elements in _oneArgFunction, _twoArgFunction and _terminals vectors.

Parameters:

ChromosomeType

- type of variables held in _terminals and calculated by fuctions.

Member Typedef Documentation

template<class ChromosomeType = double>

typedef ChromosomeType GEP::Chromosome< ChromosomeType >::CType

Type of the chromosome terminals and functions

Constructor & Destructor Documentation

template<class ChromosomeType >

GEP::Chromosome< ChromosomeType >::Chromosome ( ) [inline]

Default constructor

template<class ChromosomeType >

GEP::Chromosome< ChromosomeType >::Chromosome ( const Chromosome< ChromosomeType > & copy ) [inline]

Copy constructor

template<class ChromosomeType = double>

virtual GEP::Chromosome< ChromosomeType >::~Chromosome ( ) [inline, virtual]

template<class ChromosomeType >

GEP::Chromosome< ChromosomeType >::Chromosome ( const std::vector< CElement > & chromo ) [inline]

"We know better" Constructor - sets head, tail and the lengths.

Parameters:

chromo

- new chromosome

Member Function Documentation

template<class ChromosomeType>

void GEP::Chromosome< ChromosomeType >::assignValues	(	const std::vector< ChromosomeType > &	vals,
		const size_t	pop_age = `0`
	)			`[inline, static]`

Assigns the values of the _terminals vector.

Parameters:

	vals	values of the terminals
	pop_age	supportive parameter for ABFT analysis, by default - unused

template<class ChromosomeType>

void GEP::Chromosome< ChromosomeType >::calculateSubValues ( std::vector< std::pair< bool, ChromosomeType > > & vals ) [inline]

Calculates value of the chromosome genes. places values of genes of a given chromosome in

Parameters:

vals

template<class ChromosomeType >

ChromosomeType GEP::Chromosome< ChromosomeType >::calculateValue ( ) [inline, virtual]

Calculates value of the chromosome, linking the results of ORFs with the linking function of the chromosome.

Returns:: value of a given chromosome

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::clearFunctionPointers ( ) [inline, static]

Gracefully deletes the pointers to the linking function, one argument and two argument functions. Should be invoked after the work with GEP::Chromosome.

template<class ChromosomeType >

ChromosomeType GEP::Chromosome< ChromosomeType >::evaluateGeneTree ( const u_short & idx ) const [inline]

Evaluates value of given ORF, following ET. Uses _treeDepth[idx].

Parameters:

idx

- index of ORF to be evaluated

Returns:: value of a given tree

template<class ChromosomeType >

u_short GEP::Chromosome< ChromosomeType >::evaluateTreeDepth ( const u_short & idx ) const [inline]

Evaluates ET depth for a given ORF, results will be placed in _treeDepth[idx].

Parameters:

idx

- index of ORF to be evaluated

Returns:: tree depth (besides placing it in _treeDepth[idx])

template<class ChromosomeType >

std::string GEP::Chromosome< ChromosomeType >::geneToString ( const u_short & numGene ) const [inline]

Returns:

Parameters:

numGene

ORF represented as string.

template<class ChromosomeType = double>

const std::vector<CElement>& GEP::Chromosome< ChromosomeType >::getChromosome ( ) const [inline]

template<class ChromosomeType = double>

std::vector<CElement>& GEP::Chromosome< ChromosomeType >::getChromosome ( ) [inline]

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getChromosomeLength ( ) [inline, static]

template<class ChromosomeType >

CElement GEP::Chromosome< ChromosomeType >::getCombinedIndex ( const std::string & name ) [inline, static]

Returns the absolute index of the searched function, i.e. if the searched name will be in _twoArgFunctions vector, result will be _oneArgFunctions.size()+index of searched function.

Parameters:

name

name of the searched function

Returns:: absolute index of the searched function

template<class ChromosomeType = double>

CElement GEP::Chromosome< ChromosomeType >::getElement	(	const u_short &	gidx,
		const u_short &	idx
	)			`[inline]`

Returns:: element in given ORF (gidx) , on a given position(idx).

