bpp::BranchLikelihood Class Reference

Compute likelihood for a 4-tree. More...

#include <Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h>

Inheritance diagram for bpp::BranchLikelihood:

Collaboration diagram for bpp::BranchLikelihood:

Public Member Functions
	BranchLikelihood (const std::vector< unsigned int > &weights)
	BranchLikelihood (const BranchLikelihood &bl)
BranchLikelihood &	operator= (const BranchLikelihood &bl)
virtual	~BranchLikelihood ()
BranchLikelihood *	clone () const
void	initModel (const SubstitutionModel *model, const DiscreteDistribution *rDist)
void	initLikelihoods (const VVVdouble *array1, const VVVdouble *array2)
void	resetLikelihoods ()
void	setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
double	getValue () const throw (Exception)
void	fireParameterChanged (const ParameterList &parameters)

Protected Member Functions
void	computeAllTransitionProbabilities ()
void	computeLogLikelihood ()

Protected Attributes
const VVVdouble *	array1_
const VVVdouble *	array2_
const SubstitutionModel *	model_
const DiscreteDistribution *	rDist_
size_t	nbStates_
size_t	nbClasses_
VVVdouble	pxy_
double	lnL_
std::vector< unsigned int >	weights_

Detailed Description

Compute likelihood for a 4-tree.

This class is used internally by DRHomogeneousTreeLikelihood to test NNI movements. This function needs:

• two likelihood arrays corresponding to the conditional likelihoods at top and bottom nodes,
• a substitution model and a rate distribution, whose parameters will not be estimated but taken "as is", It takes only one parameter, the branch length.

Definition at line 62 of file NNIHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

BranchLikelihood() [1/2]

bpp::BranchLikelihood::BranchLikelihood ( const std::vector< unsigned int > &  weights )

inline

Definition at line 76 of file NNIHomogeneousTreeLikelihood.h.

Referenced by clone().

BranchLikelihood() [2/2]

bpp::BranchLikelihood::BranchLikelihood ( const BranchLikelihood &  bl )

inline

Definition at line 91 of file NNIHomogeneousTreeLikelihood.h.

~BranchLikelihood()

virtual bpp::BranchLikelihood::~BranchLikelihood ( )

inlinevirtual

Definition at line 119 of file NNIHomogeneousTreeLikelihood.h.

Member Function Documentation

clone()

BranchLikelihood* bpp::BranchLikelihood::clone ( ) const

inline

Definition at line 121 of file NNIHomogeneousTreeLikelihood.h.

References BranchLikelihood().

Referenced by bpp::NNIHomogeneousTreeLikelihood::NNIHomogeneousTreeLikelihood(), and bpp::NNIHomogeneousTreeLikelihood::operator=().

computeAllTransitionProbabilities()

void BranchLikelihood::computeAllTransitionProbabilities ( )

protected

Definition at line 72 of file NNIHomogeneousTreeLikelihood.cpp.

Referenced by fireParameterChanged().

computeLogLikelihood()

void BranchLikelihood::computeLogLikelihood ( )

protected

Definition at line 93 of file NNIHomogeneousTreeLikelihood.cpp.

Referenced by fireParameterChanged().

fireParameterChanged()

void bpp::BranchLikelihood::fireParameterChanged ( const ParameterList &  parameters )

inline

Definition at line 150 of file NNIHomogeneousTreeLikelihood.h.

References computeAllTransitionProbabilities(), and computeLogLikelihood().

getValue()

double bpp::BranchLikelihood::getValue ( ) const throw ( Exception )

inline

Definition at line 148 of file NNIHomogeneousTreeLikelihood.h.

References lnL_.

initLikelihoods()

void bpp::BranchLikelihood::initLikelihoods ( const VVVdouble *  array1, const VVVdouble *  array2  )

inline

Warning

No checking on alphabet size or number of rate classes is performed, use with care!

Definition at line 130 of file NNIHomogeneousTreeLikelihood.h.

References array1_, and array2_.

initModel()

void BranchLikelihood::initModel	(	const SubstitutionModel *	model,
		const DiscreteDistribution *	rDist
	)

Definition at line 54 of file NNIHomogeneousTreeLikelihood.cpp.

References bpp::SubstitutionModel::getNumberOfStates().

operator=()

BranchLikelihood& bpp::BranchLikelihood::operator= ( const BranchLikelihood &  bl )

inline

Definition at line 104 of file NNIHomogeneousTreeLikelihood.h.

References array1_, array2_, lnL_, model_, nbClasses_, nbStates_, pxy_, rDist_, and weights_.

resetLikelihoods()

void bpp::BranchLikelihood::resetLikelihoods ( )

inline

Definition at line 136 of file NNIHomogeneousTreeLikelihood.h.

References array1_, and array2_.

setParameters()

void bpp::BranchLikelihood::setParameters ( const ParameterList &  parameters ) throw ( ParameterNotFoundException, ConstraintException )

inline

Definition at line 142 of file NNIHomogeneousTreeLikelihood.h.

Member Data Documentation

array1_

const VVVdouble* bpp::BranchLikelihood::array1_

protected

Definition at line 67 of file NNIHomogeneousTreeLikelihood.h.

Referenced by initLikelihoods(), operator=(), and resetLikelihoods().

array2_

const VVVdouble * bpp::BranchLikelihood::array2_

protected

Definition at line 67 of file NNIHomogeneousTreeLikelihood.h.

Referenced by initLikelihoods(), operator=(), and resetLikelihoods().

lnL_

double bpp::BranchLikelihood::lnL_

protected

Definition at line 72 of file NNIHomogeneousTreeLikelihood.h.

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

model_

const SubstitutionModel* bpp::BranchLikelihood::model_

protected

Definition at line 68 of file NNIHomogeneousTreeLikelihood.h.

Referenced by operator=().

nbClasses_

size_t bpp::BranchLikelihood::nbClasses_

protected

Definition at line 70 of file NNIHomogeneousTreeLikelihood.h.

Referenced by operator=().

nbStates_

size_t bpp::BranchLikelihood::nbStates_

protected

Definition at line 70 of file NNIHomogeneousTreeLikelihood.h.

Referenced by operator=().

pxy_

VVVdouble bpp::BranchLikelihood::pxy_

protected

Definition at line 71 of file NNIHomogeneousTreeLikelihood.h.

Referenced by operator=().

rDist_

const DiscreteDistribution* bpp::BranchLikelihood::rDist_

protected

Definition at line 69 of file NNIHomogeneousTreeLikelihood.h.

Referenced by operator=().

weights_

std::vector<unsigned int> bpp::BranchLikelihood::weights_

protected

Definition at line 73 of file NNIHomogeneousTreeLikelihood.h.

Referenced by operator=().

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

• Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
• Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp