bpp-core3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::RescaledHmmLikelihood Class Referenceabstract

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)
 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)
 Set the point where the function must be computed. More...
 
double getValue () const
 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, and its derivatives. More...
 
double getDLogLikelihoodForASite (size_t site) const
 
double getD2LogLikelihoodForASite (size_t site) const
 
Vdouble getLikelihoodForEachSite () const
 Get the likelihood for each site. More...
 
void setNamespace (const std::string &nameSpace)
 Set the namespace for the parameter names. 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
 
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
 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
 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
 
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 & getParameter (const std::string &name) const =0
 Get the parameter with specified name. More...
 
virtual double getParameterValue (const std::string &name) const =0
 Get the value for parameter of name 'name'. More...
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 Set the parameters values to be equals to those of parameters. More...
 
virtual void setParameterValue (const std::string &name, double value)=0
 Set the value of parameter with name name to be equal to value. More...
 
virtual void setParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual size_t getNumberOfParameters () const =0
 Get the number of parameters. More...
 
virtual 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
 Get the parameter with specified name. More...
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const
 Get the value for parameter of name 'name'. More...
 
void setAllParametersValues (const ParameterList &parameters)
 Set the parameters values to be equals to those of parameters. More...
 
void setParameterValue (const std::string &name, double value)
 Set the value of parameter with name name to be equal to value. More...
 
void setParametersValues (const ParameterList &parameters)
 Update the parameters from parameters. More...
 
bool matchParametersValues (const ParameterList &parameters)
 Update the parameters from parameters. More...
 
size_t getNumberOfParameters () const
 Get the number of parameters. More...
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 Resolves a parameter name according to the current namespace. More...
 

Protected Member Functions

void computeForward_ ()
 
void computeBackward_ () const
 
void computeDLikelihood_ () const
 
void computeD2Likelihood_ () const
 
void computeDForward_ () const
 
void computeD2Forward_ () const
 
virtual ParameterList & getParameters_ ()=0
 Get all parameters available. More...
 
const std::shared_ptr< Parameter > & getSharedParameter (size_t i) const
 
std::shared_ptr< Parameter > & getSharedParameter (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_ ()
 Get all parameters available. More...
 

Protected Attributes

double dLogLik_
 
std::string dVariable_
 
double d2LogLik_
 
std::string d2Variable_
 

Private Attributes

std::unique_ptr< HmmStateAlphabet > hiddenAlphabet_
 The alphabet describing the hidden states. More...
 
std::unique_ptr< HmmTransitionMatrix > transitionMatrix_
 
std::unique_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_
 
ParameterList parameters_
 
std::string prefix_
 

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 61 of file RescaledHmmLikelihood.h.

Constructor & Destructor Documentation

◆ RescaledHmmLikelihood() [1/2]

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

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 51 of file RescaledHmmLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), computeForward_(), emissionProbabilities_, bpp::HmmEmissionProbabilities::getHmmStateAlphabet(), bpp::HmmTransitionMatrix::getHmmStateAlphabet(), hiddenAlphabet_, likelihood_, nbSites_, nbStates_, scales_, and transitionMatrix_.

Referenced by clone().

◆ RescaledHmmLikelihood() [2/2]

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

Definition at line 139 of file RescaledHmmLikelihood.h.

References emissionProbabilities_, hiddenAlphabet_, and transitionMatrix_.

◆ ~RescaledHmmLikelihood()

virtual bpp::RescaledHmmLikelihood::~RescaledHmmLikelihood ( )
inlinevirtual

Definition at line 189 of file RescaledHmmLikelihood.h.

Member Function Documentation

◆ addParameter_()

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 137 of file AbstractParametrizable.h.

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

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

◆ addParameters_()

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 143 of file AbstractParametrizable.h.

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

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

◆ 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 191 of file RescaledHmmLikelihood.h.

References RescaledHmmLikelihood().

◆ computeBackward_()

void RescaledHmmLikelihood::computeBackward_ ( ) const
protected

Definition at line 261 of file RescaledHmmLikelihood.cpp.

References backLikelihood_, backLikelihoodUpToDate_, breakPoints_, nbSites_, nbStates_, scales_, and transitionMatrix_.

Referenced by getHiddenStatesPosteriorProbabilities(), and getHiddenStatesPosteriorProbabilitiesForASite().