Parameters:

	gidx	- index of gene
	idx	- index of gene element

template<class ChromosomeType = double>

CElement GEP::Chromosome< ChromosomeType >::getElement	(	const u_short &	gidx,
		const u_short &	idx
	)			const `[inline]`

Returns:: element in given ORF (gidx), on a given position(idx).

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getGeneLength ( ) [inline, static]

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getHeadLength ( ) [inline, static]

template<class ChromosomeType = double>

twoArg<ChromosomeType>* GEP::Chromosome< ChromosomeType >::getLink ( const u_short & idx ) const [inline]

template<class ChromosomeType = double>

twoArg<ChromosomeType>* GEP::Chromosome< ChromosomeType >::getLink ( const u_short & idx ) [inline]

template<class ChromosomeType = double>

static std::vector< twoArg<ChromosomeType>* > GEP::Chromosome< ChromosomeType >::getLinkPool ( ) [inline, static]

template<class ChromosomeType = double>

const std::vector<u_short>& GEP::Chromosome< ChromosomeType >::getLinks ( ) const [inline]

template<class ChromosomeType = double>

std::vector<u_short>& GEP::Chromosome< ChromosomeType >::getLinks ( ) [inline]

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getNumGenes ( ) [inline, static]

template<class ChromosomeType = double>

static std::vector< oneArg<ChromosomeType>* > GEP::Chromosome< ChromosomeType >::getOneArgFunctions ( ) [inline, static]

template<class ChromosomeType = double>

const std::vector<double>& GEP::Chromosome< ChromosomeType >::getRandomConstants ( ) const [inline]

template<class ChromosomeType = double>

std::vector<double>& GEP::Chromosome< ChromosomeType >::getRandomConstants ( ) [inline]

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getRcLength ( ) [inline, static]

template<class ChromosomeType = double>

static std::vector< oneArg<ChromosomeType>* >& GEP::Chromosome< ChromosomeType >::getROneArgFunctions ( ) [inline, static]

template<class ChromosomeType = double>

static std::vector<ChromosomeType>& GEP::Chromosome< ChromosomeType >::getRTerminals ( ) [inline, static]

template<class ChromosomeType = double>

static std::vector< twoArg<ChromosomeType>* >& GEP::Chromosome< ChromosomeType >::getRTwoArgFunctions ( ) [inline, static]

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getTailLength ( ) [inline, static]

template<class ChromosomeType = double>

static std::vector<ChromosomeType> GEP::Chromosome< ChromosomeType >::getTerminals ( ) [inline, static]

template<class ChromosomeType = double>

static u_short GEP::Chromosome< ChromosomeType >::getTermLength ( ) [inline, static]

template<class ChromosomeType = double>

static std::vector< twoArg<ChromosomeType>* > GEP::Chromosome< ChromosomeType >::getTwoArgFunctions ( ) [inline, static]

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::insertHeadElement	(	const u_short &	gidx,
		const u_short &	idx,
		const CElement &	element
	)			`[inline]`

Inserts element in head of given ORF (gidx), on a given position(idx). Last element of the head is removed.

Parameters:

	gidx	- index of gene
	idx	- index of gene element
	element	- element to be placed at a given position

template<class ChromosomeType = double>

bool GEP::Chromosome< ChromosomeType >::isViable ( ) const [inline]

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::kill ( ) [inline]

template<class ChromosomeType = double>

CElement GEP::Chromosome< ChromosomeType >::operator[] ( const u_short & idx ) const [inline]

Operator[] overload.

Returns:: ORF element on a given position (

Parameters:

idx).

template<class ChromosomeType = double>

CElement& GEP::Chromosome< ChromosomeType >::operator[] ( const u_short & idx ) [inline]

Operator[] overload.

