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

Inheritance diagram for bpp::LikelihoodCalculationSingleProcess:

Collaboration diagram for bpp::LikelihoodCalculationSingleProcess:

Classes
class	ProcessNodes
	DF Nodes used in the process. ProcessTree is used without any rate multiplier. More...

class	RateCategoryTrees

Public Member Functions
	LikelihoodCalculationSingleProcess (Context &context, std::shared_ptr< const AlignmentDataInterface > sites, std::shared_ptr< const SubstitutionProcessInterface > process)

	LikelihoodCalculationSingleProcess (Context &context, std::shared_ptr< const SubstitutionProcessInterface > process)

	LikelihoodCalculationSingleProcess (std::shared_ptr< CollectionNodes > collection, std::shared_ptr< const AlignmentDataInterface > sites, size_t nProcess)

	LikelihoodCalculationSingleProcess (std::shared_ptr< CollectionNodes > collection, size_t nProcess)

	LikelihoodCalculationSingleProcess (const LikelihoodCalculationSingleProcess &lik)

LikelihoodCalculationSingleProcess *	clone () const

void	setData (std::shared_ptr< const AlignmentDataInterface > sites)

void	setNumericalDerivateConfiguration (double delta, const NumericalDerivativeType &config)
	Set derivation procedure (see DataFlowNumeric.h) More...

void	setClockLike (double rate=1)

void	makeLikelihoods ()

const DAGindexes &	getNodesIds (uint speciesId) const
	Get indexes of the nodes in the Likelihood DAG that have a given species index. More...

const DAGindexes &	getEdgesIds (uint speciesId, size_t nCat) const
	Get indexes of the non-empty edges in the Likelihood DAG that have a given species index for a given rate class index. More...

size_t	getNumberOfSites () const

size_t	getNumberOfDistinctSites () const

const SubstitutionProcessInterface &	substitutionProcess () const
	Return the ref to the SubstitutionProcess. More...

std::shared_ptr< const SubstitutionProcessInterface >	getSubstitutionProcess () const

const AlignmentDataInterface &	data () const

std::shared_ptr< const AlignmentDataInterface >	getData () const

const StateMapInterface &	stateMap () const

std::shared_ptr< const StateMapInterface >	getStateMap () const

size_t	getRootArrayPosition (size_t currentPosition) const

const PatternType &	getRootArrayPositions () const

ValueRef< PatternType >	getRootPatternLinks () const

const AlignmentDataInterface &	shrunkData () const

std::shared_ptr< const AlignmentDataInterface >	getShrunkData () 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 ()

ValueRef< Eigen::RowVectorXd >	getRootFreqs ()

ConditionalLikelihoodRef	getLikelihoodsAtNode (uint nodeId, bool shrunk=false)

size_t	getNumberOfClasses () const

ConditionalLikelihoodRef	getForwardLikelihoodsAtNodeForClass (uint nodeId, size_t nCat)

ConditionalLikelihoodRef	getBackwardLikelihoodsAtNodeForClass (uint nodeId, size_t nCat)

ConditionalLikelihoodRef	getBackwardLikelihoodsAtEdgeForClass (uint edgeId, size_t nCat)

ConditionalLikelihoodRef	getConditionalLikelihoodsAtNodeForClass (uint nodeId, size_t nCat)

SiteLikelihoodsRef	getLikelihoodsAtNodeForClass (uint nodeId, size_t nCat)
	Get shrunked conditional likelihood matrix at Node (ie just above the node), for a given rate class. More...

void	makeLikelihoodsTree ()
	make backward likelihood tree (only computed when needed) More...

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...

std::shared_ptr< ProcessTree >	getTreeNode (size_t nCat)
	Get process tree for a rate category. More...

std::shared_ptr< ForwardLikelihoodTree >	getForwardLikelihoodTree (size_t nCat)

std::shared_ptr< BackwardLikelihoodTree >	getBackwardLikelihoodTree (size_t nCat)

void	cleanAllLikelihoods ()

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	setPatterns_ ()

void	makeForwardLikelihoodTree_ ()

void	makeProcessNodes_ ()

void	makeRootFreqs_ ()

void	makeLikelihoodsAtRoot_ ()

void	makeProcessNodes_ (CollectionNodes &pl, size_t nProc)
	make DF nodes of a process in a collection, using ConfiguredParameters defined in a CollectionNodes. More...

void	makeLikelihoodsAtNode_ (uint nodeId)
	Compute the likelihood at a given node in the tree, which number may not be the same number in the DAG. More...

void	makeLikelihoodsAtDAGNode_ (uint nodeId)
	Compute the likelihood at a given node in the DAG,. More...