◆ computeD2Forward_()

void RescaledHmmLikelihood::computeD2Forward_ ( ) const
protected

Definition at line 523 of file RescaledHmmLikelihood.cpp.

References breakPoints_, d2Likelihood_, bpp::AbstractHmmLikelihood::d2LogLik_, d2Scales_, dLikelihood_, bpp::AbstractHmmLikelihood::dLogLik_, dScales_, emissionProbabilities_, bpp::ColMatrix< Scalar >::getCol(), likelihood_, nbSites_, nbStates_, scales_, bpp::VectorTools::sum(), and transitionMatrix_.

Referenced by computeD2Likelihood_().

◆ computeD2Likelihood_()

void bpp::RescaledHmmLikelihood::computeD2Likelihood_ ( ) const
inlineprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 247 of file RescaledHmmLikelihood.h.

References computeD2Forward_().

◆ computeDForward_()

void RescaledHmmLikelihood::computeDForward_ ( ) const
protected

Definition at line 407 of file RescaledHmmLikelihood.cpp.

References breakPoints_, dLikelihood_, bpp::AbstractHmmLikelihood::dLogLik_, dScales_, emissionProbabilities_, bpp::ColMatrix< Scalar >::getCol(), likelihood_, nbSites_, nbStates_, scales_, bpp::VectorTools::sum(), and transitionMatrix_.

Referenced by computeDLikelihood_().

◆ computeDLikelihood_()

void bpp::RescaledHmmLikelihood::computeDLikelihood_ ( ) const
inlineprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 242 of file RescaledHmmLikelihood.h.

References computeDForward_().

◆ computeForward_()

void RescaledHmmLikelihood::computeForward_ ( )
protected

Definition at line 129 of file RescaledHmmLikelihood.cpp.

References breakPoints_, likelihood_, logLik_, nbSites_, nbStates_, scales_, bpp::TextTools::toString(), transitionMatrix_, and bpp::ApplicationTools::warning.

Referenced by fireParameterChanged(), RescaledHmmLikelihood(), and setBreakPoints().

◆ d2f() [1/2]

virtual double bpp::DerivableSecondOrder::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
variableThe name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x^2} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 228 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 
)
inlinevirtualinherited

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

Parameters
variable1The name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
variable2The name of the $ y $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 255 of file Functions.h.

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

◆ deleteParameter_() [1/2]

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 163 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::parameters_, 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 170 of file AbstractParametrizable.h.

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

◆ deleteParameters_()

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 175 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 
)
inlinevirtualinherited

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

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 173 of file Functions.h.

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

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractHmmLikelihood::enableFirstOrderDerivatives ( ) const
inlinevirtualinherited

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 162 of file HmmLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

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

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableFirstOrder.

Definition at line 160 of file HmmLikelihood.h.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractHmmLikelihood::enableSecondOrderDerivatives ( ) const
inlinevirtualinherited

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 183 of file HmmLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

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

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableSecondOrder.

Definition at line 181 of file HmmLikelihood.h.

◆ f()

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

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

Parameters
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf 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::BrentOneDimension::doInit(), bpp::DownhillSimplexMethod::doInit(), bpp::GoldenSectionSearch::doInit(), bpp::NewtonBacktrackOneDimension::doInit(), bpp::NewtonOneDimension::doInit(), bpp::PowellMultiDimensions::doInit(), bpp::BfgsMultiDimensions::doStep(), bpp::BrentOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::NewtonOneDimension::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::FunctionWrapper::f(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::PowellMultiDimensions::optimize(), bpp::AbstractOptimizer::step(), bpp::DownhillSimplexMethod::tryExtrapolation(), and bpp::NumTools::uniRoot().

◆ fireParameterChanged()

void RescaledHmmLikelihood::fireParameterChanged ( const ParameterList &  parameters)
virtual

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 110 of file RescaledHmmLikelihood.cpp.

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

◆ getBreakPoints()

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

Implements bpp::HmmLikelihood.

Definition at line 210 of file RescaledHmmLikelihood.h.

References breakPoints_.

◆ getD2LogLikelihood()

double bpp::AbstractHmmLikelihood::getD2LogLikelihood ( ) const
inlinevirtualinherited

Implements bpp::HmmLikelihood.

Definition at line 187 of file HmmLikelihood.h.

