bpp::SitePartitionHomogeneousTreeLikelihood Class Reference

Specialization of the TreeLikelihood interface for partition models, homogeneous case. More...

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

Inheritance diagram for bpp::SitePartitionHomogeneousTreeLikelihood:

Collaboration diagram for bpp::SitePartitionHomogeneousTreeLikelihood:

Public Member Functions
SitePartitionHomogeneousTreeLikelihood *	clone () const =0
const TransitionModel *	getModel (int nodeId, size_t siteIndex) const
TransitionModel *	getModel (int nodeId, size_t siteIndex)
virtual const TransitionModel *	getModelForSite (size_t siteIndex) const =0
	Get the substitution model associated to a given node. More...
virtual TransitionModel *	getModelForSite (size_t siteIndex)=0
	Get the substitution model associated to a given node. More...

Detailed Description

Specialization of the TreeLikelihood interface for partition models, homogeneous case.

These models allow the distinct sites of an alignment to have a different model. The substitution model is however assumed to be the same along the tree. Such models are hence homogeneous in time.

Definition at line 20 of file SitePartitionTreeLikelihood.h.

Member Function Documentation

clone()

SitePartitionHomogeneousTreeLikelihood* bpp::SitePartitionHomogeneousTreeLikelihood::clone ( ) const

pure virtual

getModel() [1/2]

TransitionModel* bpp::SitePartitionHomogeneousTreeLikelihood::getModel ( int  nodeId, size_t  siteIndex  )

inline

Definition at line 32 of file SitePartitionTreeLikelihood.h.

References getModelForSite().

getModel() [2/2]

const TransitionModel* bpp::SitePartitionHomogeneousTreeLikelihood::getModel ( int  nodeId, size_t  siteIndex  ) const

inline

Definition at line 27 of file SitePartitionTreeLikelihood.h.

References getModelForSite().

getModelForSite() [1/2]

virtual const TransitionModel* bpp::SitePartitionHomogeneousTreeLikelihood::getModelForSite ( size_t  siteIndex ) const

pure virtual

Get the substitution model associated to a given node.

Parameters

siteIndex

The position in the alignment.

Returns

A pointer toward the corresponding model.

Referenced by getModel().

getModelForSite() [2/2]

virtual TransitionModel* bpp::SitePartitionHomogeneousTreeLikelihood::getModelForSite ( size_t  siteIndex )

pure virtual

Get the substitution model associated to a given node.

Parameters

siteIndex

The position in the alignment.

Returns

A pointer toward the corresponding model.

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

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