discrete Rate Across Sites, (simple) Recursive likelihood data structure. More...

#include <Bpp/Phyl/Legacy/Likelihood/DRASRTreeLikelihoodData.h>

Inheritance diagram for bpp::DRASRTreeLikelihoodData:

Collaboration diagram for bpp::DRASRTreeLikelihoodData:

Public Member Functions
	DRASRTreeLikelihoodData (std::shared_ptr< const TreeTemplate< Node >> tree, size_t nbClasses, bool usePatterns=true)

	DRASRTreeLikelihoodData (const DRASRTreeLikelihoodData &data)

DRASRTreeLikelihoodData &	operator= (const DRASRTreeLikelihoodData &data)

virtual	~DRASRTreeLikelihoodData ()

DRASRTreeLikelihoodData *	clone () const

void	setTree (std::shared_ptr< const TreeTemplate< Node >> tree)
	Set the tree associated to the data. More...

DRASRTreeLikelihoodNodeData &	getNodeData (int nodeId)

const DRASRTreeLikelihoodNodeData &	getNodeData (int nodeId) const

size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition) const

size_t	getRootArrayPosition (size_t currentPosition) const

const std::vector< size_t > &	getArrayPositions (int parentId, int sonId) const

std::vector< size_t > &	getArrayPositions (int parentId, int sonId)

size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition)

VVVdouble &	getLikelihoodArray (int nodeId)

VVVdouble &	getDLikelihoodArray (int nodeId)

VVVdouble &	getD2LikelihoodArray (int nodeId)

size_t	getNumberOfDistinctSites () const

size_t	getNumberOfSites () const

size_t	getNumberOfStates () const

size_t	getNumberOfClasses () const

void	initLikelihoods (const AlignmentDataInterface &sites, const TransitionModelInterface &model)

std::vector< size_t > &	getRootArrayPositions ()

const std::vector< size_t > &	getRootArrayPositions () const

unsigned int	getWeight (size_t pos) const

const std::vector< unsigned int > &	getWeights () const

std::shared_ptr< const Alphabet >	getAlphabet () const

std::shared_ptr< const TreeTemplate< Node > >	getTree () const

Protected Member Functions
virtual void	initLikelihoods (const Node *node, const AlignmentDataInterface &sequences, const TransitionModelInterface &model)
	This method initializes the leaves according to a sequence file. likelihood is set to 1 for the state corresponding to the sequence site, otherwise it is set to 0. More...

virtual std::unique_ptr< SitePatterns >	initLikelihoodsWithPatterns (const Node *node, const AlignmentDataInterface &sequences, const TransitionModelInterface &model)
	This method initializes the leaves according to a sequence file. More...

Protected Attributes
std::vector< size_t >	rootPatternLinks_
	Links between sites and patterns. More...

std::vector< unsigned int >	rootWeights_
	The frequency of each site. More...

std::shared_ptr< const TreeTemplate< Node > >	tree_

std::shared_ptr< const Alphabet >	alphabet_

Private Attributes
std::map< int, DRASRTreeLikelihoodNodeData >	nodeData_
	This contains all likelihood values used for computation. More...

std::map< int, std::map< int, std::vector< size_t > > >	patternLinks_
	This map defines the pattern network. More...

std::shared_ptr< AlignmentDataInterface >	shrunkData_

size_t	nbSites_

size_t	nbStates_

size_t	nbClasses_

size_t	nbDistinctSites_

bool	usePatterns_

Detailed Description

discrete Rate Across Sites, (simple) Recursive likelihood data structure.

Definition at line 86 of file DRASRTreeLikelihoodData.h.

Constructor & Destructor Documentation

◆ DRASRTreeLikelihoodData() [1/2]

bpp::DRASRTreeLikelihoodData::DRASRTreeLikelihoodData	(	std::shared_ptr< const TreeTemplate< Node >>	tree,
		size_t	nbClasses,
		bool	usePatterns = `true`
	)

inline

Definition at line 116 of file DRASRTreeLikelihoodData.h.