std::shared_ptr< SiteLikelihoodsTree >	getSiteLikelihoodsTree_ (size_t nCat)

Private Attributes
std::shared_ptr< const SubstitutionProcessInterface >	process_

std::shared_ptr< const AlignmentDataInterface >	psites_

ValueRef< PatternType >	rootPatternLinks_

std::shared_ptr< SiteWeights >	rootWeights_
	The frequency of each site. More...

std::shared_ptr< AlignmentDataInterface >	shrunkData_

ProcessNodes	processNodes_

ValueRef< Eigen::RowVectorXd >	rFreqs_

std::vector< RateCategoryTrees >	vRateCatTrees_

ValueRef< Eigen::RowVectorXd >	catProb_

std::shared_ptr< ConditionalLikelihoodTree >	condLikelihoodTree_

Context &	context_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Friends
class	LikelihoodCalculationOnABranch

Detailed Description

Definition at line 112 of file LikelihoodCalculationSingleProcess.h.

Constructor & Destructor Documentation

◆ LikelihoodCalculationSingleProcess() [1/5]

LikelihoodCalculationSingleProcess::LikelihoodCalculationSingleProcess	(	Context &	context,
		std::shared_ptr< const AlignmentDataInterface >	sites,
		std::shared_ptr< const SubstitutionProcessInterface >	process
	)

Definition at line 21 of file LikelihoodCalculationSingleProcess.cpp.

References makeProcessNodes_(), process_, setNumericalDerivateConfiguration(), setPatterns_(), and bpp::ThreePoints.

◆ LikelihoodCalculationSingleProcess() [2/5]

LikelihoodCalculationSingleProcess::LikelihoodCalculationSingleProcess	(	Context &	context,
		std::shared_ptr< const SubstitutionProcessInterface >	process
	)

Definition at line 39 of file LikelihoodCalculationSingleProcess.cpp.

References makeProcessNodes_(), process_, setNumericalDerivateConfiguration(), and bpp::ThreePoints.

◆ LikelihoodCalculationSingleProcess() [3/5]

LikelihoodCalculationSingleProcess::LikelihoodCalculationSingleProcess	(	std::shared_ptr< CollectionNodes >	collection,
		std::shared_ptr< const AlignmentDataInterface >	sites,
		size_t	nProcess
	)

Definition at line 57 of file LikelihoodCalculationSingleProcess.cpp.

References makeProcessNodes_(), process_, setNumericalDerivateConfiguration(), setPatterns_(), and bpp::ThreePoints.

◆ LikelihoodCalculationSingleProcess() [4/5]

LikelihoodCalculationSingleProcess::LikelihoodCalculationSingleProcess	(	std::shared_ptr< CollectionNodes >	collection,
		size_t	nProcess
	)

Definition at line 79 of file LikelihoodCalculationSingleProcess.cpp.

References makeProcessNodes_(), setNumericalDerivateConfiguration(), and bpp::ThreePoints.

◆ LikelihoodCalculationSingleProcess() [5/5]

LikelihoodCalculationSingleProcess::LikelihoodCalculationSingleProcess ( const LikelihoodCalculationSingleProcess & lik )

Definition at line 96 of file LikelihoodCalculationSingleProcess.cpp.

References makeProcessNodes_(), setNumericalDerivateConfiguration(), setPatterns_(), and bpp::ThreePoints.

Member Function Documentation

◆ cleanAllLikelihoods()

void LikelihoodCalculationSingleProcess::cleanAllLikelihoods ( )

virtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 806 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), condLikelihoodTree_, psites_, rootPatternLinks_, rootWeights_, shrunkData_, and vRateCatTrees_.

Referenced by setData().

◆ clone()

LikelihoodCalculationSingleProcess* bpp::LikelihoodCalculationSingleProcess::clone ( ) const

inlinevirtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 247 of file LikelihoodCalculationSingleProcess.h.

◆ data()

const AlignmentDataInterface& bpp::LikelihoodCalculationSingleProcess::data ( ) const

inline

Definition at line 337 of file LikelihoodCalculationSingleProcess.h.

References psites_.

◆ expandMatrix()

ValueRef<MatrixLik> bpp::LikelihoodCalculationSingleProcess::expandMatrix ( ValueRef< MatrixLik > matrix )

inline

Definition at line 412 of file LikelihoodCalculationSingleProcess.h.

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

Referenced by getLikelihoodsAtNode().

◆ expandVector()

ValueRef<RowLik> bpp::LikelihoodCalculationSingleProcess::expandVector ( ValueRef< RowLik > vector )

inline

Definition at line 398 of file LikelihoodCalculationSingleProcess.h.

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

Referenced by getSiteLikelihoodsForAClass(), and makeLikelihoodsAtRoot_().

