Partial implementation of HmmTransitionMatrix. More...

#include <Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h>

Inheritance diagram for bpp::AbstractHmmTransitionMatrix:

Collaboration diagram for bpp::AbstractHmmTransitionMatrix:

Public Member Functions
	AbstractHmmTransitionMatrix (std::shared_ptr< const HmmStateAlphabet > alph, const std::string &prefix="")

	AbstractHmmTransitionMatrix (const AbstractHmmTransitionMatrix &hptm)

AbstractHmmTransitionMatrix &	operator= (const AbstractHmmTransitionMatrix &hptm)

std::shared_ptr< const HmmStateAlphabet >	getHmmStateAlphabet () const

const HmmStateAlphabet &	hmmStateAlphabet () const

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

size_t	getNumberOfStates () const

std::vector< size_t >	sample (size_t size) const
	sampling of a sequence of states. Starting point is sampled from the equilibrium distribution. More...

virtual HmmTransitionMatrix *	clone () const override=0
	Create a copy of this object and send a pointer to it. More...

virtual double	Pij (size_t i, size_t j) const =0
	Get the transition probability between two states. More...

virtual const Matrix< double > &	getPij () const =0
	Get all transition probabilities as a matrix. More...

virtual const std::vector< double > &	getEquilibriumFrequencies () const =0

virtual bool	hasParameter (const std::string &name) const =0
	Tell if there is a parameter with specified name. More...

virtual const ParameterList &	getParameters () const =0
	Get all parameters available. More...

virtual const Parameter &	parameter (const std::string &name) const =0
	Get the parameter with specified name. More...

virtual double	getParameterValue (const std::string &name) const =0
	Get the value for parameter of name 'name'. More...

virtual void	setAllParametersValues (const ParameterList &parameters)=0
	Set the parameters values to be equals to those of parameters. More...

virtual void	setParameterValue (const std::string &name, double value)=0
	Set the value of parameter with name name to be equal to value. More...

virtual void	setParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...

virtual bool	matchParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...

virtual void	removeConstraint (const std::string &name)=0
	Remove the constraint associated with one parameter, if any. More...

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
	Set/Change the constraint associated with one parameter. More...

virtual size_t	getNumberOfParameters () const =0
	Get the number of parameters. More...

virtual void	setNamespace (const std::string &prefix)=0
	Set the namespace for the parameter names. More...

virtual std::string	getNamespace () const =0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
	Resolves a parameter name according to the current namespace. More...

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0
	Get all parameters available. More...

Protected Attributes
RowMatrix< double >	pij_

RowMatrix< double >	tmpmat_

Vdouble	eqFreq_

bool	upToDate_

Private Attributes
std::shared_ptr< const HmmStateAlphabet >	alph_

Detailed Description

Partial implementation of HmmTransitionMatrix.

Definition at line 19 of file AbstractHmmTransitionMatrix.h.

Constructor & Destructor Documentation

◆ AbstractHmmTransitionMatrix() [1/2]

AbstractHmmTransitionMatrix::AbstractHmmTransitionMatrix	(	std::shared_ptr< const HmmStateAlphabet >	alph,
		const std::string &	prefix = `""`
	)

Definition at line 13 of file AbstractHmmTransitionMatrix.cpp.

◆ AbstractHmmTransitionMatrix() [2/2]

AbstractHmmTransitionMatrix::AbstractHmmTransitionMatrix ( const AbstractHmmTransitionMatrix & hptm )

Definition at line 21 of file AbstractHmmTransitionMatrix.cpp.

Member Function Documentation

◆ clone()

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

overridepure virtualinherited

Create a copy of this object and send a pointer to it.

Returns: A pointer toward the copy object.

Implements bpp::Clonable.

Implemented in bpp::FullHmmTransitionMatrix, and bpp::AutoCorrelationTransitionMatrix.

◆ getEquilibriumFrequencies()

virtual const std::vector<double>& bpp::HmmTransitionMatrix::getEquilibriumFrequencies ( ) const

pure virtualinherited

Returns: The vector of equilibrium frequencies of the Markov chain described by the matrix.

Implemented in bpp::FullHmmTransitionMatrix, and bpp::AutoCorrelationTransitionMatrix.

◆ getHmmStateAlphabet()

std::shared_ptr<const HmmStateAlphabet> bpp::AbstractHmmTransitionMatrix::getHmmStateAlphabet ( ) const

inlinevirtual

Returns: A pointer toward the hidden alphabet associated to this model.

Implements bpp::HmmTransitionMatrix.

Definition at line 42 of file AbstractHmmTransitionMatrix.h.

References alph_.

◆ getNamespace()

virtual std::string bpp::Parametrizable::getNamespace ( ) const

pure virtualinherited

Returns: The current namespace used. This is an empty string if no namespace is currently defined.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getNumberOfParameters()

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const

pure virtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getNumberOfStates()

size_t bpp::AbstractHmmTransitionMatrix::getNumberOfStates ( ) const

inlinevirtual

Returns: The number of states in the model.

