bpp-phyl  2.4.0
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 ()
 
TreeLikelihoodDataclone () const =0
 
virtual const AlphabetgetAlphabet () 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 TreeLikelihoodNodeDatagetNodeData (int nodeId)=0
 
virtual const TreeLikelihoodNodeDatagetNodeData (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 97 of file TreeLikelihoodData.h.

Constructor & Destructor Documentation

bpp::TreeLikelihoodData::TreeLikelihoodData ( )
inline

Definition at line 101 of file TreeLikelihoodData.h.

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

Definition at line 102 of file TreeLikelihoodData.h.

References bpp::TreeLikelihoodNodeData::clone().

Member Function Documentation

TreeLikelihoodData* bpp::TreeLikelihoodData::clone ( ) const
pure virtual
virtual const Alphabet* bpp::TreeLikelihoodData::getAlphabet ( ) const
pure virtual
virtual size_t bpp::TreeLikelihoodData::getArrayPosition ( int  parentId,
int  sonId,
size_t  currentPosition 
) const
pure virtual
virtual TreeLikelihoodNodeData& bpp::TreeLikelihoodData::getNodeData ( int  nodeId)
pure virtual
virtual const TreeLikelihoodNodeData& bpp::TreeLikelihoodData::getNodeData ( int  nodeId) const
pure virtual
virtual size_t bpp::TreeLikelihoodData::getNumberOfDistinctSites ( ) const
pure virtual
Returns
The number of non redundant patterns.

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

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

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

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

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.

virtual size_t bpp::TreeLikelihoodData::getRootArrayPosition ( size_t  site) const
pure virtual
virtual const TreeTemplate<Node>* bpp::TreeLikelihoodData::getTree ( ) const
pure virtual
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().

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: