bpp-phyl  2.2.0
Public Member Functions | List of all members
bpp::TreeLikelihoodData Class Referenceabstract

TreeLikelihood data structure. More...

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

+ Inheritance diagram for bpp::TreeLikelihoodData:
+ Collaboration diagram for bpp::TreeLikelihoodData:

Public Member Functions

 TreeLikelihoodData ()
 
virtual ~TreeLikelihoodData ()
 
TreeLikelihoodData * clone () const =0
 
virtual const Alphabet * getAlphabet () const =0
 
virtual 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:

  • conditionnal likelihoods for each node,
  • correspondance between sites in the dataset and array indices.
See also
TreeLikelihoodNodeData

Definition at line 102 of file TreeLikelihoodData.h.

Constructor & Destructor Documentation

◆ TreeLikelihoodData()

bpp::TreeLikelihoodData::TreeLikelihoodData ( )
inline

Definition at line 106 of file TreeLikelihoodData.h.

◆ ~TreeLikelihoodData()

virtual bpp::TreeLikelihoodData::~TreeLikelihoodData ( )
inlinevirtual

Definition at line 107 of file TreeLikelihoodData.h.

Member Function Documentation

◆ clone()

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

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

◆ getAlphabet()

virtual 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::DRASDRTreeLikelihoodData, and bpp::DRASRTreeLikelihoodData.

◆ getNodeData() [1/2]

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

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

◆ getNodeData() [2/2]

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

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

◆ getNumberOfDistinctSites()

virtual size_t bpp::TreeLikelihoodData::getNumberOfDistinctSites ( ) const
pure virtual
Returns
The number of non redundant patterns.

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

◆ getNumberOfSites()

virtual size_t bpp::TreeLikelihoodData::getNumberOfSites ( ) const
pure virtual
Returns
The total number of sites.

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

◆ getNumberOfStates()

virtual size_t bpp::TreeLikelihoodData::getNumberOfStates ( ) const
pure virtual
Returns
Get the number of states used in the model.

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

◆ getRootArrayPosition()

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

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

◆ getTree()

virtual 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.

◆ getWeights()

virtual const std::vector<unsigned int>& bpp::TreeLikelihoodData::getWeights ( ) const
pure virtual
Returns
Frequencies for each pattern.

Implemented in bpp::AbstractTreeLikelihoodData.

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