Describe the transition probabilities between hidden states of a Hidden Markov Model. More...

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

Inheritance diagram for bpp::FullHmmTransitionMatrix:

Collaboration diagram for bpp::FullHmmTransitionMatrix:

Public Member Functions
	FullHmmTransitionMatrix (const HmmStateAlphabet *alph, const std::string &prefix="")

	FullHmmTransitionMatrix (const FullHmmTransitionMatrix &hptm)

FullHmmTransitionMatrix &	operator= (const FullHmmTransitionMatrix &hptm)

FullHmmTransitionMatrix *	clone () const
	Create a copy of this object and send a pointer to it. More...

void	setTransitionProbabilities (const Matrix< double > &mat)
	Set the matrix of the transition probabilities. More...

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

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

const std::vector< double > &	getEquilibriumFrequencies () const

void	fireParameterChanged (const ParameterList &parameters)
	Notify the class when one or several parameters have changed. More...

const HmmStateAlphabet *	getHmmStateAlphabet () const

void	setHmmStateAlphabet (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 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 &	getParameter (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 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...

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

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

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

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

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

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

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

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

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

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

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

std::string	getNamespace () const

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

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

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

std::shared_ptr< Parameter > &	getSharedParameter (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_ ()
	Get all parameters available. More...

Protected Attributes
RowMatrix< double >	pij_

RowMatrix< double >	tmpmat_

Vdouble	eqFreq_

bool	upToDate_

Private Attributes
std::vector< Simplex >	vSimplex_

const HmmStateAlphabet *	alph_

ParameterList	parameters_

std::string	prefix_

Detailed Description

Describe the transition probabilities between hidden states of a Hidden Markov Model.

Transition probabilities are described through simplexes.

Parameters are denoted "I.Simplex.thetaJ" where I is the line number of the transition matrix, and "thetaJ" is the matching parameter in the Ith Simplex.

See also: Simplex

Definition at line 65 of file FullHmmTransitionMatrix.h.

Constructor & Destructor Documentation

◆ FullHmmTransitionMatrix() [1/2]

FullHmmTransitionMatrix::FullHmmTransitionMatrix	(	const HmmStateAlphabet *	alph,
		const std::string &	prefix = `""`
	)

Definition at line 50 of file FullHmmTransitionMatrix.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractHmmTransitionMatrix::getNumberOfStates(), bpp::AbstractParametrizable::getParameters(), bpp::TextTools::toString(), and vSimplex_.

Referenced by clone().

◆ FullHmmTransitionMatrix() [2/2]

FullHmmTransitionMatrix::FullHmmTransitionMatrix ( const FullHmmTransitionMatrix & hptm )

Definition at line 64 of file FullHmmTransitionMatrix.cpp.

Member Function Documentation

◆ addParameter_()

virtual void bpp::AbstractParametrizable::addParameter_ ( Parameter * parameter )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 137 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::addParameter_(), bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(), and bpp::TestFunction::TestFunction().

◆ addParameters_()

virtual void bpp::AbstractParametrizable::addParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 143 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::addParameters_(), FullHmmTransitionMatrix(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(), and bpp::RescaledHmmLikelihood::RescaledHmmLikelihood().

◆ clone()

FullHmmTransitionMatrix* bpp::FullHmmTransitionMatrix::clone ( ) const

inlinevirtual

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

Returns: A pointer toward the copy object.

Implements bpp::Clonable.

Definition at line 79 of file FullHmmTransitionMatrix.h.

References FullHmmTransitionMatrix().

◆ deleteParameter_() [1/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( size_t index )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 163 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::deleteParameter_().

◆ deleteParameter_() [2/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( std::string & name )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 170 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), and bpp::AbstractParametrizable::parameters_.

◆ deleteParameters_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 175 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameters(), and bpp::AbstractParametrizable::parameters_.

◆ fireParameterChanged()

void FullHmmTransitionMatrix::fireParameterChanged ( const ParameterList & parameters )

virtual

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 139 of file FullHmmTransitionMatrix.cpp.

