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

#include <Bpp/Phyl/Legacy/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 (std::shared_ptr< const TransitionModelInterface > model, std::shared_ptr< const DiscreteDistributionInterface > rDist)

void	initLikelihoods (const VVVdouble array1, const VVVdouble array2)

void	resetLikelihoods ()

void	setParameters (const ParameterList &parameters)

double	getValue () const

void	fireParameterChanged (const ParameterList &parameters)

virtual double	f (const ParameterList &parameters)

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

void	setNamespace (const std::string &prefix) override

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

Protected Member Functions
void	computeAllTransitionProbabilities ()

void	computeLogLikelihood ()

virtual ParameterList &	getParameters_ ()=0

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

virtual void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override

Protected Attributes
const VVVdouble *	array1_

const VVVdouble *	array2_

std::shared_ptr< const TransitionModelInterface >	model_

std::shared_ptr< const DiscreteDistributionInterface >	rDist_

size_t	nbStates_

size_t	nbClasses_

VVVdouble	pxy_

double	lnL_

std::vector< unsigned int >	weights_

Private Attributes
ParameterList	parameters_

std::string	prefix_

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 27 of file NNIHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

◆ BranchLikelihood() [1/2]

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

inline

Definition at line 41 of file NNIHomogeneousTreeLikelihood.h.

References bpp::AbstractParametrizable::addParameter_().

Referenced by clone().

◆ BranchLikelihood() [2/2]

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

inline

Definition at line 56 of file NNIHomogeneousTreeLikelihood.h.

◆ ~BranchLikelihood()

virtual bpp::BranchLikelihood::~BranchLikelihood ( )

inlinevirtual

Definition at line 84 of file NNIHomogeneousTreeLikelihood.h.

Member Function Documentation

◆ clone()

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

inlinevirtual

Implements bpp::AbstractParametrizable.

Definition at line 86 of file NNIHomogeneousTreeLikelihood.h.

References BranchLikelihood().

◆ computeAllTransitionProbabilities()

void BranchLikelihood::computeAllTransitionProbabilities ( )

protected

Definition at line 39 of file NNIHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameterValue(), model_, nbClasses_, nbStates_, pxy_, and rDist_.

Referenced by fireParameterChanged().

◆ computeLogLikelihood()

void BranchLikelihood::computeLogLikelihood ( )

protected

Definition at line 60 of file NNIHomogeneousTreeLikelihood.cpp.

References array1_, lnL_, bpp::log(), nbClasses_, nbStates_, pxy_, rDist_, and weights_.

Referenced by fireParameterChanged().

◆ fireParameterChanged()

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

inlinevirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 116 of file NNIHomogeneousTreeLikelihood.h.

References computeAllTransitionProbabilities(), and computeLogLikelihood().

◆ getValue()

double bpp::BranchLikelihood::getValue ( ) const

inlinevirtual

Implements bpp::FunctionInterface.

Definition at line 114 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 97 of file NNIHomogeneousTreeLikelihood.h.

References array1_, and array2_.

◆ initModel()

void BranchLikelihood::initModel	(	std::shared_ptr< const TransitionModelInterface >	model,
		std::shared_ptr< const DiscreteDistributionInterface >	rDist
	)