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

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

+ Inheritance diagram for bpp::LikelihoodCalculationOnABranch:
+ Collaboration diagram for bpp::LikelihoodCalculationOnABranch:

Classes

class  RateCategoryEdge
 

Public Member Functions

 LikelihoodCalculationOnABranch (Context &context, LikelihoodCalculationSingleProcess &likcalsp, uint edgeId)
 
void setModel (std::shared_ptr< ConfiguredModel > model)
 
 LikelihoodCalculationOnABranch (const LikelihoodCalculationOnABranch &lik)
 
LikelihoodCalculationOnABranch * clone () const
 
const StateMapInterface & stateMap () const
 
std::shared_ptr< const StateMapInterface > getStateMap () const
 
std::shared_ptr< const Alphabet > getAlphabet () const
 
size_t getRootArrayPosition (size_t currentPosition) const
 
const PatternType & getRootArrayPositions () const
 
ValueRef< RowLik > expandVector (ValueRef< RowLik > vector)
 
ValueRef< MatrixLik > expandMatrix (ValueRef< MatrixLik > matrix)
 
unsigned int getWeight (size_t pos) const
 
std::shared_ptr< SiteWeights > getRootWeights ()
 
RowLik getSiteLikelihoodsForAClass (size_t nCat, bool shrunk=false)
 Get site likelihoods for a rate category. More...
 
AllRatesSiteLikelihoods getSiteLikelihoodsForAllClasses (bool shrunk=false)
 Output array (Classes X Sites) of likelihoods for all sites & classes. More...
 
size_t getNumberOfDistinctSites () const
 
size_t getNumberOfSites () const
 
std::shared_ptr< ConfiguredModel > getModel ()
 
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...
 
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

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 Member Functions

void makeLikelihoods ()
 
std::shared_ptr< SiteLikelihoods > getSiteLikelihoods_ (size_t nCat)
 
void cleanAllLikelihoods ()
 

Private Attributes

size_t numberOfSites_
 
MatrixDimension likelihoodMatrixDim_
 
std::shared_ptr< ConfiguredModel > model_
 
ValueRef< PatternType > rootPatternLinks_
 
std::shared_ptr< SiteWeights > rootWeights_
 The frequency of each site. More...
 
ValueRef< Eigen::RowVectorXd > catProb_
 
std::vector< RateCategoryEdge > vRateCatEdges_
 
Context & context_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Definition at line 70 of file LikelihoodCalculationOnABranch.h.

Constructor & Destructor Documentation

◆ LikelihoodCalculationOnABranch() [1/2]

LikelihoodCalculationOnABranch::LikelihoodCalculationOnABranch ( Context &  context,
LikelihoodCalculationSingleProcess &  likcalsp,
uint  edgeId 
)

Definition at line 19 of file LikelihoodCalculationOnABranch.cpp.

References bpp::LikelihoodCalculationSingleProcess::getNumberOfDistinctSites(), bpp::StateMapInterface::getNumberOfModelStates(), and bpp::LikelihoodCalculationSingleProcess::stateMap().

◆ LikelihoodCalculationOnABranch() [2/2]

LikelihoodCalculationOnABranch::LikelihoodCalculationOnABranch ( const LikelihoodCalculationOnABranch &  lik)

Definition at line 53 of file LikelihoodCalculationOnABranch.cpp.

Member Function Documentation

◆ cleanAllLikelihoods()

void LikelihoodCalculationOnABranch::cleanAllLikelihoods ( )
privatevirtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 170 of file LikelihoodCalculationOnABranch.cpp.

References bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), rootPatternLinks_, rootWeights_, and vRateCatEdges_.

◆ clone()

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

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 168 of file LikelihoodCalculationOnABranch.h.

◆ expandMatrix()

ValueRef< MatrixLik > bpp::LikelihoodCalculationOnABranch::expandMatrix ( ValueRef< MatrixLik >  matrix)
inline

Definition at line 238 of file LikelihoodCalculationOnABranch.h.

References bpp::CWisePattern< R >::create(), bpp::LikelihoodCalculation::getContext_(), numberOfSites_, and rootPatternLinks_.

◆ expandVector()

ValueRef< RowLik > bpp::LikelihoodCalculationOnABranch::expandVector ( ValueRef< RowLik >  vector)
inline

Definition at line 224 of file LikelihoodCalculationOnABranch.h.

References bpp::CWisePattern< R >::create(), bpp::LikelihoodCalculation::getContext_(), numberOfSites_, and rootPatternLinks_.

Referenced by getSiteLikelihoodsForAClass(), and makeLikelihoods().