References bpp::AbstractHmmLikelihood::d2LogLik_.

◆ getD2LogLikelihoodForASite()

double RescaledHmmLikelihood::getD2LogLikelihoodForASite ( size_t  site) const
virtual

Implements bpp::HmmLikelihood.

Definition at line 640 of file RescaledHmmLikelihood.cpp.

References d2Scales_, dScales_, and scales_.

◆ getDLogLikelihood()

double bpp::AbstractHmmLikelihood::getDLogLikelihood ( ) const
inlinevirtualinherited

Implements bpp::HmmLikelihood.

Definition at line 166 of file HmmLikelihood.h.

References bpp::AbstractHmmLikelihood::dLogLik_.

◆ getDLogLikelihoodForASite()

double RescaledHmmLikelihood::getDLogLikelihoodForASite ( size_t  site) const
virtual

Implements bpp::HmmLikelihood.

Definition at line 515 of file RescaledHmmLikelihood.cpp.

References dScales_, and scales_.

◆ getFirstOrderDerivative()

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

Get the derivative of the function at the current point.

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::DerivableFirstOrder.

Definition at line 70 of file HmmLikelihood.cpp.

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

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

◆ getHiddenStatesPosteriorProbabilities()

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

Implements bpp::HmmLikelihood.

Definition at line 383 of file RescaledHmmLikelihood.cpp.

References backLikelihood_, backLikelihoodUpToDate_, computeBackward_(), likelihood_, nbSites_, and nbStates_.

Referenced by getLikelihoodForEachSite().

◆ getHiddenStatesPosteriorProbabilitiesForASite()

Vdouble RescaledHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite ( size_t  site) const
virtual

Implements bpp::HmmLikelihood.

Definition at line 367 of file RescaledHmmLikelihood.cpp.

References backLikelihood_, backLikelihoodUpToDate_, computeBackward_(), likelihood_, and nbStates_.

Referenced by getLikelihoodForASite().

◆ getHmmEmissionProbabilities() [1/2]

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

Implements bpp::HmmLikelihood.

Definition at line 201 of file RescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmEmissionProbabilities() [2/2]

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

Implements bpp::HmmLikelihood.

Definition at line 200 of file RescaledHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmStateAlphabet() [1/2]

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

Implements bpp::HmmLikelihood.

Definition at line 195 of file RescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmStateAlphabet() [2/2]

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

Implements bpp::HmmLikelihood.

Definition at line 194 of file RescaledHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmTransitionMatrix() [1/2]

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

Implements bpp::HmmLikelihood.

Definition at line 198 of file RescaledHmmLikelihood.h.

References transitionMatrix_.

◆ getHmmTransitionMatrix() [2/2]

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

Implements bpp::HmmLikelihood.

Definition at line 197 of file RescaledHmmLikelihood.h.

References transitionMatrix_.

◆ getLikelihoodForASite()

double RescaledHmmLikelihood::getLikelihoodForASite ( size_t  site) const
virtual

Get the likelihood for a site, and its derivatives.

Parameters
siteThe site index to analyse.
Returns
The likelihood for site site.

Implements bpp::HmmLikelihood.

Definition at line 335 of file RescaledHmmLikelihood.cpp.

References getHiddenStatesPosteriorProbabilitiesForASite(), and nbStates_.

◆ 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 347 of file RescaledHmmLikelihood.cpp.

References getHiddenStatesPosteriorProbabilities(), nbSites_, and nbStates_.

◆ getLogLikelihood()

double bpp::RescaledHmmLikelihood::getLogLikelihood ( ) const
inlinevirtual

Implements bpp::HmmLikelihood.

Definition at line 219 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::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::hasIndependentParameter(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

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

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

◆ getParameter() [1/2]

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

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif 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::AbstractParameterAliasable::getFromParameters(), 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
pure virtualinherited

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

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

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

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string &  name)
inlineprotectedinherited
Parameters
nameThe name of the parameter.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 190 of file AbstractParametrizable.h.

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

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

◆ getParameter_() [2/3]

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

Definition at line 216 of file AbstractParametrizable.h.

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

◆ getParameter_() [3/3]

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

Definition at line 223 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 65 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), and bpp::AbstractParameterAliasable::shareParameters_().

