bpp-phyl3 3.0.0
Public Member Functions | Protected Member Functions | List of all members
bpp::PhyloLikelihoodInterface Class Referenceabstract

The PhyloLikelihood interface, for phylogenetic likelihood. More...

#include <Bpp/Phyl/Likelihood/PhyloLikelihoods/PhyloLikelihood.h>

+ Inheritance diagram for bpp::PhyloLikelihoodInterface:
+ Collaboration diagram for bpp::PhyloLikelihoodInterface:

Public Member Functions

 PhyloLikelihoodInterface ()
 
virtual ~PhyloLikelihoodInterface ()
 
PhyloLikelihoodInterface * clone () const =0
 
virtual LikelihoodCalculation & likelihoodCalculation () const =0
 
virtual std::shared_ptr< LikelihoodCalculation > getLikelihoodCalculation () const =0
 
virtual void enableSecondOrderDerivatives (bool yn)=0
 
virtual bool enableSecondOrderDerivatives () const=0
 
virtual double getSecondOrderDerivative (const std::string &variable) const=0
 
virtual double getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const=0
 
virtual double d2f (const std::string &variable, const ParameterList &parameters)
 
virtual double d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)
 
virtual void enableFirstOrderDerivatives (bool yn)=0
 
virtual bool enableFirstOrderDerivatives () const=0
 
virtual double getFirstOrderDerivative (const std::string &variable) const=0
 
virtual double df (const std::string &variable, const ParameterList &parameters)
 
virtual void setParameters (const ParameterList &parameters)=0
 
virtual double getValue () const=0
 
virtual double f (const ParameterList &parameters)
 
virtual bool hasParameter (const std::string &name) const=0
 
virtual const ParameterList & getParameters () const=0
 
virtual const Parameter & parameter (const std::string &name) const=0
 
virtual double getParameterValue (const std::string &name) const=0
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
virtual void setParameterValue (const std::string &name, double value)=0
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
virtual void removeConstraint (const std::string &name)=0
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
virtual size_t getNumberOfParameters () const=0
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
The data functions
virtual bool isInitialized () const =0
 
virtual const Context & context () const =0
 
virtual Context & context ()=0
 
The likelihood functions.
virtual ValueRef< DataLik > getLikelihoodNode () const =0
 
double getLogLikelihood () const
 Get the logarithm of the likelihood for the whole dataset. More...
 
Retrieve some particular independent parameters subsets.

Get the derivates of the LogLikelihood.

virtual ParameterList getNonDerivableParameters () const =0
 
virtual ParameterList getDerivableParameters () const =0
 
virtual ParameterList getBranchLengthParameters () const =0
 Get the independent branch lengths parameters. More...
 
virtual ParameterList getSubstitutionModelParameters () const =0
 Get the independent parameters associated to substitution model(s). More...
 
virtual ParameterList getRateDistributionParameters () const =0
 Get the independent parameters associated to the rate distribution(s). More...
 
virtual ParameterList getRootFrequenciesParameters () const =0
 Get the independent parameters associated to the root frequencies(s). More...
 

Protected Member Functions

virtual ParameterList & getParameters_ ()=0
 

Detailed Description

The PhyloLikelihood interface, for phylogenetic likelihood.

This interface defines the common methods needed to compute a likelihood from a sequence alignment, usually involving one or more phylogenetic trees.

Definition at line 21 of file PhyloLikelihood.h.

Constructor & Destructor Documentation

◆ PhyloLikelihoodInterface()

bpp::PhyloLikelihoodInterface::PhyloLikelihoodInterface ( )
inline

Definition at line 25 of file PhyloLikelihood.h.

◆ ~PhyloLikelihoodInterface()

virtual bpp::PhyloLikelihoodInterface::~PhyloLikelihoodInterface ( )
inlinevirtual

Definition at line 26 of file PhyloLikelihood.h.

Member Function Documentation

◆ clone()

PhyloLikelihoodInterface * bpp::PhyloLikelihoodInterface::clone ( ) const
pure virtual

Implements bpp::SecondOrderDerivable.

Implemented in bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodProduct, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodInterface, bpp::PhyloLikelihoodSetInterface, bpp::SingleDataPhyloLikelihoodInterface, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodMixture, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodSetInterface, and bpp::SequencePhyloLikelihoodInterface.

◆ context() [1/2]

virtual const Context & bpp::PhyloLikelihoodInterface::context ( ) const
pure virtual

Implemented in bpp::AbstractPhyloLikelihood.

◆ context() [2/2]

virtual Context & bpp::PhyloLikelihoodInterface::context ( )
pure virtual

Implemented in bpp::AbstractPhyloLikelihood.

◆ getBranchLengthParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getBranchLengthParameters ( ) const
pure virtual

Get the independent branch lengths parameters.

Returns
A ParameterList with all branch lengths.

Implemented in bpp::OnABranchPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractParametrizableSequencePhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

Referenced by bpp::BppPhylogeneticsApplication::displayParameters().

◆ getDerivableParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getDerivableParameters ( ) const
pure virtual

Implemented in bpp::OnABranchPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractParametrizableSequencePhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

◆ getLikelihoodCalculation()

virtual std::shared_ptr< LikelihoodCalculation > bpp::PhyloLikelihoodInterface::getLikelihoodCalculation ( ) const
pure virtual
Returns
A shared pointer toward the LikelihoodCalculation.

Implemented in bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodProduct, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodMixture, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

Referenced by bpp::AbstractPhyloLikelihood::getLikelihoodNode().

◆ getLikelihoodNode()

virtual ValueRef< DataLik > bpp::PhyloLikelihoodInterface::getLikelihoodNode ( ) const
pure virtual
Returns
the LikDF node where the Likelihood is computed.

Implemented in bpp::AbstractPhyloLikelihood.

◆ getLogLikelihood()

double bpp::PhyloLikelihoodInterface::getLogLikelihood ( ) const
inline

Get the logarithm of the likelihood for the whole dataset.

Returns
The logarithm of the likelihood of the dataset.

Definition at line 66 of file PhyloLikelihood.h.

References bpp::SecondOrderDerivable::getValue().

◆ getNonDerivableParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getNonDerivableParameters ( ) const
pure virtual

Implemented in bpp::OnABranchPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractParametrizableSequencePhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

◆ getRateDistributionParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getRateDistributionParameters ( ) const
pure virtual

Get the independent parameters associated to the rate distribution(s).

Returns
A ParameterList.

Implemented in bpp::OnABranchPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractParametrizableSequencePhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

◆ getRootFrequenciesParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getRootFrequenciesParameters ( ) const
pure virtual

Get the independent parameters associated to the root frequencies(s).

Returns
A ParameterList.

Implemented in bpp::OnABranchPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractParametrizableSequencePhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

◆ getSubstitutionModelParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getSubstitutionModelParameters ( ) const
pure virtual

Get the independent parameters associated to substitution model(s).

Returns
A ParameterList.

Implemented in bpp::OnABranchPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractParametrizableSequencePhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

◆ isInitialized()

virtual bool bpp::PhyloLikelihoodInterface::isInitialized ( ) const
pure virtual
Returns
'true' is the likelihood function has been initialized.

Implemented in bpp::AbstractPhyloLikelihood, bpp::MultiProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::SingleProcessPhyloLikelihood.

◆ likelihoodCalculation()

virtual LikelihoodCalculation & bpp::PhyloLikelihoodInterface::likelihoodCalculation ( ) const
pure virtual
Returns
The LikelihoodCalculation.

Implemented in bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodProduct, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodMixture, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, and bpp::SingleProcessPhyloLikelihood.

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