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

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

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

+ Inheritance diagram for bpp::LogsumHmmLikelihood:
+ Collaboration diagram for bpp::LogsumHmmLikelihood:

Public Member Functions

 LogsumHmmLikelihood (std::shared_ptr< HmmStateAlphabet > hiddenAlphabet, std::shared_ptr< HmmTransitionMatrix > transitionMatrix, std::shared_ptr< HmmEmissionProbabilities > emissionProbabilities, const std::string &prefix="")
 Build a new LogsumHmmLikelihood object. More...
 
 LogsumHmmLikelihood (const LogsumHmmLikelihood &lik)
 
LogsumHmmLikelihood & operator= (const LogsumHmmLikelihood &lik)
 
virtual ~LogsumHmmLikelihood ()
 
LogsumHmmLikelihood * 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
 
double getLikelihoodForASite (size_t site) const override
 Get the likelihood for a site, and its derivatives. More...
 
double getDLogLikelihoodForASite (size_t site) const override
 
double getD2LogLikelihoodForASite (size_t site) const override
 
Vdouble getLikelihoodForEachSite () const override
 Get the likelihood for each site. More...
 
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...
 
Vdouble getHiddenStatesPosteriorProbabilitiesForASite (size_t site) const override
 
void getHiddenStatesPosteriorProbabilities (std::vector< std::vector< double >> &probs, bool append=false) const override
 
void computeLikelihood ()
 
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 computeBackward_ () const
 
void computeDLikelihood_ () const override
 
void computeD2Likelihood_ () const override
 
void computeDForward_ () const
 
void computeD2Forward_ () const
 
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

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 > logLikelihood_
 The likelihood array. More...
 
std::vector< double > partialLogLikelihoods_
 
double logLik_
 
std::vector< std::vector< double > > dLogLikelihood_
 The DLogLikelihood arrays. More...
 
std::vector< double > partialDLogLikelihoods_
 
std::vector< std::vector< double > > d2LogLikelihood_
 
std::vector< double > partialD2LogLikelihoods_
 
std::vector< std::vector< double > > backLogLikelihood_
 backward logLikelihood More...
 
bool backLogLikelihoodUpToDate_
 
std::vector< size_t > breakPoints_
 
size_t nbStates_
 
size_t nbSites_
 
double dLogLik_
 
std::string dVariable_
 
double d2LogLik_
 
std::string d2Variable_
 

Detailed Description

A simple implementation of hidden Markov models recursion.

This implementation uses the logsum method described in Durbin et al "Biological sequence analysis", Cambridge University Press, and further developped in Tobias P. Mann "Numerically Stable Hidden Markov Model Implementation" (2006) http://bozeman.genome.washington.edu/compbio/mbt599_2006/hmm_scaling_revised.pdf . It also offer the possibility to specify "breakpoints", where the chain will be reset to the equilibrium frequencies.

Although probably more numerically accurate, this method is slower than the rescaling, as it involves one exponentiation per site and per hidden state!

See also
RescaledHmmLikelihood

Definition at line 31 of file LogsumHmmLikelihood.h.

Constructor & Destructor Documentation

◆ LogsumHmmLikelihood() [1/2]

LogsumHmmLikelihood::LogsumHmmLikelihood ( std::shared_ptr< HmmStateAlphabet >  hiddenAlphabet,
std::shared_ptr< HmmTransitionMatrix >  transitionMatrix,
std::shared_ptr< HmmEmissionProbabilities >  emissionProbabilities,
const std::string &  prefix = "" 
)

Build a new LogsumHmmLikelihood object.

Warning
the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null and point toward the same HmmStateAlphabet instance.

Definition at line 13 of file LogsumHmmLikelihood.cpp.

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

Referenced by clone().

◆ LogsumHmmLikelihood() [2/2]

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

Definition at line 96 of file LogsumHmmLikelihood.h.

References emissionProbabilities_, hiddenAlphabet_, and transitionMatrix_.

◆ ~LogsumHmmLikelihood()

virtual bpp::LogsumHmmLikelihood::~LogsumHmmLikelihood ( )
inlinevirtual

Definition at line 152 of file LogsumHmmLikelihood.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(), LogsumHmmLikelihood(), bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(), and bpp::RescaledHmmLikelihood::RescaledHmmLikelihood().