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

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), 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::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::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameters_() [1/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )
inlineprotectedvirtualinherited

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 231 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameters_() [2/2]

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::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameterValue() [1/2]

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

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 89 of file AbstractParametrizable.h.

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

Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ConstantDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

◆ getParameterValue() [2/2]

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

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

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

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

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name)
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 202 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name) const
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 211 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ 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
variableThe name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x^2} $.
Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::DerivableSecondOrder.

Definition at line 82 of file HmmLikelihood.cpp.

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

◆ 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
variable1The name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
variable2The name of the $ y $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Implements bpp::DerivableSecondOrder.

Definition at line 192 of file HmmLikelihood.h.

◆ getSharedParameter() [1/3]

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

Definition at line 84 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getSharedParameter() [2/3]

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

Definition at line 242 of file AbstractParametrizable.h.

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

◆ getSharedParameter() [3/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( 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 237 of file AbstractParametrizable.h.

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

◆ getValue()

double bpp::RescaledHmmLikelihood::getValue ( ) const
inlinevirtual

Get the value of the function at the current point.

Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 217 of file RescaledHmmLikelihood.h.

References logLik_.

◆ hasParameter() [1/2]

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

Tell if there is a parameter with specified name.

Parameters
nameThe 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_.

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

◆ hasParameter() [2/2]

virtual bool bpp::Parametrizable::hasParameter ( const std::string &  name) const
pure virtualinherited

Tell if there is a parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
y/n.

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

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

◆ includeParameters_()

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 158 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [1/2]

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

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 112 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::TestFunction::setParameters(), 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
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

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

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ operator=()

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

Definition at line 163 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 180 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)
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
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 94 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)
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
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

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

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

◆ setBreakPoints()

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

Implements bpp::HmmLikelihood.

Definition at line 203 of file RescaledHmmLikelihood.h.

References backLikelihoodUpToDate_, breakPoints_, and computeForward_().

◆ setNamespace()

void RescaledHmmLikelihood::setNamespace ( const std::string &  prefix)
virtual

Set the namespace for the parameter names.

Parameters
prefixThe '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 101 of file RescaledHmmLikelihood.cpp.

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

◆ setParameters()

void bpp::RescaledHmmLikelihood::setParameters ( const ParameterList &  parameters)
inlinevirtual

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

Implements bpp::Function.

Definition at line 212 of file RescaledHmmLikelihood.h.

References bpp::AbstractParametrizable::setParametersValues().

◆ setParametersValues() [1/2]

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

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 106 of file AbstractParametrizable.h.

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

Referenced by bpp::LogsumHmmLikelihood::setParameters(), bpp::LowMemoryRescaledHmmLikelihood::setParameters(), and 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
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

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

Referenced by bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue() [1/2]

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

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

Parameters
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 100 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, 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
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

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

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

◆ shareParameter_()

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 148 of file AbstractParametrizable.h.

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

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

◆ shareParameters_()

virtual void bpp::AbstractParametrizable::shareParameters_ ( const ParameterList &  parameters)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 153 of file AbstractParametrizable.h.

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

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

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 104 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), and operator=().

◆ backLikelihoodUpToDate_

bool bpp::RescaledHmmLikelihood::backLikelihoodUpToDate_
mutableprivate

Definition at line 105 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), fireParameterChanged(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), operator=(), and setBreakPoints().

◆ breakPoints_

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

Definition at line 120 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getBreakPoints(), operator=(), and setBreakPoints().

◆ d2Likelihood_

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

Definition at line 95 of file RescaledHmmLikelihood.h.

Referenced by computeD2Forward_(), and operator=().

◆ d2LogLik_

double bpp::AbstractHmmLikelihood::d2LogLik_
mutableprotectedinherited

Definition at line 145 of file HmmLikelihood.h.

Referenced by bpp::LogsumHmmLikelihood::computeD2Forward_(), computeD2Forward_(), bpp::AbstractHmmLikelihood::getD2LogLikelihood(), bpp::AbstractHmmLikelihood::getSecondOrderDerivative(), and bpp::AbstractHmmLikelihood::operator=().

◆ d2Scales_

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

Definition at line 117 of file RescaledHmmLikelihood.h.

Referenced by computeD2Forward_(), getD2LogLikelihoodForASite(), and operator=().

