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:

List of all members.

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.
void	setNode (const Node *node)
	Set the node associated to this data.
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_

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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.

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Constructor & Destructor Documentation

bpp::DRASRTreeLikelihoodNodeData::DRASRTreeLikelihoodNodeData

(

)

[inline]

Definition at line 83 of file DRASRTreeLikelihoodData.h.

Referenced by clone().

bpp::DRASRTreeLikelihoodNodeData::DRASRTreeLikelihoodNodeData

(

const DRASRTreeLikelihoodNodeData &

data

)

[inline]

Definition at line 85 of file DRASRTreeLikelihoodData.h.

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Member Function Documentation

DRASRTreeLikelihoodNodeData* bpp::DRASRTreeLikelihoodNodeData::clone

(

)

const [inline, virtual]

Implements bpp::TreeLikelihoodNodeData.

Definition at line 106 of file DRASRTreeLikelihoodData.h.

References DRASRTreeLikelihoodNodeData().

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray

(

)

[inline]

Definition at line 121 of file DRASRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

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

const VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getD2LikelihoodArray

(

)

const [inline]

Definition at line 122 of file DRASRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray

(

)

[inline]

Definition at line 118 of file DRASRTreeLikelihoodData.h.

References nodeDLikelihoods_.

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

const VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getDLikelihoodArray

(

)

const [inline]

Definition at line 119 of file DRASRTreeLikelihoodData.h.

References nodeDLikelihoods_.

VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray

(

)

[inline]

Definition at line 115 of file DRASRTreeLikelihoodData.h.

References nodeLikelihoods_.

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

const VVVdouble& bpp::DRASRTreeLikelihoodNodeData::getLikelihoodArray

(

)

const [inline]

Definition at line 116 of file DRASRTreeLikelihoodData.h.

References nodeLikelihoods_.

const Node* bpp::DRASRTreeLikelihoodNodeData::getNode

(

)

const [inline, virtual]

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_.

DRASRTreeLikelihoodNodeData& bpp::DRASRTreeLikelihoodNodeData::operator=

(

const DRASRTreeLikelihoodNodeData &

data

)

[inline]

Definition at line 92 of file DRASRTreeLikelihoodData.h.

References node_, nodeD2Likelihoods_, nodeDLikelihoods_, and nodeLikelihoods_.

void bpp::DRASRTreeLikelihoodNodeData::setNode

(

const Node *

node

)

[inline, virtual]

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().

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Member Data Documentation

const Node* bpp::DRASRTreeLikelihoodNodeData::node_ [private]

Definition at line 80 of file DRASRTreeLikelihoodData.h.

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

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeD2Likelihoods_ [mutable, private]

Definition at line 79 of file DRASRTreeLikelihoodData.h.

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

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeDLikelihoods_ [mutable, private]

Definition at line 78 of file DRASRTreeLikelihoodData.h.

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

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeLikelihoods_ [mutable, private]

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