bpp::LocusInfo Class Reference

The LocusInfo class. More...

#include <Bpp/PopGen/LocusInfo.h>

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 &locus_info)
	Copy constructor. More...
virtual	~LocusInfo ()
	Destroy the LocusInfo. More...
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< AlleleInfo * >	alleles_

Detailed Description

The LocusInfo class.

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

Author

Sylvain Gaillard

Definition at line 63 of file LocusInfo.h.

Constructor & Destructor Documentation

LocusInfo() [1/2]

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

Build a new LocusInfo object.

Parameters

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

Definition at line 55 of file LocusInfo.cpp.

LocusInfo() [2/2]

LocusInfo::LocusInfo

(

const LocusInfo &

locus_info

)

Copy constructor.

Definition at line 59 of file LocusInfo.cpp.

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

~LocusInfo()

LocusInfo::~LocusInfo ( )

virtual

Destroy the LocusInfo.

Definition at line 71 of file LocusInfo.cpp.

References alleles_.

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 83 of file LocusInfo.cpp.

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

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

clear()

void LocusInfo::clear

(

)

Delete all alleles from the locus.

Definition at line 126 of file LocusInfo.cpp.

References alleles_.

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 94 of file LocusInfo.cpp.

References alleles_.

getAlleleInfoByKey()

const AlleleInfo & LocusInfo::getAlleleInfoByKey

(

size_t

key

)

const

Retrieve an AlleleInfo object of the LocusInfo.

Exceptions

IndexOutOfBoundsException

if key excedes the number of alleles.

Definition at line 104 of file LocusInfo.cpp.

References alleles_.

Referenced by LocusInfo(), 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 111 of file LocusInfo.cpp.

References alleles_.

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

getName()

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

inline

Get the name of the locus.

Definition at line 101 of file LocusInfo.h.

References name_.

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

getNumberOfAlleles()

size_t LocusInfo::getNumberOfAlleles

(

)

const

Get the number of alleles at this locus.

Definition at line 121 of file LocusInfo.cpp.

References alleles_.

Referenced by LocusInfo(), 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 108 of file LocusInfo.h.

References ploidy_.

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

Member Data Documentation

alleles_

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

private

Definition at line 68 of file LocusInfo.h.

Referenced by addAlleleInfo(), clear(), getAlleleInfoById(), getAlleleInfoByKey(), getAlleleInfoKey(), getNumberOfAlleles(), LocusInfo(), and ~LocusInfo().

DIPLOID

unsigned int LocusInfo::DIPLOID = 2

static

Definition at line 73 of file LocusInfo.h.

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

HAPLODIPLOID

unsigned int LocusInfo::HAPLODIPLOID = 0

static

Definition at line 71 of file LocusInfo.h.

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

HAPLOID

unsigned int LocusInfo::HAPLOID = 1

static

Definition at line 72 of file LocusInfo.h.

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

name_

std::string bpp::LocusInfo::name_

private

Definition at line 66 of file LocusInfo.h.

Referenced by getName().

ploidy_

unsigned int bpp::LocusInfo::ploidy_

private

Definition at line 67 of file LocusInfo.h.

Referenced by getPloidy().

UNKNOWN

unsigned int LocusInfo::UNKNOWN = 9999

static

Definition at line 74 of file LocusInfo.h.

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

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

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