◆ d2Variable_

std::string bpp::AbstractHmmLikelihood::d2Variable_
mutableprotectedinherited

Definition at line 146 of file HmmLikelihood.h.

Referenced by bpp::LogsumHmmLikelihood::computeD2Forward_(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::AbstractHmmLikelihood::getSecondOrderDerivative(), and 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 94 of file RescaledHmmLikelihood.h.

Referenced by computeD2Forward_(), computeDForward_(), and operator=().

◆ dLogLik_

double bpp::AbstractHmmLikelihood::dLogLik_
mutableprotectedinherited

Definition at line 142 of file HmmLikelihood.h.

Referenced by computeD2Forward_(), bpp::LogsumHmmLikelihood::computeDForward_(), computeDForward_(), bpp::AbstractHmmLikelihood::getDLogLikelihood(), bpp::AbstractHmmLikelihood::getFirstOrderDerivative(), and bpp::AbstractHmmLikelihood::operator=().

◆ dScales_

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

Definition at line 116 of file RescaledHmmLikelihood.h.

Referenced by computeD2Forward_(), computeDForward_(), getD2LogLikelihoodForASite(), getDLogLikelihoodForASite(), and operator=().

◆ dVariable_

std::string bpp::AbstractHmmLikelihood::dVariable_
mutableprotectedinherited

Definition at line 143 of file HmmLikelihood.h.

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

◆ emissionProbabilities_

std::unique_ptr<HmmEmissionProbabilities> bpp::RescaledHmmLikelihood::emissionProbabilities_
private

Definition at line 71 of file RescaledHmmLikelihood.h.

Referenced by computeD2Forward_(), computeDForward_(), fireParameterChanged(), getHmmEmissionProbabilities(), operator=(), RescaledHmmLikelihood(), and setNamespace().

◆ hiddenAlphabet_

std::unique_ptr<HmmStateAlphabet> bpp::RescaledHmmLikelihood::hiddenAlphabet_
private

The alphabet describing the hidden states.

Definition at line 69 of file RescaledHmmLikelihood.h.

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

◆ 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 85 of file RescaledHmmLikelihood.h.

Referenced by computeD2Forward_(), computeDForward_(), computeForward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), operator=(), and RescaledHmmLikelihood().

◆ logLik_

double bpp::RescaledHmmLikelihood::logLik_
private

Definition at line 118 of file RescaledHmmLikelihood.h.

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

◆ nbSites_

size_t bpp::RescaledHmmLikelihood::nbSites_
private

Definition at line 122 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getHiddenStatesPosteriorProbabilities(), getLikelihoodForEachSite(), operator=(), and RescaledHmmLikelihood().

◆ nbStates_

size_t bpp::RescaledHmmLikelihood::nbStates_
private

Definition at line 122 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), getLikelihoodForASite(), getLikelihoodForEachSite(), operator=(), and RescaledHmmLikelihood().

◆ parameters_

ParameterList bpp::AbstractParametrizable::parameters_
privateinherited

Definition at line 66 of file AbstractParametrizable.h.

Referenced by bpp::AbstractParametrizable::addParameter_(), bpp::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::deleteParameter_(), bpp::AbstractParametrizable::deleteParameters_(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::includeParameters_(), bpp::AbstractParametrizable::matchParametersValues(), bpp::AbstractParametrizable::resetParameters_(), bpp::AbstractParametrizable::setAllParametersValues(), bpp::AbstractParametrizable::setParametersValues(), bpp::AbstractParametrizable::setParameterValue(), bpp::AbstractParametrizable::shareParameter_(), and bpp::AbstractParametrizable::shareParameters_().

◆ prefix_

std::string bpp::AbstractParametrizable::prefix_
privateinherited

Definition at line 67 of file AbstractParametrizable.h.

Referenced by bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), and bpp::AbstractParametrizable::setParameterValue().

◆ 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 114 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getD2LogLikelihoodForASite(), getDLogLikelihoodForASite(), operator=(), and RescaledHmmLikelihood().

◆ transitionMatrix_

std::unique_ptr<HmmTransitionMatrix> bpp::RescaledHmmLikelihood::transitionMatrix_
private

Definition at line 70 of file RescaledHmmLikelihood.h.

Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), fireParameterChanged(), getHmmTransitionMatrix(), operator=(), RescaledHmmLikelihood(), and setNamespace().

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