Partial implementation of the TreeLikelihoodData interface. More...

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

Inheritance diagram for bpp::AbstractTreeLikelihoodData:

Collaboration diagram for bpp::AbstractTreeLikelihoodData:

Public Member Functions
	AbstractTreeLikelihoodData (std::shared_ptr< const TreeTemplate< Node >> tree)

	AbstractTreeLikelihoodData (const AbstractTreeLikelihoodData &atd)

AbstractTreeLikelihoodData &	operator= (const AbstractTreeLikelihoodData &atd)

virtual	~AbstractTreeLikelihoodData ()

std::vector< size_t > &	getRootArrayPositions ()

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

size_t	getRootArrayPosition (const size_t site) 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

TreeLikelihoodData *	clone () const =0

virtual size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition) const =0

virtual TreeLikelihoodNodeData &	getNodeData (int nodeId)=0

virtual const TreeLikelihoodNodeData &	getNodeData (int nodeId) const =0

virtual size_t	getNumberOfDistinctSites () const =0

virtual size_t	getNumberOfSites () const =0

virtual size_t	getNumberOfStates () const =0

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_

Detailed Description

Partial implementation of the TreeLikelihoodData interface.

This data structure provides a simple compression, by performing and storing computations only one time per identical sites.

The compression is achieved by the TreeLikelihood object. The correspondence between sites in the dataset and the arrays in the structures is given by the rootPatternLinks_ array: the array indice for site if given by:

rootPatternLinks_[i]

bpp::AbstractTreeLikelihoodData::rootPatternLinks_

std::vector< size_t > rootPatternLinks_

Links between sites and patterns.

Definition: AbstractTreeLikelihoodData.h:50

Finally, the rootWeights_ array gives for each array position, the number of sites with this pattern. The global likelihood is then given by the product of all likelihoods for each array position, weighted by the corresponding number of sites.

Definition at line 35 of file AbstractTreeLikelihoodData.h.

Constructor & Destructor Documentation

◆ AbstractTreeLikelihoodData() [1/2]

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

inline

Definition at line 62 of file AbstractTreeLikelihoodData.h.

◆ AbstractTreeLikelihoodData() [2/2]

bpp::AbstractTreeLikelihoodData::AbstractTreeLikelihoodData ( const AbstractTreeLikelihoodData & atd )

inline

Definition at line 65 of file AbstractTreeLikelihoodData.h.

◆ ~AbstractTreeLikelihoodData()

virtual bpp::AbstractTreeLikelihoodData::~AbstractTreeLikelihoodData ( )

inlinevirtual

Definition at line 82 of file AbstractTreeLikelihoodData.h.

Member Function Documentation

◆ clone()

TreeLikelihoodData* bpp::TreeLikelihoodData::clone ( ) const

pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

◆ getAlphabet()

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

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 100 of file AbstractTreeLikelihoodData.h.

References alphabet_.

◆ getArrayPosition()

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

pure virtualinherited

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

◆ getNodeData() [1/2]

virtual const TreeLikelihoodNodeData& bpp::TreeLikelihoodData::getNodeData ( int nodeId ) const

pure virtualinherited

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

◆ getNodeData() [2/2]

virtual TreeLikelihoodNodeData& bpp::TreeLikelihoodData::getNodeData ( int nodeId )

pure virtualinherited

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

◆ getNumberOfDistinctSites()

virtual size_t bpp::TreeLikelihoodData::getNumberOfDistinctSites ( ) const

pure virtualinherited

Returns: The number of non redundant patterns.

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies().

◆ getNumberOfSites()

virtual size_t bpp::TreeLikelihoodData::getNumberOfSites ( ) const

pure virtualinherited

Returns: The total number of sites.

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

◆ getNumberOfStates()

virtual size_t bpp::TreeLikelihoodData::getNumberOfStates ( ) const

pure virtualinherited

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

Implemented in bpp::DRASRTreeLikelihoodData, and bpp::DRASDRTreeLikelihoodData.

◆ getRootArrayPosition()

size_t bpp::AbstractTreeLikelihoodData::getRootArrayPosition ( const size_t site ) const

inlinevirtual

Implements bpp::TreeLikelihoodData.

Reimplemented in bpp::DRASRTreeLikelihoodData.

Definition at line 87 of file AbstractTreeLikelihoodData.h.

References rootPatternLinks_.

◆ getRootArrayPositions() [1/2]

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

inline

Definition at line 85 of file AbstractTreeLikelihoodData.h.

References rootPatternLinks_.

◆ getRootArrayPositions() [2/2]

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

inline

Definition at line 86 of file AbstractTreeLikelihoodData.h.

References rootPatternLinks_.

◆ getTree()

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

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 102 of file AbstractTreeLikelihoodData.h.

References tree_.

◆ getWeight()

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

inlinevirtual

Returns: The frequency of a given pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 91 of file AbstractTreeLikelihoodData.h.

References rootWeights_.

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

◆ getWeights()

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

inlinevirtual

Returns: Frequencies for each pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 95 of file AbstractTreeLikelihoodData.h.

References rootWeights_.

◆ operator=()

AbstractTreeLikelihoodData& bpp::AbstractTreeLikelihoodData::operator= ( const AbstractTreeLikelihoodData & atd )

inline

Definition at line 72 of file AbstractTreeLikelihoodData.h.

References alphabet_, rootPatternLinks_, rootWeights_, and tree_.

Referenced by bpp::DRASDRTreeLikelihoodData::operator=(), and bpp::DRASRTreeLikelihoodData::operator=().

Member Data Documentation

◆ alphabet_

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

protected

Definition at line 59 of file AbstractTreeLikelihoodData.h.

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

◆ rootPatternLinks_

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

protected

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 getRootArrayPosition(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), getRootArrayPositions(), and operator=().