#include <Bpp/Phyl/App/BppPhylogeneticsApplication.h>

Inheritance diagram for bpp::BppPhylogeneticsApplication:

Collaboration diagram for bpp::BppPhylogeneticsApplication:

Public Member Functions
	BppPhylogeneticsApplication (int argc, char *argv[], const std::string &name)

virtual void	fixLikelihood (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< PhyloLikelihoodInterface > phylolik, const std::string &suffix="", bool suffixIsOptional=true) const
	Method to have a clean likelihood (ie not saturated, nor infinite). More...

virtual void	displayParameters (const PhyloLikelihoodInterface &tl, bool displaylL=true) const
	Display parameter values. More...

virtual std::shared_ptr< Alphabet >	getAlphabet (const string &suffix="", bool suffixIsOptional=true, bool allowGeneric=false) const

virtual std::shared_ptr< GeneticCode >	getGeneticCode (std::shared_ptr< const Alphabet > &alphabet, const string &suffix="", bool suffixIsOptional=true) const

virtual std::map< size_t, std::unique_ptr< AlignmentDataInterface > >	getAlignmentsMap (std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const

virtual std::map< size_t, std::unique_ptr< const AlignmentDataInterface > >	getConstAlignmentsMap (std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const

virtual void	startTimer ()

virtual void	done ()

virtual const std::map< std::string, std::string > &	getParams () const

virtual std::map< std::string, std::string > &	getParams ()

virtual const std::string &	getParam (const std::string &name) const

virtual std::string &	getParam (const std::string &name)

virtual bool	isVerbose () const

virtual int	getWarningLevel () const

virtual void	help (const std::string &program) const


virtual std::map< size_t, std::shared_ptr< PhyloTree > >	getPhyloTreesMap (const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mSites, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const
	Methods to build objects. More...

virtual std::unique_ptr< SubstitutionProcessCollection >	getCollection (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mSites, const std::map< size_t, std::shared_ptr< PhyloTree >> &mpTree, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const
	get the collection of objects necessary to build substitution processes. More...

virtual std::unique_ptr< SubstitutionProcessCollection >	getCollection (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mSites, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const

virtual std::map< size_t, std::unique_ptr< SequenceEvolution > >	getProcesses (std::shared_ptr< SubstitutionProcessCollection > collection, std::map< std::string, std::string > &unparsedParams, const std::string &suffix="", bool suffixIsOptional=true) const
	get the substitution processes. More...

virtual std::shared_ptr< PhyloLikelihoodContainer >	getPhyloLikelihoods (Context &context, std::map< size_t, std::shared_ptr< SequenceEvolution >> mSeqEvol, std::shared_ptr< SubstitutionProcessCollection > collection, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mSites, const std::string &suffix="", bool suffixIsOptional=true) const
	get the phylolikelihoods. More...

Protected Attributes
std::string	appName_

std::map< std::string, std::string >	params_

bool	timerStarted_

bool	verbose_

int	warn_

Detailed Description

Definition at line 26 of file BppPhylogeneticsApplication.h.

Constructor & Destructor Documentation

◆ BppPhylogeneticsApplication()

bpp::BppPhylogeneticsApplication::BppPhylogeneticsApplication	(	int	argc,
		char *	argv[],
		const std::string &	name
	)

inline

Definition at line 30 of file BppPhylogeneticsApplication.h.

Member Function Documentation

◆ displayParameters()

void BppPhylogeneticsApplication::displayParameters	(	const PhyloLikelihoodInterface &	tl,
		bool	displaylL = `true`
	)		const

virtual

Display parameter values.

Parameters

tl	the phylolikelihood
displaylL	if log-likelihood is displayed (default: true)

Definition at line 286 of file BppPhylogeneticsApplication.cpp.

