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

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

+ Inheritance diagram for bpp::AlignedLikelihoodCalculation:
+ Collaboration diagram for bpp::AlignedLikelihoodCalculation:

Public Member Functions

 AlignedLikelihoodCalculation (Context &context)
 
 AlignedLikelihoodCalculation (const AlignedLikelihoodCalculation &lik)
 
AlignedLikelihoodCalculation * clone () const
 
SiteLikelihoodsRef getSiteLikelihoods (bool shrunk=false)
 
void setSiteLikelihoods (SiteLikelihoodsRef ll, bool shrunk=false)
 
DataLik getLikelihoodForASite (size_t pos, bool shrunk=false)
 
DataLik getLogLikelihoodForASite (size_t pos, bool shrunk=false)
 
VDataLik getLikelihoodPerSite ()
 Get the likelihood for each site. More...
 
void cleanAllLikelihoods ()
 
ValueRef< DataLik > getLikelihoodNode ()
 
virtual bool isInitialized () const
 
const Context & getContext () const
 
void setLikelihoodNode (ValueRef< DataLik > ll)
 
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

SiteLikelihoodsRef siteLikelihoods_
 
SiteLikelihoodsRef patternedSiteLikelihoods_
 
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

Definition at line 124 of file LikelihoodCalculation.h.

Constructor & Destructor Documentation

◆ AlignedLikelihoodCalculation() [1/2]

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

Definition at line 128 of file LikelihoodCalculation.h.

◆ AlignedLikelihoodCalculation() [2/2]

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

Definition at line 131 of file LikelihoodCalculation.h.

Member Function Documentation

◆ cleanAllLikelihoods()

void bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods ( )
inlinevirtual

Reimplemented from bpp::LikelihoodCalculation.

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

Definition at line 235 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::cleanAllLikelihoods(), bpp::Context::erase(), bpp::LikelihoodCalculation::getContext_(), patternedSiteLikelihoods_, and siteLikelihoods_.

Referenced by bpp::LikelihoodCalculationOnABranch::cleanAllLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::cleanAllLikelihoods().

◆ clone()

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

Reimplemented from bpp::LikelihoodCalculation.

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

Definition at line 136 of file LikelihoodCalculation.h.

◆ getContext()

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

Definition at line 76 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::context_.

◆ getContext_()

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

Definition at line 110 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::context_.

Referenced by bpp::LikelihoodCalculation::cleanAllLikelihoods(), 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_().

◆ getLikelihoodForASite()

DataLik bpp::AlignedLikelihoodCalculation::getLikelihoodForASite ( size_t  pos,
bool  shrunk = false 
)
inline

Definition at line 198 of file LikelihoodCalculation.h.

References makeLikelihoods(), patternedSiteLikelihoods_, and siteLikelihoods_.

Referenced by bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite(), and getLogLikelihoodForASite().

◆ getLikelihoodNode()

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

Definition at line 63 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_, and bpp::LikelihoodCalculation::makeLikelihoods().

◆ getLikelihoodNode_()

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

Definition at line 115 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_.

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

◆ getLikelihoodPerSite()

VDataLik bpp::AlignedLikelihoodCalculation::getLikelihoodPerSite ( )
inline

Get the likelihood for each site.

Returns
A vector with all site likelihoods.

Definition at line 221 of file LikelihoodCalculation.h.

References bpp::copyEigenToBpp(), and getSiteLikelihoods().

◆ getLogLikelihoodForASite()

DataLik bpp::AlignedLikelihoodCalculation::getLogLikelihoodForASite ( size_t  pos,
bool  shrunk = false 
)
inline

Definition at line 209 of file LikelihoodCalculation.h.

References getLikelihoodForASite(), and bpp::log().

◆ getSiteLikelihoods()

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::getSiteLikelihoods ( bool  shrunk = false)
inline

Definition at line 165 of file LikelihoodCalculation.h.

References makeLikelihoods(), patternedSiteLikelihoods_, and siteLikelihoods_.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), and getLikelihoodPerSite().

◆ isInitialized()

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

Definition at line 71 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::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::AlignedLikelihoodCalculation::makeLikelihoods ( )
inlineprotectedvirtual

Reimplemented from bpp::LikelihoodCalculation.

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

Definition at line 252 of file LikelihoodCalculation.h.

Referenced by getLikelihoodForASite(), and getSiteLikelihoods().

◆ setLikelihoodNode()

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

Definition at line 85 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_.

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

◆ setSiteLikelihoods()

void bpp::AlignedLikelihoodCalculation::setSiteLikelihoods ( SiteLikelihoodsRef  ll,
bool  shrunk = false 
)
inline

Definition at line 184 of file LikelihoodCalculation.h.

References patternedSiteLikelihoods_, and siteLikelihoods_.

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

Member Data Documentation

◆ context_

Context& bpp::LikelihoodCalculation::context_
privateinherited

Definition at line 24 of file LikelihoodCalculation.h.

Referenced by bpp::LikelihoodCalculation::getContext(), and bpp::LikelihoodCalculation::getContext_().

◆ likelihood_

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

Likelihoods

Definition at line 30 of file LikelihoodCalculation.h.

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

◆ patternedSiteLikelihoods_

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_
mutableprotected

Definition at line 155 of file LikelihoodCalculation.h.

Referenced by cleanAllLikelihoods(), getLikelihoodForASite(), getSiteLikelihoods(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_(), and setSiteLikelihoods().

◆ siteLikelihoods_

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::siteLikelihoods_
mutableprotected

Site Likelihoods

Definition at line 149 of file LikelihoodCalculation.h.

Referenced by cleanAllLikelihoods(), getLikelihoodForASite(), getSiteLikelihoods(), and setSiteLikelihoods().

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