bpp::DRASDRTreeLikelihoodNodeData Class Reference

Likelihood data structure for a node. More...

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

Inheritance diagram for bpp::DRASDRTreeLikelihoodNodeData:

Collaboration diagram for bpp::DRASDRTreeLikelihoodNodeData:

Public Member Functions
	DRASDRTreeLikelihoodNodeData ()
	DRASDRTreeLikelihoodNodeData (const DRASDRTreeLikelihoodNodeData &data)
DRASDRTreeLikelihoodNodeData &	operator= (const DRASDRTreeLikelihoodNodeData &data)
virtual	~DRASDRTreeLikelihoodNodeData ()
DRASDRTreeLikelihoodNodeData *	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...
const std::map< int, VVVdouble > &	getLikelihoodArrays () const
std::map< int, VVVdouble > &	getLikelihoodArrays ()
VVVdouble &	getLikelihoodArrayForNeighbor (int neighborId)
const VVVdouble &	getLikelihoodArrayForNeighbor (int neighborId) const
Vdouble &	getDLikelihoodArray ()
const Vdouble &	getDLikelihoodArray () const
Vdouble &	getD2LikelihoodArray ()
const Vdouble &	getD2LikelihoodArrayForNeighbor () const
bool	isNeighbor (int neighborId) const
void	eraseNeighborArrays ()

Private Attributes
std::map< int, VVVdouble >	nodeLikelihoods_
	This contains all likelihood values used for computation. More...
Vdouble	nodeDLikelihoods_
	This contains all likelihood first order derivatives values used for computation. More...
Vdouble	nodeD2Likelihoods_
	This contains all likelihood second order derivatives values used for computation. More...
const Node *	node_

Detailed Description

Likelihood data structure for a node.

This class is for use with the DRASDRTreeLikelihoodData class.

Store for each neighbor node an array with conditional likelihoods.

See also

DRASDRTreeLikelihoodData

Definition at line 72 of file DRASDRTreeLikelihoodData.h.

Constructor & Destructor Documentation

DRASDRTreeLikelihoodNodeData() [1/2]

bpp::DRASDRTreeLikelihoodNodeData::DRASDRTreeLikelihoodNodeData ( )

inline

Definition at line 115 of file DRASDRTreeLikelihoodData.h.

Referenced by clone().

DRASDRTreeLikelihoodNodeData() [2/2]

bpp::DRASDRTreeLikelihoodNodeData::DRASDRTreeLikelihoodNodeData ( const DRASDRTreeLikelihoodNodeData &  data )

inline

Definition at line 117 of file DRASDRTreeLikelihoodData.h.

~DRASDRTreeLikelihoodNodeData()

virtual bpp::DRASDRTreeLikelihoodNodeData::~DRASDRTreeLikelihoodNodeData ( )

inlinevirtual

Definition at line 133 of file DRASDRTreeLikelihoodData.h.

Member Function Documentation

clone()

DRASDRTreeLikelihoodNodeData* bpp::DRASDRTreeLikelihoodNodeData::clone ( ) const

inlinevirtual

Implements bpp::TreeLikelihoodNodeData.

Definition at line 135 of file DRASDRTreeLikelihoodData.h.

References DRASDRTreeLikelihoodNodeData().

eraseNeighborArrays()

void bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays ( )

inline

Definition at line 172 of file DRASDRTreeLikelihoodData.h.

References nodeD2Likelihoods_, nodeDLikelihoods_, and nodeLikelihoods_.

Referenced by bpp::DRASDRTreeLikelihoodData::reInit().

getD2LikelihoodArray()

Vdouble& bpp::DRASDRTreeLikelihoodNodeData::getD2LikelihoodArray ( )

inline

Definition at line 163 of file DRASDRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASDRTreeLikelihoodData::reInit().

getD2LikelihoodArrayForNeighbor()

const Vdouble& bpp::DRASDRTreeLikelihoodNodeData::getD2LikelihoodArrayForNeighbor ( ) const

inline

Definition at line 165 of file DRASDRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

getDLikelihoodArray() [1/2]

Vdouble& bpp::DRASDRTreeLikelihoodNodeData::getDLikelihoodArray ( )

inline

Definition at line 159 of file DRASDRTreeLikelihoodData.h.