Referenced by clone().

◆ DRASRTreeLikelihoodData() [2/2]

bpp::DRASRTreeLikelihoodData::DRASRTreeLikelihoodData ( const DRASRTreeLikelihoodData & data )

inline

Definition at line 122 of file DRASRTreeLikelihoodData.h.

References shrunkData_.

◆ ~DRASRTreeLikelihoodData()

virtual bpp::DRASRTreeLikelihoodData::~DRASRTreeLikelihoodData ( )

inlinevirtual

Definition at line 152 of file DRASRTreeLikelihoodData.h.

Member Function Documentation

◆ clone()

DRASRTreeLikelihoodData* bpp::DRASRTreeLikelihoodData::clone ( ) const

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 154 of file DRASRTreeLikelihoodData.h.

References DRASRTreeLikelihoodData().

Referenced by bpp::RHomogeneousTreeLikelihood::operator=(), and bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractTreeLikelihoodData::getAlphabet ( ) const

inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Definition at line 100 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::alphabet_.

◆ getArrayPosition() [1/2]

size_t bpp::DRASRTreeLikelihoodData::getArrayPosition	(	int	parentId,
		int	sonId,
		size_t	currentPosition
	)

inline

Definition at line 200 of file DRASRTreeLikelihoodData.h.

References patternLinks_.

◆ getArrayPosition() [2/2]

size_t bpp::DRASRTreeLikelihoodData::getArrayPosition	(	int	parentId,
		int	sonId,
		size_t	currentPosition
	)		const

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 184 of file DRASRTreeLikelihoodData.h.

References patternLinks_.

◆ getArrayPositions() [1/2]

std::vector<size_t>& bpp::DRASRTreeLikelihoodData::getArrayPositions	(	int	parentId,
		int	sonId
	)

inline

Definition at line 196 of file DRASRTreeLikelihoodData.h.

References patternLinks_.

◆ getArrayPositions() [2/2]

const std::vector<size_t>& bpp::DRASRTreeLikelihoodData::getArrayPositions	(	int	parentId,
		int	sonId
	)		const

inline

Definition at line 192 of file DRASRTreeLikelihoodData.h.

References patternLinks_.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), and bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood().

◆ getD2LikelihoodArray()

VVVdouble& bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray ( int nodeId )

inline

Definition at line 215 of file DRASRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), and bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass().

◆ getDLikelihoodArray()

VVVdouble& bpp::DRASRTreeLikelihoodData::getDLikelihoodArray ( int nodeId )

inline

Definition at line 210 of file DRASRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), and bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass().

◆ getLikelihoodArray()

VVVdouble& bpp::DRASRTreeLikelihoodData::getLikelihoodArray ( int nodeId )

inline

Definition at line 205 of file DRASRTreeLikelihoodData.h.

References nodeData_.

◆ getNodeData() [1/2]

DRASRTreeLikelihoodNodeData& bpp::DRASRTreeLikelihoodData::getNodeData ( int nodeId )

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 176 of file DRASRTreeLikelihoodData.h.

References nodeData_.

◆ getNodeData() [2/2]

const DRASRTreeLikelihoodNodeData& bpp::DRASRTreeLikelihoodData::getNodeData ( int nodeId ) const

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 180 of file DRASRTreeLikelihoodData.h.

References nodeData_.

◆ getNumberOfClasses()

size_t bpp::DRASRTreeLikelihoodData::getNumberOfClasses ( ) const

inline

Definition at line 223 of file DRASRTreeLikelihoodData.h.

References nbClasses_.

◆ getNumberOfDistinctSites()

size_t bpp::DRASRTreeLikelihoodData::getNumberOfDistinctSites ( ) const

inlinevirtual

Returns: The number of non redundant patterns.

Implements bpp::TreeLikelihoodData.

