A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage. More...

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

Inheritance diagram for bpp::LowMemoryRescaledHmmLikelihood:

Collaboration diagram for bpp::LowMemoryRescaledHmmLikelihood:

Public Member Functions
	LowMemoryRescaledHmmLikelihood (std::shared_ptr< HmmStateAlphabet > hiddenAlphabet, std::shared_ptr< HmmTransitionMatrix > transitionMatrix, std::shared_ptr< HmmEmissionProbabilities > emissionProbabilities, const std::string &prefix, size_t maxSize=1000000)
	Build a new LowMemoryRescaledHmmLikelihood object. More...

	LowMemoryRescaledHmmLikelihood (const LowMemoryRescaledHmmLikelihood &lik)

LowMemoryRescaledHmmLikelihood &	operator= (const LowMemoryRescaledHmmLikelihood &lik)

virtual	~LowMemoryRescaledHmmLikelihood ()

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

const HmmStateAlphabet &	hmmStateAlphabet () const override

std::shared_ptr< const HmmStateAlphabet >	getHmmStateAlphabet () const override

HmmStateAlphabet &	hmmStateAlphabet () override

std::shared_ptr< HmmStateAlphabet >	getHmmStateAlphabet () override

const HmmTransitionMatrix &	hmmTransitionMatrix () const override

std::shared_ptr< const HmmTransitionMatrix >	getHmmTransitionMatrix () const override

HmmTransitionMatrix &	hmmTransitionMatrix () override

std::shared_ptr< HmmTransitionMatrix >	getHmmTransitionMatrix () override

const HmmEmissionProbabilities &	hmmEmissionProbabilities () const override

std::shared_ptr< const HmmEmissionProbabilities >	getHmmEmissionProbabilities () const override

HmmEmissionProbabilities &	hmmEmissionProbabilities () override

std::shared_ptr< HmmEmissionProbabilities >	getHmmEmissionProbabilities () override

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

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

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

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

double	getLogLikelihood () const override

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

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

double	getLikelihoodForASite (size_t site) const override
	Get the likelihood for a site, and its derivatives. More...

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

Vdouble	getHiddenStatesPosteriorProbabilitiesForASite (size_t site) const override

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

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

virtual double	f (const ParameterList &parameters)
	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 &	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 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 override
	Tell if there is a parameter with specified name. More...

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

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

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

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

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

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

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

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

void	removeConstraint (const std::string &name) override
	Remove the constraint associated with one parameter, if any. More...

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
	Set/Change the constraint associated with one parameter. More...

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

std::string	getNamespace () const override

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


void	enableFirstOrderDerivatives (bool yn)
	From FirstOrder: More...

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

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

double	getDLogLikelihood () const


void	enableSecondOrderDerivatives (bool yn)
	From SecondOrder: More...

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

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

double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const
	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	computeDLikelihood_ () const override

void	computeD2Likelihood_ () const override

double	getDLogLikelihoodForASite (size_t site) const override

double	getD2LogLikelihoodForASite (size_t site) const override

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

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

std::shared_ptr< Parameter > &	getParameter (size_t i)

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

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

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

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

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

ParameterList &	getParameters_ () override
	Get all parameters available. More...

Protected Attributes
double	dLogLik_

std::string	dVariable_

double	d2LogLik_

std::string	d2Variable_

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

std::shared_ptr< HmmTransitionMatrix >	transitionMatrix_

std::shared_ptr< HmmEmissionProbabilities >	emissionProbabilities_

std::vector< double >	likelihood1_
	The likelihood array. More...

std::vector< double >	likelihood2_

double	logLik_

size_t	maxSize_

std::vector< size_t >	breakPoints_

size_t	nbStates_

size_t	nbSites_

Detailed Description

A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage.

This implementation is similar to the one used in the RescaledHmmLikelihood class, but does not store the full likelihood array. The benefit of it is a significantly reduced memory usage, allowing to compute likelihood for very large data sets.

The drawback is that this class can't compute posterior probabilities, neither derivatives of the likelihoods, and can hence only be used to compute likelihoods.

Definition at line 32 of file LowMemoryRescaledHmmLikelihood.h.

