This is the complete list of members for bpp::LegacyOptimizationTools, including all inherited members.

buildDistanceTree(DistanceEstimation &estimationMethod, AgglomerativeDistanceMethodInterface &reconstructionMethod, const std::string &param, OptimizationOptions &optopt)	bpp::OptimizationTools	static
DISTANCEMETHOD_INIT	bpp::OptimizationTools	static
DISTANCEMETHOD_ITERATIONS	bpp::OptimizationTools	static
DISTANCEMETHOD_PAIRWISE	bpp::OptimizationTools	static
estimateDistanceMatrix(DistanceEstimation &estimationMethod, const ParameterList &parametersToIgnore, const std::string &param=DISTANCEMETHOD_INIT, unsigned int verbose=0)	bpp::OptimizationTools	static
LegacyOptimizationTools()	bpp::LegacyOptimizationTools
OPTIMIZATION_BFGS	bpp::OptimizationTools	static
OPTIMIZATION_BRENT	bpp::OptimizationTools	static
OPTIMIZATION_GRADIENT	bpp::OptimizationTools	static
OPTIMIZATION_NEWTON	bpp::OptimizationTools	static
OptimizationTools()	bpp::OptimizationTools
optimizeBranchLengthsParameters(std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface > tl, const ParameterList &parameters, std::shared_ptr< OptimizationListener > listener=nullptr, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON)	bpp::LegacyOptimizationTools	static
optimizeNumericalParameters(std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface > tl, const ParameterList &parameters, std::shared_ptr< OptimizationListener > listener=nullptr, unsigned int nstep=1, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON, const std::string &optMethodModel=OPTIMIZATION_BRENT)	bpp::LegacyOptimizationTools	static
bpp::OptimizationTools::optimizeNumericalParameters(std::shared_ptr< PhyloLikelihoodInterface > lik, const OptimizationOptions &optopt)	bpp::OptimizationTools	static
optimizeNumericalParameters2(std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface > tl, const ParameterList &parameters, std::shared_ptr< OptimizationListener > listener=nullptr, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, bool useClock=false, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON)	bpp::LegacyOptimizationTools	static
bpp::OptimizationTools::optimizeNumericalParameters2(std::shared_ptr< PhyloLikelihoodInterface > lik, const OptimizationOptions &optopt)	bpp::OptimizationTools	static
bpp::OptimizationTools::optimizeNumericalParameters2(std::shared_ptr< SingleProcessPhyloLikelihood > lik, const OptimizationOptions &optopt)	bpp::OptimizationTools	static
optimizeTreeNNI(std::shared_ptr< NNIHomogeneousTreeLikelihood > tl, const ParameterList &parameters, bool optimizeNumFirst=true, double tolBefore=100, double tolDuring=100, unsigned int tlEvalMax=1000000, unsigned int numStep=1, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethod=OptimizationTools::OPTIMIZATION_NEWTON, unsigned int nStep=1, const std::string &nniMethod=NNITopologySearch::PHYML)	bpp::LegacyOptimizationTools	static
optimizeTreeNNI(std::shared_ptr< DRTreeParsimonyScore > tp, unsigned int verbose=1)	bpp::LegacyOptimizationTools	static
optimizeTreeNNI2(std::shared_ptr< NNIHomogeneousTreeLikelihood > tl, const ParameterList &parameters, bool optimizeNumFirst=true, double tolBefore=100, double tolDuring=100, unsigned int tlEvalMax=1000000, unsigned int numStep=1, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethod=OptimizationTools::OPTIMIZATION_NEWTON, const std::string &nniMethod=NNITopologySearch::PHYML)	bpp::LegacyOptimizationTools	static
optimizeTreeScale(std::shared_ptr< TreeLikelihoodInterface > tl, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, unsigned int verbose=1)	bpp::LegacyOptimizationTools	static
~LegacyOptimizationTools()	bpp::LegacyOptimizationTools	virtual
~OptimizationTools()	bpp::OptimizationTools	virtual