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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)
 
DRASRTreeLikelihoodNodeDataoperator= (const DRASRTreeLikelihoodNodeData &data)
 
DRASRTreeLikelihoodNodeDataclone () const
 
const NodegetNode () const
 Get the node associated to this data structure. More...
 
void setNode (const Node *node)
 Set the node associated to this data. More...
 
VVVdoublegetLikelihoodArray ()
 
const VVVdoublegetLikelihoodArray () const
 
VVVdoublegetDLikelihoodArray ()
 
const VVVdoublegetDLikelihoodArray () const
 
VVVdoublegetD2LikelihoodArray ()
 
const VVVdoublegetD2LikelihoodArray () const
 

Private Attributes

VVVdouble nodeLikelihoods_
 
VVVdouble nodeDLikelihoods_
 
VVVdouble nodeD2Likelihoods_
 
const Nodenode_
 

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

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.

Member Function Documentation

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

Implements bpp::TreeLikelihoodNodeData.

Definition at line 106 of file DRASRTreeLikelihoodData.h.

References DRASRTreeLikelihoodNodeData().

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

Definition at line 122 of file DRASRTreeLikelihoodData.h.

References nodeD2Likelihoods_.

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

Definition at line 119 of file DRASRTreeLikelihoodData.h.

References nodeDLikelihoods_.

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

Definition at line 116 of file DRASRTreeLikelihoodData.h.

References nodeLikelihoods_.

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_.

DRASRTreeLikelihoodNodeData& bpp::DRASRTreeLikelihoodNodeData::operator= ( const DRASRTreeLikelihoodNodeData data)
inline
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 113 of file DRASRTreeLikelihoodData.h.

References node_.

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

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_
mutableprivate

Definition at line 79 of file DRASRTreeLikelihoodData.h.

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

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeDLikelihoods_
mutableprivate

Definition at line 78 of file DRASRTreeLikelihoodData.h.

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

VVVdouble bpp::DRASRTreeLikelihoodNodeData::nodeLikelihoods_
mutableprivate

Definition at line 77 of file DRASRTreeLikelihoodData.h.

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


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