bpp::DRASRTreeLikelihoodNodeData Class Reference

Likelihood data structure for a node. More...

#include <Bpp/Phyl/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 conditionnal 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 73 of file DRASRTreeLikelihoodData.h.

Constructor & Destructor Documentation

DRASRTreeLikelihoodNodeData() [1/2]

bpp::DRASRTreeLikelihoodNodeData::DRASRTreeLikelihoodNodeData ( )

inline

Definition at line 83 of file DRASRTreeLikelihoodData.h.

Referenced by clone().

DRASRTreeLikelihoodNodeData() [2/2]

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

inline

Definition at line 85 of file DRASRTreeLikelihoodData.h.

Member Function Documentation

clone()

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

inlinevirtual

Implements bpp::TreeLikelihoodNodeData.

Definition at line 106 of file DRASRTreeLikelihoodData.h.

References DRASRTreeLikelihoodNodeData().

getD2LikelihoodArray() [1/2]

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray ( )

inline

Definition at line 121 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 122 of file DRASRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

getDLikelihoodArray() [1/2]

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray ( )

inline

Definition at line 118 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 119 of file DRASRTreeLikelihoodData.h.

References nodeDLikelihoods_.

getLikelihoodArray() [1/2]

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray ( )

inline

Definition at line 115 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 116 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 112 of file DRASRTreeLikelihoodData.h.

References node_.

operator=()

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

inline

Definition at line 92 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

node	The node to be associated to this data.

Implements bpp::TreeLikelihoodNodeData.

Definition at line 113 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 80 of file DRASRTreeLikelihoodData.h.

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

nodeD2Likelihoods_

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeD2Likelihoods_

mutableprivate

Definition at line 79 of file DRASRTreeLikelihoodData.h.

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

nodeDLikelihoods_

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeDLikelihoods_

mutableprivate

Definition at line 78 of file DRASRTreeLikelihoodData.h.

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

nodeLikelihoods_

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeLikelihoods_

mutableprivate

Definition at line 77 of file DRASRTreeLikelihoodData.h.

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

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

• Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h