bpp::PhyloLikelihoodContainer Class Reference

The PhyloLikelihoodContainer, owns and assigns numbers to Phylolikelihoods. More...

#include <Bpp/Phyl/Likelihood/PhyloLikelihoods/PhyloLikelihoodContainer.h>

Inheritance diagram for bpp::PhyloLikelihoodContainer:

Collaboration diagram for bpp::PhyloLikelihoodContainer:

Public Member Functions
	PhyloLikelihoodContainer (Context &context, std::shared_ptr< SubstitutionProcessCollection > sColl)
	PhyloLikelihoodContainer (Context &context, std::shared_ptr< CollectionNodes > sColl)
PhyloLikelihoodContainer *	clone () const override
virtual	~PhyloLikelihoodContainer ()
	Abstract class destructor. More...
void	addPhyloLikelihood (size_t pos, std::shared_ptr< PhyloLikelihoodInterface > Ap)
bool	hasPhyloLikelihood (size_t pos) const
std::shared_ptr< const PhyloLikelihoodInterface >	operator[] (size_t pos) const
std::shared_ptr< PhyloLikelihoodInterface >	operator[] (size_t pos)
std::shared_ptr< const PhyloLikelihoodInterface >	getPhyloLikelihood (size_t pos) const
std::shared_ptr< PhyloLikelihoodInterface >	getPhyloLikelihood (size_t pos)
size_t	getSize () const
std::vector< size_t >	getNumbersOfPhyloLikelihoods () const
std::shared_ptr< const CollectionNodes >	getCollectionNodes () const
	Manage Collection Nodes. More...
std::shared_ptr< CollectionNodes >	getCollectionNodes ()
void	setData (std::shared_ptr< const AlignmentDataInterface > sites, size_t nPhyl)
	Set the dataset for which the likelihood must be evaluated, iff the pointed PhyloLikelihood is a SingleDataPhyloLikelihood. More...
std::shared_ptr< const AlignmentDataInterface >	getData (size_t nPhyl) const
	Get the dataset for which the likelihood must be evaluated. More...

Protected Attributes
std::map< size_t, std::shared_ptr< PhyloLikelihoodInterface > >	mPhylo_

Private Attributes
Context &	context_
std::shared_ptr< CollectionNodes >	collectionNodes_

Detailed Description

The PhyloLikelihoodContainer, owns and assigns numbers to Phylolikelihoods.

It owns the PhyloLikelihoods

Definition at line 25 of file PhyloLikelihoodContainer.h.

Constructor & Destructor Documentation

PhyloLikelihoodContainer() [1/2]

bpp::PhyloLikelihoodContainer::PhyloLikelihoodContainer ( Context &  context, std::shared_ptr< SubstitutionProcessCollection >  sColl  )

inline

Definition at line 37 of file PhyloLikelihoodContainer.h.

PhyloLikelihoodContainer() [2/2]

bpp::PhyloLikelihoodContainer::PhyloLikelihoodContainer ( Context &  context, std::shared_ptr< CollectionNodes >  sColl  )

inline

Definition at line 45 of file PhyloLikelihoodContainer.h.

~PhyloLikelihoodContainer()

virtual bpp::PhyloLikelihoodContainer::~PhyloLikelihoodContainer ( )

inlinevirtual

Abstract class destructor.

Definition at line 60 of file PhyloLikelihoodContainer.h.

Member Function Documentation

addPhyloLikelihood()

void bpp::PhyloLikelihoodContainer::addPhyloLikelihood ( size_t  pos, std::shared_ptr< PhyloLikelihoodInterface >  Ap  )

inline

Definition at line 71 of file PhyloLikelihoodContainer.h.

References mPhylo_, and bpp::TextTools::toString().

clone()

PhyloLikelihoodContainer* bpp::PhyloLikelihoodContainer::clone ( ) const

inlineoverridevirtual

Implements bpp::Clonable.

Definition at line 51 of file PhyloLikelihoodContainer.h.

getCollectionNodes() [1/2]

std::shared_ptr<CollectionNodes> bpp::PhyloLikelihoodContainer::getCollectionNodes ( )

inline

Definition at line 133 of file PhyloLikelihoodContainer.h.

