bpp::HmmTransitionMatrix Class Reference

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

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

Inheritance diagram for bpp::HmmTransitionMatrix:

Collaboration diagram for bpp::HmmTransitionMatrix:

Public Member Functions
virtual const HmmStateAlphabet *	getHmmStateAlphabet () const =0
virtual void	setHmmStateAlphabet (const HmmStateAlphabet *stateAlphabet)=0
	Set the new hidden state alphabet. More...
virtual size_t	getNumberOfStates () const =0
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 &	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...
virtual Clonable *	clone () const =0
	Create a copy of this object and send a pointer to it. More...

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

Detailed Description

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

This class is part of the HMM framework.

Definition at line 60 of file HmmTransitionMatrix.h.

Member Function Documentation

clone()

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

pure virtualinherited

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

Returns

A pointer toward the copy object.

Implemented in bpp::TransformedParameter, bpp::MultipleDiscreteDistribution, bpp::DiscreteDistribution, bpp::ParameterListener, bpp::BppNumberI, bpp::HmmLikelihood, bpp::HmmEmissionProbabilities, bpp::Optimizer, bpp::OptimizationStopCondition, bpp::DerivableSecondOrder, bpp::DerivableFirstOrder, bpp::AbstractNumericalDerivative, bpp::Constraint, bpp::OutputStream, bpp::PlaceboTransformedParameter, bpp::IntervalTransformedParameter, bpp::RTransformedParameter, bpp::Table< T >, bpp::PrincipalComponentAnalysis, bpp::DualityDiagram, bpp::CorrespondenceAnalysis, bpp::ContingencyTableTest, bpp::Range< T >, bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::Simplex, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::ConstantDistribution, bpp::BetaDiscreteDistribution, bpp::ParametrizableCollection< N >, bpp::ParameterList, bpp::Parameter, bpp::ParameterEvent, bpp::BppUnsignedInteger, bpp::BppInteger, bpp::BppDouble, bpp::Number< T >, bpp::Number< double >, bpp::Number< int >, bpp::Number< unsigned int >, bpp::BppNotANumber, bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, bpp::FullHmmTransitionMatrix, bpp::AutoCorrelationTransitionMatrix, bpp::TwoPointsNumericalDerivative, bpp::ThreePointsNumericalDerivative, bpp::SimpleNewtonMultiDimensions, bpp::SimpleMultiDimensions, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::ReparametrizationFunctionWrapper, bpp::PowellMultiDimensions, bpp::PowellMultiDimensions::PMDStopCondition, bpp::FunctionStopCondition, bpp::ParametersStopCondition, bpp::NegativeOperator, bpp::MathOperator, bpp::FunctionOperator< F >, bpp::ConstantOperator, bpp::ComputationTree, bpp::BinaryOperator, bpp::NewtonOneDimension, bpp::NewtonBacktrackOneDimension, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::MetaOptimizer, bpp::MetaOptimizerInfos, bpp::GoldenSectionSearch, bpp::GoldenSectionSearch::GSSStopCondition, bpp::TestFunction, bpp::InfinityDerivableSecondOrderWrapper, bpp::InfinityDerivableFirstOrderWrapper, bpp::InfinityFunctionWrapper, bpp::FivePointsNumericalDerivative, bpp::DownhillSimplexMethod, bpp::DownhillSimplexMethod::DSMStopCondition, bpp::DirectionFunction, bpp::ConjugateGradientMultiDimensions, bpp::BrentOneDimension, bpp::BrentOneDimension::BODStopCondition, bpp::BfgsMultiDimensions, bpp::DataTable, bpp::IntervalConstraint, bpp::AutoParameter, bpp::AliasParameterListener, bpp::StdErr, bpp::StdOut, bpp::StlOutputStreamWrapper, bpp::StlOutputStream, bpp::NullOutputStream, bpp::RGBColor, bpp::Point2D< T >, bpp::Font, bpp::GlobalGraph, bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl >, bpp::BppVector< T >, bpp::BppString, and bpp::BppBoolean.

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

getEquilibriumFrequencies()

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

pure virtual

Returns

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

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

Referenced by bpp::LogsumHmmLikelihood::computeForward_().

getHmmStateAlphabet()

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

pure virtual

Returns

The hidden alphabet associated to this model.

Implemented in bpp::AbstractHmmTransitionMatrix.

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

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

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

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

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

getNumberOfStates()

virtual size_t bpp::HmmTransitionMatrix::getNumberOfStates ( ) const

pure virtual

Returns

The number of states in the model.

Implemented in bpp::AbstractHmmTransitionMatrix.

getParameter()

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().

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

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

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::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_()

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()

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().

getPij()

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

pure virtual

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 bpp::LogsumHmmLikelihood::computeD2Forward_(), bpp::LogsumHmmLikelihood::computeDForward_(), and bpp::AbstractHmmTransitionMatrix::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::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

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

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::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().

Pij()

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

pure virtual

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.

Referenced by bpp::LogsumHmmLikelihood::computeBackward_(), and bpp::LogsumHmmLikelihood::computeForward_().

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

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

setHmmStateAlphabet()

virtual void bpp::HmmTransitionMatrix::setHmmStateAlphabet ( const HmmStateAlphabet *  stateAlphabet )

pure 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).

Implemented in bpp::AbstractHmmTransitionMatrix.

Referenced by bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), and bpp::LogsumHmmLikelihood::operator=().

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::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()

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()

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().

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

• Bpp/Numeric/Hmm/HmmTransitionMatrix.h