References bpp::AbstractHmmTransitionMatrix::getNumberOfStates(), bpp::AbstractHmmTransitionMatrix::upToDate_, and vSimplex_.

◆ getEquilibriumFrequencies()

const std::vector< double > & FullHmmTransitionMatrix::getEquilibriumFrequencies ( ) const

virtual

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

Implements bpp::HmmTransitionMatrix.

Definition at line 118 of file FullHmmTransitionMatrix.cpp.

References bpp::AbstractHmmTransitionMatrix::eqFreq_, bpp::AbstractHmmTransitionMatrix::getNumberOfStates(), getPij(), bpp::AbstractHmmTransitionMatrix::pij_, bpp::MatrixTools::pow(), bpp::AbstractHmmTransitionMatrix::tmpmat_, and bpp::AbstractHmmTransitionMatrix::upToDate_.

◆ getHmmStateAlphabet()

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

inlinevirtualinherited

Returns: The hidden alphabet associated to this model.

Implements bpp::HmmTransitionMatrix.

Definition at line 79 of file AbstractHmmTransitionMatrix.h.

References bpp::AbstractHmmTransitionMatrix::alph_.

Referenced by bpp::AbstractHmmTransitionMatrix::sample().

◆ getNamespace() [1/2]

std::string bpp::AbstractParametrizable::getNamespace ( ) const

inlinevirtualinherited

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

Implements bpp::Parametrizable.

Definition at line 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::hasIndependentParameter(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getNamespace() [2/2]

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

Referenced by bpp::FunctionWrapper::getNamespace().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlinevirtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 121 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractParameterAliasable::operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ getNumberOfParameters() [2/2]

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

Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getNumberOfStates()

size_t bpp::AbstractHmmTransitionMatrix::getNumberOfStates ( ) const

inlinevirtualinherited

Returns: The number of states in the model.

Implements bpp::HmmTransitionMatrix.

Definition at line 95 of file AbstractHmmTransitionMatrix.h.

References bpp::AbstractHmmTransitionMatrix::alph_, and bpp::HmmStateAlphabet::getNumberOfStates().

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

◆ getParameter() [1/2]

const Parameter& bpp::AbstractParametrizable::getParameter ( const std::string & name ) const

inlinevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 79 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::TestFunction::getValue().

◆ getParameter() [2/2]

virtual const Parameter& bpp::Parametrizable::getParameter ( 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::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameter().

◆ getParameter_() [1/3]

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

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ConstantDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getParameter_() [2/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index )

inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

◆ getParameter_() [3/3]

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index ) const

inlineprotectedinherited

Definition at line 223 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace() [1/2]

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

virtualinherited

Resolves a parameter name according to the current namespace.

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

Implements bpp::Parametrizable.

Definition at line 65 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), and bpp::AbstractParameterAliasable::shareParameters_().

◆ getParameterNameWithoutNamespace() [2/2]

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

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), and bpp::BppOParametrizableFormat::write().

◆ getParameters() [1/2]

const ParameterList& bpp::AbstractParametrizable::getParameters ( ) const

inlinevirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 77 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), FullHmmTransitionMatrix(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::ParametrizableCollection< N >::removeObject().

◆ getParameters() [2/2]

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

Referenced by bpp::NewtonOneDimension::doStep(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::FunctionWrapper::getParameters(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::AbstractNumericalDerivative::setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().

◆ getParameters_() [1/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineprotectedvirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 231 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), and bpp::AbstractParameterAliasable::operator=().

◆ getParameters_() [2/2]

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::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameters_().

◆ getParameterValue() [1/2]

double bpp::AbstractParametrizable::getParameterValue ( const std::string & name ) const

inlinevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 89 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter(), and bpp::Parameter::getValue().

◆ getParameterValue() [2/2]

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

Referenced by bpp::FunctionWrapper::getParameterValue().

◆ getParameterWithNamespace_() [1/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 202 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 211 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getPij()

const Matrix< double > & FullHmmTransitionMatrix::getPij ( ) const

virtual

Get all transition probabilities as a matrix.

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

Implements bpp::HmmTransitionMatrix.

