bpp::SitePatterns Class Reference

Data structure for site patterns. More...

#include <Bpp/Phyl/SitePatterns.h>

Inheritance diagram for bpp::SitePatterns:

Collaboration diagram for bpp::SitePatterns:

Classes
class	SortableSite
	Class used for site pattern sorting. More...

Public Types
typedef Eigen::Matrix< size_t, 1, -1 >	IndicesType

Public Member Functions
	SitePatterns (const AlignmentDataInterface &sequences, std::vector< std::string > names={})
	Build a new SitePattern object. More...
SitePatterns *	clone () const
const std::vector< unsigned int > &	getWeights () const
const IndicesType &	getIndices () const
std::unique_ptr< AlignmentDataInterface >	getSites () const

Private Member Functions
void	init_ (const AlignmentDataInterface &sequences, std::vector< std::string > names={})

Private Attributes
std::vector< std::string >	names_
std::vector< std::shared_ptr< const CoreSiteInterface > >	sites_
std::vector< unsigned int >	weights_
IndicesType	indices_
std::shared_ptr< const Alphabet >	alpha_

Detailed Description

Data structure for site patterns.

'names' are the sequence names 'sites' points toward a unique site 'weights' is the number of sites identical to this sites 'indices' are the positions in the original container

Definition at line 33 of file SitePatterns.h.

Member Typedef Documentation

IndicesType

typedef Eigen::Matrix<size_t, 1, -1> bpp::SitePatterns::IndicesType

Definition at line 37 of file SitePatterns.h.

Constructor & Destructor Documentation

SitePatterns()

SitePatterns::SitePatterns	(	const AlignmentDataInterface &	sequences,
		std::vector< std::string >	names = {}
	)

Build a new SitePattern object.

Look for patterns (unique sites) within a site container.

Parameters

sequences	The container to look in.
names	The vector of the names of the sequences that are effectively used in the computation. If not empty, the sites are filtered with the sequences names.

Definition at line 17 of file SitePatterns.cpp.

References bpp::TemplateAlignmentDataInterface< class >::getSequenceNames(), init_(), names_, and bpp::VectorTools::vectorIntersection().

Referenced by clone().

Member Function Documentation

clone()

SitePatterns * bpp::SitePatterns::clone ( ) const

inlinevirtual

Implements bpp::Clonable.

Definition at line 88 of file SitePatterns.h.

References SitePatterns().

getIndices()

const IndicesType & bpp::SitePatterns::getIndices ( ) const

inline

Returns

The position of each unique site.

Definition at line 103 of file SitePatterns.h.

References indices_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::setPatterns_().

getSites()

unique_ptr< AlignmentDataInterface > SitePatterns::getSites

(

)

const

Returns

A new container with each unique site.

Definition at line 110 of file SitePatterns.cpp.

References alpha_, names_, and sites_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::setPatterns_().

getWeights()

const std::vector< unsigned int > & bpp::SitePatterns::getWeights ( ) const

inline

Returns

The number of times each unique site was found.

Definition at line 99 of file SitePatterns.h.

References weights_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::setPatterns_().

init_()

void SitePatterns::init_ ( const AlignmentDataInterface &  sequences, std::vector< std::string >  names = {}  )

private

Definition at line 32 of file SitePatterns.cpp.

References bpp::SymbolListTools::areSymbolListsIdentical(), bpp::CoreSiteInterface::clone(), bpp::CoreSiteInterface::deleteElement(), bpp::TemplateAlignmentDataInterface< class >::getNumberOfSequences(), bpp::TemplateAlignmentDataInterface< class >::getNumberOfSites(), bpp::TemplateAlignmentDataInterface< class >::getSequencePosition(), indices_, bpp::SitePatterns::SortableSite::originalPosition, bpp::TemplateAlignmentDataInterface< class >::site(), bpp::SitePatterns::SortableSite::siteP, bpp::SitePatterns::SortableSite::siteS, sites_, bpp::CoreSiteInterface::toString(), and weights_.

Referenced by SitePatterns().

Member Data Documentation

alpha_

std::shared_ptr<const Alphabet> bpp::SitePatterns::alpha_

private

Definition at line 71 of file SitePatterns.h.

Referenced by getSites().

indices_

IndicesType bpp::SitePatterns::indices_

private

Definition at line 70 of file SitePatterns.h.

Referenced by getIndices(), and init_().

names_

std::vector<std::string> bpp::SitePatterns::names_

private

Definition at line 67 of file SitePatterns.h.

Referenced by getSites(), and SitePatterns().

sites_

std::vector<std::shared_ptr<const CoreSiteInterface> > bpp::SitePatterns::sites_

private

Definition at line 68 of file SitePatterns.h.

Referenced by getSites(), and init_().

weights_

std::vector<unsigned int> bpp::SitePatterns::weights_

private

Definition at line 69 of file SitePatterns.h.

Referenced by getWeights(), and init_().

---

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

• Bpp/Phyl/SitePatterns.h
• Bpp/Phyl/SitePatterns.cpp