◆ getAlphabet()

std::shared_ptr< const Alphabet > bpp::LikelihoodCalculationOnABranch::getAlphabet ( ) const
inline

Definition at line 183 of file LikelihoodCalculationOnABranch.h.

References bpp::StateMapInterface::getAlphabet(), and stateMap().

◆ 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(), bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), expandMatrix(), bpp::LikelihoodCalculationSingleProcess::expandMatrix(), expandVector(), bpp::LikelihoodCalculationSingleProcess::expandVector(), bpp::HmmLikelihood_DF::HmmLikelihood_DF(), bpp::LikelihoodCalculationSingleProcess::makeForwardLikelihoodTree_(), 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 
)
inlineinherited

Definition at line 198 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::makeLikelihoods(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

Referenced by bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite(), and bpp::AlignedLikelihoodCalculation::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 ( )
inlineinherited

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 bpp::AlignedLikelihoodCalculation::getSiteLikelihoods().

◆ getLogLikelihoodForASite()

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

Definition at line 209 of file LikelihoodCalculation.h.

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

◆ getModel()

std::shared_ptr< ConfiguredModel > bpp::LikelihoodCalculationOnABranch::getModel ( )
inline

Definition at line 295 of file LikelihoodCalculationOnABranch.h.

References model_.

Referenced by makeLikelihoods().

◆ getNumberOfDistinctSites()

size_t bpp::LikelihoodCalculationOnABranch::getNumberOfDistinctSites ( ) const
inline

Definition at line 285 of file LikelihoodCalculationOnABranch.h.

References bpp::MatrixDimension::cols, and likelihoodMatrixDim_.

Referenced by bpp::OnABranchPhyloLikelihood::getNumberOfDistinctSites(), getSiteLikelihoodsForAllClasses(), and makeLikelihoods().

◆ getNumberOfSites()

size_t bpp::LikelihoodCalculationOnABranch::getNumberOfSites ( ) const
inline

Definition at line 290 of file LikelihoodCalculationOnABranch.h.

References numberOfSites_.

Referenced by bpp::OnABranchPhyloLikelihood::getNumberOfSites().

◆ getRootArrayPosition()

size_t bpp::LikelihoodCalculationOnABranch::getRootArrayPosition ( size_t  currentPosition) const
inline

Definition at line 202 of file LikelihoodCalculationOnABranch.h.

References rootPatternLinks_.

◆ getRootArrayPositions()

const PatternType & bpp::LikelihoodCalculationOnABranch::getRootArrayPositions ( ) const
inline

Definition at line 216 of file LikelihoodCalculationOnABranch.h.

References rootPatternLinks_.

◆ getRootWeights()

std::shared_ptr< SiteWeights > bpp::LikelihoodCalculationOnABranch::getRootWeights ( )
inline

Definition at line 256 of file LikelihoodCalculationOnABranch.h.

References rootWeights_.

◆ getSiteLikelihoods()

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

Definition at line 165 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::makeLikelihoods(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

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

◆ getSiteLikelihoods_()

std::shared_ptr< SiteLikelihoods > bpp::LikelihoodCalculationOnABranch::getSiteLikelihoods_ ( size_t  nCat)
private

◆ getSiteLikelihoodsForAClass()

RowLik LikelihoodCalculationOnABranch::getSiteLikelihoodsForAClass ( size_t  nCat,
bool  shrunk = false 
)

Get site likelihoods for a rate category.

Parameters
nCat: index of the rate category
shrunk: if returns on shrunked data (default: false)

Definition at line 64 of file LikelihoodCalculationOnABranch.cpp.

References expandVector(), and vRateCatEdges_.

Referenced by getSiteLikelihoodsForAllClasses().

◆ getSiteLikelihoodsForAllClasses()

AllRatesSiteLikelihoods LikelihoodCalculationOnABranch::getSiteLikelihoodsForAllClasses ( bool  shrunk = false)

Output array (Classes X Sites) of likelihoods for all sites & classes.

Parameters
shrunk: if returns on shrunked data (default: false)

Definition at line 72 of file LikelihoodCalculationOnABranch.cpp.

References getNumberOfDistinctSites(), getSiteLikelihoodsForAClass(), numberOfSites_, and vRateCatEdges_.

◆ getStateMap()

std::shared_ptr< const StateMapInterface > bpp::LikelihoodCalculationOnABranch::getStateMap ( ) const
inline

Definition at line 178 of file LikelihoodCalculationOnABranch.h.

References model_.

