Hidden states alphabet. More...

#include <Bpp/Phyl/Likelihood/HmmProcessAlphabet.h>

Inheritance diagram for bpp::HmmProcessAlphabet:

Collaboration diagram for bpp::HmmProcessAlphabet:

Public Member Functions
	HmmProcessAlphabet (std::shared_ptr< const SubstitutionProcessCollection > pSub, std::vector< size_t > nProc)

	HmmProcessAlphabet (const HmmProcessAlphabet &hpa)

HmmProcessAlphabet &	operator= (const HmmProcessAlphabet &hpa)

HmmProcessAlphabet *	clone () const override

virtual	~HmmProcessAlphabet ()

const Clonable &	getState (size_t stateIndex) const override

size_t	getNumberOfStates () const override

bool	worksWith (const HmmStateAlphabet &stateAlphabet) const override
	Tell if this instance can work with the instance of alphabet given as input. More...

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

void	setNamespace (const std::string &prefix) override

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

virtual void	fireParameterChanged (const ParameterList &parameters)

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

virtual void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override

Private Attributes
std::shared_ptr< const SubstitutionProcessCollection >	processColl_

std::vector< size_t >	nProc_
	the vector of the substitution process numbers. More...

ParameterList	parameters_

std::string	prefix_

Detailed Description

Hidden states alphabet.

Implementation of HmmStateAlphabet where Alphabet States are Substitution Process belonging to a collection.

Definition at line 23 of file HmmProcessAlphabet.h.

Constructor & Destructor Documentation

◆ HmmProcessAlphabet() [1/2]

bpp::HmmProcessAlphabet::HmmProcessAlphabet	(	std::shared_ptr< const SubstitutionProcessCollection >	pSub,
		std::vector< size_t >	nProc
	)

inline

Definition at line 36 of file HmmProcessAlphabet.h.

Referenced by clone().

◆ HmmProcessAlphabet() [2/2]

bpp::HmmProcessAlphabet::HmmProcessAlphabet ( const HmmProcessAlphabet & hpa )

inline

Definition at line 44 of file HmmProcessAlphabet.h.

◆ ~HmmProcessAlphabet()

virtual bpp::HmmProcessAlphabet::~HmmProcessAlphabet ( )

inlinevirtual

Definition at line 61 of file HmmProcessAlphabet.h.

Member Function Documentation

◆ clone()

HmmProcessAlphabet* bpp::HmmProcessAlphabet::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParametrizable.

Definition at line 59 of file HmmProcessAlphabet.h.

References HmmProcessAlphabet().

◆ getNumberOfStates()

size_t bpp::HmmProcessAlphabet::getNumberOfStates ( ) const

inlineoverridevirtual

Implements bpp::HmmStateAlphabet.

Definition at line 73 of file HmmProcessAlphabet.h.

References nProc_.

◆ getState()

const Clonable& bpp::HmmProcessAlphabet::getState ( size_t stateIndex ) const

inlineoverridevirtual

Parameters

stateIndex The index of a hidden state.

Returns: The corresponding hidden state.

See also: getNumberOfStates

Implements bpp::HmmStateAlphabet.

Definition at line 68 of file HmmProcessAlphabet.h.

References nProc_, and processColl_.

◆ operator=()

HmmProcessAlphabet& bpp::HmmProcessAlphabet::operator= ( const HmmProcessAlphabet & hpa )

inline

Definition at line 50 of file HmmProcessAlphabet.h.

References nProc_, and processColl_.

◆ worksWith()

bool bpp::HmmProcessAlphabet::worksWith ( const HmmStateAlphabet & stateAlphabet ) const

inlineoverridevirtual

Tell if this instance can work with the instance of alphabet given as input.

In many case, this will return true if the pointer provided as argument refers to this object.

Parameters

stateAlphabet The alphabet to check.

Returns: true if the matrix is compatible with the given alphabet.

Implements bpp::HmmStateAlphabet.

Definition at line 86 of file HmmProcessAlphabet.h.

Member Data Documentation

◆ nProc_

std::vector<size_t> bpp::HmmProcessAlphabet::nProc_

private

the vector of the substitution process numbers.

Definition at line 33 of file HmmProcessAlphabet.h.

Referenced by getNumberOfStates(), getState(), and operator=().

◆ processColl_

std::shared_ptr<const SubstitutionProcessCollection> bpp::HmmProcessAlphabet::processColl_

private

Definition at line 28 of file HmmProcessAlphabet.h.

Referenced by getState(), and operator=().

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

Bpp/Phyl/Likelihood/HmmProcessAlphabet.h

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HmmProcessAlphabet() [1/2]

◆ HmmProcessAlphabet() [2/2]

◆ ~HmmProcessAlphabet()

Member Function Documentation

◆ clone()

◆ getNumberOfStates()

◆ getState()

◆ operator=()

◆ worksWith()

Member Data Documentation

◆ nProc_

◆ processColl_