A simple implementation of hidden Markov models recursion. More...

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

Inheritance diagram for bpp::RescaledHmmLikelihood:

Collaboration diagram for bpp::RescaledHmmLikelihood:

Public Member Functions
	RescaledHmmLikelihood (HmmStateAlphabet hiddenAlphabet, HmmTransitionMatrix transitionMatrix, HmmEmissionProbabilities *emissionProbabilities, const std::string &prefix) throw (Exception)
	Build a new RescaledHmmLikelihood object. More...

	RescaledHmmLikelihood (const RescaledHmmLikelihood &lik)

RescaledHmmLikelihood &	operator= (const RescaledHmmLikelihood &lik)

virtual	~RescaledHmmLikelihood ()

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

const HmmStateAlphabet &	getHmmStateAlphabet () const

HmmStateAlphabet &	getHmmStateAlphabet ()

const HmmTransitionMatrix &	getHmmTransitionMatrix () const

HmmTransitionMatrix &	getHmmTransitionMatrix ()

const HmmEmissionProbabilities &	getHmmEmissionProbabilities () const

HmmEmissionProbabilities &	getHmmEmissionProbabilities ()

void	setBreakPoints (const std::vector< size_t > &breakPoints)

const std::vector< size_t > &	getBreakPoints () const

void	setParameters (const ParameterList &pl) throw (Exception)
	Set the point where the function must be computed. More...

double	getValue () const throw (Exception)
	Get the value of the function at the current point. More...

double	getLogLikelihood () const

double	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site. More...

Vdouble	getLikelihoodForEachSite () const
	Get the likelihood for each site. More...

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

Vdouble	getHiddenStatesPosteriorProbabilitiesForASite (size_t site) const

void	getHiddenStatesPosteriorProbabilities (std::vector< std::vector< double > > &probs, bool append=false) const throw (Exception)

virtual double	d2f (const std::string &variable, const ParameterList &parameters) throw (Exception)
	Get the value of the second order derivative of the function according to a given set of parameters. More...

virtual double	d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters) throw (Exception)
	Get the value of the cross derivative of the function according to a given set of parameters. More...

virtual double	df (const std::string &variable, const ParameterList &parameters) throw (Exception)
	Get the value of the first derivative of the function according to a given set of parameters. More...

virtual double	f (const ParameterList &parameters) throw (Exception)
	Get the value of the function according to a given set of parameters. 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 throw (ParameterNotFoundException)
	Get the parameter with specified name. More...

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

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

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

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

virtual bool	matchParametersValues (const ParameterList &parameters)=0 throw (ConstraintException)
	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 throw (ParameterNotFoundException)
	Get the parameter with specified name. More...

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

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

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

void	setParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Update the parameters from parameters. More...

bool	matchParametersValues (const ParameterList &parameters) throw (ConstraintException)
	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...


void	enableFirstOrderDerivatives (bool yn)
	Tell if derivatives must be computed. More...

bool	enableFirstOrderDerivatives () const
	Tell if derivatives must be computed. More...

double	getFirstOrderDerivative (const std::string &variable) const throw (Exception)
	Get the derivative of the function at the current point. More...

double	getDLogLikelihood () const

void	enableSecondOrderDerivatives (bool yn)
	Tell if derivatives must be computed. More...

bool	enableSecondOrderDerivatives () const
	Tell if derivatives must be computed. More...

double	getSecondOrderDerivative (const std::string &variable) const throw (Exception)
	Get the second order derivative of the function at the current point. More...

double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const throw (Exception)
	Get the value of the cross derivative of the function according to a given set of parameters. More...

double	getD2LogLikelihood () const

Protected Member Functions
void	computeForward_ ()

void	computeBackward_ () const

void	computeDLikelihood_ () const

void	computeD2Likelihood_ () const

void	computeDForward_ () const

void	computeD2Forward_ () const

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index) throw (IndexOutOfBoundsException)

void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name) throw (ParameterNotFoundException)

Parameter &	getParameter_ (size_t index) throw (IndexOutOfBoundsException)

const Parameter &	getParameter_ (size_t index) const throw (IndexOutOfBoundsException)