◆ getBackwardLikelihoodsAtEdgeForClass()

ConditionalLikelihoodRef LikelihoodCalculationSingleProcess::getBackwardLikelihoodsAtEdgeForClass	(	uint	edgeId,
		size_t	nCat
	)

Definition at line 744 of file LikelihoodCalculationSingleProcess.cpp.

References condLikelihoodTree_, getTreeNode(), makeLikelihoodsAtNode_(), bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), and bpp::RewardMappingTools::computeRewardVectors().

◆ getBackwardLikelihoodsAtNodeForClass()

ConditionalLikelihoodRef LikelihoodCalculationSingleProcess::getBackwardLikelihoodsAtNodeForClass	(	uint	nodeId,
		size_t	nCat
	)

Definition at line 760 of file LikelihoodCalculationSingleProcess.cpp.

References makeLikelihoodsAtDAGNode_(), bpp::TextTools::toString(), and vRateCatTrees_.

◆ getBackwardLikelihoodTree()

std::shared_ptr< BackwardLikelihoodTree > LikelihoodCalculationSingleProcess::getBackwardLikelihoodTree ( size_t nCat )

Definition at line 798 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::TextTools::toString(), and vRateCatTrees_.

◆ getConditionalLikelihoodsAtNodeForClass()

ConditionalLikelihoodRef LikelihoodCalculationSingleProcess::getConditionalLikelihoodsAtNodeForClass	(	uint	nodeId,
		size_t	nCat
	)

Definition at line 717 of file LikelihoodCalculationSingleProcess.cpp.

References makeLikelihoodsAtDAGNode_(), bpp::TextTools::toString(), and vRateCatTrees_.

◆ 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

◆ getData()

std::shared_ptr<const AlignmentDataInterface> bpp::LikelihoodCalculationSingleProcess::getData ( ) const

inline

Definition at line 342 of file LikelihoodCalculationSingleProcess.h.

References psites_.

Referenced by expandMatrix(), expandVector(), and bpp::SingleProcessPhyloLikelihood::getData().

◆ getEdgesIds()

const DAGindexes & LikelihoodCalculationSingleProcess::getEdgesIds	(	uint	speciesId,
		size_t	nCat
	)		const

Get indexes of the non-empty edges in the Likelihood DAG that have a given species index for a given rate class index.

Parameters

speciesId	Looked species Index
nCat	Rate class category

Definition at line 782 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), and bpp::RewardMappingTools::computeRewardVectors().

◆ getForwardLikelihoodsAtNodeForClass()

ConditionalLikelihoodRef LikelihoodCalculationSingleProcess::getForwardLikelihoodsAtNodeForClass	(	uint	nodeId,
		size_t	nCat
	)

Definition at line 703 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::LikelihoodCalculation::getLikelihoodNode_(), makeLikelihoods(), bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), and bpp::RewardMappingTools::computeRewardVectors().

◆ getForwardLikelihoodTree()

std::shared_ptr< ForwardLikelihoodTree > LikelihoodCalculationSingleProcess::getForwardLikelihoodTree ( size_t nCat )

Definition at line 790 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), and bpp::RewardMappingTools::computeRewardVectors().

◆ 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 getForwardLikelihoodsAtNodeForClass(), and 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().

◆ getLikelihoodsAtNode()

ConditionalLikelihoodRef bpp::LikelihoodCalculationSingleProcess::getLikelihoodsAtNode	(	uint	nodeId,
		bool	shrunk = `false`
	)

inline

Definition at line 452 of file LikelihoodCalculationSingleProcess.h.

References condLikelihoodTree_, expandMatrix(), and makeLikelihoodsAtNode_().

◆ getLikelihoodsAtNodeForClass()

SiteLikelihoodsRef LikelihoodCalculationSingleProcess::getLikelihoodsAtNodeForClass	(	uint	nodeId,
		size_t	nCat
	)

Get shrunked conditional likelihood matrix at Node (ie just above the node), for a given rate class.

These likelihoods are multiplied by the probability of the node.

Parameters

nodeId	Node Index in the forward tree (! ie in the computation tree, not the species tree).
nCat	Rate class category

Definition at line 730 of file LikelihoodCalculationSingleProcess.cpp.

References makeLikelihoodsAtDAGNode_(), bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), and bpp::RewardMappingTools::computeRewardVectors().

◆ 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().

◆ getNodesIds()

const DAGindexes & LikelihoodCalculationSingleProcess::getNodesIds ( uint speciesId ) const

Get indexes of the nodes in the Likelihood DAG that have a given species index.

Parameters

speciesId Looked species Index

Definition at line 774 of file LikelihoodCalculationSingleProcess.cpp.

References vRateCatTrees_.