◆ clone()

LogsumHmmLikelihood* bpp::LogsumHmmLikelihood::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 155 of file LogsumHmmLikelihood.h.

References LogsumHmmLikelihood().

◆ computeBackward_()

void LogsumHmmLikelihood::computeBackward_ ( ) const
protected

Definition at line 205 of file LogsumHmmLikelihood.cpp.

References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, bpp::NumTools::logsum(), nbSites_, nbStates_, and transitionMatrix_.

Referenced by getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), and getLogLikelihood().

◆ computeD2Forward_()

void LogsumHmmLikelihood::computeD2Forward_ ( ) const
protected

Definition at line 483 of file LogsumHmmLikelihood.cpp.

References breakPoints_, bpp::AbstractHmmLikelihood::d2LogLik_, d2LogLikelihood_, bpp::AbstractHmmLikelihood::d2Variable_, dLogLikelihood_, emissionProbabilities_, bpp::AbstractHmmLikelihood::getFirstOrderDerivative(), logLikelihood_, nbSites_, nbStates_, partialD2LogLikelihoods_, partialDLogLikelihoods_, bpp::VectorTools::sumExp(), transitionMatrix_, and bpp::VectorTools::whichMax().

Referenced by computeD2Likelihood_().

◆ computeD2Likelihood_()

void bpp::LogsumHmmLikelihood::computeD2Likelihood_ ( ) const
inlineoverrideprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 222 of file LogsumHmmLikelihood.h.

References computeD2Forward_(), and computeDForward_().

◆ computeDForward_()

void LogsumHmmLikelihood::computeDForward_ ( ) const
protected

Definition at line 378 of file LogsumHmmLikelihood.cpp.

References breakPoints_, bpp::AbstractHmmLikelihood::dLogLik_, dLogLikelihood_, emissionProbabilities_, logLikelihood_, nbSites_, nbStates_, partialDLogLikelihoods_, bpp::VectorTools::sumExp(), transitionMatrix_, and bpp::VectorTools::whichMax().

Referenced by computeD2Likelihood_(), and computeDLikelihood_().

◆ computeDLikelihood_()

void bpp::LogsumHmmLikelihood::computeDLikelihood_ ( ) const
inlineoverrideprotectedvirtual

Implements bpp::HmmLikelihood.

Definition at line 217 of file LogsumHmmLikelihood.h.

References computeDForward_().

◆ computeForward_()

void LogsumHmmLikelihood::computeForward_ ( )
protected

Definition at line 98 of file LogsumHmmLikelihood.cpp.

References breakPoints_, logLik_, logLikelihood_, bpp::NumTools::logsum(), nbSites_, nbStates_, partialLogLikelihoods_, and transitionMatrix_.

Referenced by computeLikelihood(), getLogLikelihood(), LogsumHmmLikelihood(), and setBreakPoints().

◆ computeLikelihood()

void LogsumHmmLikelihood::computeLikelihood ( )

Definition at line 91 of file LogsumHmmLikelihood.cpp.

References computeForward_().

Referenced by fireParameterChanged(), and getLogLikelihood().

◆ 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
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 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
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 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
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 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
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 82 of file Functions.h.

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

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

◆ fireParameterChanged()

void LogsumHmmLikelihood::fireParameterChanged ( const ParameterList &  parameters)
overridevirtual

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 71 of file LogsumHmmLikelihood.cpp.

References backLogLikelihoodUpToDate_, computeLikelihood(), bpp::AbstractHmmLikelihood::d2Variable_, bpp::AbstractHmmLikelihood::dVariable_, emissionProbabilities_, hiddenAlphabet_, and transitionMatrix_.

Referenced by getLogLikelihood().

◆ getBreakPoints()

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

Implements bpp::HmmLikelihood.

Definition at line 183 of file LogsumHmmLikelihood.h.

References breakPoints_.

◆ getD2LogLikelihood()

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

Implements bpp::HmmLikelihood.

Definition at line 158 of file HmmLikelihood.h.