◆ getWeight()

unsigned int bpp::LikelihoodCalculationOnABranch::getWeight ( size_t  pos) const
inline

Definition at line 251 of file LikelihoodCalculationOnABranch.h.

References rootWeights_.

◆ 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()

void LikelihoodCalculationOnABranch::makeLikelihoods ( )
privatevirtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 89 of file LikelihoodCalculationOnABranch.cpp.

References catProb_, bpp::ConstantOne< T >::create(), bpp::SumOfLogarithms< F >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::Convert< R, F >::create(), expandVector(), bpp::LikelihoodCalculation::getContext_(), getModel(), getNumberOfDistinctSites(), bpp::Context::getZero(), likelihoodMatrixDim_, model_, bpp::numeric::one(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, rootPatternLinks_, rootWeights_, bpp::LikelihoodCalculation::setLikelihoodNode(), bpp::AlignedLikelihoodCalculation::setSiteLikelihoods(), stateMap(), bpp::transitionMatrixDimension(), vRateCatEdges_, and bpp::numeric::zero().

Referenced by setModel().

◆ 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(), makeLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_().

◆ setModel()

void bpp::LikelihoodCalculationOnABranch::setModel ( std::shared_ptr< ConfiguredModel >  model)
inline

Definition at line 157 of file LikelihoodCalculationOnABranch.h.

References makeLikelihoods(), model_, and bpp::AbstractParameterAliasable::shareParameters_().

◆ setSiteLikelihoods()

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

Definition at line 184 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

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

◆ stateMap()

const StateMapInterface & bpp::LikelihoodCalculationOnABranch::stateMap ( ) const
inline

Definition at line 173 of file LikelihoodCalculationOnABranch.h.

References model_.

Referenced by getAlphabet(), and makeLikelihoods().

Member Data Documentation

◆ catProb_

ValueRef<Eigen::RowVectorXd> bpp::LikelihoodCalculationOnABranch::catProb_
private

Definition at line 148 of file LikelihoodCalculationOnABranch.h.

Referenced by makeLikelihoods().

◆ 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().

◆ likelihoodMatrixDim_

MatrixDimension bpp::LikelihoodCalculationOnABranch::likelihoodMatrixDim_
private

Definition at line 111 of file LikelihoodCalculationOnABranch.h.

Referenced by getNumberOfDistinctSites(), and makeLikelihoods().

◆ model_

std::shared_ptr<ConfiguredModel> bpp::LikelihoodCalculationOnABranch::model_
private

Definition at line 118 of file LikelihoodCalculationOnABranch.h.

Referenced by getModel(), getStateMap(), makeLikelihoods(), setModel(), and stateMap().

◆ numberOfSites_

size_t bpp::LikelihoodCalculationOnABranch::numberOfSites_
private

Definition at line 105 of file LikelihoodCalculationOnABranch.h.

Referenced by expandMatrix(), expandVector(), getNumberOfSites(), and getSiteLikelihoodsForAllClasses().

◆ patternedSiteLikelihoods_

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_
mutableprotectedinherited

Definition at line 155 of file LikelihoodCalculation.h.

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

◆ rootPatternLinks_

ValueRef<PatternType> bpp::LikelihoodCalculationOnABranch::rootPatternLinks_
private

Definition at line 135 of file LikelihoodCalculationOnABranch.h.

Referenced by cleanAllLikelihoods(), expandMatrix(), expandVector(), getRootArrayPosition(), getRootArrayPositions(), and makeLikelihoods().

◆ rootWeights_

std::shared_ptr<SiteWeights> bpp::LikelihoodCalculationOnABranch::rootWeights_
private

The frequency of each site.

Definition at line 141 of file LikelihoodCalculationOnABranch.h.

Referenced by cleanAllLikelihoods(), getRootWeights(), getWeight(), and makeLikelihoods().

◆ siteLikelihoods_

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::siteLikelihoods_
mutableprotectedinherited

Site Likelihoods

Definition at line 149 of file LikelihoodCalculation.h.

Referenced by bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), bpp::AlignedLikelihoodCalculation::getLikelihoodForASite(), bpp::AlignedLikelihoodCalculation::getSiteLikelihoods(), and bpp::AlignedLikelihoodCalculation::setSiteLikelihoods().

◆ vRateCatEdges_

std::vector<RateCategoryEdge> bpp::LikelihoodCalculationOnABranch::vRateCatEdges_
private

Definition at line 151 of file LikelihoodCalculationOnABranch.h.

Referenced by cleanAllLikelihoods(), getSiteLikelihoodsForAClass(), getSiteLikelihoodsForAllClasses(), and makeLikelihoods().

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