Parameter &	getParameterWithNamespace_ (const std::string &name) throw (ParameterNotFoundException)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const throw (ParameterNotFoundException)

ParameterList &	getParameters_ ()

Protected Attributes
double	dLogLik_

std::string	dVariable_

double	d2LogLik_

std::string	d2Variable_

Private Attributes
std::auto_ptr< HmmStateAlphabet >	hiddenAlphabet_
	The alphabet describing the hidden states. More...

std::auto_ptr< HmmTransitionMatrix >	transitionMatrix_

std::auto_ptr< HmmEmissionProbabilities >	emissionProbabilities_

std::vector< double >	likelihood_
	The likelihood arrays. More...

std::vector< std::vector< double > >	dLikelihood_
	derivatec of forward likelihood More...

std::vector< std::vector< double > >	d2Likelihood_

std::vector< std::vector< double > >	backLikelihood_
	backward likelihood More...

bool	backLikelihoodUpToDate_

std::vector< double >	scales_
	scales for likelihood computing More...

std::vector< double >	dScales_

std::vector< double >	d2Scales_

double	logLik_

std::vector< size_t >	breakPoints_

size_t	nbStates_

size_t	nbSites_

Detailed Description

A simple implementation of hidden Markov models recursion.

This implementation uses the rescaling method described in Durbin et al "Biological sequence analysis", Cambridge University Press. It also offer the possibility to specify "breakpoints", where the chain will be reset to the equilibrium frequencies.

Definition at line 59 of file RescaledHmmLikelihood.h.

Constructor & Destructor Documentation

◆ RescaledHmmLikelihood() [1/2]

RescaledHmmLikelihood::RescaledHmmLikelihood	(	HmmStateAlphabet *	hiddenAlphabet,
		HmmTransitionMatrix *	transitionMatrix,
		HmmEmissionProbabilities *	emissionProbabilities,
		const std::string &	prefix
	)
throw	(	Exception
	)

Build a new RescaledHmmLikelihood object.

Warning: the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to be destroyed with this object.

Definition at line 50 of file RescaledHmmLikelihood.cpp.

Referenced by clone().

◆ RescaledHmmLikelihood() [2/2]

bpp::RescaledHmmLikelihood::RescaledHmmLikelihood ( const RescaledHmmLikelihood & lik )

inline

Definition at line 137 of file RescaledHmmLikelihood.h.

References emissionProbabilities_, hiddenAlphabet_, and transitionMatrix_.

◆ ~RescaledHmmLikelihood()

virtual bpp::RescaledHmmLikelihood::~RescaledHmmLikelihood ( )

inlinevirtual

Definition at line 187 of file RescaledHmmLikelihood.h.

Member Function Documentation

◆ addParameter_()

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

inlineprotectedinherited

Definition at line 137 of file AbstractParametrizable.h.

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

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

◆ addParameters_()

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

inlineprotectedinherited

Definition at line 143 of file AbstractParametrizable.h.

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

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

◆ clone()

RescaledHmmLikelihood* bpp::RescaledHmmLikelihood::clone ( ) const

inlinevirtual

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

Returns: A pointer toward the copy object.

Implements bpp::HmmLikelihood.

Definition at line 194 of file RescaledHmmLikelihood.h.

References RescaledHmmLikelihood().

◆ computeBackward_()

void RescaledHmmLikelihood::computeBackward_ ( ) const

protected

Definition at line 240 of file RescaledHmmLikelihood.cpp.

◆ computeD2Forward_()

void RescaledHmmLikelihood::computeD2Forward_ ( ) const

protected

Definition at line 474 of file RescaledHmmLikelihood.cpp.

References bpp::VectorTools::sum().

Referenced by computeD2Likelihood_().

◆ computeD2Likelihood_()

void bpp::RescaledHmmLikelihood::computeD2Likelihood_ ( ) const

inlineprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 244 of file RescaledHmmLikelihood.h.

References computeD2Forward_().

