Compute A simple distance using observed counts. More...

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

Inheritance diagram for bpp::MaximumLikelihoodDistanceEstimationMafIterator:

Collaboration diagram for bpp::MaximumLikelihoodDistanceEstimationMafIterator:

Public Member Functions
	MaximumLikelihoodDistanceEstimationMafIterator (MafIterator iterator, DistanceEstimation distEst, double propGapsToKeep=0, bool gapsAsUnresolved=true, const string &paramOpt=OptimizationTools::DISTANCEMETHOD_INIT, bool verbose=true)
	Build a new distance estimation maf iterator, based on the DistanceEstimation class. More...

std::string	getPropertyName () const

DistanceMatrix *	estimateDistanceMatrixForBlock (const MafBlock &block)

Private Member Functions
	MaximumLikelihoodDistanceEstimationMafIterator (const MaximumLikelihoodDistanceEstimationMafIterator &iterator)

MaximumLikelihoodDistanceEstimationMafIterator &	operator= (const MaximumLikelihoodDistanceEstimationMafIterator &iterator)

Private Attributes
std::auto_ptr< DistanceEstimation >	distEst_

double	propGapsToKeep_

bool	gapsAsUnresolved_

std::string	paramOpt_

Detailed Description

Compute A simple distance using observed counts.

Definition at line 53 of file MaximumLikelihoodDistanceEstimationMafIterator.h.

Constructor & Destructor Documentation

◆ MaximumLikelihoodDistanceEstimationMafIterator() [1/2]

bpp::MaximumLikelihoodDistanceEstimationMafIterator::MaximumLikelihoodDistanceEstimationMafIterator	(	MafIterator *	iterator,
		DistanceEstimation *	distEst,
		double	propGapsToKeep = `0`,
		bool	gapsAsUnresolved = `true`,
		const string &	paramOpt = `OptimizationTools::DISTANCEMETHOD_INIT`,
		bool	verbose = `true`
	)

inline

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

See also: DistanceEstimation

Parameters

iterator	The input iterator.
distEst	A DistanceEstimation object, initialized with an appropriate substitution model.
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.
paramOpt	Tell if substitution model parameters should be optimized in a pairwise manner or not. See OptimizationTools::estimateDistanceMatrix for more details.
verbose	Tell if some information should be output in the default message stream.

Definition at line 74 of file MaximumLikelihoodDistanceEstimationMafIterator.h.

References distEst_.

◆ MaximumLikelihoodDistanceEstimationMafIterator() [2/2]

bpp::MaximumLikelihoodDistanceEstimationMafIterator::MaximumLikelihoodDistanceEstimationMafIterator ( const MaximumLikelihoodDistanceEstimationMafIterator & iterator )

inlineprivate

Definition at line 88 of file MaximumLikelihoodDistanceEstimationMafIterator.h.

Member Function Documentation

◆ estimateDistanceMatrixForBlock()

DistanceMatrix * MaximumLikelihoodDistanceEstimationMafIterator::estimateDistanceMatrixForBlock ( const MafBlock & block )

virtual

Implements bpp::AbstractDistanceEstimationMafIterator.

Definition at line 47 of file MaximumLikelihoodDistanceEstimationMafIterator.cpp.

References distEst_, gapsAsUnresolved_, paramOpt_, and propGapsToKeep_.

◆ getPropertyName()

std::string bpp::MaximumLikelihoodDistanceEstimationMafIterator::getPropertyName ( ) const

inlinevirtual

Implements bpp::AbstractDistanceEstimationMafIterator.

Definition at line 104 of file MaximumLikelihoodDistanceEstimationMafIterator.h.

◆ operator=()

MaximumLikelihoodDistanceEstimationMafIterator& bpp::MaximumLikelihoodDistanceEstimationMafIterator::operator= ( const MaximumLikelihoodDistanceEstimationMafIterator & iterator )

inlineprivate

Definition at line 94 of file MaximumLikelihoodDistanceEstimationMafIterator.h.

References distEst_, gapsAsUnresolved_, paramOpt_, and propGapsToKeep_.