#include <Bpp/PopGen/LocusInfo.h>

Inheritance diagram for bpp::LocusInfo:

Collaboration diagram for bpp::LocusInfo:

Public Member Functions
	LocusInfo (const std::string &name, const unsigned int ploidy=DIPLOID)
	Build a new LocusInfo object. More...

	LocusInfo (const LocusInfo &locusInfo)
	Copy constructor. More...

LocusInfo &	operator= (const LocusInfo &locusInfo)

virtual	~LocusInfo ()=default
	Destroy the LocusInfo. More...

LocusInfo *	clone () const override

const std::string &	getName () const
	Get the name of the locus. More...

unsigned int	getPloidy () const
	Get the ploidy of the locus. More...

void	addAlleleInfo (const AlleleInfo &allele)
	Add an AlleleInfo to the LocusInfo. More...

const AlleleInfo &	getAlleleInfoById (const std::string &id) const
	Retrieve an AlleleInfo object of the LocusInfo. More...

const AlleleInfo &	getAlleleInfoByKey (size_t key) const
	Retrieve an AlleleInfo object of the LocusInfo. More...

unsigned int	getAlleleInfoKey (const std::string &id) const
	Get the position of an AlleleInfo. More...

size_t	getNumberOfAlleles () const
	Get the number of alleles at this locus. More...

void	clear ()
	Delete all alleles from the locus. More...

Static Public Attributes
static unsigned int	HAPLODIPLOID = 0

static unsigned int	HAPLOID = 1

static unsigned int	DIPLOID = 2

static unsigned int	UNKNOWN = 9999

Private Attributes
std::string	name_

unsigned int	ploidy_

std::vector< std::unique_ptr< AlleleInfo > >	alleles_

Detailed Description

The LocusInfo class.

This is an AlleleInfo container with additional data like a name, the ploidy and some comments.

Author: Sylvain Gaillard

Definition at line 29 of file LocusInfo.h.

Constructor & Destructor Documentation

◆ LocusInfo() [1/2]

bpp::LocusInfo::LocusInfo	(	const std::string &	name,
		const unsigned int	ploidy = `DIPLOID`
	)

inline

Build a new LocusInfo object.

Parameters

name	The name of the locus.
ploidy	The ploidy of the locus.

Definition at line 51 of file LocusInfo.h.

Referenced by clone().

◆ LocusInfo() [2/2]

bpp::LocusInfo::LocusInfo ( const LocusInfo & locusInfo )

inline

Copy constructor.

Definition at line 60 of file LocusInfo.h.

References alleles_, bpp::AlleleInfo::clone(), getAlleleInfoByKey(), and getNumberOfAlleles().

◆ ~LocusInfo()

virtual bpp::LocusInfo::~LocusInfo ( )

virtualdefault

Destroy the LocusInfo.

Member Function Documentation

◆ addAlleleInfo()

void LocusInfo::addAlleleInfo ( const AlleleInfo & allele )

Add an AlleleInfo to the LocusInfo.

Exceptions

BadIdentifierException if the AlleleInfo's id already exists.

Definition at line 21 of file LocusInfo.cpp.

References bpp::AlleleInfo::clone(), and bpp::AlleleInfo::getId().

Referenced by bpp::Genetix::read().

◆ clear()

void bpp::LocusInfo::clear ( )

inline

Delete all alleles from the locus.

Definition at line 139 of file LocusInfo.h.

References alleles_.

◆ clone()

LocusInfo* bpp::LocusInfo::clone ( ) const

inlineoverridevirtual

Implements bpp::Clonable.

Definition at line 88 of file LocusInfo.h.

References LocusInfo().

Referenced by bpp::AnalyzedLoci::setLocusInfo().

◆ getAlleleInfoById()

const AlleleInfo & LocusInfo::getAlleleInfoById ( const std::string & id ) const

Retrieve an AlleleInfo object of the LocusInfo.

Exceptions

AlleleNotFoundException if the id is not found.

Definition at line 32 of file LocusInfo.cpp.

