bpp::HmmStateAlphabet Class Reference

Hidden states alphabet. More...

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

Inheritance diagram for bpp::HmmStateAlphabet:

Collaboration diagram for bpp::HmmStateAlphabet:

Public Member Functions
	HmmStateAlphabet ()
virtual	~HmmStateAlphabet ()
virtual const Clonable &	getState (size_t stateIndex) const =0
virtual size_t	getNumberOfStates () const =0
virtual bool	worksWith (const HmmStateAlphabet *stateAlphabet) const =0
	Tell if this instance can work with the instance of alphabet given as input. 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...
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

Hidden states alphabet.

Implementations of this interface describe the set of hidden states of a Hidden Markov Model.

Definition at line 64 of file HmmStateAlphabet.h.

Constructor & Destructor Documentation

HmmStateAlphabet()

bpp::HmmStateAlphabet::HmmStateAlphabet ( )

inline

Definition at line 68 of file HmmStateAlphabet.h.

~HmmStateAlphabet()

virtual bpp::HmmStateAlphabet::~HmmStateAlphabet ( )

inlinevirtual

Definition at line 69 of file HmmStateAlphabet.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=().

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::HmmStateAlphabet::getNumberOfStates ( ) const

pure virtual

Referenced by bpp::AbstractHmmTransitionMatrix::getNumberOfStates(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), and bpp::AbstractHmmTransitionMatrix::sample().

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().

getState()

virtual const Clonable& bpp::HmmStateAlphabet::getState ( size_t  stateIndex ) const

pure virtual

Parameters

stateIndex

The index of a hidden state.

Returns

The corresponding hidden state.

See also

getNumberOfStates

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().

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().

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().

worksWith()

virtual bool bpp::HmmStateAlphabet::worksWith ( const HmmStateAlphabet *  stateAlphabet ) const

pure virtual

Tell if this instance can work with the instance of alphabet given as input.

In many case, this will return true is 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.

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

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

• Bpp/Numeric/Hmm/HmmStateAlphabet.h