Listener used internally by the optimizeTreeNNI2 method. More...

#include <Bpp/Phyl/Legacy/OptimizationTools.h>

Inheritance diagram for bpp::NNITopologyListener2:

Collaboration diagram for bpp::NNITopologyListener2:

Public Member Functions
	NNITopologyListener2 (std::shared_ptr< NNITopologySearch > ts, const ParameterList &parameters, double tolerance, std::shared_ptr< OutputStream > messenger, std::shared_ptr< OutputStream > profiler, unsigned int verbose, const std::string &optMethod, bool reparametrization)
	Build a new NNITopologyListener2 object. More...

	NNITopologyListener2 (const NNITopologyListener2 &tl)

NNITopologyListener2 &	operator= (const NNITopologyListener2 &tl)

NNITopologyListener2 *	clone () const

virtual	~NNITopologyListener2 ()

void	topologyChangeTested (const TopologyChangeEvent &event)
	Notify a topology change event. More...

void	topologyChangeSuccessful (const TopologyChangeEvent &event)
	Tell that a topology change is definitive. More...

void	setNumericalOptimizationCounter (unsigned int c)

virtual void	topologyChangePerformed (const TopologyChangeEvent &event)
	Notify a topology change event. More...

Private Attributes
std::shared_ptr< NNITopologySearch >	topoSearch_

ParameterList	parameters_

double	tolerance_

std::shared_ptr< OutputStream >	messenger_

std::shared_ptr< OutputStream >	profiler_

unsigned int	verbose_

unsigned int	optimizeCounter_

unsigned int	optimizeNumerical_

std::string	optMethod_

bool	reparametrization_

Detailed Description

Listener used internally by the optimizeTreeNNI2 method.

Definition at line 122 of file OptimizationTools.h.

Constructor & Destructor Documentation

◆ NNITopologyListener2() [1/2]

bpp::NNITopologyListener2::NNITopologyListener2	(	std::shared_ptr< NNITopologySearch >	ts,
		const ParameterList &	parameters,
		double	tolerance,
		std::shared_ptr< OutputStream >	messenger,
		std::shared_ptr< OutputStream >	profiler,
		unsigned int	verbose,
		const std::string &	optMethod,
		bool	reparametrization
	)

inline

Build a new NNITopologyListener2 object.

This listener listens to a NNITopologySearch object, and optimizes numerical parameters every n topological movements. Optimization is performed using the optimizeNumericalParameters2 method (see there documentation for more details).

Parameters

ts	The NNITopologySearch object attached to this listener.
parameters	The list of parameters to optimize. Use ts->getIndependentParameters() in order to estimate all parameters.
tolerance	Tolerance to use during optimization.
messenger	Where to output messages.
profiler	Where to output optimization steps.
verbose	Verbose level during optimization.
optMethod	Optimization method to use.
reparametrization	Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower.

Definition at line 154 of file OptimizationTools.h.

Referenced by clone().

◆ NNITopologyListener2() [2/2]

bpp::NNITopologyListener2::NNITopologyListener2 ( const NNITopologyListener2 & tl )

inline

Definition at line 174 of file OptimizationTools.h.

◆ ~NNITopologyListener2()

virtual bpp::NNITopologyListener2::~NNITopologyListener2 ( )

inlinevirtual

Definition at line 204 of file OptimizationTools.h.

Member Function Documentation

◆ clone()

NNITopologyListener2* bpp::NNITopologyListener2::clone ( ) const

inlinevirtual

Implements bpp::TopologyListener.

Definition at line 202 of file OptimizationTools.h.

References NNITopologyListener2().

◆ operator=()

NNITopologyListener2& bpp::NNITopologyListener2::operator= ( const NNITopologyListener2 & tl )

inline

Definition at line 187 of file OptimizationTools.h.

References messenger_, optimizeCounter_, optimizeNumerical_, optMethod_, parameters_, profiler_, reparametrization_, tolerance_, topoSearch_, and verbose_.

