bpp::HmmEmissionProbabilities_Eigen Class Reference

Interface for computing emission probabilities in a Hidden Markov Model. More...

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

Inheritance diagram for bpp::HmmEmissionProbabilities_Eigen:

Collaboration diagram for bpp::HmmEmissionProbabilities_Eigen:

Public Member Functions
virtual HmmEmissionProbabilities_Eigen *	clone () const =0
virtual const HmmStateAlphabet *	getHmmStateAlphabet () const =0
virtual void	setHmmStateAlphabet (std::shared_ptr< HmmStateAlphabet > stateAlphabet)=0
	Set the new hidden state alphabet. More...
virtual DataLik	operator() (size_t pos, size_t state) const =0
	Operator access to the emission probabilities. More...
virtual VectorLik	operator() (size_t pos) const =0
	Operator access to the emission probabilities. More...
virtual size_t	getNumberOfPositions () const =0
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

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

Detailed Description

Interface for computing emission probabilities in a Hidden Markov Model.

This class is part of the HMM framework. It compute the probabilities of the data conditioned on each hidden state. The emission probabilities class also has in charge the data, its putative compression, and the number of position in the sequence of observed states.

See also

HmmStateAlphabet

HmmTransitionMatrix

Definition at line 29 of file HmmEmissionProbabilities_Eigen.h.

Member Function Documentation

clone()

virtual HmmEmissionProbabilities_Eigen* bpp::HmmEmissionProbabilities_Eigen::clone ( ) const

pure virtual

Implements bpp::Parametrizable.

Implemented in bpp::HmmPhyloEmissionProbabilities.

getHmmStateAlphabet()

virtual const HmmStateAlphabet* bpp::HmmEmissionProbabilities_Eigen::getHmmStateAlphabet ( ) const

pure virtual

Implemented in bpp::HmmPhyloEmissionProbabilities.

getNumberOfPositions()

virtual size_t bpp::HmmEmissionProbabilities_Eigen::getNumberOfPositions ( ) const

pure virtual

Returns

The number of positions in the data.

Implemented in bpp::HmmPhyloEmissionProbabilities.

operator()() [1/2]

virtual VectorLik bpp::HmmEmissionProbabilities_Eigen::operator() ( size_t  pos ) const

pure virtual

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 getEmissionProbability 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.

Implemented in bpp::HmmPhyloEmissionProbabilities.

operator()() [2/2]

virtual DataLik bpp::HmmEmissionProbabilities_Eigen::operator() ( size_t  pos, size_t  state  ) const

pure virtual

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 getEmissionProbability 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.

Implemented in bpp::HmmPhyloEmissionProbabilities.

setHmmStateAlphabet()

virtual void bpp::HmmEmissionProbabilities_Eigen::setHmmStateAlphabet ( std::shared_ptr< HmmStateAlphabet >  stateAlphabet )

pure virtual

Set the new hidden state alphabet.

Parameters

stateAlphabet

The new state alphabet.

Exceptions

UnvalidStateAlphabetException

if the new alphabet is incorrect (for instance is NULL pointer).

Implemented in bpp::HmmPhyloEmissionProbabilities.

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

• Bpp/Phyl/Likelihood/HmmEmissionProbabilities_Eigen.h