Constructor & Destructor Documentation

◆ LowMemoryRescaledHmmLikelihood() [1/2]

LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood	(	std::shared_ptr< HmmStateAlphabet >	hiddenAlphabet,
		std::shared_ptr< HmmTransitionMatrix >	transitionMatrix,
		std::shared_ptr< HmmEmissionProbabilities >	emissionProbabilities,
		const std::string &	prefix,
		size_t	maxSize = `1000000`
	)

Build a new LowMemoryRescaledHmmLikelihood 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.

Parameters

hiddenAlphabet	The hidden states alphabet to use.
transitionMatrix	The transition matrix to use.
emissionProbabilities	The emission probabilities to use.
prefix	A namespace for parameter names.
maxSize	the maximum size of the vector of scales. If this size is exceeded, then a temporary likelihood computation is made and stored, and the vector is reset. the size of the vector specify the memory usage of the class. A two low value can lead to numerical precision errors.

Definition at line 13 of file LowMemoryRescaledHmmLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), computeForward_(), emissionProbabilities_, hiddenAlphabet_, likelihood1_, likelihood2_, nbSites_, nbStates_, and transitionMatrix_.

Referenced by clone().

◆ LowMemoryRescaledHmmLikelihood() [2/2]

bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood ( const LowMemoryRescaledHmmLikelihood & lik )

inline

Definition at line 81 of file LowMemoryRescaledHmmLikelihood.h.

◆ ~LowMemoryRescaledHmmLikelihood()

virtual bpp::LowMemoryRescaledHmmLikelihood::~LowMemoryRescaledHmmLikelihood ( )

inlinevirtual

Definition at line 121 of file LowMemoryRescaledHmmLikelihood.h.

Member Function Documentation

◆ addParameter_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 111 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter().

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

◆ addParameters_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 117 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters().

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

◆ clone()

LowMemoryRescaledHmmLikelihood* bpp::LowMemoryRescaledHmmLikelihood::clone ( ) const

inlineoverridevirtual

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 123 of file LowMemoryRescaledHmmLikelihood.h.

References LowMemoryRescaledHmmLikelihood().

◆ computeD2Likelihood_()

void bpp::LowMemoryRescaledHmmLikelihood::computeD2Likelihood_ ( ) const

inlineoverrideprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 194 of file LowMemoryRescaledHmmLikelihood.h.

◆ computeDLikelihood_()

void bpp::LowMemoryRescaledHmmLikelihood::computeDLikelihood_ ( ) const

inlineoverrideprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 189 of file LowMemoryRescaledHmmLikelihood.h.

◆ computeForward_()

void LowMemoryRescaledHmmLikelihood::computeForward_ ( )

protected

Definition at line 85 of file LowMemoryRescaledHmmLikelihood.cpp.

References breakPoints_, likelihood1_, likelihood2_, logLik_, maxSize_, nbSites_, nbStates_, and transitionMatrix_.

Referenced by fireParameterChanged(), getHiddenStatesPosteriorProbabilities(), LowMemoryRescaledHmmLikelihood(), and setBreakPoints().

◆ d2f() [1/2]

virtual double bpp::SecondOrderDerivable::d2f	(	const std::string &	variable,
		const ParameterList &	parameters
	)

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 193 of file Functions.h.

References bpp::FunctionInterface::setParameters().

◆ d2f() [2/2]

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

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 220 of file Functions.h.

References bpp::FunctionInterface::setParameters().

◆ deleteParameter_() [1/2]

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 137 of file AbstractParametrizable.h.

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

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

◆ deleteParameter_() [2/2]

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 144 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter().

◆ deleteParameters_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 149 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameters().

◆ df()

virtual double bpp::FirstOrderDerivable::df	(	const std::string &	variable,
		const ParameterList &	parameters
	)

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 138 of file Functions.h.

References bpp::FunctionInterface::setParameters().

◆ enableFirstOrderDerivatives() [1/2]

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

inlinevirtualinherited

From FirstOrder:

Implements bpp::FirstOrderDerivable.

Definition at line 132 of file HmmLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

bool bpp::AbstractHmmLikelihood::enableFirstOrderDerivatives ( ) const

inlinevirtualinherited

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::FirstOrderDerivable.

Definition at line 134 of file HmmLikelihood.h.

References bpp::FirstOrderDerivable::getFirstOrderDerivative().

◆ enableSecondOrderDerivatives() [1/2]

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

inlinevirtualinherited

From SecondOrder:

Implements bpp::SecondOrderDerivable.