References bpp::ParameterList::deleteParameters(), bpp::PhyloLikelihoodInterface::getBranchLengthParameters(), bpp::SecondOrderDerivable::getNumberOfParameters(), bpp::ParameterList::getParameterNames(), bpp::SecondOrderDerivable::getParameters(), bpp::SecondOrderDerivable::getValue(), and bpp::ParameterList::size().

◆ fixLikelihood()

void BppPhylogeneticsApplication::fixLikelihood	(	std::shared_ptr< const Alphabet >	alphabet,
		std::shared_ptr< const GeneticCode >	gCode,
		std::shared_ptr< PhyloLikelihoodInterface >	phylolik,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`
	)		const

virtual

Method to have a clean likelihood (ie not saturated, nor infinite).

Definition at line 111 of file BppPhylogeneticsApplication.cpp.

References bpp::ProbabilisticSite::getCoordinate(), bpp::Site::getCoordinate(), bpp::ProbabilisticSite::getStateValueAt(), bpp::Site::getValue(), bpp::ParameterList::matchParametersValues(), bpp::ParameterList::size(), bpp::ProbabilisticSite::size(), and bpp::Site::size().

◆ getCollection() [1/2]

std::unique_ptr< SubstitutionProcessCollection > BppPhylogeneticsApplication::getCollection	(	std::shared_ptr< const Alphabet >	alphabet,
		std::shared_ptr< const GeneticCode >	gCode,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mSites,
		const std::map< size_t, std::shared_ptr< PhyloTree >> &	mpTree,
		std::map< std::string, std::string > &	unparsedParams,
		const std::string &	prefix = `"input."`,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`
	)		const

virtual

get the collection of objects necessary to build substitution processes.

Definition at line 61 of file BppPhylogeneticsApplication.cpp.

◆ getCollection() [2/2]

unique_ptr< SubstitutionProcessCollection > BppPhylogeneticsApplication::getCollection	(	std::shared_ptr< const Alphabet >	alphabet,
		std::shared_ptr< const GeneticCode >	gCode,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mSites,
		std::map< std::string, std::string > &	unparsedParams,
		const std::string &	prefix = `"input."`,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`
	)		const

virtual

Definition at line 47 of file BppPhylogeneticsApplication.cpp.

◆ getPhyloLikelihoods()

std::shared_ptr< PhyloLikelihoodContainer > BppPhylogeneticsApplication::getPhyloLikelihoods	(	Context &	context,
		std::map< size_t, std::shared_ptr< SequenceEvolution >>	mSeqEvol,
		std::shared_ptr< SubstitutionProcessCollection >	collection,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mSites,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`
	)		const

virtual

get the phylolikelihoods.

Definition at line 98 of file BppPhylogeneticsApplication.cpp.

◆ getPhyloTreesMap()

map< size_t, std::shared_ptr< PhyloTree > > BppPhylogeneticsApplication::getPhyloTreesMap	(	const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mSites,
		std::map< std::string, std::string > &	unparsedParams,
		const std::string &	prefix = `"input."`,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`
	)		const

virtual

Methods to build objects.

Get the std::map of initial phylo trees

Definition at line 19 of file BppPhylogeneticsApplication.cpp.

◆ getProcesses()

map< size_t, std::unique_ptr< SequenceEvolution > > BppPhylogeneticsApplication::getProcesses	(	std::shared_ptr< SubstitutionProcessCollection >	collection,
		std::map< std::string, std::string > &	unparsedParams,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`
	)		const

virtual

get the substitution processes.

Definition at line 87 of file BppPhylogeneticsApplication.cpp.

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

Bpp/Phyl/App/BppPhylogeneticsApplication.h
Bpp/Phyl/App/BppPhylogeneticsApplication.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BppPhylogeneticsApplication()

Member Function Documentation

◆ displayParameters()

◆ fixLikelihood()

◆ getCollection() [1/2]

◆ getCollection() [2/2]

◆ getPhyloLikelihoods()

◆ getPhyloTreesMap()

◆ getProcesses()