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 229 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 215 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 286 of file LikelihoodCalculationOnABranch.h.

References model_.

Referenced by makeLikelihoods().

getNumberOfDistinctSites()

size_t bpp::LikelihoodCalculationOnABranch::getNumberOfDistinctSites ( ) const

inline

Definition at line 276 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 281 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 207 of file LikelihoodCalculationOnABranch.h.

References rootPatternLinks_.

getRootWeights()

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

inline

Definition at line 247 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 242 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().

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

• Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculationOnABranch.h
• Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculationOnABranch.cpp