◆ getD2LogLikelihoodForASite()

double LogsumHmmLikelihood::getD2LogLikelihoodForASite ( size_t  site) const
overridevirtual

Implements bpp::HmmLikelihood.

Definition at line 600 of file LogsumHmmLikelihood.cpp.

References partialD2LogLikelihoods_.

Referenced by getLogLikelihood().

◆ getDLogLikelihood()

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

Implements bpp::HmmLikelihood.

Definition at line 138 of file HmmLikelihood.h.

◆ getDLogLikelihoodForASite()

double LogsumHmmLikelihood::getDLogLikelihoodForASite ( size_t  site) const
overridevirtual

Implements bpp::HmmLikelihood.

Definition at line 476 of file LogsumHmmLikelihood.cpp.

References partialDLogLikelihoods_.

Referenced by getLogLikelihood().

◆ 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::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 computeD2Forward_().

◆ getHiddenStatesPosteriorProbabilities()

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

Implements bpp::HmmLikelihood.

Definition at line 338 of file LogsumHmmLikelihood.cpp.

References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, computeBackward_(), logLikelihood_, nbSites_, nbStates_, and partialLogLikelihoods_.

Referenced by getLikelihoodForEachSite(), and getLogLikelihood().

◆ getHiddenStatesPosteriorProbabilitiesForASite()

Vdouble LogsumHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite ( size_t  site) const
overridevirtual

Implements bpp::HmmLikelihood.

Definition at line 312 of file LogsumHmmLikelihood.cpp.

References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, computeBackward_(), logLikelihood_, nbStates_, and partialLogLikelihoods_.

Referenced by getLikelihoodForASite(), and getLogLikelihood().

◆ getHmmEmissionProbabilities() [1/2]

std::shared_ptr<const HmmEmissionProbabilities> bpp::LogsumHmmLikelihood::getHmmEmissionProbabilities ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 171 of file LogsumHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmEmissionProbabilities() [2/2]

std::shared_ptr<HmmEmissionProbabilities> bpp::LogsumHmmLikelihood::getHmmEmissionProbabilities ( )
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 174 of file LogsumHmmLikelihood.h.

References emissionProbabilities_.

◆ getHmmStateAlphabet() [1/2]

std::shared_ptr<const HmmStateAlphabet> bpp::LogsumHmmLikelihood::getHmmStateAlphabet ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 159 of file LogsumHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmStateAlphabet() [2/2]

std::shared_ptr<HmmStateAlphabet> bpp::LogsumHmmLikelihood::getHmmStateAlphabet ( )
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 162 of file LogsumHmmLikelihood.h.

References hiddenAlphabet_.

◆ getHmmTransitionMatrix() [1/2]

std::shared_ptr<const HmmTransitionMatrix> bpp::LogsumHmmLikelihood::getHmmTransitionMatrix ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 165 of file LogsumHmmLikelihood.h.

References transitionMatrix_.

◆ getHmmTransitionMatrix() [2/2]

std::shared_ptr<HmmTransitionMatrix> bpp::LogsumHmmLikelihood::getHmmTransitionMatrix ( )
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 168 of file LogsumHmmLikelihood.h.

References transitionMatrix_.

◆ getLikelihoodForASite()

double LogsumHmmLikelihood::getLikelihoodForASite ( size_t  site) const
overridevirtual

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 279 of file LogsumHmmLikelihood.cpp.

References getHiddenStatesPosteriorProbabilitiesForASite(), and nbStates_.

Referenced by getLogLikelihood().

◆ getLikelihoodForEachSite()

Vdouble LogsumHmmLikelihood::getLikelihoodForEachSite ( ) const
overridevirtual

Get the likelihood for each site.

Returns
A vector with all likelihoods for each site.

Implements bpp::HmmLikelihood.

Definition at line 291 of file LogsumHmmLikelihood.cpp.

References getHiddenStatesPosteriorProbabilities(), nbSites_, and nbStates_.

Referenced by getLogLikelihood().

◆ getLogLikelihood()

double bpp::LogsumHmmLikelihood::getLogLikelihood ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 192 of file LogsumHmmLikelihood.h.