◆ getNumberOfClasses()

size_t bpp::LikelihoodCalculationSingleProcess::getNumberOfClasses ( ) const

inline

Definition at line 466 of file LikelihoodCalculationSingleProcess.h.

References vRateCatTrees_.

◆ getNumberOfDistinctSites()

size_t bpp::LikelihoodCalculationSingleProcess::getNumberOfDistinctSites ( ) const

inline

Definition at line 316 of file LikelihoodCalculationSingleProcess.h.

References getNumberOfSites(), and shrunkData_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::RewardMappingTools::computeRewardVectors(), bpp::SingleProcessPhyloLikelihood::getNumberOfDistinctSites(), getSiteLikelihoodsForAllClasses(), bpp::LikelihoodCalculationOnABranch::LikelihoodCalculationOnABranch(), makeLikelihoodsAtDAGNode_(), makeLikelihoodsAtNode_(), and makeLikelihoodsAtRoot_().

◆ getNumberOfSites()

size_t bpp::LikelihoodCalculationSingleProcess::getNumberOfSites ( ) const

inline

Definition at line 311 of file LikelihoodCalculationSingleProcess.h.

References psites_.

Referenced by expandMatrix(), expandVector(), getNumberOfDistinctSites(), bpp::SingleProcessPhyloLikelihood::getNumberOfSites(), and getSiteLikelihoodsForAllClasses().

◆ getRootArrayPosition()

size_t bpp::LikelihoodCalculationSingleProcess::getRootArrayPosition ( size_t currentPosition ) const

inline

Definition at line 370 of file LikelihoodCalculationSingleProcess.h.

References rootPatternLinks_.

◆ getRootArrayPositions()

const PatternType& bpp::LikelihoodCalculationSingleProcess::getRootArrayPositions ( ) const

inline

Definition at line 375 of file LikelihoodCalculationSingleProcess.h.

References rootPatternLinks_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), and bpp::RewardMappingTools::computeRewardVectors().

◆ getRootFreqs()

ValueRef<Eigen::RowVectorXd> bpp::LikelihoodCalculationSingleProcess::getRootFreqs ( )

inline

Definition at line 435 of file LikelihoodCalculationSingleProcess.h.

References rFreqs_.

◆ getRootPatternLinks()

ValueRef<PatternType> bpp::LikelihoodCalculationSingleProcess::getRootPatternLinks ( ) const

inline

Definition at line 377 of file LikelihoodCalculationSingleProcess.h.

References rootPatternLinks_.

◆ getRootWeights()

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

inline

Definition at line 430 of file LikelihoodCalculationSingleProcess.h.

References rootWeights_.

◆ getShrunkData()

std::shared_ptr<const AlignmentDataInterface> bpp::LikelihoodCalculationSingleProcess::getShrunkData ( ) const

inline

Definition at line 387 of file LikelihoodCalculationSingleProcess.h.

References shrunkData_.

Referenced by bpp::SingleProcessPhyloLikelihood::getShrunkData(), and makeForwardLikelihoodTree_().

◆ 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().

◆ getSiteLikelihoodsForAClass()

RowLik LikelihoodCalculationSingleProcess::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 344 of file LikelihoodCalculationSingleProcess.cpp.

References expandVector(), and getSiteLikelihoodsTree_().

Referenced by getSiteLikelihoodsForAllClasses().

◆ getSiteLikelihoodsForAllClasses()

AllRatesSiteLikelihoods LikelihoodCalculationSingleProcess::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 352 of file LikelihoodCalculationSingleProcess.cpp.

References getNumberOfDistinctSites(), getNumberOfSites(), getSiteLikelihoodsForAClass(), and vRateCatTrees_.

◆ getSiteLikelihoodsTree_()

std::shared_ptr< SiteLikelihoodsTree > LikelihoodCalculationSingleProcess::getSiteLikelihoodsTree_ ( size_t nCat )

private

Definition at line 685 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::LikelihoodCalculation::getLikelihoodNode_(), getTreeNode(), makeLikelihoodsAtNode_(), makeLikelihoodsAtRoot_(), shrunkData_, bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by getSiteLikelihoodsForAClass().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::LikelihoodCalculationSingleProcess::getStateMap ( ) const

inline

Definition at line 352 of file LikelihoodCalculationSingleProcess.h.

References bpp::LikelihoodCalculationSingleProcess::ProcessNodes::modelNode_, and processNodes_.

Referenced by bpp::SubstitutionMappingTools::computeOneJumpCounts().

◆ getSubstitutionProcess()

std::shared_ptr<const SubstitutionProcessInterface> bpp::LikelihoodCalculationSingleProcess::getSubstitutionProcess ( ) const

inline

Definition at line 332 of file LikelihoodCalculationSingleProcess.h.