Implements bpp::HmmTransitionMatrix.

Definition at line 65 of file AbstractHmmTransitionMatrix.h.

References sample().

Referenced by bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::FullHmmTransitionMatrix::fireParameterChanged(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::FullHmmTransitionMatrix::getEquilibriumFrequencies(), bpp::AutoCorrelationTransitionMatrix::getPij(), and bpp::AutoCorrelationTransitionMatrix::Pij().

◆ getParameterNameWithoutNamespace()

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string & name ) const

pure virtualinherited

Resolves a parameter name according to the current namespace.

Returns: The parameter name without the namespace prefix, if any.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters()

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const

pure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::ParameterAliasableAdapter::getIndependentParameters(), bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters_()

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )

protectedpure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getParameterValue()

virtual double bpp::Parametrizable::getParameterValue ( const std::string & name ) const

pure virtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getPij()

virtual const Matrix<double>& bpp::HmmTransitionMatrix::getPij ( ) const

pure virtualinherited

Get all transition probabilities as a matrix.

Returns: A n*n matrix will all transition probabilities (n being the number of hidden states).

Implemented in bpp::FullHmmTransitionMatrix, and bpp::AutoCorrelationTransitionMatrix.

Referenced by sample().

◆ hasParameter()

virtual bool bpp::Parametrizable::hasParameter ( const std::string & name ) const

pure virtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ hmmStateAlphabet()

const HmmStateAlphabet& bpp::AbstractHmmTransitionMatrix::hmmStateAlphabet ( ) const

inlinevirtual

Returns: The hidden alphabet associated to this model.

Implements bpp::HmmTransitionMatrix.

Definition at line 50 of file AbstractHmmTransitionMatrix.h.

References alph_, and setHmmStateAlphabet().

Referenced by sample().

◆ matchParametersValues()

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList & parameters )

pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters A list of parameters.

Returns: True if at least one parameter value has been changed.

Exceptions

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::TestFunction::setParameters(), and bpp::Parametrizable::~Parametrizable().

◆ operator=()

AbstractHmmTransitionMatrix & AbstractHmmTransitionMatrix::operator= ( const AbstractHmmTransitionMatrix & hptm )

Definition at line 29 of file AbstractHmmTransitionMatrix.cpp.

References alph_, eqFreq_, pij_, tmpmat_, and upToDate_.

Referenced by bpp::AutoCorrelationTransitionMatrix::operator=(), and bpp::FullHmmTransitionMatrix::operator=().

◆ parameter()

virtual const Parameter& bpp::Parametrizable::parameter ( const std::string & name ) const

pure virtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: The parameter with given name.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::TestFunction::getValue(), and bpp::Parametrizable::~Parametrizable().

◆ Pij()

virtual double bpp::HmmTransitionMatrix::Pij	(	size_t	i,
		size_t	j
	)		const

pure virtualinherited

Get the transition probability between two states.

Parameters

i	initial state.
j	final state.

Returns: the transition probability between the two states.

Implemented in bpp::FullHmmTransitionMatrix, and bpp::AutoCorrelationTransitionMatrix.

◆ removeConstraint()

virtual void bpp::Parametrizable::removeConstraint ( const std::string & name )

pure virtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ sample()

vector< size_t > AbstractHmmTransitionMatrix::sample ( size_t size ) const

sampling of a sequence of states. Starting point is sampled from the equilibrium distribution.

Parameters

size	the length of the sequence

Returns: a vector of states index sampled from the Transition probabilities

Definition at line 48 of file AbstractHmmTransitionMatrix.cpp.

References eqFreq_, bpp::HmmStateAlphabet::getNumberOfStates(), bpp::HmmTransitionMatrix::getPij(), bpp::RowMatrix< Scalar >::getRow(), bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), hmmStateAlphabet(), and pij_.

Referenced by getNumberOfStates().

◆ setAllParametersValues()

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList & parameters )

pure virtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

parameters A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setConstraint()

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

pure virtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setHmmStateAlphabet()

void AbstractHmmTransitionMatrix::setHmmStateAlphabet ( std::shared_ptr< const HmmStateAlphabet > stateAlphabet )

virtual

Set the new hidden state alphabet.

Parameters

stateAlphabet The new state alphabet

Exceptions

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

Implements bpp::HmmTransitionMatrix.

Definition at line 40 of file AbstractHmmTransitionMatrix.cpp.

References alph_.

Referenced by hmmStateAlphabet().

◆ setNamespace()

virtual void bpp::Parametrizable::setNamespace ( const std::string & prefix )

pure virtualinherited

Set the namespace for the parameter names.

Parameters

prefix The 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setParametersValues()

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList & parameters )

pure virtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setParameterValue()

virtual void bpp::Parametrizable::setParameterValue	(	const std::string &	name,
		double	value
	)

pure virtualinherited

Set the value of parameter with name name to be equal to value.

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().