bpp-phyl3  3.0.0
Public Member Functions | Private Attributes | List of all members
bpp::DRASRTreeLikelihoodNodeData Class Reference

Likelihood data structure for a node. More...

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

+ Inheritance diagram for bpp::DRASRTreeLikelihoodNodeData:
+ Collaboration diagram for bpp::DRASRTreeLikelihoodNodeData:

Public Member Functions

 DRASRTreeLikelihoodNodeData ()
 
 DRASRTreeLikelihoodNodeData (const DRASRTreeLikelihoodNodeData &data)
 
DRASRTreeLikelihoodNodeData & operator= (const DRASRTreeLikelihoodNodeData &data)
 
DRASRTreeLikelihoodNodeData * clone () const
 
const Node * getNode () const
 Get the node associated to this data structure. More...
 
void setNode (const Node *node)
 Set the node associated to this data. More...
 
VVVdouble & getLikelihoodArray ()
 
const VVVdouble & getLikelihoodArray () const
 
VVVdouble & getDLikelihoodArray ()
 
const VVVdouble & getDLikelihoodArray () const
 
VVVdouble & getD2LikelihoodArray ()
 
const VVVdouble & getD2LikelihoodArray () const
 

Private Attributes

VVVdouble nodeLikelihoods_
 
VVVdouble nodeDLikelihoods_
 
VVVdouble nodeD2Likelihoods_
 
const Node * node_
 

Detailed Description

Likelihood data structure for a node.

This class is for use with the DRASRTreeParsimonyData class.

Store all conditional likelihoods: 

x[i][c][s]
  |---------> Site i
     |------> Rate class c
        |---> Ancestral state s

We call this the likelihood array for each node. In the same way, we store first and second order derivatives.

See also
DRASRTreeLikelihoodData

Definition at line 36 of file DRASRTreeLikelihoodData.h.

Constructor & Destructor Documentation

◆ DRASRTreeLikelihoodNodeData() [1/2]

bpp::DRASRTreeLikelihoodNodeData::DRASRTreeLikelihoodNodeData ( )
inline

Definition at line 46 of file DRASRTreeLikelihoodData.h.

Referenced by clone().

◆ DRASRTreeLikelihoodNodeData() [2/2]

bpp::DRASRTreeLikelihoodNodeData::DRASRTreeLikelihoodNodeData ( const DRASRTreeLikelihoodNodeData &  data)
inline

Definition at line 48 of file DRASRTreeLikelihoodData.h.

Member Function Documentation

◆ clone()

DRASRTreeLikelihoodNodeData* bpp::DRASRTreeLikelihoodNodeData::clone ( ) const
inlinevirtual

Implements bpp::TreeLikelihoodNodeData.

Definition at line 64 of file DRASRTreeLikelihoodData.h.

References DRASRTreeLikelihoodNodeData().

◆ getD2LikelihoodArray() [1/2]

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray ( )
inline

Definition at line 79 of file DRASRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

Referenced by bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

◆ getD2LikelihoodArray() [2/2]

const VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray ( ) const
inline

Definition at line 80 of file DRASRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

◆ getDLikelihoodArray() [1/2]

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray ( )
inline

Definition at line 76 of file DRASRTreeLikelihoodData.h.

References nodeDLikelihoods_.

Referenced by bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

◆ getDLikelihoodArray() [2/2]

const VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray ( ) const
inline

Definition at line 77 of file DRASRTreeLikelihoodData.h.

References nodeDLikelihoods_.

◆ getLikelihoodArray() [1/2]

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray ( )
inline

Definition at line 73 of file DRASRTreeLikelihoodData.h.

References nodeLikelihoods_.

Referenced by bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

◆ getLikelihoodArray() [2/2]

const VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray ( ) const
inline

Definition at line 74 of file DRASRTreeLikelihoodData.h.

References nodeLikelihoods_.

◆ getNode()

const Node* bpp::DRASRTreeLikelihoodNodeData::getNode ( ) const
inlinevirtual

Get the node associated to this data structure.

Returns
The node associated to this structure.

Implements bpp::TreeLikelihoodNodeData.

Definition at line 70 of file DRASRTreeLikelihoodData.h.

References node_.

◆ operator=()

DRASRTreeLikelihoodNodeData& bpp::DRASRTreeLikelihoodNodeData::operator= ( const DRASRTreeLikelihoodNodeData &  data)
inline

Definition at line 55 of file DRASRTreeLikelihoodData.h.

References node_, nodeD2Likelihoods_, nodeDLikelihoods_, and nodeLikelihoods_.

◆ setNode()

void bpp::DRASRTreeLikelihoodNodeData::setNode ( const Node *  node)
inlinevirtual

Set the node associated to this data.

A pointer toward this node will be created and associated to this data.

Parameters
nodeThe node to be associated to this data.

Implements bpp::TreeLikelihoodNodeData.

Definition at line 71 of file DRASRTreeLikelihoodData.h.

References node_.

Referenced by bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

Member Data Documentation

◆ node_

const Node* bpp::DRASRTreeLikelihoodNodeData::node_
private

Definition at line 43 of file DRASRTreeLikelihoodData.h.

Referenced by getNode(), operator=(), and setNode().

◆ nodeD2Likelihoods_

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeD2Likelihoods_
mutableprivate

Definition at line 42 of file DRASRTreeLikelihoodData.h.

Referenced by getD2LikelihoodArray(), and operator=().

◆ nodeDLikelihoods_

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeDLikelihoods_
mutableprivate

Definition at line 41 of file DRASRTreeLikelihoodData.h.

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

◆ nodeLikelihoods_

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeLikelihoods_
mutableprivate

Definition at line 40 of file DRASRTreeLikelihoodData.h.

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

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