References process_.

Referenced by bpp::SingleProcessPhyloLikelihood::getSubstitutionProcess().

◆ getTreeNode()

std::shared_ptr<ProcessTree> bpp::LikelihoodCalculationSingleProcess::getTreeNode ( size_t nCat )

inline

Get process tree for a rate category.

Parameters

nCat	: index of the rate category

Definition at line 579 of file LikelihoodCalculationSingleProcess.h.

References bpp::TextTools::toString(), and vRateCatTrees_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::RewardMappingTools::computeRewardVectors(), getBackwardLikelihoodsAtEdgeForClass(), and getSiteLikelihoodsTree_().

◆ getWeight()

unsigned int bpp::LikelihoodCalculationSingleProcess::getWeight ( size_t pos ) const

inline

Definition at line 425 of file LikelihoodCalculationSingleProcess.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 setData().

◆ makeForwardLikelihoodTree_()

void LikelihoodCalculationSingleProcess::makeForwardLikelihoodTree_ ( )

private

Definition at line 381 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::CategoryFromDiscreteDistribution::create(), bpp::LikelihoodCalculation::getContext_(), getShrunkData(), bpp::LikelihoodCalculationSingleProcess::ProcessNodes::modelNode_, processNodes_, psites_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::ratesNode_, stateMap(), bpp::LikelihoodCalculationSingleProcess::ProcessNodes::treeNode_, and vRateCatTrees_.

Referenced by makeLikelihoodsAtDAGNode_(), makeLikelihoodsAtNode_(), and makeLikelihoodsAtRoot_().

◆ makeLikelihoods()

void bpp::LikelihoodCalculationSingleProcess::makeLikelihoods ( )

inlinevirtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 285 of file LikelihoodCalculationSingleProcess.h.

References makeLikelihoodsAtRoot_(), and psites_.

Referenced by getForwardLikelihoodsAtNodeForClass().

◆ makeLikelihoodsAtDAGNode_()

void LikelihoodCalculationSingleProcess::makeLikelihoodsAtDAGNode_ ( uint nodeId )

private

Compute the likelihood at a given node in the DAG,.

This is not enough to compute likelihoods at species nodes, use makeLikelihoodsAtNode_ instead.

Parameters

nodeId : index of the node in the DAG

Definition at line 634 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::conditionalLikelihoodDimension(), bpp::ConstantOne< T >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::LikelihoodCalculation::getContext_(), getNumberOfDistinctSites(), makeForwardLikelihoodTree_(), makeRootFreqs_(), bpp::numeric::one(), rFreqs_, stateMap(), and vRateCatTrees_.

Referenced by getBackwardLikelihoodsAtNodeForClass(), getConditionalLikelihoodsAtNodeForClass(), and getLikelihoodsAtNodeForClass().

◆ makeLikelihoodsAtNode_()

void LikelihoodCalculationSingleProcess::makeLikelihoodsAtNode_ ( uint nodeId )

private

Compute the likelihood at a given node in the tree, which number may not be the same number in the DAG.

Several nodes in the DAG may be related to this tree node, in which case a sum is computed.

Parameters

nodeId : index of the node in the phylo Tree

Definition at line 497 of file LikelihoodCalculationSingleProcess.cpp.

References catProb_, bpp::conditionalLikelihoodDimension(), condLikelihoodTree_, bpp::ConstantOne< T >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::Convert< R, F >::create(), bpp::LikelihoodCalculation::getContext_(), getNumberOfDistinctSites(), makeForwardLikelihoodTree_(), makeRootFreqs_(), bpp::numeric::one(), process_, processNodes_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::ratesNode_, rFreqs_, stateMap(), and vRateCatTrees_.

Referenced by getBackwardLikelihoodsAtEdgeForClass(), getLikelihoodsAtNode(), getSiteLikelihoodsTree_(), and makeLikelihoodsTree().

◆ makeLikelihoodsAtRoot_()

void LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_ ( )

private

Definition at line 428 of file LikelihoodCalculationSingleProcess.cpp.

References catProb_, bpp::ProbabilitiesFromDiscreteDistribution::create(), bpp::SumOfLogarithms< F >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::Convert< R, F >::create(), bpp::DetailedNodeInfo, expandVector(), bpp::LikelihoodCalculation::getContext_(), getNumberOfDistinctSites(), bpp::Context::getZero(), bpp::LikelihoodCalculation::likelihood_, makeForwardLikelihoodTree_(), makeRootFreqs_(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, processNodes_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::ratesNode_, rFreqs_, rootPatternLinks_, rootWeights_, bpp::LikelihoodCalculation::setLikelihoodNode(), bpp::AlignedLikelihoodCalculation::setSiteLikelihoods(), vRateCatTrees_, bpp::writeGraphToDot(), and bpp::numeric::zero().

