bpp::TreeLikelihoodData Class Reference

TreeLikelihood data structure. More...

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

Inheritance diagram for bpp::TreeLikelihoodData:

Collaboration diagram for bpp::TreeLikelihoodData:

Public Member Functions
	TreeLikelihoodData ()
virtual	~TreeLikelihoodData ()
TreeLikelihoodData *	clone () const =0
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
virtual std::shared_ptr< const TreeTemplate< Node > >	getTree () const =0
virtual size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition) const =0
virtual size_t	getRootArrayPosition (size_t site) 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
virtual unsigned int	getWeight (size_t pos) const =0
virtual const std::vector< unsigned int > &	getWeights () const =0

Detailed Description

TreeLikelihood data structure.

Stores all the inner computations:

• conditional likelihoods for each node,
• correspondence between sites in the dataset and array indices.

See also

TreeLikelihoodNodeData

Definition at line 61 of file TreeLikelihoodData.h.

Constructor & Destructor Documentation

TreeLikelihoodData()

bpp::TreeLikelihoodData::TreeLikelihoodData ( )

inline

Definition at line 65 of file TreeLikelihoodData.h.

~TreeLikelihoodData()

virtual bpp::TreeLikelihoodData::~TreeLikelihoodData ( )

inlinevirtual

Definition at line 66 of file TreeLikelihoodData.h.

Member Function Documentation

clone()

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

pure virtual

Implements bpp::Clonable.

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

getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::TreeLikelihoodData::getAlphabet ( ) const

pure virtual

Implemented in bpp::AbstractTreeLikelihoodData.

getArrayPosition()

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

pure virtual

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

getNodeData() [1/2]

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

pure virtual

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

getNodeData() [2/2]

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

pure virtual

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

getNumberOfDistinctSites()

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

pure virtual

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 virtual

Returns

The total number of sites.

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

getNumberOfStates()

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

pure virtual

Returns

Get the number of states used in the model.

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

getRootArrayPosition()

virtual size_t bpp::TreeLikelihoodData::getRootArrayPosition ( size_t  site ) const

pure virtual

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

getTree()

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

pure virtual

Implemented in bpp::AbstractTreeLikelihoodData.

getWeight()

virtual unsigned int bpp::TreeLikelihoodData::getWeight ( size_t  pos ) const

pure virtual

Returns

The frequency of a given pattern.

Implemented in bpp::AbstractTreeLikelihoodData.

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

getWeights()

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

pure virtual

Returns

Frequencies for each pattern.

Implemented in bpp::AbstractTreeLikelihoodData.

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

• Bpp/Phyl/Legacy/Likelihood/TreeLikelihoodData.h