Fit a substitution model. More...

#include <Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h>

Inheritance diagram for bpp::MaximumLikelihoodModelFitMafStatistics:

Collaboration diagram for bpp::MaximumLikelihoodModelFitMafStatistics:

Public Member Functions
	MaximumLikelihoodModelFitMafStatistics (SubstitutionModel model, DiscreteDistribution rDist, NucleotideFrequenciesSet *rootFreqs, const std::string &treePropertyIn, const std::vector< std::string > &parametersOut, const ParameterList &fixedParameters, bool reestimateBrLen=true, double propGapsToKeep=0, bool gapsAsUnresolved=true)
	Build a new distance estimation maf mafstat, based on the DistanceEstimation class. More...

	MaximumLikelihoodModelFitMafStatistics (SubstitutionModel model, DiscreteDistribution rDist, NucleotideFrequenciesSet rootFreqs, const Tree tree, const std::vector< std::string > &parametersOut, const ParameterList &fixedParameters, bool reestimateBrLen=true, double propGapsToKeep=0, bool gapsAsUnresolved=true)
	Build a new distance estimation maf mafstat, based on the DistanceEstimation class. More...

std::string	getShortName () const

std::string	getFullName () const

void	compute (const MafBlock &block)

std::vector< std::string >	getSupportedTags () const

Static Public Attributes
static const std::string	NO_PROPERTY = "RESERVED_NOPROPERTY"

Private Member Functions
	MaximumLikelihoodModelFitMafStatistics (const MaximumLikelihoodModelFitMafStatistics &mafstat)

MaximumLikelihoodModelFitMafStatistics &	operator= (const MaximumLikelihoodModelFitMafStatistics &mafstat)

void	init_ ()

Private Attributes
std::auto_ptr< SubstitutionModel >	model_

std::auto_ptr< SubstitutionModelSet >	modelSet_

std::auto_ptr< DiscreteDistribution >	rDist_

std::auto_ptr< NucleotideFrequenciesSet >	rootFreqs_

std::string	treePropertyIn_

std::auto_ptr< const Tree >	tree_

std::vector< std::string >	parametersOut_

bool	reestimateBrLen_

double	propGapsToKeep_

bool	gapsAsUnresolved_

ParameterList	initParameters_

ParameterList	fixedParameters_

Detailed Description

Fit a substitution model.

All nucleotide substitution models and rate distributions are supported. Only time-homogeneous models are allowed though.

Definition at line 64 of file MaximumLikelihoodModelFitMafStatistics.h.

Constructor & Destructor Documentation

◆ MaximumLikelihoodModelFitMafStatistics() [1/3]

bpp::MaximumLikelihoodModelFitMafStatistics::MaximumLikelihoodModelFitMafStatistics	(	SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		NucleotideFrequenciesSet *	rootFreqs,
		const std::string &	treePropertyIn,
		const std::vector< std::string > &	parametersOut,
		const ParameterList &	fixedParameters,
		bool	reestimateBrLen = `true`,
		double	propGapsToKeep = `0`,
		bool	gapsAsUnresolved = `true`
	)

inline

Build a new distance estimation maf mafstat, based on the DistanceEstimation class.

A tree must be associated to each block before this analysis can be run.

Parameters

model	The substitution model.
rDist	The distribution of rates.
rootFreqs	Root frequencies for non-stationary model. If set to 0, then a stationary model is assumed.
treePropertyIn	The name of the property where the input tree is stored for each block.
parametersOut	Parameters to output.
fixedParameters	Parameter which should not be estimated but fixed to the given value instead.
reestimateBrLen	If the branch length from the tree should be reestimated (otherwise kept as is).
propGapsToKeep	The maximum gapfrequency in a site to include it in the analysis.
gapsAsUnresolved	Tell if gap characters should be considered as unresolved states. In ost cases it should be set to true, as very few substitution models consider gaps as genuine states.

Definition at line 98 of file MaximumLikelihoodModelFitMafStatistics.h.

References init_().

◆ MaximumLikelihoodModelFitMafStatistics() [2/3]

bpp::MaximumLikelihoodModelFitMafStatistics::MaximumLikelihoodModelFitMafStatistics	(	SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		NucleotideFrequenciesSet *	rootFreqs,
		const Tree *	tree,
		const std::vector< std::string > &	parametersOut,
		const ParameterList &	fixedParameters,
		bool	reestimateBrLen = `true`,
		double	propGapsToKeep = `0`,
		bool	gapsAsUnresolved = `true`
	)

inline

Build a new distance estimation maf mafstat, based on the DistanceEstimation class.

This analysis use the same input tree for all blocks.

Parameters

model	The substitution model.
rDist	The distribution of rates.
rootFreqs	Root frequencies for non-stationary model. If set to 0, then a stationary model is assumed.
tree	The tree to use for fitting the model.
parametersOut	Parameters to output.
fixedParameters	Parameter which should not be estimated but fixed to the given value instead.
reestimateBrLen	If the branch length from the tree should be reestimated (otherwise kept as is).
propGapsToKeep	The maximum gapfrequency in a site to include it in the analysis.
gapsAsUnresolved	Tell if gap characters should be considered as unresolved states. In ost cases it should be set to true, as very few substitution models consider gaps as genuine states.

Definition at line 135 of file MaximumLikelihoodModelFitMafStatistics.h.

References init_(), and modelSet_.

◆ MaximumLikelihoodModelFitMafStatistics() [3/3]

bpp::MaximumLikelihoodModelFitMafStatistics::MaximumLikelihoodModelFitMafStatistics ( const MaximumLikelihoodModelFitMafStatistics & mafstat )

inlineprivate

Definition at line 157 of file MaximumLikelihoodModelFitMafStatistics.h.

Member Function Documentation

◆ compute()

void MaximumLikelihoodModelFitMafStatistics::compute ( const MafBlock & block )

Definition at line 56 of file MaximumLikelihoodModelFitMafStatistics.cpp.

◆ getFullName()

std::string bpp::MaximumLikelihoodModelFitMafStatistics::getFullName ( ) const

inline

Definition at line 184 of file MaximumLikelihoodModelFitMafStatistics.h.

◆ getShortName()

std::string bpp::MaximumLikelihoodModelFitMafStatistics::getShortName ( ) const

inline

Definition at line 183 of file MaximumLikelihoodModelFitMafStatistics.h.

◆ getSupportedTags()

std::vector<std::string> bpp::MaximumLikelihoodModelFitMafStatistics::getSupportedTags ( ) const

inline

Definition at line 186 of file MaximumLikelihoodModelFitMafStatistics.h.

References parametersOut_.

◆ init_()

void MaximumLikelihoodModelFitMafStatistics::init_ ( )

private

Definition at line 105 of file MaximumLikelihoodModelFitMafStatistics.cpp.

Referenced by MaximumLikelihoodModelFitMafStatistics().

◆ operator=()

MaximumLikelihoodModelFitMafStatistics& bpp::MaximumLikelihoodModelFitMafStatistics::operator= ( const MaximumLikelihoodModelFitMafStatistics & mafstat )

inlineprivate

Definition at line 165 of file MaximumLikelihoodModelFitMafStatistics.h.

References fixedParameters_, gapsAsUnresolved_, initParameters_, model_, modelSet_, parametersOut_, propGapsToKeep_, rDist_, reestimateBrLen_, rootFreqs_, tree_, and treePropertyIn_.