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

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

Inheritance diagram for bpp::NNITopologyListener:

Collaboration diagram for bpp::NNITopologyListener:

Public Member Functions
	NNITopologyListener (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, unsigned int nStep, bool reparametrization)
	Build a new NNITopologyListener object. More...

	NNITopologyListener (const NNITopologyListener &tl)

NNITopologyListener &	operator= (const NNITopologyListener &tl)

NNITopologyListener *	clone () const

virtual	~NNITopologyListener ()

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_

unsigned int	nStep_

bool	reparametrization_

Detailed Description

Listener used internally by the optimizeTreeNNI method.

Definition at line 23 of file OptimizationTools.h.

Constructor & Destructor Documentation

◆ NNITopologyListener() [1/2]

bpp::NNITopologyListener::NNITopologyListener	(	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,
		unsigned int	nStep,
		bool	reparametrization
	)

inline

Build a new NNITopologyListener object.

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

Parameters

ts	The NNITopologySearch object attached to this listener.
parameters	The list of parameters to optimize. Use tl->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.
nStep	The number of optimization steps to perform.
reparametrization	Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower.

Definition at line 57 of file OptimizationTools.h.

Referenced by clone().

◆ NNITopologyListener() [2/2]

bpp::NNITopologyListener::NNITopologyListener ( const NNITopologyListener & tl )

inline

Definition at line 79 of file OptimizationTools.h.

◆ ~NNITopologyListener()

virtual bpp::NNITopologyListener::~NNITopologyListener ( )

inlinevirtual

Definition at line 111 of file OptimizationTools.h.

Member Function Documentation

◆ clone()

NNITopologyListener* bpp::NNITopologyListener::clone ( ) const

inlinevirtual

Implements bpp::TopologyListener.

Definition at line 109 of file OptimizationTools.h.

References NNITopologyListener().

◆ operator=()

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

inline

Definition at line 93 of file OptimizationTools.h.

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

◆ setNumericalOptimizationCounter()

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

inline

Definition at line 116 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 NNITopologyListener::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 358 of file OptimizationTools.cpp.

References bpp::LegacyOptimizationTools::optimizeNumericalParameters().

◆ topologyChangeTested()

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

inlinevirtual

Notify a topology change event.

Parameters

event The topology change event.

Implements bpp::TopologyListener.

Definition at line 114 of file OptimizationTools.h.

Member Data Documentation

◆ messenger_

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

private

Definition at line 30 of file OptimizationTools.h.

Referenced by operator=().

◆ nStep_

unsigned int bpp::NNITopologyListener::nStep_

private

Definition at line 36 of file OptimizationTools.h.

Referenced by operator=().

◆ optimizeCounter_

unsigned int bpp::NNITopologyListener::optimizeCounter_

private

Definition at line 33 of file OptimizationTools.h.

Referenced by operator=().

◆ optimizeNumerical_

unsigned int bpp::NNITopologyListener::optimizeNumerical_

private

Definition at line 34 of file OptimizationTools.h.

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

◆ optMethod_

std::string bpp::NNITopologyListener::optMethod_

private

Definition at line 35 of file OptimizationTools.h.

Referenced by operator=().

◆ parameters_

ParameterList bpp::NNITopologyListener::parameters_

private

Definition at line 28 of file OptimizationTools.h.

Referenced by operator=().

◆ profiler_

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

private

Definition at line 31 of file OptimizationTools.h.

Referenced by operator=().

◆ reparametrization_

bool bpp::NNITopologyListener::reparametrization_

private

Definition at line 37 of file OptimizationTools.h.

Referenced by operator=().

◆ tolerance_

double bpp::NNITopologyListener::tolerance_

private

Definition at line 29 of file OptimizationTools.h.

Referenced by operator=().

◆ topoSearch_

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

private

Definition at line 27 of file OptimizationTools.h.

Referenced by operator=().

◆ verbose_

unsigned int bpp::NNITopologyListener::verbose_

private

Definition at line 32 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

◆ NNITopologyListener() [1/2]

◆ NNITopologyListener() [2/2]

◆ ~NNITopologyListener()

Member Function Documentation

◆ clone()

◆ operator=()

◆ setNumericalOptimizationCounter()

◆ topologyChangePerformed()

◆ topologyChangeSuccessful()

◆ topologyChangeTested()

Member Data Documentation

◆ messenger_

◆ nStep_

◆ optimizeCounter_

◆ optimizeNumerical_

◆ optMethod_

◆ parameters_

◆ profiler_

◆ reparametrization_

◆ tolerance_

◆ topoSearch_

◆ verbose_