Definition at line 152 of file HmmLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

bool bpp::AbstractHmmLikelihood::enableSecondOrderDerivatives ( ) const

inlinevirtualinherited

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::SecondOrderDerivable.

Definition at line 154 of file HmmLikelihood.h.

References bpp::SecondOrderDerivable::getSecondOrderDerivative().

◆ f()

virtual double bpp::FunctionInterface::f ( const ParameterList & parameters )

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 82 of file Functions.h.

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

Referenced by bpp::NumTools::uniRoot().

◆ fireParameterChanged()

void LowMemoryRescaledHmmLikelihood::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 67 of file LowMemoryRescaledHmmLikelihood.cpp.

References computeForward_(), emissionProbabilities_, hiddenAlphabet_, and transitionMatrix_.

Referenced by getLogLikelihood().

◆ getBreakPoints()

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

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 150 of file LowMemoryRescaledHmmLikelihood.h.

References breakPoints_.

◆ getD2LogLikelihood()

double bpp::AbstractHmmLikelihood::getD2LogLikelihood ( ) const

inlinevirtualinherited

Implements bpp::HmmLikelihood.

Definition at line 158 of file HmmLikelihood.h.

◆ getD2LogLikelihoodForASite()

double bpp::LowMemoryRescaledHmmLikelihood::getD2LogLikelihoodForASite ( size_t site ) const

inlineoverrideprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 205 of file LowMemoryRescaledHmmLikelihood.h.

◆ getDLogLikelihood()

double bpp::AbstractHmmLikelihood::getDLogLikelihood ( ) const

inlinevirtualinherited

Implements bpp::HmmLikelihood.

Definition at line 138 of file HmmLikelihood.h.

◆ getDLogLikelihoodForASite()

double bpp::LowMemoryRescaledHmmLikelihood::getDLogLikelihoodForASite ( size_t site ) const

inlineoverrideprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 199 of file LowMemoryRescaledHmmLikelihood.h.

◆ getFirstOrderDerivative()

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

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::FirstOrderDerivable.

Definition at line 33 of file HmmLikelihood.cpp.

References bpp::HmmEmissionProbabilities::computeDEmissionProbabilities(), bpp::HmmLikelihood::computeDLikelihood_(), bpp::AbstractHmmLikelihood::dLogLik_, bpp::AbstractHmmLikelihood::dVariable_, and bpp::HmmLikelihood::hmmEmissionProbabilities().

Referenced by bpp::LogsumHmmLikelihood::computeD2Forward_().

◆ getHiddenStatesPosteriorProbabilities()

void bpp::LowMemoryRescaledHmmLikelihood::getHiddenStatesPosteriorProbabilities	(	std::vector< std::vector< double >> &	probs,
		bool	append = `false`
	)		const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 181 of file LowMemoryRescaledHmmLikelihood.h.

References computeForward_().

◆ getHiddenStatesPosteriorProbabilitiesForASite()

Vdouble bpp::LowMemoryRescaledHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite ( size_t site ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 176 of file LowMemoryRescaledHmmLikelihood.h.

◆ getHmmEmissionProbabilities() [1/2]

std::shared_ptr<const HmmEmissionProbabilities> bpp::LowMemoryRescaledHmmLikelihood::getHmmEmissionProbabilities ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 139 of file LowMemoryRescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmEmissionProbabilities() [2/2]

std::shared_ptr<HmmEmissionProbabilities> bpp::LowMemoryRescaledHmmLikelihood::getHmmEmissionProbabilities ( )

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 142 of file LowMemoryRescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmStateAlphabet() [1/2]

std::shared_ptr<const HmmStateAlphabet> bpp::LowMemoryRescaledHmmLikelihood::getHmmStateAlphabet ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 127 of file LowMemoryRescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmStateAlphabet() [2/2]

std::shared_ptr<HmmStateAlphabet> bpp::LowMemoryRescaledHmmLikelihood::getHmmStateAlphabet ( )

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 130 of file LowMemoryRescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmTransitionMatrix() [1/2]

std::shared_ptr<const HmmTransitionMatrix> bpp::LowMemoryRescaledHmmLikelihood::getHmmTransitionMatrix ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 133 of file LowMemoryRescaledHmmLikelihood.h.