◆ computeDForward_()

void RescaledHmmLikelihood::computeDForward_ ( ) const

protected

Definition at line 375 of file RescaledHmmLikelihood.cpp.

References bpp::VectorTools::sum().

Referenced by computeDLikelihood_().

◆ computeDLikelihood_()

void bpp::RescaledHmmLikelihood::computeDLikelihood_ ( ) const

inlineprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 239 of file RescaledHmmLikelihood.h.

References computeDForward_().

◆ computeForward_()

void RescaledHmmLikelihood::computeForward_ ( )

protected

Definition at line 114 of file RescaledHmmLikelihood.cpp.

References bpp::TextTools::toString(), and bpp::ApplicationTools::warning.

Referenced by setBreakPoints().

◆ d2f() [1/2]

virtual double bpp::DerivableSecondOrder::d2f	(	const std::string &	variable,
		const ParameterList &	parameters
	)
throw	(	Exception
	)

inlinevirtualinherited

Get the value of the second order derivative of the function according to a given set of parameters.

Parameters

variable	The name of the variable in $\frac{\partial^2 f}{\partial x^2}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 236 of file Functions.h.

References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().

◆ d2f() [2/2]

virtual double bpp::DerivableSecondOrder::d2f	(	const std::string &	variable1,
		const std::string &	variable2,
		const ParameterList &	parameters
	)
throw	(	Exception
	)

inlinevirtualinherited

Get the value of the cross derivative of the function according to a given set of parameters.

Parameters

variable1	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .
variable2	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 263 of file Functions.h.

References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().

◆ deleteParameter_() [1/2]

void bpp::AbstractParametrizable::deleteParameter_	(	size_t	index	)
throw	(	IndexOutOfBoundsException
	)

inlineprotectedinherited

Definition at line 148 of file AbstractParametrizable.h.

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

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

◆ deleteParameter_() [2/2]

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

inlineprotectedinherited

Definition at line 155 of file AbstractParametrizable.h.

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

◆ deleteParameters_()

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

inlineprotectedinherited

Definition at line 160 of file AbstractParametrizable.h.

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

◆ df()

virtual double bpp::DerivableFirstOrder::df	(	const std::string &	variable,
		const ParameterList &	parameters
	)
throw	(	Exception
	)

inlinevirtualinherited

Get the value of the first derivative of the function according to a given set of parameters.

Parameters

variable	The name of the variable in $\frac{df}{dx}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 176 of file Functions.h.

References bpp::DerivableFirstOrder::getFirstOrderDerivative(), and bpp::Function::setParameters().

◆ enableFirstOrderDerivatives() [1/2]

void bpp::AbstractHmmLikelihood::enableFirstOrderDerivatives ( bool yn )

inlinevirtualinherited

Tell if derivatives must be computed.

Parameters

yn yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 163 of file HmmLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

bool bpp::AbstractHmmLikelihood::enableFirstOrderDerivatives ( ) const

inlinevirtualinherited

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 165 of file HmmLikelihood.h.

◆ enableSecondOrderDerivatives() [1/2]

void bpp::AbstractHmmLikelihood::enableSecondOrderDerivatives ( bool yn )

inlinevirtualinherited

Tell if derivatives must be computed.

Parameters

yn yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 185 of file HmmLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

bool bpp::AbstractHmmLikelihood::enableSecondOrderDerivatives ( ) const

inlinevirtualinherited

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 187 of file HmmLikelihood.h.

◆ f()

virtual double bpp::Function::f	(	const ParameterList &	parameters	)
throw	(	Exception
	)

inlinevirtualinherited

Get the value of the function according to a given set of parameters.

Parameters

parameters The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Reimplemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, and bpp::AbstractNumericalDerivative.

Definition at line 117 of file Functions.h.

References bpp::Function::getValue(), and bpp::Function::setParameters().

Referenced by bpp::NewtonOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::BfgsMultiDimensions::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::GoldenSectionSearch::doStep(), bpp::BrentOneDimension::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::FunctionWrapper::f(), bpp::PowellMultiDimensions::optimize(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::AbstractOptimizer::step(), and bpp::DownhillSimplexMethod::tryExtrapolation().