Definition at line 220 of file DRASRTreeLikelihoodData.h.

References nbDistinctSites_.

Referenced by bpp::RHomogeneousTreeLikelihood::setData().

◆ getNumberOfSites()

size_t bpp::DRASRTreeLikelihoodData::getNumberOfSites ( ) const

inlinevirtual

Returns: The total number of sites.

Implements bpp::TreeLikelihoodData.

Definition at line 221 of file DRASRTreeLikelihoodData.h.

References nbSites_.

Referenced by bpp::RHomogeneousTreeLikelihood::setData().

◆ getNumberOfStates()

size_t bpp::DRASRTreeLikelihoodData::getNumberOfStates ( ) const

inlinevirtual

Returns: Get the number of states used in the model.

Implements bpp::TreeLikelihoodData.

Definition at line 222 of file DRASRTreeLikelihoodData.h.

References nbStates_.

Referenced by bpp::RHomogeneousTreeLikelihood::setData().

◆ getRootArrayPosition()

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

inlinevirtual

Reimplemented from bpp::AbstractTreeLikelihoodData.

Definition at line 188 of file DRASRTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

Referenced by bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), and bpp::RHomogeneousTreeLikelihood::getSiteIndex().

◆ getRootArrayPositions() [1/2]

std::vector<size_t>& bpp::AbstractTreeLikelihoodData::getRootArrayPositions ( )

inlineinherited

Definition at line 85 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

◆ getRootArrayPositions() [2/2]

const std::vector<size_t>& bpp::AbstractTreeLikelihoodData::getRootArrayPositions ( ) const

inlineinherited

Definition at line 86 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

◆ getTree()

std::shared_ptr< const TreeTemplate<Node> > bpp::AbstractTreeLikelihoodData::getTree ( ) const

inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Definition at line 102 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::tree_.

◆ getWeight()

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

inlinevirtualinherited

Returns: The frequency of a given pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 91 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootWeights_.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

◆ getWeights()

const std::vector<unsigned int>& bpp::AbstractTreeLikelihoodData::getWeights ( ) const

inlinevirtualinherited

Returns: Frequencies for each pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 95 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootWeights_.

◆ initLikelihoods() [1/2]

void DRASRTreeLikelihoodData::initLikelihoods	(	const AlignmentDataInterface &	sites,
		const TransitionModelInterface &	model
	)

Definition at line 19 of file DRASRTreeLikelihoodData.cpp.

References bpp::BranchModelInterface::getAlphabet(), bpp::TemplateAlignmentDataInterface< class >::getAlphabet(), bpp::TemplateAlignmentDataInterface< class >::getNumberOfSequences(), bpp::TemplateAlignmentDataInterface< class >::getNumberOfSites(), and bpp::BranchModelInterface::getNumberOfStates().

Referenced by bpp::RHomogeneousTreeLikelihood::setData().

◆ initLikelihoods() [2/2]

void DRASRTreeLikelihoodData::initLikelihoods	(	const Node *	node,
		const AlignmentDataInterface &	sequences,
		const TransitionModelInterface &	model
	)

protectedvirtual

This method initializes the leaves according to a sequence file. likelihood is set to 1 for the state corresponding to the sequence site, otherwise it is set to 0.

All likelihood arrays at each nodes are initialized according to alphabet size and sequences length, and filled with 1.

NB: This method is recursive.

Parameters

node	The node defining the subtree to analyse.
sequences	The data to be used for initialization.
model	The model to use.

Definition at line 60 of file DRASRTreeLikelihoodData.cpp.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray(), bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray(), bpp::Node::getName(), bpp::Node::getNumberOfSons(), bpp::TemplateAlignmentDataInterface< class >::getSequencePosition(), bpp::TemplateAlignmentDataInterface< class >::getStateValueAt(), bpp::Node::isLeaf(), and bpp::DRASRTreeLikelihoodNodeData::setNode().