◆ setNumericalOptimizationCounter()

void bpp::NNITopologyListener2::setNumericalOptimizationCounter ( unsigned int c )

inline

Definition at line 209 of file OptimizationTools.h.

References optimizeNumerical_.

◆ topologyChangePerformed()

virtual void bpp::TopologyListener::topologyChangePerformed ( const TopologyChangeEvent & event )

inlinevirtualinherited

Notify a topology change event.

This method is to be invoked after one or several NNI are performed. It allows appropriate recomputations.

In most case, this is the same as topologyChangeTested() + topologyChangeSuccessful().

Parameters

event The topology change event.

Definition at line 67 of file TopologySearch.h.

References bpp::TopologyListener::topologyChangeSuccessful(), and bpp::TopologyListener::topologyChangeTested().

◆ topologyChangeSuccessful()

void NNITopologyListener2::topologyChangeSuccessful ( const TopologyChangeEvent & event )

virtual

Tell that a topology change is definitive.

This method is called after the topologyChangeTested() method.

Parameters

event The topology change event.

Implements bpp::TopologyListener.

Definition at line 372 of file OptimizationTools.cpp.

References bpp::LegacyOptimizationTools::optimizeNumericalParameters2().

◆ topologyChangeTested()

void bpp::NNITopologyListener2::topologyChangeTested ( const TopologyChangeEvent & event )

inlinevirtual

Notify a topology change event.

Parameters

event The topology change event.

Implements bpp::TopologyListener.

Definition at line 207 of file OptimizationTools.h.

Member Data Documentation

◆ messenger_

std::shared_ptr<OutputStream> bpp::NNITopologyListener2::messenger_

private

Definition at line 129 of file OptimizationTools.h.

Referenced by operator=().

◆ optimizeCounter_

unsigned int bpp::NNITopologyListener2::optimizeCounter_

private

Definition at line 132 of file OptimizationTools.h.

Referenced by operator=().

◆ optimizeNumerical_

unsigned int bpp::NNITopologyListener2::optimizeNumerical_

private

Definition at line 133 of file OptimizationTools.h.

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

◆ optMethod_

std::string bpp::NNITopologyListener2::optMethod_

private

Definition at line 134 of file OptimizationTools.h.

Referenced by operator=().

◆ parameters_

ParameterList bpp::NNITopologyListener2::parameters_

private

Definition at line 127 of file OptimizationTools.h.

Referenced by operator=().

◆ profiler_

std::shared_ptr<OutputStream> bpp::NNITopologyListener2::profiler_

private

Definition at line 130 of file OptimizationTools.h.

Referenced by operator=().

◆ reparametrization_

bool bpp::NNITopologyListener2::reparametrization_

private

Definition at line 135 of file OptimizationTools.h.

Referenced by operator=().

◆ tolerance_

double bpp::NNITopologyListener2::tolerance_

private

Definition at line 128 of file OptimizationTools.h.

Referenced by operator=().

◆ topoSearch_

std::shared_ptr<NNITopologySearch> bpp::NNITopologyListener2::topoSearch_

private

Definition at line 126 of file OptimizationTools.h.

Referenced by operator=().

◆ verbose_

unsigned int bpp::NNITopologyListener2::verbose_

private

Definition at line 131 of file OptimizationTools.h.

Referenced by operator=().

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

Bpp/Phyl/Legacy/OptimizationTools.h
Bpp/Phyl/Legacy/OptimizationTools.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NNITopologyListener2() [1/2]

◆ NNITopologyListener2() [2/2]

◆ ~NNITopologyListener2()

Member Function Documentation

◆ clone()

◆ operator=()

◆ setNumericalOptimizationCounter()

◆ topologyChangePerformed()

◆ topologyChangeSuccessful()

◆ topologyChangeTested()

Member Data Documentation

◆ messenger_

◆ optimizeCounter_

◆ optimizeNumerical_

◆ optMethod_

◆ parameters_

◆ profiler_

◆ reparametrization_

◆ tolerance_

◆ topoSearch_

◆ verbose_