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:

List of all members.

Classes
class	SortableSite
	Class used for site pattern sorting. More...
Public Member Functions
	SitePatterns (const SiteContainer *sequences, bool own=false)
	Build a new SitePattern object.
virtual	~SitePatterns ()
	SitePatterns (const SitePatterns &patterns)
SitePatterns &	operator= (const SitePatterns &patterns)
SitePatterns *	clone () const
const std::vector< unsigned int > &	getWeights () const
const std::vector< size_t > &	getIndices () const
SiteContainer *	getSites () const
Private Attributes
std::vector< std::string >	names_
	Class used for site pattern sorting.
std::vector< const Site * >	sites_
std::vector< unsigned int >	weights_
std::vector< size_t >	indices_
const SiteContainer *	sequences_
const Alphabet *	alpha_
bool	own_

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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 69 of file SitePatterns.h.

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Constructor & Destructor Documentation

SitePatterns::SitePatterns	(	const SiteContainer *	sequences,
		bool	own = false
	)

Build a new SitePattern object.

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

Parameters:

sequences	The container to look in.
own	Tel is the class own the sequence container. If yes, the sequences wll be deleted together with this instance.

Definition at line 52 of file SitePatterns.cpp.

References bpp::SiteTools::areSitesIdentical(), bpp::SiteContainer::getNumberOfSites(), bpp::SiteContainer::getSite(), indices_, bpp::SitePatterns::SortableSite::originalPosition, bpp::SitePatterns::SortableSite::siteP, bpp::SitePatterns::SortableSite::siteS, sites_, bpp::Site::toString(), and weights_.

Referenced by clone().

virtual bpp::SitePatterns::~SitePatterns

(

)

[inline, virtual]

Definition at line 129 of file SitePatterns.h.

References own_, and sequences_.

bpp::SitePatterns::SitePatterns

(

const SitePatterns &

patterns

)

[inline]

Definition at line 134 of file SitePatterns.h.

References bpp::SiteContainer::clone(), own_, and sequences_.

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Member Function Documentation

SitePatterns* bpp::SitePatterns::clone

(

)

const [inline, virtual]

Implements bpp::Clonable.

Definition at line 165 of file SitePatterns.h.

References SitePatterns().

const std::vector<size_t>& bpp::SitePatterns::getIndices

(

)

const [inline]

Returns:

The position of each unique site.

Definition at line 175 of file SitePatterns.h.

References indices_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().

SiteContainer * SitePatterns::getSites

(

)

const

Returns:

A new container with each unique site.

Definition at line 110 of file SitePatterns.cpp.

References alpha_, names_, bpp::SiteContainer::setSequencesNames(), and sites_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().

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

(

)

const [inline]

Returns:

The number of times each unique site was found.

Definition at line 171 of file SitePatterns.h.

References weights_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().

SitePatterns& bpp::SitePatterns::operator=

(

const SitePatterns &

patterns

)

[inline]

Definition at line 147 of file SitePatterns.h.

References alpha_, bpp::SiteContainer::clone(), indices_, names_, own_, sequences_, sites_, and weights_.

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Member Data Documentation

const Alphabet* bpp::SitePatterns::alpha_ [private]

Definition at line 114 of file SitePatterns.h.

Referenced by getSites(), and operator=().

std::vector<size_t> bpp::SitePatterns::indices_ [private]

Definition at line 112 of file SitePatterns.h.

Referenced by getIndices(), operator=(), and SitePatterns().

std::vector<std::string> bpp::SitePatterns::names_ [private]

Class used for site pattern sorting.

Definition at line 109 of file SitePatterns.h.

Referenced by getSites(), and operator=().

bool bpp::SitePatterns::own_ [private]

Definition at line 115 of file SitePatterns.h.

Referenced by operator=(), SitePatterns(), and ~SitePatterns().

const SiteContainer* bpp::SitePatterns::sequences_ [private]

Definition at line 113 of file SitePatterns.h.

Referenced by operator=(), SitePatterns(), and ~SitePatterns().

std::vector<const Site *> bpp::SitePatterns::sites_ [private]

Definition at line 110 of file SitePatterns.h.

Referenced by getSites(), operator=(), and SitePatterns().

std::vector<unsigned int> bpp::SitePatterns::weights_ [private]

Definition at line 111 of file SitePatterns.h.

Referenced by getWeights(), operator=(), and SitePatterns().

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

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