Definition at line 101 of file FullHmmTransitionMatrix.cpp.

References bpp::AbstractHmmTransitionMatrix::pij_, bpp::AbstractHmmTransitionMatrix::upToDate_, and vSimplex_.

Referenced by getEquilibriumFrequencies().

◆ getSharedParameter() [1/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( const std::string & name ) const

inlineinherited

Definition at line 84 of file AbstractParametrizable.h.

References bpp::ParameterList::getSharedParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getSharedParameter() [2/3]

std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( size_t i )

inlineprotectedinherited

Definition at line 242 of file AbstractParametrizable.h.

References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.

◆ getSharedParameter() [3/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( size_t i ) const

inlineprotectedinherited

Returns: The shared_ptr parameter at a given position.

Warning: No check is performed on the validity of the index given as input!

Definition at line 237 of file AbstractParametrizable.h.

References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.

◆ hasParameter() [1/2]

bool bpp::AbstractParametrizable::hasParameter ( const std::string & name ) const

inlinevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implements bpp::Parametrizable.

Definition at line 75 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AbstractParametrizable::getParameter_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ hasParameter() [2/2]

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

Referenced by bpp::FunctionWrapper::hasParameter().

◆ includeParameters_()

virtual void bpp::AbstractParametrizable::includeParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 158 of file AbstractParametrizable.h.

References bpp::ParameterList::includeParameters(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::includeParameters_().

◆ matchParametersValues() [1/2]

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList & parameters )

inlinevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 112 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareSubList().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::TestFunction::setParameters(), bpp::ReparametrizationFunctionWrapper::setParameters(), and setTransitionProbabilities().

◆ matchParametersValues() [2/2]

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

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ operator=()

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

Definition at line 70 of file FullHmmTransitionMatrix.cpp.

References bpp::AbstractHmmTransitionMatrix::operator=().

◆ Pij()

double bpp::FullHmmTransitionMatrix::Pij	(	size_t	i,
		size_t	j
	)		const

inlinevirtual

Get the transition probability between two states.

Parameters

i	initial state.
j	final state.

Returns: the transition probability between the two states.

Implements bpp::HmmTransitionMatrix.

Definition at line 95 of file FullHmmTransitionMatrix.h.

References vSimplex_.

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 180 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::reset().

Referenced by bpp::AbstractParameterAliasable::resetParameters_().

◆ sample()

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

inherited

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 85 of file AbstractHmmTransitionMatrix.cpp.

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

◆ setAllParametersValues() [1/2]

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList & parameters )

inlinevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 94 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setAllParametersValues().

◆ setAllParametersValues() [2/2]

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

Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

◆ setHmmStateAlphabet()

void AbstractHmmTransitionMatrix::setHmmStateAlphabet ( const HmmStateAlphabet * stateAlphabet )

virtualinherited

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 77 of file AbstractHmmTransitionMatrix.cpp.

References bpp::AbstractHmmTransitionMatrix::alph_.

◆ setNamespace() [1/2]

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

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.

Implements bpp::Parametrizable.

Reimplemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, and bpp::LogsumHmmLikelihood.

Definition at line 47 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::LogsumHmmLikelihood::setNamespace(), bpp::LowMemoryRescaledHmmLikelihood::setNamespace(), bpp::RescaledHmmLikelihood::setNamespace(), and bpp::AbstractParameterAliasable::setNamespace().

◆ setNamespace() [2/2]

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

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::LogsumHmmLikelihood::setNamespace(), bpp::FunctionWrapper::setNamespace(), and bpp::InvariantMixedDiscreteDistribution::setNamespace().

◆ setParametersValues() [1/2]

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList & parameters )

inlinevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 106 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setParametersValues().

Referenced by bpp::LogsumHmmLikelihood::setParameters(), bpp::LowMemoryRescaledHmmLikelihood::setParameters(), and bpp::RescaledHmmLikelihood::setParameters().

◆ setParametersValues() [2/2]

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

Referenced by bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue() [1/2]

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

inlinevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 100 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, and bpp::ParameterList::setParameterValue().

◆ setParameterValue() [2/2]

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

Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().