References nodeDLikelihoods_.

Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASDRTreeLikelihoodData::reInit().

getDLikelihoodArray() [2/2]

const Vdouble& bpp::DRASDRTreeLikelihoodNodeData::getDLikelihoodArray ( ) const

inline

Definition at line 161 of file DRASDRTreeLikelihoodData.h.

References nodeDLikelihoods_.

getLikelihoodArrayForNeighbor() [1/2]

VVVdouble& bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrayForNeighbor ( int  neighborId )

inline

Definition at line 149 of file DRASDRTreeLikelihoodData.h.

References nodeLikelihoods_.

Referenced by bpp::DRASDRTreeLikelihoodData::reInit(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

getLikelihoodArrayForNeighbor() [2/2]

const VVVdouble& bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrayForNeighbor ( int  neighborId ) const

inline

Definition at line 154 of file DRASDRTreeLikelihoodData.h.

References nodeLikelihoods_.

getLikelihoodArrays() [1/2]

std::map<int, VVVdouble>& bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrays ( )

inline

Definition at line 147 of file DRASDRTreeLikelihoodData.h.

References nodeLikelihoods_.

getLikelihoodArrays() [2/2]

const std::map<int, VVVdouble>& bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrays ( ) const

inline

Definition at line 145 of file DRASDRTreeLikelihoodData.h.

References nodeLikelihoods_.

Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods().

getNode()

const Node* bpp::DRASDRTreeLikelihoodNodeData::getNode ( ) const

inlinevirtual

Get the node associated to this data structure.

Returns

The node associated to this structure.

Implements bpp::TreeLikelihoodNodeData.

Definition at line 141 of file DRASDRTreeLikelihoodData.h.

References node_.

isNeighbor()

bool bpp::DRASDRTreeLikelihoodNodeData::isNeighbor ( int  neighborId ) const

inline

Definition at line 167 of file DRASDRTreeLikelihoodData.h.

References nodeLikelihoods_.

operator=()

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

inline

Definition at line 124 of file DRASDRTreeLikelihoodData.h.

References node_, nodeD2Likelihoods_, nodeDLikelihoods_, and nodeLikelihoods_.

setNode()

void bpp::DRASDRTreeLikelihoodNodeData::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 143 of file DRASDRTreeLikelihoodData.h.

References node_.

Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASDRTreeLikelihoodData::reInit().

Member Data Documentation

node_

const Node* bpp::DRASDRTreeLikelihoodNodeData::node_

private

Definition at line 112 of file DRASDRTreeLikelihoodData.h.

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

nodeD2Likelihoods_

Vdouble bpp::DRASDRTreeLikelihoodNodeData::nodeD2Likelihoods_

mutableprivate

This contains all likelihood second order derivatives values used for computation.

  x[i]
|---------> Site i
  

We call this the d2Likelihood array for each node.

Definition at line 110 of file DRASDRTreeLikelihoodData.h.

Referenced by eraseNeighborArrays(), getD2LikelihoodArray(), getD2LikelihoodArrayForNeighbor(), and operator=().

nodeDLikelihoods_

Vdouble bpp::DRASDRTreeLikelihoodNodeData::nodeDLikelihoods_

mutableprivate

This contains all likelihood first order derivatives values used for computation.

x[i]
  |---------> Site i

We call this the dLikelihood array for each node.

Definition at line 99 of file DRASDRTreeLikelihoodData.h.

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

nodeLikelihoods_

std::map<int, VVVdouble> bpp::DRASDRTreeLikelihoodNodeData::nodeLikelihoods_

mutableprivate

This contains all likelihood values used for computation.

x[b][i][c][s]
  |------------> Neighbor node of n (id)
    |---------> Site i
        |------> Rate class c
           |---> Ancestral state s

We call this the likelihood array for each node.

Definition at line 89 of file DRASDRTreeLikelihoodData.h.

Referenced by eraseNeighborArrays(), getLikelihoodArrayForNeighbor(), getLikelihoodArrays(), isNeighbor(), and operator=().

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

• Bpp/Phyl/Legacy/Likelihood/DRASDRTreeLikelihoodData.h