◆ fireParameterChanged()

void RescaledHmmLikelihood::fireParameterChanged ( const ParameterList & parameters )

virtual

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Implements bpp::AbstractParametrizable.

Definition at line 97 of file RescaledHmmLikelihood.cpp.

◆ getBreakPoints()

const std::vector<size_t>& bpp::RescaledHmmLikelihood::getBreakPoints ( ) const

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 212 of file RescaledHmmLikelihood.h.

References breakPoints_.

◆ getD2LogLikelihood()

double bpp::AbstractHmmLikelihood::getD2LogLikelihood ( ) const

inlinevirtualinherited

Implements bpp::HmmLikelihood.

Definition at line 191 of file HmmLikelihood.h.

References bpp::AbstractHmmLikelihood::d2LogLik_.

◆ getDLogLikelihood()

double bpp::AbstractHmmLikelihood::getDLogLikelihood ( ) const

inlinevirtualinherited

Implements bpp::HmmLikelihood.

Definition at line 169 of file HmmLikelihood.h.

References bpp::AbstractHmmLikelihood::dLogLik_.

◆ getFirstOrderDerivative()

double AbstractHmmLikelihood::getFirstOrderDerivative	(	const std::string &	variable	)	const
throw	(	Exception
	)

virtualinherited

Get the derivative of the function at the current point.

Parameters

variable The name of the variable in $\frac{df}{dx}$ .

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::DerivableFirstOrder.

Definition at line 68 of file HmmLikelihood.cpp.

◆ getHiddenStatesPosteriorProbabilities()

void RescaledHmmLikelihood::getHiddenStatesPosteriorProbabilities	(	std::vector< std::vector< double > > &	probs,
		bool	append = `false`
	)		const
throw	(	Exception
	)

virtual

Implements bpp::HmmLikelihood.

Definition at line 351 of file RescaledHmmLikelihood.cpp.

◆ getHiddenStatesPosteriorProbabilitiesForASite()

Vdouble RescaledHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite ( size_t site ) const

virtual

Implements bpp::HmmLikelihood.

Definition at line 335 of file RescaledHmmLikelihood.cpp.

◆ getHmmEmissionProbabilities() [1/2]

const HmmEmissionProbabilities& bpp::RescaledHmmLikelihood::getHmmEmissionProbabilities ( ) const

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 203 of file RescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmEmissionProbabilities() [2/2]

HmmEmissionProbabilities& bpp::RescaledHmmLikelihood::getHmmEmissionProbabilities ( )

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 204 of file RescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmStateAlphabet() [1/2]

const HmmStateAlphabet& bpp::RescaledHmmLikelihood::getHmmStateAlphabet ( ) const

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 197 of file RescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmStateAlphabet() [2/2]

HmmStateAlphabet& bpp::RescaledHmmLikelihood::getHmmStateAlphabet ( )

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 198 of file RescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmTransitionMatrix() [1/2]

const HmmTransitionMatrix& bpp::RescaledHmmLikelihood::getHmmTransitionMatrix ( ) const

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 200 of file RescaledHmmLikelihood.h.

References transitionMatrix_.

◆ getHmmTransitionMatrix() [2/2]

HmmTransitionMatrix& bpp::RescaledHmmLikelihood::getHmmTransitionMatrix ( )

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 201 of file RescaledHmmLikelihood.h.

References transitionMatrix_.

◆ getLikelihoodForASite()

double RescaledHmmLikelihood::getLikelihoodForASite ( size_t site ) const

virtual

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implements bpp::HmmLikelihood.

Definition at line 307 of file RescaledHmmLikelihood.cpp.

◆ getLikelihoodForEachSite()

Vdouble RescaledHmmLikelihood::getLikelihoodForEachSite ( ) const

virtual

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

Implements bpp::HmmLikelihood.

Definition at line 317 of file RescaledHmmLikelihood.cpp.

◆ getLogLikelihood()

double bpp::RescaledHmmLikelihood::getLogLikelihood ( ) const

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 221 of file RescaledHmmLikelihood.h.