Referenced by getSiteLikelihoodsTree_(), makeLikelihoods(), and setData().

◆ makeLikelihoodsTree()

void bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsTree ( )

inline

make backward likelihood tree (only computed when needed)

Definition at line 544 of file LikelihoodCalculationSingleProcess.h.

References makeLikelihoodsAtNode_(), and process_.

◆ makeProcessNodes_() [1/2]

void LikelihoodCalculationSingleProcess::makeProcessNodes_ ( )

private

Definition at line 124 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::AbstractParameterAliasable::aliasParameters(), bpp::ConfiguredParameter::create(), bpp::LikelihoodCalculation::getContext_(), bpp::AbstractParameterAliasable::getParameters_(), bpp::ProcessTree::makeProcessTree(), bpp::LikelihoodCalculationSingleProcess::ProcessNodes::modelNode_, process_, processNodes_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::ratesNode_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::rootFreqsNode_, bpp::AbstractParameterAliasable::shareParameter_(), bpp::TextTools::toString(), and bpp::LikelihoodCalculationSingleProcess::ProcessNodes::treeNode_.

Referenced by LikelihoodCalculationSingleProcess().

◆ makeProcessNodes_() [2/2]

void LikelihoodCalculationSingleProcess::makeProcessNodes_	(	CollectionNodes &	pl,
		size_t	nProc
	)

private

make DF nodes of a process in a collection, using ConfiguredParameters defined in a CollectionNodes.

Definition at line 197 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::AbstractParameterAliasable::aliasParameters(), bpp::CollectionNodes::collection(), bpp::ConfiguredParameter::create(), bpp::LikelihoodCalculation::getContext_(), bpp::CollectionNodes::getFrequencies(), bpp::AbstractParameterAliasable::getIndependentParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParameterAliasable::getParameters_(), bpp::CollectionNodes::getRateDistribution(), bpp::AbstractParametrizable::hasParameter(), bpp::ProcessTree::makeProcessTree(), bpp::LikelihoodCalculationSingleProcess::ProcessNodes::modelNode_, processNodes_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::ratesNode_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::rootFreqsNode_, bpp::AbstractParameterAliasable::shareParameter_(), bpp::SubstitutionProcessCollection::substitutionProcess(), and bpp::LikelihoodCalculationSingleProcess::ProcessNodes::treeNode_.

◆ makeRootFreqs_()

void LikelihoodCalculationSingleProcess::makeRootFreqs_ ( )

private

Definition at line 369 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::LikelihoodCalculation::getContext_(), bpp::StateMapInterface::getNumberOfModelStates(), bpp::LikelihoodCalculationSingleProcess::ProcessNodes::modelNode_, processNodes_, rFreqs_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::rootFreqsNode_, and stateMap().

Referenced by makeLikelihoodsAtDAGNode_(), makeLikelihoodsAtNode_(), and makeLikelihoodsAtRoot_().

◆ setClockLike()

void LikelihoodCalculationSingleProcess::setClockLike ( double rate = 1 )

Set Tree ClockLike :

add a RateNode parameter for multiplying all branch lengths
remove all branch lengths parameters from the parameters

Definition at line 305 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::ValueFromConfiguredParameter::create(), bpp::ConfiguredParameter::create(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::LikelihoodCalculation::getContext_(), bpp::ParameterList::getParameterNames(), bpp::AbstractParameterAliasable::getParameters(), processNodes_, bpp::Parameter::R_PLUS_STAR, bpp::ConfiguredParameter::resetDependencies(), bpp::AbstractParameterAliasable::shareParameter_(), and bpp::LikelihoodCalculationSingleProcess::ProcessNodes::treeNode_.

◆ setData()

void bpp::LikelihoodCalculationSingleProcess::setData ( std::shared_ptr< const AlignmentDataInterface > sites )

inline

Definition at line 252 of file LikelihoodCalculationSingleProcess.h.

References cleanAllLikelihoods(), bpp::LikelihoodCalculation::isInitialized(), makeLikelihoodsAtRoot_(), psites_, setPatterns_(), and vRateCatTrees_.

Referenced by bpp::OneProcessSequencePhyloLikelihood::setData(), and bpp::SingleProcessPhyloLikelihood::setData().

◆ 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 makeLikelihoodsAtRoot_().