References transitionMatrix_.

◆ getHmmTransitionMatrix() [2/2]

std::shared_ptr<HmmTransitionMatrix> bpp::LowMemoryRescaledHmmLikelihood::getHmmTransitionMatrix ( )

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 136 of file LowMemoryRescaledHmmLikelihood.h.

References transitionMatrix_.

◆ getLikelihoodForASite()

double bpp::LowMemoryRescaledHmmLikelihood::getLikelihoodForASite ( size_t site ) const

inlineoverridevirtual

Get the likelihood for a site, and its derivatives.

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implements bpp::HmmLikelihood.

Definition at line 165 of file LowMemoryRescaledHmmLikelihood.h.

◆ getLikelihoodForEachSite()

Vdouble bpp::LowMemoryRescaledHmmLikelihood::getLikelihoodForEachSite ( ) const

inlineoverridevirtual

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

Implements bpp::HmmLikelihood.

Definition at line 171 of file LowMemoryRescaledHmmLikelihood.h.

◆ getLogLikelihood()

double bpp::LowMemoryRescaledHmmLikelihood::getLogLikelihood ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 159 of file LowMemoryRescaledHmmLikelihood.h.

References fireParameterChanged(), logLik_, and setNamespace().

◆ getNamespace() [1/2]

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

inlineoverridevirtualinherited

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

Implements bpp::Parametrizable.

Definition at line 99 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), and bpp::AbstractParametrizable::prefix_.

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

◆ 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::Parametrizable::~Parametrizable().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlineoverridevirtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 95 of file AbstractParametrizable.h.

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

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

◆ getNumberOfParameters() [2/2]

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const

pure virtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

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

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getParameter() [1/3]

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

inlineinherited

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

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

◆ getParameter() [2/3]

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

inlineprotectedinherited

Returns: The shared_ptr parameter at a given position.

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

Definition at line 211 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter() [3/3]

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

inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter_() [1/3]

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

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns: A reference toward the corresponding parameter.

Exceptions

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

Definition at line 164 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::hasParameter(), and bpp::ParameterList::parameter().

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

◆ getParameter_() [2/3]

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

inlineprotectedinherited

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameter_() [3/3]

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

inlineprotectedinherited

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace() [1/2]

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

overridevirtualinherited

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 28 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

◆ 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::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters() [1/2]

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

inlineoverridevirtualinherited

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 41 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameters() [2/2]

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const

pure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

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

Referenced by bpp::ParameterAliasableAdapter::getIndependentParameters(), bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters_() [1/2]

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )

protectedpure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getParameters_() [2/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineoverrideprotectedvirtualinherited

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 205 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue() [1/2]

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

inlineoverridevirtualinherited

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 53 of file AbstractParametrizable.h.

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

◆ getParameterValue() [2/2]

virtual double bpp::Parametrizable::getParameterValue ( const std::string & name ) const

pure virtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

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

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getParameterWithNamespace_() [1/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

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

Definition at line 176 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

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

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameter().

◆ getSecondOrderDerivative() [1/2]

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

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::SecondOrderDerivable.

Definition at line 45 of file HmmLikelihood.cpp.

References bpp::HmmEmissionProbabilities::computeD2EmissionProbabilities(), bpp::HmmLikelihood::computeD2Likelihood_(), bpp::AbstractHmmLikelihood::d2LogLik_, bpp::AbstractHmmLikelihood::d2Variable_, and bpp::HmmLikelihood::hmmEmissionProbabilities().

◆ getSecondOrderDerivative() [2/2]

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

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::SecondOrderDerivable.

Definition at line 163 of file HmmLikelihood.h.

◆ getValue()

double bpp::LowMemoryRescaledHmmLikelihood::getValue ( ) const

inlineoverridevirtual

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::FunctionInterface.

Definition at line 157 of file LowMemoryRescaledHmmLikelihood.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::Parametrizable::~Parametrizable().

◆ hasParameter() [2/2]

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

inlineoverridevirtualinherited

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 39 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter().