References logLik_.

◆ 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::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::write().

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

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

◆ getParameter() [1/2]

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

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::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
throw	(	ParameterNotFoundException
	)

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::FunctionWrapper::getParameter().

◆ getParameter_() [1/3]

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

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 175 of file AbstractParametrizable.h.

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

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

◆ getParameter_() [2/3]

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

inlineprotectedinherited

Definition at line 199 of file AbstractParametrizable.h.

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

◆ getParameter_() [3/3]

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

inlineprotectedinherited

Definition at line 205 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 63 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), bpp::BppODiscreteDistributionFormat::read(), 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(), bpp::AbstractParameterAliasable::fireParameterChanged(), 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::FunctionWrapper, bpp::ParametrizableAdapter, bpp::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineprotectedinherited

Definition at line 212 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue() [1/2]

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

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 84 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
throw	(	ParameterNotFoundException
	)

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::FunctionWrapper::getParameterValue(), and bpp::BppODiscreteDistributionFormat::read().

◆ getParameterWithNamespace_() [1/2]

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

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 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

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

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 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getSecondOrderDerivative() [1/2]

double AbstractHmmLikelihood::getSecondOrderDerivative	(	const std::string &	variable	)	const
throw	(	Exception
	)

virtualinherited

Get the second order derivative of the function at the current point.

Parameters

variable The name of the variable in $\frac{\partial^2 f}{\partial x^2}$ .

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::DerivableSecondOrder.

Definition at line 80 of file HmmLikelihood.cpp.

◆ getSecondOrderDerivative() [2/2]

double bpp::AbstractHmmLikelihood::getSecondOrderDerivative	(	const std::string &	variable1,
		const std::string &	variable2
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Get the value of the cross derivative of the function according to a given set of parameters.

Parameters

variable1	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .
variable2	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Implements bpp::DerivableSecondOrder.

Definition at line 196 of file HmmLikelihood.h.

◆ getValue()

double bpp::RescaledHmmLikelihood::getValue	(		)	const
throw	(	Exception
	)

inlinevirtual

Get the value of the function at the current point.

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 219 of file RescaledHmmLikelihood.h.

References logLik_.

◆ hasParameter() [1/2]

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

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

◆ hasParameter() [2/2]

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_.

◆ matchParametersValues() [1/2]

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

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 111 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [2/2]

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

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::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ operator=()

RescaledHmmLikelihood& bpp::RescaledHmmLikelihood::operator= ( const RescaledHmmLikelihood & lik )

inline

Definition at line 161 of file RescaledHmmLikelihood.h.

References backLikelihood_, backLikelihoodUpToDate_, breakPoints_, d2Likelihood_, d2Scales_, dLikelihood_, dScales_, emissionProbabilities_, hiddenAlphabet_, likelihood_, logLik_, nbSites_, nbStates_, bpp::AbstractHmmLikelihood::operator=(), scales_, and transitionMatrix_.

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 165 of file AbstractParametrizable.h.

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

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

◆ setAllParametersValues() [1/2]

void bpp::AbstractParametrizable::setAllParametersValues	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

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 90 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	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

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

◆ setBreakPoints()

void bpp::RescaledHmmLikelihood::setBreakPoints ( const std::vector< size_t > & breakPoints )

inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 206 of file RescaledHmmLikelihood.h.

References backLikelihoodUpToDate_, breakPoints_, and computeForward_().

◆ 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, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 45 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by 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::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

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

◆ setParameters()

void bpp::RescaledHmmLikelihood::setParameters	(	const ParameterList &	parameters	)
throw	(	Exception
	)

inlinevirtual

Set the point where the function must be computed.

Parameters

parameters The parameter set to pass to the function.

Implements bpp::Function.

Definition at line 214 of file RescaledHmmLikelihood.h.

References bpp::AbstractParametrizable::setParametersValues().

◆ setParametersValues() [1/2]

void bpp::AbstractParametrizable::setParametersValues	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

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 104 of file AbstractParametrizable.h.