◆ getAlleleInfoByKey()

const AlleleInfo & LocusInfo::getAlleleInfoByKey ( size_t key ) const

Retrieve an AlleleInfo object of the LocusInfo.

Exceptions

IndexOutOfBoundsException if key exceeds the number of alleles.

Definition at line 42 of file LocusInfo.cpp.

Referenced by LocusInfo(), operator=(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getAlleleInfoKey()

unsigned int LocusInfo::getAlleleInfoKey ( const std::string & id ) const

Get the position of an AlleleInfo.

Exceptions

AlleleNotFoundException if the AlleleInfo's id is not found.

Definition at line 49 of file LocusInfo.cpp.

Referenced by bpp::MultilocusGenotype::setMonolocusGenotypeByAlleleId().

◆ getName()

const std::string& bpp::LocusInfo::getName ( ) const

inline

Get the name of the locus.

Definition at line 94 of file LocusInfo.h.

References name_.

Referenced by bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getNumberOfAlleles()

size_t bpp::LocusInfo::getNumberOfAlleles ( ) const

inline

Get the number of alleles at this locus.

Definition at line 134 of file LocusInfo.h.

References alleles_.

Referenced by LocusInfo(), operator=(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getPloidy()

unsigned int bpp::LocusInfo::getPloidy ( ) const

inline

Get the ploidy of the locus.

Returns: The ploidy as an unsigned integer.

Definition at line 101 of file LocusInfo.h.

References ploidy_.

Referenced by bpp::PopgenlibIO::write().

◆ operator=()

LocusInfo& bpp::LocusInfo::operator= ( const LocusInfo & locusInfo )

inline

Definition at line 71 of file LocusInfo.h.

References alleles_, bpp::AlleleInfo::clone(), getAlleleInfoByKey(), getNumberOfAlleles(), name_, and ploidy_.

Member Data Documentation

◆ alleles_

std::vector<std::unique_ptr<AlleleInfo> > bpp::LocusInfo::alleles_

private

Definition at line 35 of file LocusInfo.h.

Referenced by clear(), getNumberOfAlleles(), LocusInfo(), and operator=().

◆ DIPLOID

unsigned int LocusInfo::DIPLOID = 2

static

Definition at line 40 of file LocusInfo.h.

Referenced by bpp::PopgenlibIO::parseLoci_(), and bpp::PopgenlibIO::write().

◆ HAPLODIPLOID

unsigned int LocusInfo::HAPLODIPLOID = 0

static

Definition at line 38 of file LocusInfo.h.

Referenced by bpp::PopgenlibIO::parseLoci_(), and bpp::PopgenlibIO::write().

◆ HAPLOID

unsigned int LocusInfo::HAPLOID = 1

static

Definition at line 39 of file LocusInfo.h.

Referenced by bpp::PopgenlibIO::parseLoci_(), and bpp::PopgenlibIO::write().

◆ name_

std::string bpp::LocusInfo::name_

private

Definition at line 33 of file LocusInfo.h.

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

◆ ploidy_

unsigned int bpp::LocusInfo::ploidy_

private

Definition at line 34 of file LocusInfo.h.

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

◆ UNKNOWN

unsigned int LocusInfo::UNKNOWN = 9999

static

Definition at line 41 of file LocusInfo.h.

Referenced by bpp::PopgenlibIO::parseLoci_(), bpp::GeneMapperCsvExport::read(), and bpp::PopgenlibIO::write().

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

Bpp/PopGen/LocusInfo.h
Bpp/PopGen/LocusInfo.cpp

Public Member Functions

Static Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ LocusInfo() [1/2]

◆ LocusInfo() [2/2]

◆ ~LocusInfo()

Member Function Documentation

◆ addAlleleInfo()

◆ clear()

◆ clone()

◆ getAlleleInfoById()

◆ getAlleleInfoByKey()

◆ getAlleleInfoKey()

◆ getName()

◆ getNumberOfAlleles()

◆ getPloidy()

◆ operator=()

Member Data Documentation

◆ alleles_

◆ DIPLOID

◆ HAPLODIPLOID

◆ HAPLOID

◆ name_

◆ ploidy_

◆ UNKNOWN