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

◆ hmmEmissionProbabilities() [1/2]

const HmmEmissionProbabilities& bpp::LowMemoryRescaledHmmLikelihood::hmmEmissionProbabilities ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 138 of file LowMemoryRescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ hmmEmissionProbabilities() [2/2]

HmmEmissionProbabilities& bpp::LowMemoryRescaledHmmLikelihood::hmmEmissionProbabilities ( )

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 141 of file LowMemoryRescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ hmmStateAlphabet() [1/2]

const HmmStateAlphabet& bpp::LowMemoryRescaledHmmLikelihood::hmmStateAlphabet ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 126 of file LowMemoryRescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ hmmStateAlphabet() [2/2]

HmmStateAlphabet& bpp::LowMemoryRescaledHmmLikelihood::hmmStateAlphabet ( )

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 129 of file LowMemoryRescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ hmmTransitionMatrix() [1/2]

const HmmTransitionMatrix& bpp::LowMemoryRescaledHmmLikelihood::hmmTransitionMatrix ( ) const

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 132 of file LowMemoryRescaledHmmLikelihood.h.

References transitionMatrix_.

◆ hmmTransitionMatrix() [2/2]

HmmTransitionMatrix& bpp::LowMemoryRescaledHmmLikelihood::hmmTransitionMatrix ( )

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 135 of file LowMemoryRescaledHmmLikelihood.h.

References transitionMatrix_.

◆ includeParameters_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 132 of file AbstractParametrizable.h.

References bpp::ParameterList::includeParameters().

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

◆ matchParametersValues() [1/2]

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

inlineoverridevirtualinherited

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 76 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [2/2]

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

pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters A list of parameters.

Returns: True if at least one parameter value has been changed.

Exceptions

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

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

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::TestFunction::setParameters(), and bpp::Parametrizable::~Parametrizable().

◆ operator=()

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

inline

Definition at line 100 of file LowMemoryRescaledHmmLikelihood.h.

References breakPoints_, emissionProbabilities_, hiddenAlphabet_, likelihood1_, likelihood2_, logLik_, maxSize_, nbSites_, nbStates_, bpp::AbstractHmmLikelihood::operator=(), and transitionMatrix_.

◆ parameter() [1/2]

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

inlineoverridevirtualinherited

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 43 of file AbstractParametrizable.h.

References bpp::ParameterList::parameter().

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

◆ parameter() [2/2]

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() [1/2]

void bpp::AbstractParametrizable::removeConstraint ( const std::string & name )

inlineoverridevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 85 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::removeConstraint().

◆ removeConstraint() [2/2]

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().

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 154 of file AbstractParametrizable.h.

References bpp::ParameterList::reset().

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

◆ setAllParametersValues() [1/2]

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

inlineoverridevirtualinherited

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 58 of file AbstractParametrizable.h.

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

◆ setAllParametersValues() [2/2]

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList & parameters )

pure virtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

parameters A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setBreakPoints()

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

inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 144 of file LowMemoryRescaledHmmLikelihood.h.

References computeForward_().

◆ setConstraint() [1/2]

void bpp::AbstractParametrizable::setConstraint	(	const std::string &	name,
		std::shared_ptr< ConstraintInterface >	constraint
	)

inlineoverridevirtualinherited

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.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::setConstraint().

Referenced by bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ setConstraint() [2/2]

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()

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

overridevirtual

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.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 58 of file LowMemoryRescaledHmmLikelihood.cpp.

References emissionProbabilities_, hiddenAlphabet_, bpp::AbstractParametrizable::setNamespace(), and transitionMatrix_.

Referenced by getLogLikelihood().

◆ setParameters()

void bpp::LowMemoryRescaledHmmLikelihood::setParameters ( const ParameterList & parameters )

inlineoverridevirtual

Set the point where the function must be computed.

Parameters

parameters The parameter set to pass to the function.

Implements bpp::FunctionInterface.

Definition at line 152 of file LowMemoryRescaledHmmLikelihood.h.

References bpp::AbstractParametrizable::setParametersValues().

◆ setParametersValues() [1/2]

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

inlineoverridevirtualinherited

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 70 of file AbstractParametrizable.h.

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

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

◆ setParametersValues() [2/2]

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList & parameters )

pure virtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setParameterValue() [1/2]

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

inlineoverridevirtualinherited

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 64 of file AbstractParametrizable.h.

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

◆ setParameterValue() [2/2]

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

pure virtualinherited

Set the value of parameter with name name to be equal to value.

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

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

Referenced by bpp::Parametrizable::~Parametrizable().