bpp::GlobalClockTreeLikelihoodFunctionWrapper Class Reference

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

Inheritance diagram for bpp::GlobalClockTreeLikelihoodFunctionWrapper:

Collaboration diagram for bpp::GlobalClockTreeLikelihoodFunctionWrapper:

Public Member Functions
	GlobalClockTreeLikelihoodFunctionWrapper (TreeLikelihood *tl)
	GlobalClockTreeLikelihoodFunctionWrapper (const GlobalClockTreeLikelihoodFunctionWrapper &gctlfw)
GlobalClockTreeLikelihoodFunctionWrapper &	operator= (const GlobalClockTreeLikelihoodFunctionWrapper &gctlfw)
GlobalClockTreeLikelihoodFunctionWrapper *	clone () const
void	setParameters (const ParameterList &pl) throw (Exception)
double	getValue () const throw (Exception)
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 throw (Exception)
double	getSecondOrderDerivative (const std::string &variable) const throw (Exception)
double	getFirstOrderDerivative (const std::string &variable) const throw (Exception)
ParameterList	getHeightParameters () const

Private Member Functions
void	initParameters_ ()
void	computeBranchLengthsFromHeights_ (const Node *node, double height, ParameterList &brlenPl) throw (Exception)

Private Attributes
TreeLikelihood *	tl_

Detailed Description

Definition at line 48 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

Constructor & Destructor Documentation

GlobalClockTreeLikelihoodFunctionWrapper() [1/2]

bpp::GlobalClockTreeLikelihoodFunctionWrapper::GlobalClockTreeLikelihoodFunctionWrapper ( TreeLikelihood *  tl )

inline

Definition at line 56 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References initParameters_().

Referenced by clone().

GlobalClockTreeLikelihoodFunctionWrapper() [2/2]

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

inline

Definition at line 63 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

Member Function Documentation

clone()

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

inline

Definition at line 73 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References GlobalClockTreeLikelihoodFunctionWrapper().

Referenced by initParameters_().

computeBranchLengthsFromHeights_()

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

private

Definition at line 106 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References bpp::Node::getId(), bpp::Node::getSon(), and bpp::Node::isLeaf().

Referenced by fireParameterChanged().

enableFirstOrderDerivatives() [1/2]

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

inline

Definition at line 87 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

enableFirstOrderDerivatives() [2/2]

bool bpp::GlobalClockTreeLikelihoodFunctionWrapper::enableFirstOrderDerivatives ( ) const

inline

Definition at line 88 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

enableSecondOrderDerivatives() [1/2]

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

inline

Definition at line 85 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

enableSecondOrderDerivatives() [2/2]

bool bpp::GlobalClockTreeLikelihoodFunctionWrapper::enableSecondOrderDerivatives ( ) const

inline

Definition at line 86 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

fireParameterChanged()

void GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged

(

const bpp::ParameterList &

pl

)

Definition at line 44 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References computeBranchLengthsFromHeights_(), bpp::TreeLikelihood::getTree(), and tl_.

Referenced by initParameters_().

getFirstOrderDerivative()

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

inline

Definition at line 91 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

getHeightParameters()

ParameterList GlobalClockTreeLikelihoodFunctionWrapper::getHeightParameters

(

)

const

Definition at line 64 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

Referenced by bpp::OptimizationTools::optimizeNumericalParameters2().

getSecondOrderDerivative() [1/2]

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

inline

Definition at line 89 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

getSecondOrderDerivative() [2/2]

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

inline

Definition at line 90 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

getValue()

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

inline

Definition at line 81 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

initParameters_()

void GlobalClockTreeLikelihoodFunctionWrapper::initParameters_ ( )

private

Definition at line 77 of file GlobalClockTreeLikelihoodFunctionWrapper.cpp.

References clone(), fireParameterChanged(), bpp::TreeTemplateTools::getHeights(), bpp::TreeLikelihood::getTree(), bpp::TreeTemplateTools::isMultifurcating(), and tl_.

Referenced by GlobalClockTreeLikelihoodFunctionWrapper().

operator=()

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

inline

Definition at line 67 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

References tl_.

setParameters()

void bpp::GlobalClockTreeLikelihoodFunctionWrapper::setParameters ( const ParameterList &  pl ) throw ( Exception )

inline

Definition at line 76 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

Member Data Documentation

tl_

TreeLikelihood* bpp::GlobalClockTreeLikelihoodFunctionWrapper::tl_

private

Definition at line 53 of file GlobalClockTreeLikelihoodFunctionWrapper.h.

Referenced by enableFirstOrderDerivatives(), enableSecondOrderDerivatives(), fireParameterChanged(), getFirstOrderDerivative(), getSecondOrderDerivative(), getValue(), initParameters_(), and operator=().

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

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