bpp::OptimizationTools::OptimizationOptions Class Reference

#include <Bpp/Phyl/OptimizationTools.h>

Collaboration diagram for bpp::OptimizationTools::OptimizationOptions:

Public Member Functions
	OptimizationOptions ()
	OptimizationOptions (std::shared_ptr< PhyloLikelihoodInterface > lik, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verb=true, int warn=1)

Public Attributes
ParameterList	parameters
std::shared_ptr< OptimizationListener >	listener
std::string	backupFile
unsigned int	nstep
double	tolerance
unsigned int	nbEvalMax
std::shared_ptr< OutputStream >	messenger
std::shared_ptr< OutputStream >	profiler
bool	reparametrization
bool	useClock
unsigned int	verbose
std::string	optMethodDeriv
std::string	optMethodModel

Detailed Description

Class used to register Optimization options parameters The list of parameters to optimize. Use tl->getIndependentParameters() in order to estimate all parameters. listener A pointer toward an optimization listener, if needed. nstep The number of progressive steps to perform (see NewtonBrentMetaOptimizer). 1 means full precision from start. tolerance The tolerance to use in the algorithm. nbEvalMax The maximum number of function evaluations. messenger The massage handler. profiler The profiler. reparametrization Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower. useClock True if follows the tree clock verbose The verbose level. optMethodDeriv Optimization type for derivable parameters (first or second order derivatives).

See also

OPTIMIZATION_NEWTON, OPTIMIZATION_GRADIENT optMethodModel Optimization type for model parameters (Brent or BFGS).

OPTIMIZATION_BRENT, OPTIMIZATION_BFGS

Exceptions

Exception

any exception thrown by the Optimizer.

Definition at line 97 of file OptimizationTools.h.

Constructor & Destructor Documentation

OptimizationOptions() [1/2]

bpp::OptimizationTools::OptimizationOptions::OptimizationOptions ( )

inline

Definition at line 115 of file OptimizationTools.h.

OptimizationOptions() [2/2]

OptimizationTools::OptimizationOptions::OptimizationOptions	(	std::shared_ptr< PhyloLikelihoodInterface >	lik,
		const std::map< std::string, std::string > &	params,
		const std::string &	suffix = "",
		bool	suffixIsOptional = true,
		bool	verb = true,
		int	warn = 1
	)

Get the method

Definition at line 41 of file OptimizationTools.cpp.

References bpp::abs(), backupFile, bpp::convert(), bpp::ParameterList::deleteParameter(), bpp::ParameterList::deleteParameters(), bpp::ApplicationTools::displayError(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::FileTools::fileExists(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getBooleanParameter(), bpp::Parameter::getConstraint(), bpp::ApplicationTools::getDoubleParameter(), bpp::Parameter::getName(), bpp::ParameterList::getParameterNames(), bpp::ApplicationTools::getStringParameter(), bpp::Parameter::hasConstraint(), bpp::StringTokenizer::hasMoreToken(), bpp::ParameterList::hasParameter(), bpp::TextTools::isEmpty(), listener, bpp::ApplicationTools::matchingParameters(), bpp::ApplicationTools::message, messenger, nbEvalMax, bpp::StringTokenizer::nextToken(), nstep, bpp::StringTokenizer::numberOfRemainingTokens(), bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_BRENT, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, optMethodDeriv, optMethodModel, bpp::ParameterNotFoundException::parameter(), bpp::ParameterList::parameter(), parameters, bpp::KeyvalTools::parseProcedure(), profiler, bpp::FileTools::putStreamIntoVectorOfStrings(), reparametrization, bpp::ParameterList::reset(), bpp::Parameter::setConstraint(), bpp::ParameterList::setParameter(), bpp::TextTools::toDouble(), tolerance, bpp::TextTools::toString(), useClock, verbose, and bpp::ParameterList::whichParameterHasName().

Member Data Documentation

backupFile

std::string bpp::OptimizationTools::OptimizationOptions::backupFile

Definition at line 102 of file OptimizationTools.h.

Referenced by OptimizationOptions(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

listener

std::shared_ptr<OptimizationListener> bpp::OptimizationTools::OptimizationOptions::listener

Definition at line 101 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), and bpp::OptimizationTools::optimizeNumericalParameters2().

messenger

std::shared_ptr<OutputStream> bpp::OptimizationTools::OptimizationOptions::messenger

Definition at line 106 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

nbEvalMax

unsigned int bpp::OptimizationTools::OptimizationOptions::nbEvalMax

Definition at line 105 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

nstep

unsigned int bpp::OptimizationTools::OptimizationOptions::nstep

Definition at line 103 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

optMethodDeriv

std::string bpp::OptimizationTools::OptimizationOptions::optMethodDeriv

Definition at line 111 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), and bpp::OptimizationTools::optimizeNumericalParameters2().

optMethodModel

std::string bpp::OptimizationTools::OptimizationOptions::optMethodModel

Definition at line 112 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

parameters

ParameterList bpp::OptimizationTools::OptimizationOptions::parameters

Definition at line 100 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::buildDistanceTree(), OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

profiler

std::shared_ptr<OutputStream> bpp::OptimizationTools::OptimizationOptions::profiler

Definition at line 107 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

reparametrization

bool bpp::OptimizationTools::OptimizationOptions::reparametrization

Definition at line 108 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), and bpp::OptimizationTools::optimizeNumericalParameters2().

tolerance

double bpp::OptimizationTools::OptimizationOptions::tolerance

Definition at line 104 of file OptimizationTools.h.

Referenced by OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

useClock

bool bpp::OptimizationTools::OptimizationOptions::useClock

Definition at line 109 of file OptimizationTools.h.

Referenced by OptimizationOptions().

verbose

unsigned int bpp::OptimizationTools::OptimizationOptions::verbose

Definition at line 110 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::buildDistanceTree(), OptimizationOptions(), bpp::OptimizationTools::optimizeNumericalParameters(), and bpp::OptimizationTools::optimizeNumericalParameters2().

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

• Bpp/Phyl/OptimizationTools.h
• Bpp/Phyl/OptimizationTools.cpp