◆ setNumericalDerivateConfiguration()

void LikelihoodCalculationSingleProcess::setNumericalDerivateConfiguration	(	double	delta,
		const NumericalDerivativeType &	config
	)

Set derivation procedure (see DataFlowNumeric.h)

Definition at line 264 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::NumericMutable< T >::create(), bpp::LikelihoodCalculation::getContext_(), processNodes_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::ratesNode_, bpp::LikelihoodCalculationSingleProcess::ProcessNodes::rootFreqsNode_, and bpp::LikelihoodCalculationSingleProcess::ProcessNodes::treeNode_.

Referenced by LikelihoodCalculationSingleProcess().

◆ setPatterns_()

void LikelihoodCalculationSingleProcess::setPatterns_ ( )

private

Definition at line 110 of file LikelihoodCalculationSingleProcess.cpp.

References bpp::NumericConstant< T >::create(), bpp::LikelihoodCalculation::getContext_(), bpp::SitePatterns::getIndices(), bpp::SitePatterns::getSites(), bpp::SitePatterns::getWeights(), process_, psites_, rootPatternLinks_, rootWeights_, and shrunkData_.

Referenced by LikelihoodCalculationSingleProcess(), and setData().

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

◆ shrunkData()

const AlignmentDataInterface& bpp::LikelihoodCalculationSingleProcess::shrunkData ( ) const

inline

Definition at line 382 of file LikelihoodCalculationSingleProcess.h.

References shrunkData_.

◆ stateMap()

const StateMapInterface& bpp::LikelihoodCalculationSingleProcess::stateMap ( ) const

inline

Definition at line 347 of file LikelihoodCalculationSingleProcess.h.

References bpp::LikelihoodCalculationSingleProcess::ProcessNodes::modelNode_, and processNodes_.

Referenced by bpp::SingleProcessPhyloLikelihood::getAlphabet(), bpp::LikelihoodCalculationOnABranch::LikelihoodCalculationOnABranch(), makeForwardLikelihoodTree_(), makeLikelihoodsAtDAGNode_(), makeLikelihoodsAtNode_(), and makeRootFreqs_().

◆ substitutionProcess()

const SubstitutionProcessInterface& bpp::LikelihoodCalculationSingleProcess::substitutionProcess ( ) const

inline

Return the ref to the SubstitutionProcess.

Warning; the process parameter values may not be up to date with some of the LikelihoodCalculationSingleProcess

Definition at line 327 of file LikelihoodCalculationSingleProcess.h.

References process_.

Friends And Related Function Documentation

◆ LikelihoodCalculationOnABranch

friend class LikelihoodCalculationOnABranch

friend

Definition at line 634 of file LikelihoodCalculationSingleProcess.h.

Member Data Documentation

◆ catProb_

ValueRef<Eigen::RowVectorXd> bpp::LikelihoodCalculationSingleProcess::catProb_

private

Definition at line 210 of file LikelihoodCalculationSingleProcess.h.

Referenced by makeLikelihoodsAtNode_(), and makeLikelihoodsAtRoot_().

◆ condLikelihoodTree_

std::shared_ptr<ConditionalLikelihoodTree> bpp::LikelihoodCalculationSingleProcess::condLikelihoodTree_

private

Definition at line 213 of file LikelihoodCalculationSingleProcess.h.

Referenced by cleanAllLikelihoods(), getBackwardLikelihoodsAtEdgeForClass(), getLikelihoodsAtNode(), and makeLikelihoodsAtNode_().

◆ 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(), makeLikelihoodsAtRoot_(), and bpp::LikelihoodCalculation::setLikelihoodNode().

◆ 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(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), makeLikelihoodsAtRoot_(), and bpp::AlignedLikelihoodCalculation::setSiteLikelihoods().

◆ process_

std::shared_ptr<const SubstitutionProcessInterface> bpp::LikelihoodCalculationSingleProcess::process_

private

Definition at line 169 of file LikelihoodCalculationSingleProcess.h.

Referenced by getSubstitutionProcess(), LikelihoodCalculationSingleProcess(), makeLikelihoodsAtNode_(), makeLikelihoodsTree(), makeProcessNodes_(), setPatterns_(), and substitutionProcess().

◆ processNodes_

ProcessNodes bpp::LikelihoodCalculationSingleProcess::processNodes_

private

Definition at line 198 of file LikelihoodCalculationSingleProcess.h.

Referenced by getStateMap(), makeForwardLikelihoodTree_(), makeLikelihoodsAtNode_(), makeLikelihoodsAtRoot_(), makeProcessNodes_(), makeRootFreqs_(), setClockLike(), setNumericalDerivateConfiguration(), and stateMap().

◆ psites_

std::shared_ptr<const AlignmentDataInterface> bpp::LikelihoodCalculationSingleProcess::psites_

private

Definition at line 170 of file LikelihoodCalculationSingleProcess.h.