Returns:: ORF element on a given position (

Parameters:

idx).

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::readConfig ( const ConfigArgs & cfg ) [inline, static]

Reads the config stored in

Parameters:

cfg

of type ConfigArgs.

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::readConfig ( const std::string & path ) [inline, static]

Reads the config stored in the file indicated by

Parameters:

path

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::setChromosome ( const std::vector< CElement > & fchromo ) [inline]

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::setElement	(	const u_short &	gidx,
		const u_short &	idx,
		const CElement &	element
	)			`[inline]`

Sets element in given ORF (gidx), on a given position(idx) to element.

Parameters:

	gidx	- index of gene
	idx	- index of gene element
	element	- element to be placed at a given position

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::setEmpty ( ) [inline]

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::setHeadLength ( const u_short & fhead ) [inline, static]

Function setting head, tail and result lengths.

Parameters:

fhead

size of the head part of the chromosome

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::setLink	(	const u_short &	link,
		const size_t &	pos
	)			`[inline]`

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setLinkPool ( const twoArg< ChromosomeType > *& pool ) [inline, static]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setLinkPool ( const std::vector< twoArg< ChromosomeType > * > & pool ) [inline, static]

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::setLinkPool ( const std::string & easy ) [inline, static]

Sets the linking function on the basis of the given symbol - the name of the function. Looks up only functions in the basic Function set.

Parameters:

easy

symbol of the linking functions pool

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::setLinks ( const std::vector< u_short > & links ) [inline]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setNumGenes ( const u_short & fgenes ) [inline, static]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setOneArgFunctions ( const std::vector< oneArg< ChromosomeType > * > & ones ) [inline, static]

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::setOneArgFunctions ( const std::string & easyones ) [inline, static]

Sets the vector of one argument functiona on the basis of the vector of given symbols - the names of the functions. Looks up only functions in the basic Function set.

Parameters:

easyones

- vector of symbols of the one argument functions.

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::setRandomConstants ( const std::vector< double > & rcs ) [inline]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setRcLength ( const u_short & length ) [inline, static]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setTerminal	(	const ChromosomeType &	term,
		const size_t &	idx
	)			`[inline, static]`

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setTerminals ( const u_short & tSize ) [static]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setTerminals ( const std::vector< ChromosomeType > & terms ) [inline, static]

template<class ChromosomeType = double>

static void GEP::Chromosome< ChromosomeType >::setTwoArgFunctions ( const std::vector< twoArg< ChromosomeType > * > & twos ) [inline, static]

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::setTwoArgFunctions ( const std::string & easytwos ) [inline, static]

Sets the vector of two argument functiona on the basis of the vector of given symbols - the names of the functions. Looks up only functions in the basic Function set.

Parameters:

easytwos

- vector of symbols of the two argument functions.

template<class ChromosomeType = double>

void GEP::Chromosome< ChromosomeType >::setViable ( const bool & b ) [inline]

template<class ChromosomeType >

std::string GEP::Chromosome< ChromosomeType >::symbolic ( const CElement & a ) [inline, static]

Returns:: the symbol of a given element in the chromosome (

Parameters:

a).

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::terminalsUsed ( std::vector< short > & ref ) const [inline]

Provides the set of indexes of terminals used by functions in the chromosome.

Returns:: vector of indexes of terminals used by the chromosome

template<class ChromosomeType >

void GEP::Chromosome< ChromosomeType >::terminalsUsed	(	const u_short &	idx,
		std::vector< short > &	ref,
		const bool &	append = `false`
	)			const `[inline]`

Provides the set of indexes of terminals used by functions in a given gene.

Parameters:

	idx	index of a gene to check
	ref	target vector
	append	if false, ref will be cleared

Returns:: vector of indexes of terminals used by this gene

template<class ChromosomeType >

std::string GEP::Chromosome< ChromosomeType >::terminalToLetter ( const u_short & a ) [inline, static]

Returns:: the letter representing a given terminal in the chromosome (

Parameters:

a).

template<class ChromosomeType >

std::string GEP::Chromosome< ChromosomeType >::toString ( ) const [inline, virtual]

Returns:: this chromosome represented as string.

