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

Inheritance diagram for bpp::GlobalClockTreeLikelihoodFunctionWrapper:

Collaboration diagram for bpp::GlobalClockTreeLikelihoodFunctionWrapper:

Public Member Functions
	GlobalClockTreeLikelihoodFunctionWrapper (std::shared_ptr< TreeLikelihoodInterface > tl)

	GlobalClockTreeLikelihoodFunctionWrapper (const GlobalClockTreeLikelihoodFunctionWrapper &gctlfw)

GlobalClockTreeLikelihoodFunctionWrapper &	operator= (const GlobalClockTreeLikelihoodFunctionWrapper &gctlfw)

GlobalClockTreeLikelihoodFunctionWrapper *	clone () const

void	setParameters (const ParameterList &pl)

double	getValue () const

void	fireParameterChanged (const bpp::ParameterList &pl)

void	enableSecondOrderDerivatives (bool yn)

bool	enableSecondOrderDerivatives () const

void	enableFirstOrderDerivatives (bool yn)

bool	enableFirstOrderDerivatives () const

double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const

double	getSecondOrderDerivative (const std::string &variable) const

double	getFirstOrderDerivative (const std::string &variable) const

ParameterList	getHeightParameters () const

virtual double	d2f (const std::string &variable, const ParameterList &parameters)

virtual double	d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)

virtual double	df (const std::string &variable, 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
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

Private Member Functions
void	initParameters_ ()

void	computeBranchLengthsFromHeights_ (const Node *node, double height, ParameterList &brlenPl)

Private Attributes
std::shared_ptr< TreeLikelihoodInterface >	tl_

ParameterList	parameters_

std::string	prefix_

Detailed Description

Definition at line 13 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

Constructor & Destructor Documentation

◆ GlobalClockTreeLikelihoodFunctionWrapper() [1/2]

bpp::GlobalClockTreeLikelihoodFunctionWrapper::GlobalClockTreeLikelihoodFunctionWrapper ( std::shared_ptr< TreeLikelihoodInterface > tl )

inline

Definition at line 21 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References initParameters_().

Referenced by clone().

◆ GlobalClockTreeLikelihoodFunctionWrapper() [2/2]

bpp::GlobalClockTreeLikelihoodFunctionWrapper::GlobalClockTreeLikelihoodFunctionWrapper ( const GlobalClockTreeLikelihoodFunctionWrapper & gctlfw )

inline

Definition at line 28 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

Member Function Documentation

◆ clone()

GlobalClockTreeLikelihoodFunctionWrapper * bpp::GlobalClockTreeLikelihoodFunctionWrapper::clone ( ) const

inlinevirtual

Implements bpp::AbstractParametrizable.

Definition at line 39 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References GlobalClockTreeLikelihoodFunctionWrapper().

Referenced by initParameters_().

◆ computeBranchLengthsFromHeights_()

void GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_	(	const Node *	node,
		double	height,
		ParameterList &	brlenPl
	)

private

Definition at line 73 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References bpp::ParameterList::addParameter(), computeBranchLengthsFromHeights_(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Parameter::getValue(), bpp::Node::isLeaf(), bpp::AbstractParametrizable::parameter(), and bpp::TextTools::toString().

Referenced by computeBranchLengthsFromHeights_(), and fireParameterChanged().

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::GlobalClockTreeLikelihoodFunctionWrapper::enableFirstOrderDerivatives ( ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 55 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ enableFirstOrderDerivatives() [2/2]

void bpp::GlobalClockTreeLikelihoodFunctionWrapper::enableFirstOrderDerivatives ( bool yn )

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 54 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::GlobalClockTreeLikelihoodFunctionWrapper::enableSecondOrderDerivatives ( ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 53 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ enableSecondOrderDerivatives() [2/2]

void bpp::GlobalClockTreeLikelihoodFunctionWrapper::enableSecondOrderDerivatives ( bool yn )

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 52 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ fireParameterChanged()

void GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged ( const bpp::ParameterList & pl )

virtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 9 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References bpp::ParameterList::addParameter(), computeBranchLengthsFromHeights_(), bpp::TreeTemplate< N >::getRootNode(), getValue(), bpp::AbstractParametrizable::parameter(), bpp::ParameterList::size(), and tl_.

Referenced by initParameters_().

◆ getFirstOrderDerivative()

double bpp::GlobalClockTreeLikelihoodFunctionWrapper::getFirstOrderDerivative ( const std::string & variable ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 58 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ getHeightParameters()

ParameterList GlobalClockTreeLikelihoodFunctionWrapper::getHeightParameters ( ) const

Definition at line 29 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References bpp::ParameterList::addParameter(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getNumberOfParameters(), and bpp::AbstractParametrizable::getParameter_().

◆ getSecondOrderDerivative() [1/2]

double bpp::GlobalClockTreeLikelihoodFunctionWrapper::getSecondOrderDerivative ( const std::string & variable ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 57 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ getSecondOrderDerivative() [2/2]

double bpp::GlobalClockTreeLikelihoodFunctionWrapper::getSecondOrderDerivative	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 56 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

◆ getValue()

double bpp::GlobalClockTreeLikelihoodFunctionWrapper::getValue ( ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 48 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

Referenced by fireParameterChanged().

◆ initParameters_()

void GlobalClockTreeLikelihoodFunctionWrapper::initParameters_ ( )

private

Definition at line 42 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References bpp::AbstractParametrizable::addParameter_(), clone(), fireParameterChanged(), bpp::TreeTemplateTools::getHeights(), bpp::AbstractParametrizable::getParameters(), bpp::TreeTemplate< N >::getRootNode(), bpp::TreeTemplateTools::isMultifurcating(), bpp::TreeTemplate< N >::isRooted(), bpp::Parameter::PROP_CONSTRAINT_IN, bpp::Parameter::R_PLUS_STAR, bpp::ParameterList::size(), tl_, and bpp::TextTools::toString().

Referenced by GlobalClockTreeLikelihoodFunctionWrapper().

◆ operator=()

GlobalClockTreeLikelihoodFunctionWrapper & bpp::GlobalClockTreeLikelihoodFunctionWrapper::operator= ( const GlobalClockTreeLikelihoodFunctionWrapper & gctlfw )

inline

Definition at line 32 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.