References computeBackward_(), computeForward_(), computeLikelihood(), fireParameterChanged(), getD2LogLikelihoodForASite(), getDLogLikelihoodForASite(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), getLikelihoodForASite(), getLikelihoodForEachSite(), 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
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 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::SimpleDiscreteDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::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
nameThe 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().

Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::ConstantDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::Simplex::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::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
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 176 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 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
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::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
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::SecondOrderDerivable.

Definition at line 163 of file HmmLikelihood.h.

◆ getValue()

double bpp::LogsumHmmLikelihood::getValue ( ) const
inlineoverridevirtual

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::FunctionInterface.

Definition at line 190 of file LogsumHmmLikelihood.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
nameThe 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
nameThe 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::LogsumHmmLikelihood::hmmEmissionProbabilities ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 170 of file LogsumHmmLikelihood.h.

References emissionProbabilities_.

◆ hmmEmissionProbabilities() [2/2]

HmmEmissionProbabilities& bpp::LogsumHmmLikelihood::hmmEmissionProbabilities ( )
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 173 of file LogsumHmmLikelihood.h.

References emissionProbabilities_.

◆ hmmStateAlphabet() [1/2]

const HmmStateAlphabet& bpp::LogsumHmmLikelihood::hmmStateAlphabet ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 158 of file LogsumHmmLikelihood.h.

References hiddenAlphabet_.

◆ hmmStateAlphabet() [2/2]

HmmStateAlphabet& bpp::LogsumHmmLikelihood::hmmStateAlphabet ( )
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 161 of file LogsumHmmLikelihood.h.

References hiddenAlphabet_.

◆ hmmTransitionMatrix() [1/2]

const HmmTransitionMatrix& bpp::LogsumHmmLikelihood::hmmTransitionMatrix ( ) const
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 164 of file LogsumHmmLikelihood.h.

References transitionMatrix_.

◆ hmmTransitionMatrix() [2/2]

HmmTransitionMatrix& bpp::LogsumHmmLikelihood::hmmTransitionMatrix ( )
inlineoverridevirtual

Implements bpp::HmmLikelihood.

Definition at line 167 of file LogsumHmmLikelihood.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
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 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
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::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

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

◆ operator=()

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

Definition at line 124 of file LogsumHmmLikelihood.h.

References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, d2LogLikelihood_, dLogLikelihood_, emissionProbabilities_, hiddenAlphabet_, logLik_, logLikelihood_, nbSites_, nbStates_, bpp::AbstractHmmLikelihood::operator=(), partialD2LogLikelihoods_, partialDLogLikelihoods_, partialLogLikelihoods_, and transitionMatrix_.

◆ parameter() [1/2]

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

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 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
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::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
nameThe name of the parameter to look for.
Exceptions
ParameterNotFoundExceptionif 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
nameThe name of the parameter to look for.
Exceptions
ParameterNotFoundExceptionif 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
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 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
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::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

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

◆ setBreakPoints()

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

Implements bpp::HmmLikelihood.

Definition at line 176 of file LogsumHmmLikelihood.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
nameThe name of the parameter to look for.
constraintA pointer to the constraint (may be null)
Exceptions
ParameterNotFoundExceptionif 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
nameThe name of the parameter to look for.
constraintA pointer to the constraint (may be null)
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

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

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

◆ setNamespace()

void LogsumHmmLikelihood::setNamespace ( const std::string &  prefix)
overridevirtual

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 62 of file LogsumHmmLikelihood.cpp.

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

Referenced by getLogLikelihood().

◆ setParameters()

void bpp::LogsumHmmLikelihood::setParameters ( const ParameterList &  parameters)
inlineoverridevirtual

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

Implements bpp::FunctionInterface.

Definition at line 185 of file LogsumHmmLikelihood.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
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 70 of file AbstractParametrizable.h.

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

Referenced by bpp::LowMemoryRescaledHmmLikelihood::setParameters(), bpp::RescaledHmmLikelihood::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::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
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 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
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::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

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

◆ shareParameter_()

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

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 122 of file AbstractParametrizable.h.

References 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 127 of file AbstractParametrizable.h.

References bpp::ParameterList::shareParameters().