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

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

◆ setParametersValues() [2/2]

virtual void bpp::Parametrizable::setParametersValues	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

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::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue() [1/2]

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

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 97 of file AbstractParametrizable.h.

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

◆ setParameterValue() [2/2]

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

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

Member Data Documentation

◆ backLikelihood_

std::vector<std::vector<double> > bpp::RescaledHmmLikelihood::backLikelihood_

mutableprivate

backward likelihood

backLikelihood_[i][j] corresponds to Pr(x_i+1...x_n | yi=j), where the x are the observed states, and y the hidden states.

Definition at line 102 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ backLikelihoodUpToDate_

bool bpp::RescaledHmmLikelihood::backLikelihoodUpToDate_

mutableprivate

Definition at line 103 of file RescaledHmmLikelihood.h.

Referenced by operator=(), and setBreakPoints().

◆ breakPoints_

std::vector<size_t> bpp::RescaledHmmLikelihood::breakPoints_

private

Definition at line 118 of file RescaledHmmLikelihood.h.

Referenced by getBreakPoints(), operator=(), and setBreakPoints().

◆ d2Likelihood_

std::vector<std::vector<double> > bpp::RescaledHmmLikelihood::d2Likelihood_

mutableprivate

Definition at line 93 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ d2LogLik_

double bpp::AbstractHmmLikelihood::d2LogLik_

mutableprotectedinherited

Definition at line 147 of file HmmLikelihood.h.

Referenced by bpp::AbstractHmmLikelihood::getD2LogLikelihood(), and bpp::AbstractHmmLikelihood::operator=().

◆ d2Scales_

std::vector<double> bpp::RescaledHmmLikelihood::d2Scales_

mutableprivate

Definition at line 115 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ d2Variable_

std::string bpp::AbstractHmmLikelihood::d2Variable_

mutableprotectedinherited

Definition at line 148 of file HmmLikelihood.h.

Referenced by bpp::AbstractHmmLikelihood::operator=().

◆ dLikelihood_

std::vector<std::vector<double> > bpp::RescaledHmmLikelihood::dLikelihood_

mutableprivate

derivatec of forward likelihood

dlikelihood_[i][j] corresponds to d(Pr(x_1...x_i, y_i=j))/Pr(x_1...x_i)), where the x are the observed states, and y the hidden states.

Definition at line 92 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ dLogLik_

double bpp::AbstractHmmLikelihood::dLogLik_

mutableprotectedinherited

Definition at line 144 of file HmmLikelihood.h.

Referenced by bpp::AbstractHmmLikelihood::getDLogLikelihood(), and bpp::AbstractHmmLikelihood::operator=().

◆ dScales_

std::vector<double> bpp::RescaledHmmLikelihood::dScales_

mutableprivate

Definition at line 114 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ dVariable_

std::string bpp::AbstractHmmLikelihood::dVariable_

mutableprotectedinherited

Definition at line 145 of file HmmLikelihood.h.

Referenced by bpp::AbstractHmmLikelihood::operator=().

◆ emissionProbabilities_

std::auto_ptr<HmmEmissionProbabilities> bpp::RescaledHmmLikelihood::emissionProbabilities_

private

Definition at line 69 of file RescaledHmmLikelihood.h.

Referenced by getHmmEmissionProbabilities(), operator=(), and RescaledHmmLikelihood().

◆ hiddenAlphabet_

std::auto_ptr<HmmStateAlphabet> bpp::RescaledHmmLikelihood::hiddenAlphabet_

private

The alphabet describing the hidden states.

Definition at line 67 of file RescaledHmmLikelihood.h.

Referenced by getHmmStateAlphabet(), operator=(), and RescaledHmmLikelihood().

◆ likelihood_

std::vector<double> bpp::RescaledHmmLikelihood::likelihood_

private

The likelihood arrays.

forward likelihood

likelihood_[i * nbStates_ + j] corresponds to Pr(x_1...x_i, y_i=j)/Pr(x_1...x_i), where the x are the observed states, and y the hidden states.