◆ initLikelihoodsWithPatterns()

std::unique_ptr< SitePatterns > DRASRTreeLikelihoodData::initLikelihoodsWithPatterns	(	const Node *	node,
		const AlignmentDataInterface &	sequences,
		const TransitionModelInterface &	model
	)

protectedvirtual

This method initializes the leaves according to a sequence file.

likelihood is set to 1 for the state corresponding to the sequence site, otherwise it is set to 0.

All likelihood arrays at each nodes are initialized according to alphabet size and sequences length, and filled with 1.

NB: This method is recursive.

Parameters

node	The node defining the subtree to analyse.
sequences	The data to be used for initialization.
model	The model to use.

Returns: The shrunk sub-dataset + indices for the subtree defined by node.

Definition at line 159 of file DRASRTreeLikelihoodData.cpp.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray(), bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray(), bpp::Node::getId(), bpp::TreeTemplateTools::getLeaves(), bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray(), bpp::Node::getName(), bpp::Node::getNumberOfSons(), bpp::PatternTools::getSequenceSubset(), bpp::Node::isLeaf(), and bpp::DRASRTreeLikelihoodNodeData::setNode().

◆ operator=()

DRASRTreeLikelihoodData& bpp::DRASRTreeLikelihoodData::operator= ( const DRASRTreeLikelihoodData & data )

inline

Definition at line 135 of file DRASRTreeLikelihoodData.h.

References nbClasses_, nbDistinctSites_, nbSites_, nbStates_, nodeData_, bpp::AbstractTreeLikelihoodData::operator=(), patternLinks_, shrunkData_, and usePatterns_.

◆ setTree()

void bpp::DRASRTreeLikelihoodData::setTree ( std::shared_ptr< const TreeTemplate< Node >> tree )

inline

Set the tree associated to the data.

All node data will be actualized accordingly by calling the setNode() method on the corresponding nodes.

Warning: : the old tree and the new tree must be two clones! And particularly, they have to share the same topology and nodes id.

Parameters

tree	The tree to be associated to this data.

Definition at line 166 of file DRASRTreeLikelihoodData.h.

References nodeData_, and bpp::AbstractTreeLikelihoodData::tree_.

Referenced by bpp::RHomogeneousTreeLikelihood::operator=(), and bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTreeLikelihoodData::alphabet_

protectedinherited

Definition at line 59 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getAlphabet(), and bpp::AbstractTreeLikelihoodData::operator=().

◆ nbClasses_

size_t bpp::DRASRTreeLikelihoodData::nbClasses_

private

Definition at line 111 of file DRASRTreeLikelihoodData.h.

Referenced by getNumberOfClasses(), and operator=().

◆ nbDistinctSites_

size_t bpp::DRASRTreeLikelihoodData::nbDistinctSites_

private

Definition at line 112 of file DRASRTreeLikelihoodData.h.

Referenced by getNumberOfDistinctSites(), and operator=().

◆ nbSites_

size_t bpp::DRASRTreeLikelihoodData::nbSites_

private

Definition at line 109 of file DRASRTreeLikelihoodData.h.

Referenced by getNumberOfSites(), and operator=().

◆ nbStates_

size_t bpp::DRASRTreeLikelihoodData::nbStates_

private

Definition at line 110 of file DRASRTreeLikelihoodData.h.

Referenced by getNumberOfStates(), and operator=().

◆ nodeData_

std::map<int, DRASRTreeLikelihoodNodeData> bpp::DRASRTreeLikelihoodData::nodeData_

mutableprivate

This contains all likelihood values used for computation.

Definition at line 93 of file DRASRTreeLikelihoodData.h.

Referenced by getD2LikelihoodArray(), getDLikelihoodArray(), getLikelihoodArray(), getNodeData(), operator=(), and setTree().

