Hidden states alphabet. More...

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

Inheritance diagram for bpp::HmmPhyloAlphabet:

Collaboration diagram for bpp::HmmPhyloAlphabet:

Public Member Functions
	HmmPhyloAlphabet (AlignedPhyloLikelihoodSetInterface &soap)

	HmmPhyloAlphabet (MultiProcessSequencePhyloLikelihood &mpsp)

	HmmPhyloAlphabet (const HmmPhyloAlphabet &hpa)

HmmPhyloAlphabet *	clone () const override

virtual	~HmmPhyloAlphabet ()

Context &	getContext ()

const Clonable &	getState (size_t stateIndex) const override

const AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t stateIndex) const

std::shared_ptr< const AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t stateIndex) const

size_t	getNumberOfStates () const override

size_t	getNumberOfSites () const

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
Context &	context_

std::vector< std::shared_ptr< AlignedPhyloLikelihoodInterface > >	vAP_
	vector of aligned phylolikelihoods. These phylolikelihoods are not owned by the alphabet. More...

size_t	nbSites_

ParameterList	parameters_

std::string	prefix_

Detailed Description

Hidden states alphabet.

Implementation of HmmStateAlphabet where Alphabet States are all the PhyloLikelihoods belonging to a AlignedPhyloLikelihoodSet.

Definition at line 24 of file HmmPhyloAlphabet.h.

Constructor & Destructor Documentation

◆ HmmPhyloAlphabet() [1/3]

bpp::HmmPhyloAlphabet::HmmPhyloAlphabet ( AlignedPhyloLikelihoodSetInterface & soap )

inline

Definition at line 40 of file HmmPhyloAlphabet.h.

References bpp::AlignedPhyloLikelihoodSetInterface::getAlignedPhyloLikelihood(), bpp::AlignedPhyloLikelihoodInterface::getNumberOfSites(), bpp::PhyloLikelihoodSetInterface::getNumbersOfPhyloLikelihoods(), bpp::AbstractParametrizable::includeParameters_(), nbSites_, and vAP_.

Referenced by clone().

◆ HmmPhyloAlphabet() [2/3]

bpp::HmmPhyloAlphabet::HmmPhyloAlphabet ( MultiProcessSequencePhyloLikelihood & mpsp )

inline

Definition at line 58 of file HmmPhyloAlphabet.h.

References getContext(), bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodCalculationForAProcess(), bpp::MultiProcessSequencePhyloLikelihood::getNumberOfSubstitutionProcess(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::includeParameters_(), nbSites_, and vAP_.

◆ HmmPhyloAlphabet() [3/3]

bpp::HmmPhyloAlphabet::HmmPhyloAlphabet ( const HmmPhyloAlphabet & hpa )

inline

Definition at line 83 of file HmmPhyloAlphabet.h.

◆ ~HmmPhyloAlphabet()

virtual bpp::HmmPhyloAlphabet::~HmmPhyloAlphabet ( )

inlinevirtual

Definition at line 92 of file HmmPhyloAlphabet.h.

Member Function Documentation

◆ alignedPhyloLikelihood()

const AlignedPhyloLikelihoodInterface& bpp::HmmPhyloAlphabet::alignedPhyloLikelihood ( size_t stateIndex ) const

inline

Definition at line 106 of file HmmPhyloAlphabet.h.

References vAP_.

◆ clone()

HmmPhyloAlphabet* bpp::HmmPhyloAlphabet::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParametrizable.

Definition at line 90 of file HmmPhyloAlphabet.h.

References HmmPhyloAlphabet().

◆ getAlignedPhyloLikelihood()

std::shared_ptr<const AlignedPhyloLikelihoodInterface> bpp::HmmPhyloAlphabet::getAlignedPhyloLikelihood ( size_t stateIndex ) const

inline

Definition at line 111 of file HmmPhyloAlphabet.h.

References vAP_.

◆ getContext()

Context& bpp::HmmPhyloAlphabet::getContext ( )

inline

Definition at line 94 of file HmmPhyloAlphabet.h.

References context_.

Referenced by HmmPhyloAlphabet().

◆ getNumberOfSites()

size_t bpp::HmmPhyloAlphabet::getNumberOfSites ( ) const

inline

Definition at line 121 of file HmmPhyloAlphabet.h.

References nbSites_.

◆ getNumberOfStates()

size_t bpp::HmmPhyloAlphabet::getNumberOfStates ( ) const

inlineoverridevirtual

Implements bpp::HmmStateAlphabet.

Definition at line 116 of file HmmPhyloAlphabet.h.

References vAP_.

◆ getState()

const Clonable& bpp::HmmPhyloAlphabet::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 101 of file HmmPhyloAlphabet.h.

References vAP_.

◆ worksWith()

bool bpp::HmmPhyloAlphabet::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 134 of file HmmPhyloAlphabet.h.

Member Data Documentation

◆ context_

Context& bpp::HmmPhyloAlphabet::context_

private

Definition at line 29 of file HmmPhyloAlphabet.h.

Referenced by getContext().

◆ nbSites_

size_t bpp::HmmPhyloAlphabet::nbSites_

private

Definition at line 37 of file HmmPhyloAlphabet.h.

Referenced by getNumberOfSites(), and HmmPhyloAlphabet().

◆ vAP_

std::vector<std::shared_ptr<AlignedPhyloLikelihoodInterface> > bpp::HmmPhyloAlphabet::vAP_

private

vector of aligned phylolikelihoods. These phylolikelihoods are not owned by the alphabet.

Definition at line 35 of file HmmPhyloAlphabet.h.

Referenced by alignedPhyloLikelihood(), getAlignedPhyloLikelihood(), getNumberOfStates(), getState(), and HmmPhyloAlphabet().

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/HmmPhyloAlphabet.h

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HmmPhyloAlphabet() [1/3]

◆ HmmPhyloAlphabet() [2/3]

◆ HmmPhyloAlphabet() [3/3]

◆ ~HmmPhyloAlphabet()

Member Function Documentation

◆ alignedPhyloLikelihood()

◆ clone()

◆ getAlignedPhyloLikelihood()

◆ getContext()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getState()

◆ worksWith()

Member Data Documentation

◆ context_

◆ nbSites_

◆ vAP_