References collectionNodes_.

getCollectionNodes() [2/2]

std::shared_ptr<const CollectionNodes> bpp::PhyloLikelihoodContainer::getCollectionNodes ( ) const

inline

Manage Collection Nodes.

Definition at line 128 of file PhyloLikelihoodContainer.h.

References collectionNodes_.

getData()

std::shared_ptr<const AlignmentDataInterface> bpp::PhyloLikelihoodContainer::getData ( size_t  nPhyl ) const

inline

Get the dataset for which the likelihood must be evaluated.

Returns

A pointer toward the site container where the sequences are stored.

Definition at line 162 of file PhyloLikelihoodContainer.h.

References mPhylo_.

getNumbersOfPhyloLikelihoods()

std::vector<size_t> bpp::PhyloLikelihoodContainer::getNumbersOfPhyloLikelihoods ( ) const

inline

Definition at line 112 of file PhyloLikelihoodContainer.h.

References mPhylo_.

Referenced by bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

getPhyloLikelihood() [1/2]

std::shared_ptr<PhyloLikelihoodInterface> bpp::PhyloLikelihoodContainer::getPhyloLikelihood ( size_t  pos )

inline

Definition at line 101 of file PhyloLikelihoodContainer.h.

References mPhylo_.

getPhyloLikelihood() [2/2]

std::shared_ptr<const PhyloLikelihoodInterface> bpp::PhyloLikelihoodContainer::getPhyloLikelihood ( size_t  pos ) const

inline

Definition at line 95 of file PhyloLikelihoodContainer.h.

References mPhylo_.

getSize()

size_t bpp::PhyloLikelihoodContainer::getSize ( ) const

inline

Definition at line 107 of file PhyloLikelihoodContainer.h.

References mPhylo_.

hasPhyloLikelihood()

bool bpp::PhyloLikelihoodContainer::hasPhyloLikelihood ( size_t  pos ) const

inline

Definition at line 78 of file PhyloLikelihoodContainer.h.

References mPhylo_.

operator[]() [1/2]

std::shared_ptr<PhyloLikelihoodInterface> bpp::PhyloLikelihoodContainer::operator[] ( size_t  pos )

inline

Definition at line 89 of file PhyloLikelihoodContainer.h.

References mPhylo_.

operator[]() [2/2]

std::shared_ptr<const PhyloLikelihoodInterface> bpp::PhyloLikelihoodContainer::operator[] ( size_t  pos ) const

inline

Definition at line 83 of file PhyloLikelihoodContainer.h.

References mPhylo_.

setData()

void bpp::PhyloLikelihoodContainer::setData ( std::shared_ptr< const AlignmentDataInterface >  sites, size_t  nPhyl  )

inline

Set the dataset for which the likelihood must be evaluated, iff the pointed PhyloLikelihood is a SingleDataPhyloLikelihood.

Parameters

nPhyl	The number of the Likelihood.
sites	The data set to use.

Definition at line 145 of file PhyloLikelihoodContainer.h.

References mPhylo_.

Member Data Documentation

collectionNodes_

std::shared_ptr<CollectionNodes> bpp::PhyloLikelihoodContainer::collectionNodes_

private

Definition at line 31 of file PhyloLikelihoodContainer.h.

Referenced by getCollectionNodes().

context_

Context& bpp::PhyloLikelihoodContainer::context_

private

Definition at line 29 of file PhyloLikelihoodContainer.h.

mPhylo_

std::map<size_t, std::shared_ptr<PhyloLikelihoodInterface> > bpp::PhyloLikelihoodContainer::mPhylo_

protected

Definition at line 34 of file PhyloLikelihoodContainer.h.

Referenced by addPhyloLikelihood(), getData(), getNumbersOfPhyloLikelihoods(), getPhyloLikelihood(), getSize(), hasPhyloLikelihood(), operator[](), and setData().

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

• Bpp/Phyl/Likelihood/PhyloLikelihoods/PhyloLikelihoodContainer.h