◆ patternLinks_

std::map<int, std::map<int, std::vector<size_t> > > bpp::DRASRTreeLikelihoodData::patternLinks_

mutableprivate

This map defines the pattern network.

Let n1 be the id of a node in the tree, and n11 and n12 the ids of its sons. Providing the likelihood array is known for nodes n11 and n12, the likelihood array for node n1 and site i (likelihood[n1][i]) must be computed using arrays patternLinks[n1][n11][i] and patternLinks_[n1][n12][i]. This network is initialized once for all in the constructor of this class.

The double map contains the position of the site to use (second dimension) of the likelihoods array.

Definition at line 107 of file DRASRTreeLikelihoodData.h.

Referenced by getArrayPosition(), getArrayPositions(), and operator=().

◆ rootPatternLinks_

std::vector<size_t> bpp::AbstractTreeLikelihoodData::rootPatternLinks_

protectedinherited

Links between sites and patterns.

The size of this vector is equal to the number of sites in the container, each element corresponds to a site in the container and points to the corresponding column in the likelihood array of the root node. If the container contains no repeated site, there will be a strict equivalence between each site and the likelihood array of the root node. However, if this is not the case, some pointers may point toward the same element in the likelihood array.

Definition at line 50 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), getRootArrayPosition(), bpp::AbstractTreeLikelihoodData::getRootArrayPositions(), and bpp::AbstractTreeLikelihoodData::operator=().

◆ rootWeights_

std::vector<unsigned int> bpp::AbstractTreeLikelihoodData::rootWeights_

protectedinherited

The frequency of each site.

Definition at line 55 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getWeight(), bpp::AbstractTreeLikelihoodData::getWeights(), and bpp::AbstractTreeLikelihoodData::operator=().

◆ shrunkData_

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

private

Definition at line 108 of file DRASRTreeLikelihoodData.h.

Referenced by DRASRTreeLikelihoodData(), and operator=().

◆ tree_

std::shared_ptr<const TreeTemplate<Node> > bpp::AbstractTreeLikelihoodData::tree_

protectedinherited

Definition at line 57 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getTree(), bpp::AbstractTreeLikelihoodData::operator=(), bpp::DRASDRTreeLikelihoodData::setTree(), and setTree().

◆ usePatterns_

bool bpp::DRASRTreeLikelihoodData::usePatterns_

private

Definition at line 113 of file DRASRTreeLikelihoodData.h.

Referenced by operator=().

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

Bpp/Phyl/Legacy/Likelihood/DRASRTreeLikelihoodData.h
Bpp/Phyl/Legacy/Likelihood/DRASRTreeLikelihoodData.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DRASRTreeLikelihoodData() [1/2]

◆ DRASRTreeLikelihoodData() [2/2]

◆ ~DRASRTreeLikelihoodData()

Member Function Documentation

◆ clone()

◆ getAlphabet()

◆ getArrayPosition() [1/2]

◆ getArrayPosition() [2/2]

◆ getArrayPositions() [1/2]

◆ getArrayPositions() [2/2]

◆ getD2LikelihoodArray()

◆ getDLikelihoodArray()

◆ getLikelihoodArray()

◆ getNodeData() [1/2]

◆ getNodeData() [2/2]

◆ getNumberOfClasses()

◆ getNumberOfDistinctSites()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getRootArrayPosition()

◆ getRootArrayPositions() [1/2]

◆ getRootArrayPositions() [2/2]

◆ getTree()

◆ getWeight()

◆ getWeights()

◆ initLikelihoods() [1/2]

◆ initLikelihoods() [2/2]

◆ initLikelihoodsWithPatterns()

◆ operator=()

◆ setTree()

Member Data Documentation

◆ alphabet_

◆ nbClasses_

◆ nbDistinctSites_

◆ nbSites_

◆ nbStates_

◆ nodeData_

◆ patternLinks_

◆ rootPatternLinks_

◆ rootWeights_

◆ shrunkData_

◆ tree_

◆ usePatterns_