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

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 &	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...

Detailed Description

Hidden states alphabet.

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

Definition at line 28 of file HmmStateAlphabet.h.

Constructor & Destructor Documentation

◆ HmmStateAlphabet()

bpp::HmmStateAlphabet::HmmStateAlphabet ( )

inline

Definition at line 32 of file HmmStateAlphabet.h.

◆ ~HmmStateAlphabet()

virtual bpp::HmmStateAlphabet::~HmmStateAlphabet ( )

inlinevirtual

Definition at line 33 of file HmmStateAlphabet.h.

References clone(), getNumberOfStates(), getState(), and worksWith().

Member Function Documentation

◆ clone()

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

overridepure virtual

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

Returns: A pointer toward the copy object.

Implements bpp::Clonable.

Referenced by ~HmmStateAlphabet().

◆ 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()

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

pure virtual

Referenced by bpp::AbstractHmmTransitionMatrix::sample(), and ~HmmStateAlphabet().

◆ 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().

◆ 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

Referenced by ~HmmStateAlphabet().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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 ~HmmStateAlphabet().

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

Bpp/Numeric/Hmm/HmmStateAlphabet.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ HmmStateAlphabet()

◆ ~HmmStateAlphabet()

Member Function Documentation

◆ clone()

◆ getNamespace()

◆ getNumberOfParameters()

◆ getNumberOfStates()

◆ getParameterNameWithoutNamespace()

◆ getParameters()

◆ getParameters_()

◆ getParameterValue()

◆ getState()

◆ hasParameter()

◆ matchParametersValues()

◆ parameter()

◆ removeConstraint()

◆ setAllParametersValues()

◆ setConstraint()

◆ setNamespace()

◆ setParametersValues()

◆ setParameterValue()

◆ worksWith()