Referenced by cleanAllLikelihoods(), data(), getData(), getNumberOfSites(), makeForwardLikelihoodTree_(), makeLikelihoods(), setData(), and setPatterns_().

◆ rFreqs_

ValueRef<Eigen::RowVectorXd> bpp::LikelihoodCalculationSingleProcess::rFreqs_

private

Definition at line 200 of file LikelihoodCalculationSingleProcess.h.

Referenced by getRootFreqs(), makeLikelihoodsAtDAGNode_(), makeLikelihoodsAtNode_(), makeLikelihoodsAtRoot_(), and makeRootFreqs_().

◆ rootPatternLinks_

ValueRef<PatternType> bpp::LikelihoodCalculationSingleProcess::rootPatternLinks_

private

Definition at line 186 of file LikelihoodCalculationSingleProcess.h.

Referenced by cleanAllLikelihoods(), expandMatrix(), expandVector(), getRootArrayPosition(), getRootArrayPositions(), getRootPatternLinks(), makeLikelihoodsAtRoot_(), and setPatterns_().

◆ rootWeights_

std::shared_ptr<SiteWeights> bpp::LikelihoodCalculationSingleProcess::rootWeights_

private

The frequency of each site.

Definition at line 192 of file LikelihoodCalculationSingleProcess.h.

Referenced by cleanAllLikelihoods(), getRootWeights(), getWeight(), makeLikelihoodsAtRoot_(), and setPatterns_().

◆ shrunkData_

std::shared_ptr<AlignmentDataInterface> bpp::LikelihoodCalculationSingleProcess::shrunkData_

private

Definition at line 193 of file LikelihoodCalculationSingleProcess.h.

Referenced by cleanAllLikelihoods(), getNumberOfDistinctSites(), getShrunkData(), getSiteLikelihoodsTree_(), setPatterns_(), and shrunkData().

◆ 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().

◆ vRateCatTrees_

std::vector<RateCategoryTrees> bpp::LikelihoodCalculationSingleProcess::vRateCatTrees_

private

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

Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculationSingleProcess.h
Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculationSingleProcess.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ LikelihoodCalculationSingleProcess() [1/5]

◆ LikelihoodCalculationSingleProcess() [2/5]

◆ LikelihoodCalculationSingleProcess() [3/5]

◆ LikelihoodCalculationSingleProcess() [4/5]

◆ LikelihoodCalculationSingleProcess() [5/5]

Member Function Documentation

◆ cleanAllLikelihoods()

◆ clone()

◆ data()

◆ expandMatrix()

◆ expandVector()

◆ getBackwardLikelihoodsAtEdgeForClass()

◆ getBackwardLikelihoodsAtNodeForClass()

◆ getBackwardLikelihoodTree()

◆ getConditionalLikelihoodsAtNodeForClass()

◆ getContext()

◆ getContext_()

◆ getData()

◆ getEdgesIds()

◆ getForwardLikelihoodsAtNodeForClass()

◆ getForwardLikelihoodTree()

◆ getLikelihoodForASite()

◆ getLikelihoodNode()

◆ getLikelihoodNode_()

◆ getLikelihoodPerSite()

◆ getLikelihoodsAtNode()

◆ getLikelihoodsAtNodeForClass()

◆ getLogLikelihoodForASite()

◆ getNodesIds()

◆ getNumberOfClasses()

◆ getNumberOfDistinctSites()

◆ getNumberOfSites()

◆ getRootArrayPosition()

◆ getRootArrayPositions()

◆ getRootFreqs()

◆ getRootPatternLinks()

◆ getRootWeights()

◆ getShrunkData()

◆ getSiteLikelihoods()

◆ getSiteLikelihoodsForAClass()

◆ getSiteLikelihoodsForAllClasses()

◆ getSiteLikelihoodsTree_()

◆ getStateMap()

◆ getSubstitutionProcess()

◆ getTreeNode()

◆ getWeight()

◆ isInitialized()

◆ makeForwardLikelihoodTree_()

◆ makeLikelihoods()

◆ makeLikelihoodsAtDAGNode_()

◆ makeLikelihoodsAtNode_()

◆ makeLikelihoodsAtRoot_()

◆ makeLikelihoodsTree()

◆ makeProcessNodes_() [1/2]

◆ makeProcessNodes_() [2/2]

◆ makeRootFreqs_()

◆ setClockLike()

◆ setData()

◆ setLikelihoodNode()

◆ setNumericalDerivateConfiguration()

◆ setPatterns_()

◆ setSiteLikelihoods()

◆ shrunkData()

◆ stateMap()

◆ substitutionProcess()

Friends And Related Function Documentation

◆ LikelihoodCalculationOnABranch

Member Data Documentation

◆ catProb_

◆ condLikelihoodTree_

◆ context_