bpp-phyl3 3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::LikelihoodCalculation Class Reference

#include <Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculation.h>

+ Inheritance diagram for bpp::LikelihoodCalculation:
+ Collaboration diagram for bpp::LikelihoodCalculation:

Public Member Functions

 LikelihoodCalculation (Context &context)
 
 LikelihoodCalculation (Context &context, ParameterList &paramList)
 
 LikelihoodCalculation (const LikelihoodCalculation &lik)
 
LikelihoodCalculation * clone () const
 
ValueRef< DataLik > getLikelihoodNode ()
 
virtual bool isInitialized () const
 
const Context & getContext () const
 
void setLikelihoodNode (ValueRef< DataLik > ll)
 
virtual void cleanAllLikelihoods ()
 
void setNamespace (const std::string &prefix)
 
bool hasIndependentParameter (const std::string &name) const
 
const ParameterList & getIndependentParameters () const
 
size_t getNumberOfIndependentParameters () const
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const
 
std::string getFrom (const std::string &name) const
 
bool hasParameter (const std::string &name) const override
 
const ParameterList & getParameters () const override
 
const Parameter & parameter (const std::string &name) const override
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const override
 
void setAllParametersValues (const ParameterList &parameters) override
 
void setParameterValue (const std::string &name, double value) override
 
void setParametersValues (const ParameterList &parameters) override
 
bool matchParametersValues (const ParameterList &parameters) override
 
void removeConstraint (const std::string &name) override
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
size_t getNumberOfParameters () const override
 
std::string getNamespace () const override
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
virtual void fireParameterChanged (const ParameterList &parameters)
 

Protected Member Functions

virtual void makeLikelihoods ()
 
Context & getContext_ ()
 
ValueRef< DataLik > getLikelihoodNode_ ()
 
const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
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
 

Protected Attributes

ValueRef< DataLik > likelihood_
 

Private Attributes

Context & context_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Base classes for Likelihood calculations. Also used to store shared_ptr.

Definition at line 20 of file LikelihoodCalculation.h.

Constructor & Destructor Documentation

◆ LikelihoodCalculation() [1/3]

bpp::LikelihoodCalculation::LikelihoodCalculation ( Context &  context)
inline

Definition at line 33 of file LikelihoodCalculation.h.

◆ LikelihoodCalculation() [2/3]

bpp::LikelihoodCalculation::LikelihoodCalculation ( Context &  context,
ParameterList &  paramList 
)
inline

Definition at line 38 of file LikelihoodCalculation.h.

References bpp::AbstractParameterAliasable::shareParameters_().

◆ LikelihoodCalculation() [3/3]

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

Definition at line 52 of file LikelihoodCalculation.h.

Member Function Documentation

◆ cleanAllLikelihoods()

virtual void bpp::LikelihoodCalculation::cleanAllLikelihoods ( )
inlinevirtual

Reimplemented in bpp::AlignedLikelihoodCalculation, bpp::LikelihoodCalculationOnABranch, and bpp::LikelihoodCalculationSingleProcess.

Definition at line 90 of file LikelihoodCalculation.h.

References bpp::Context::erase(), getContext_(), and likelihood_.

Referenced by bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods().

◆ clone()

LikelihoodCalculation * bpp::LikelihoodCalculation::clone ( ) const
inlinevirtual

Implements bpp::AbstractParameterAliasable.

Reimplemented in bpp::AlignedLikelihoodCalculation, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, and bpp::HmmLikelihood_DF.

Definition at line 58 of file LikelihoodCalculation.h.

◆ getContext()

const Context & bpp::LikelihoodCalculation::getContext ( ) const
inline

Definition at line 76 of file LikelihoodCalculation.h.

References context_.

◆ getContext_()

Context & bpp::LikelihoodCalculation::getContext_ ( )
inlineprotected

Definition at line 110 of file LikelihoodCalculation.h.

References context_.

Referenced by cleanAllLikelihoods(), bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), bpp::LikelihoodCalculationOnABranch::expandMatrix(), bpp::LikelihoodCalculationSingleProcess::expandMatrix(), bpp::LikelihoodCalculationOnABranch::expandVector(), bpp::LikelihoodCalculationSingleProcess::expandVector(), bpp::HmmLikelihood_DF::HmmLikelihood_DF(), bpp::LikelihoodCalculationSingleProcess::makeForwardLikelihoodTree_(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtDAGNode_(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtNode_(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_(), bpp::LikelihoodCalculationSingleProcess::makeProcessNodes_(), bpp::LikelihoodCalculationSingleProcess::makeRootFreqs_(), bpp::LikelihoodCalculationSingleProcess::setClockLike(), bpp::LikelihoodCalculationSingleProcess::setNumericalDerivateConfiguration(), and bpp::LikelihoodCalculationSingleProcess::setPatterns_().

◆ getLikelihoodNode()

ValueRef< DataLik > bpp::LikelihoodCalculation::getLikelihoodNode ( )
inline

Definition at line 63 of file LikelihoodCalculation.h.

References likelihood_, and makeLikelihoods().

◆ getLikelihoodNode_()

ValueRef< DataLik > bpp::LikelihoodCalculation::getLikelihoodNode_ ( )
inlineprotected

Definition at line 115 of file LikelihoodCalculation.h.

References likelihood_.

Referenced by bpp::LikelihoodCalculationSingleProcess::getForwardLikelihoodsAtNodeForClass(), and bpp::LikelihoodCalculationSingleProcess::getSiteLikelihoodsTree_().

◆ isInitialized()

virtual bool bpp::LikelihoodCalculation::isInitialized ( ) const
inlinevirtual

Definition at line 71 of file LikelihoodCalculation.h.

References likelihood_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::RewardMappingTools::computeRewardVectors(), bpp::OnABranchPhyloLikelihood::isInitialized(), bpp::OneProcessSequencePhyloLikelihood::isInitialized(), bpp::SingleProcessPhyloLikelihood::isInitialized(), and bpp::LikelihoodCalculationSingleProcess::setData().

◆ makeLikelihoods()

virtual void bpp::LikelihoodCalculation::makeLikelihoods ( )
inlineprotectedvirtual

Reimplemented in bpp::AlignedLikelihoodCalculation, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, and bpp::HmmLikelihood_DF.

Definition at line 105 of file LikelihoodCalculation.h.

Referenced by getLikelihoodNode().

◆ setLikelihoodNode()

void bpp::LikelihoodCalculation::setLikelihoodNode ( ValueRef< DataLik >  ll)
inline

Definition at line 85 of file LikelihoodCalculation.h.

References likelihood_.

Referenced by bpp::HmmLikelihood_DF::HmmLikelihood_DF(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_().

Member Data Documentation

◆ context_

Context& bpp::LikelihoodCalculation::context_
private

Definition at line 24 of file LikelihoodCalculation.h.

Referenced by getContext(), and getContext_().

◆ likelihood_

ValueRef<DataLik> bpp::LikelihoodCalculation::likelihood_
mutableprotected

Likelihoods

Definition at line 30 of file LikelihoodCalculation.h.

Referenced by cleanAllLikelihoods(), getLikelihoodNode(), getLikelihoodNode_(), isInitialized(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_(), and setLikelihoodNode().

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