Friends And Related Function Documentation

template<class ChromosomeType = double>

template<class T2 >

std::ostream& operator<<	(	std::ostream &	os,
		const Chromosome< T2 > &	a
	)			`[friend]`

Member Data Documentation

template<class ChromosomeType = double>

std::vector<CElement> GEP::Chromosome< ChromosomeType >::_chromosome [protected]

GEP Chromosome - a vector of CElements holding indexes of elements in _oneArgFunction, _twoArgFunction and _terminals vectors. CElement.first describes the type anf CElement.second the value of an element

template<class ChromosomeType = double>

u_short GEP::Chromosome< ChromosomeType >::_geneLength = Chromosome<ChromosomeType>::_headLength + Chromosome<ChromosomeType>::_tailLength [inline, static, protected]

Gene length

template<class ChromosomeType = double>

u_short GEP::Chromosome< ChromosomeType >::_headLength = 10 [inline, static, protected]

Head length

template<class ChromosomeType = double>

std::vector< twoArg< ChromosomeType > * > GEP::Chromosome< ChromosomeType >::_linkPool = std::vector< twoArg<ChromosomeType>* >() [inline, static, protected]

Linking function. Two argument, as it has to link values of genes, thus take more than one value and return one value.

template<class ChromosomeType = double>

std::vector<u_short> GEP::Chromosome< ChromosomeType >::_links [protected]

Linking functions between the genes.

template<class ChromosomeType = double>

u_short GEP::Chromosome< ChromosomeType >::_numGenes = 3 [inline, static, protected]

Number of genes in one chromosome

template<class ChromosomeType = double>

std::vector< oneArg< ChromosomeType > * > GEP::Chromosome< ChromosomeType >::_oneArgFunctions = std::vector< oneArg<ChromosomeType>* >() [inline, static, protected]

One Argument Functions

template<class ChromosomeType = double>

u_short GEP::Chromosome< ChromosomeType >::_rcLength = 0 [inline, static, protected]

'Random constants' vector length

template<class ChromosomeType = double>

std::vector<double> GEP::Chromosome< ChromosomeType >::_rconstants [protected]

Random constants vector.

template<class ChromosomeType = double>

std::vector< ChromosomeType > GEP::Chromosome< ChromosomeType >::_results = std::vector<ChromosomeType>() [inline, static, protected]

Holds the results of evaluation

template<class ChromosomeType = double>

u_short GEP::Chromosome< ChromosomeType >::_tailLength = (_headLength + 1) [inline, static, protected]

Tail length

template<class ChromosomeType = double>

std::vector< ChromosomeType > GEP::Chromosome< ChromosomeType >::_terminals = std::vector<ChromosomeType>() [inline, static, protected]

Terminals

template<class ChromosomeType = double>

u_short GEP::Chromosome< ChromosomeType >::_termLength = 0 [inline, static, protected]

'Terminals' vector length

template<class ChromosomeType = double>

std::vector< twoArg< ChromosomeType > * > GEP::Chromosome< ChromosomeType >::_twoArgFunctions = std::vector< twoArg<ChromosomeType>* >() [inline, static, protected]

Two Argument Functions

template<class ChromosomeType = double>

bool GEP::Chromosome< ChromosomeType >::_viable [protected]

Is this chromosome viable.

The documentation for this class was generated from the following file:

Chromosome.h

GEP::Chromosome< ChromosomeType > Class Template Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Static Protected Attributes

Friends

Detailed Description

template<class ChromosomeType = double> class GEP::Chromosome< ChromosomeType >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<class ChromosomeType = double>
class GEP::Chromosome< ChromosomeType >