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

Member Data Documentation

◆ backLogLikelihood_

std::vector<std::vector<double> > bpp::LogsumHmmLikelihood::backLogLikelihood_
mutableprotected

backward logLikelihood

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

Definition at line 75 of file LogsumHmmLikelihood.h.

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

◆ backLogLikelihoodUpToDate_

bool bpp::LogsumHmmLikelihood::backLogLikelihoodUpToDate_
mutableprotected

Definition at line 76 of file LogsumHmmLikelihood.h.

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

◆ breakPoints_

std::vector<size_t> bpp::LogsumHmmLikelihood::breakPoints_
protected

Definition at line 78 of file LogsumHmmLikelihood.h.

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

◆ d2LogLik_

double bpp::AbstractHmmLikelihood::d2LogLik_
mutableprotectedinherited

Definition at line 116 of file HmmLikelihood.h.

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

◆ d2LogLikelihood_

std::vector< std::vector<double> > bpp::LogsumHmmLikelihood::d2LogLikelihood_
mutableprotected

Definition at line 66 of file LogsumHmmLikelihood.h.

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

◆ d2Variable_

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

Definition at line 117 of file HmmLikelihood.h.

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

◆ dLogLik_

double bpp::AbstractHmmLikelihood::dLogLik_
mutableprotectedinherited

Definition at line 113 of file HmmLikelihood.h.

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

◆ dLogLikelihood_

std::vector< std::vector<double> > bpp::LogsumHmmLikelihood::dLogLikelihood_
mutableprotected

The DLogLikelihood arrays.

dLogLikelihood_[i][j] corresponds to d(log(Pr(x1...xi, yi=j))), where the x are the observed states, and y the hidden states.

d2LogLikelihood_[i][j] corresponds to d2(log(Pr(x1...xi, yi=j))), where the x are the observed states, and y the hidden states.

Definition at line 63 of file LogsumHmmLikelihood.h.

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

◆ dVariable_

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

Definition at line 114 of file HmmLikelihood.h.

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

◆ emissionProbabilities_

std::shared_ptr<HmmEmissionProbabilities> bpp::LogsumHmmLikelihood::emissionProbabilities_
protected

Definition at line 41 of file LogsumHmmLikelihood.h.

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

◆ hiddenAlphabet_

std::shared_ptr<HmmStateAlphabet> bpp::LogsumHmmLikelihood::hiddenAlphabet_
protected

The alphabet describing the hidden states.

Definition at line 39 of file LogsumHmmLikelihood.h.

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

◆ logLik_

double bpp::LogsumHmmLikelihood::logLik_
protected

Definition at line 51 of file LogsumHmmLikelihood.h.

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

◆ logLikelihood_

std::vector<double> bpp::LogsumHmmLikelihood::logLikelihood_
protected

The likelihood array.

logLikelihood_[i * nbStates_ + j] corresponds to log(Pr(x1...xi, yi=j)), where the x are the observed states, and y the hidden states.

Definition at line 49 of file LogsumHmmLikelihood.h.

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

◆ nbSites_

size_t bpp::LogsumHmmLikelihood::nbSites_
protected

Definition at line 80 of file LogsumHmmLikelihood.h.

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

◆ nbStates_

size_t bpp::LogsumHmmLikelihood::nbStates_
protected

Definition at line 80 of file LogsumHmmLikelihood.h.

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

◆ partialD2LogLikelihoods_

std::vector<double> bpp::LogsumHmmLikelihood::partialD2LogLikelihoods_
mutableprotected

Definition at line 67 of file LogsumHmmLikelihood.h.

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

◆ partialDLogLikelihoods_

std::vector<double> bpp::LogsumHmmLikelihood::partialDLogLikelihoods_
mutableprotected

Definition at line 64 of file LogsumHmmLikelihood.h.

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

◆ partialLogLikelihoods_

std::vector<double> bpp::LogsumHmmLikelihood::partialLogLikelihoods_
protected

Definition at line 50 of file LogsumHmmLikelihood.h.

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

◆ transitionMatrix_

std::shared_ptr<HmmTransitionMatrix> bpp::LogsumHmmLikelihood::transitionMatrix_
protected

Definition at line 40 of file LogsumHmmLikelihood.h.

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

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