Definition at line 83 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ logLik_

double bpp::RescaledHmmLikelihood::logLik_

private

Definition at line 116 of file RescaledHmmLikelihood.h.

Referenced by getLogLikelihood(), getValue(), and operator=().

◆ nbSites_

size_t bpp::RescaledHmmLikelihood::nbSites_

private

Definition at line 120 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ nbStates_

size_t bpp::RescaledHmmLikelihood::nbStates_

private

Definition at line 120 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ scales_

std::vector<double> bpp::RescaledHmmLikelihood::scales_

private

scales for likelihood computing

scales_[i * nbStates_ + j] corresponds to Pr(x_1...x_i)/Pr(x_1...x_{i-1}) where the x are the observed states.

Definition at line 112 of file RescaledHmmLikelihood.h.

Referenced by operator=().

◆ transitionMatrix_

std::auto_ptr<HmmTransitionMatrix> bpp::RescaledHmmLikelihood::transitionMatrix_

private

Definition at line 68 of file RescaledHmmLikelihood.h.

Referenced by getHmmTransitionMatrix(), operator=(), and RescaledHmmLikelihood().

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

Bpp/Numeric/Hmm/RescaledHmmLikelihood.h
Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RescaledHmmLikelihood() [1/2]

◆ RescaledHmmLikelihood() [2/2]

◆ ~RescaledHmmLikelihood()

Member Function Documentation

◆ addParameter_()

◆ addParameters_()

◆ clone()

◆ computeBackward_()

◆ computeD2Forward_()

◆ computeD2Likelihood_()

◆ computeDForward_()

◆ computeDLikelihood_()

◆ computeForward_()

◆ d2f() [1/2]

◆ d2f() [2/2]

◆ deleteParameter_() [1/2]

◆ deleteParameter_() [2/2]

◆ deleteParameters_()

◆ df()

◆ enableFirstOrderDerivatives() [1/2]

◆ enableFirstOrderDerivatives() [2/2]

◆ enableSecondOrderDerivatives() [1/2]

◆ enableSecondOrderDerivatives() [2/2]

◆ f()

◆ fireParameterChanged()

◆ getBreakPoints()

◆ getD2LogLikelihood()

◆ getDLogLikelihood()

◆ getFirstOrderDerivative()

◆ getHiddenStatesPosteriorProbabilities()

◆ getHiddenStatesPosteriorProbabilitiesForASite()

◆ getHmmEmissionProbabilities() [1/2]

◆ getHmmEmissionProbabilities() [2/2]

◆ getHmmStateAlphabet() [1/2]

◆ getHmmStateAlphabet() [2/2]

◆ getHmmTransitionMatrix() [1/2]

◆ getHmmTransitionMatrix() [2/2]

◆ getLikelihoodForASite()

◆ getLikelihoodForEachSite()

◆ getLogLikelihood()

◆ getNamespace() [1/2]

◆ getNamespace() [2/2]

◆ getNumberOfParameters() [1/2]

◆ getNumberOfParameters() [2/2]

◆ getParameter() [1/2]

◆ getParameter() [2/2]

◆ getParameter_() [1/3]

◆ getParameter_() [2/3]

◆ getParameter_() [3/3]

◆ getParameterNameWithoutNamespace() [1/2]

◆ getParameterNameWithoutNamespace() [2/2]

◆ getParameters() [1/2]

◆ getParameters() [2/2]

◆ getParameters_()

◆ getParameterValue() [1/2]

◆ getParameterValue() [2/2]

◆ getParameterWithNamespace_() [1/2]

◆ getParameterWithNamespace_() [2/2]

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getValue()

◆ hasParameter() [1/2]

◆ hasParameter() [2/2]

◆ matchParametersValues() [1/2]

◆ matchParametersValues() [2/2]

◆ operator=()

◆ resetParameters_()

◆ setAllParametersValues() [1/2]

◆ setAllParametersValues() [2/2]

◆ setBreakPoints()

◆ setNamespace() [1/2]

◆ setNamespace() [2/2]

◆ setParameters()

◆ setParametersValues() [1/2]