Emission probabilities in the context of DF phylolikeihoods. More...

#include <Bpp/Phyl/Likelihood/PhyloLikelihoods/HmmPhyloEmissionProbabilities.h>

Inheritance diagram for bpp::HmmPhyloEmissionProbabilities:

Collaboration diagram for bpp::HmmPhyloEmissionProbabilities:

Public Member Functions
	HmmPhyloEmissionProbabilities (std::shared_ptr< HmmPhyloAlphabet > alphabet)

	HmmPhyloEmissionProbabilities (const HmmPhyloEmissionProbabilities &hEP)

HmmPhyloEmissionProbabilities *	clone () const

const HmmStateAlphabet *	getHmmStateAlphabet () const

size_t	getNumberOfStates () const

size_t	getNumberOfSites () const

void	setHmmStateAlphabet (std::shared_ptr< HmmStateAlphabet > stateAlphabet)
	Set the new hidden state alphabet. More...

DataLik	operator() (size_t pos, size_t state) const
	Operator access to the emission probabilities. More...

ValueRef< MatrixLik >	getEmissionProbabilities ()

VectorLik	operator() (size_t pos) const
	Operator access to the emission probabilities. More...

size_t	getNumberOfPositions () const

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
Context &	context_

std::shared_ptr< HmmPhyloAlphabet >	phylAlph_

ValueRef< MatrixLik >	emProb_

size_t	nbSites_

ParameterList	parameters_

std::string	prefix_

Detailed Description

Emission probabilities in the context of DF phylolikeihoods.

Definition at line 23 of file HmmPhyloEmissionProbabilities.h.

Constructor & Destructor Documentation

◆ HmmPhyloEmissionProbabilities() [1/2]

HmmPhyloEmissionProbabilities::HmmPhyloEmissionProbabilities ( std::shared_ptr< HmmPhyloAlphabet > alphabet )

Definition at line 10 of file HmmPhyloEmissionProbabilities.cpp.

References setHmmStateAlphabet().

Referenced by clone().

◆ HmmPhyloEmissionProbabilities() [2/2]

bpp::HmmPhyloEmissionProbabilities::HmmPhyloEmissionProbabilities ( const HmmPhyloEmissionProbabilities & hEP )

inline

Definition at line 45 of file HmmPhyloEmissionProbabilities.h.

Member Function Documentation

◆ clone()

HmmPhyloEmissionProbabilities * bpp::HmmPhyloEmissionProbabilities::clone ( ) const

inlinevirtual

Implements bpp::AbstractParametrizable.

Definition at line 53 of file HmmPhyloEmissionProbabilities.h.

References HmmPhyloEmissionProbabilities().

◆ getEmissionProbabilities()

ValueRef< MatrixLik > bpp::HmmPhyloEmissionProbabilities::getEmissionProbabilities ( )

inline

Definition at line 93 of file HmmPhyloEmissionProbabilities.h.

References emProb_.

◆ getHmmStateAlphabet()

const HmmStateAlphabet * bpp::HmmPhyloEmissionProbabilities::getHmmStateAlphabet ( ) const

inlinevirtual

Implements bpp::HmmEmissionProbabilities_Eigen.

Definition at line 55 of file HmmPhyloEmissionProbabilities.h.

References phylAlph_.

◆ getNumberOfPositions()

size_t bpp::HmmPhyloEmissionProbabilities::getNumberOfPositions ( ) const

inlinevirtual

Returns: The number of positions in the data.

Implements bpp::HmmEmissionProbabilities_Eigen.

Definition at line 115 of file HmmPhyloEmissionProbabilities.h.

References nbSites_.

◆ getNumberOfSites()

size_t bpp::HmmPhyloEmissionProbabilities::getNumberOfSites ( ) const

inline

Definition at line 65 of file HmmPhyloEmissionProbabilities.h.

References nbSites_.

◆ getNumberOfStates()

size_t bpp::HmmPhyloEmissionProbabilities::getNumberOfStates ( ) const

inline

Definition at line 60 of file HmmPhyloEmissionProbabilities.h.

References phylAlph_.

◆ operator()() [1/2]

VectorLik bpp::HmmPhyloEmissionProbabilities::operator() ( size_t pos ) const

inlinevirtual

Operator access to the emission probabilities.

This is the fastest way to get the values, but no checking is performed on the indices. For debugging purpose, the getPhyloEmissionProbability would be a safer use.

Parameters

pos	The position of the sequential data to consider.

Returns: A vector of probabilities, whose size is the number of hidden states.

Implements bpp::HmmEmissionProbabilities_Eigen.

Definition at line 107 of file HmmPhyloEmissionProbabilities.h.

References emProb_.

◆ operator()() [2/2]

DataLik bpp::HmmPhyloEmissionProbabilities::operator()	(	size_t	pos,
		size_t	state
	)		const

inlinevirtual

Operator access to the emission probabilities.

This is the fastest way to get the values, but no checking is performed on the indices. For debugging purpose, the getPhyloEmissionProbability would be a safer use.

Parameters

pos	The position of the sequential data to consider.
state	The index of the hidden state to consider, as defined by the HmmStateAlphabet object associated to this class

Implements bpp::HmmEmissionProbabilities_Eigen.

Definition at line 88 of file HmmPhyloEmissionProbabilities.h.

References emProb_.