bpp::AnalyzedLoci Class Reference

The AnalyzedLoci class. More...

#include <Bpp/PopGen/DataSet/AnalyzedLoci.h>

Inheritance diagram for bpp::AnalyzedLoci:

Collaboration diagram for bpp::AnalyzedLoci:

Public Member Functions
	AnalyzedLoci (size_t numberOfLoci)
	Build a void AnalyzedLoci with a specific number of loci. More...
	AnalyzedLoci (const AnalyzedLoci &analyzedLoci)
	Copy constructor. More...
AnalyzedLoci &	operator= (const AnalyzedLoci &analyzedLoci)
virtual	~AnalyzedLoci ()=default
	Destroy the AnalyzedLoci. More...
AnalyzedLoci *	clone () const
void	setLocusInfo (size_t locusPosition, const LocusInfo &locus)
	Set a LocusInfo. More...
size_t	getLocusInfoPosition (const std::string &locusName) const
	Get the position of a LocusInfo. More...
const LocusInfo &	getLocusInfoByName (const std::string &locusName) const
	Get a LocusInfo by name. More...
const LocusInfo &	getLocusInfoAtPosition (size_t locusPosition) const
	Get a LocusInfo by its position. More...
void	addAlleleInfoByLocusName (const std::string &locusName, const AlleleInfo &allele)
	Add an AlleleInfo to a LocusInfo by LocusInfo name. More...
void	addAlleleInfoByLocusPosition (size_t locusosition, const AlleleInfo &allele)
	Add an AlleleInfo to a LocusInfo by its position. More...
size_t	getNumberOfLoci () const
	Get the number of loci. More...
std::vector< size_t >	getNumberOfAlleles () const
	Get the number of alleles at each locus. More...
unsigned int	getPloidyByLocusName (const std::string &locusName) const
	Get the ploidy of a locus by name. More...
unsigned int	getPloidyByLocusPosition (size_t locusPosition) const
	Get the ploidy of a locus by its position. More...

Private Attributes
std::vector< std::unique_ptr< LocusInfo > >	loci_

Detailed Description

The AnalyzedLoci class.

This is a LocusInfo container. Its instantiation requires a number of locus which is fixed and can't be modified.

Author

Sylvain Gaillard

Definition at line 29 of file AnalyzedLoci.h.

Constructor & Destructor Documentation

AnalyzedLoci() [1/2]

bpp::AnalyzedLoci::AnalyzedLoci ( size_t  numberOfLoci )

inline

Build a void AnalyzedLoci with a specific number of loci.

Definition at line 40 of file AnalyzedLoci.h.

Referenced by clone().

AnalyzedLoci() [2/2]

bpp::AnalyzedLoci::AnalyzedLoci ( const AnalyzedLoci &  analyzedLoci )

inline

Copy constructor.

Definition at line 45 of file AnalyzedLoci.h.

References loci_.

~AnalyzedLoci()

virtual bpp::AnalyzedLoci::~AnalyzedLoci ( )

virtualdefault

Destroy the AnalyzedLoci.

Member Function Documentation

addAlleleInfoByLocusName()

void AnalyzedLoci::addAlleleInfoByLocusName	(	const std::string &	locusName,
		const AlleleInfo &	allele
	)

Add an AlleleInfo to a LocusInfo by LocusInfo name.

Exceptions

BadIdentifierException	if the allele's id is already in use.
LocusNotFoundException	if locus_name is not found.

Definition at line 66 of file AnalyzedLoci.cpp.

References bpp::BadIdentifierException::getIdentifier().

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

addAlleleInfoByLocusPosition()

void AnalyzedLoci::addAlleleInfoByLocusPosition	(	size_t	locusosition,
		const AlleleInfo &	allele
	)

Add an AlleleInfo to a LocusInfo by its position.

Exceptions

BadIdentifierException	if the allele's id is already in use.
IndexOutOfBoundsException	if locus_position is out of bounds.

Definition at line 92 of file AnalyzedLoci.cpp.

References bpp::BadIdentifierException::getIdentifier().

clone()

AnalyzedLoci* bpp::AnalyzedLoci::clone ( ) const

inlinevirtual

Implements bpp::Clonable.

Definition at line 71 of file AnalyzedLoci.h.

References AnalyzedLoci().

Referenced by bpp::DataSet::setAnalyzedLoci().

getLocusInfoAtPosition()

const LocusInfo & AnalyzedLoci::getLocusInfoAtPosition

(

size_t

locusPosition

)

const

Get a LocusInfo by its position.

Exceptions

NullPointerException	if the LocusInfo is not defined.
IndexOutOfBoundsException	if locus_position is out of bounds.

Definition at line 52 of file AnalyzedLoci.cpp.

getLocusInfoByName()

const LocusInfo & AnalyzedLoci::getLocusInfoByName

(

const std::string &

locusName

)

const

Get a LocusInfo by name.

Exceptions

BadIdentifierException

if locus_name is not found.

Definition at line 38 of file AnalyzedLoci.cpp.

getLocusInfoPosition()

size_t AnalyzedLoci::getLocusInfoPosition

(

const std::string &

locusName

)

const

Get the position of a LocusInfo.

Exceptions

BadIdentifierException

if locus_name is not found.

Definition at line 25 of file AnalyzedLoci.cpp.

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

getNumberOfAlleles()

std::vector< size_t > AnalyzedLoci::getNumberOfAlleles

(

)

const

Get the number of alleles at each locus.

Definition at line 113 of file AnalyzedLoci.cpp.

getNumberOfLoci()

size_t bpp::AnalyzedLoci::getNumberOfLoci ( ) const

inline

Get the number of loci.

Definition at line 125 of file AnalyzedLoci.h.

References loci_.

getPloidyByLocusName()

unsigned int AnalyzedLoci::getPloidyByLocusName

(

const std::string &

locusName

)

const

Get the ploidy of a locus by name.

Exceptions

LocusNotFoundException

if locus_name is not found.

Definition at line 125 of file AnalyzedLoci.cpp.

getPloidyByLocusPosition()

unsigned int AnalyzedLoci::getPloidyByLocusPosition

(

size_t

locusPosition

)

const

Get the ploidy of a locus by its position.

Exceptions

IndexOutOfBoundsException

if locus_position is out of bounds.

Definition at line 138 of file AnalyzedLoci.cpp.

operator=()

AnalyzedLoci& bpp::AnalyzedLoci::operator= ( const AnalyzedLoci &  analyzedLoci )

inline

Definition at line 55 of file AnalyzedLoci.h.

References loci_.

setLocusInfo()

void AnalyzedLoci::setLocusInfo	(	size_t	locusPosition,
		const LocusInfo &	locus
	)

Set a LocusInfo.

Exceptions

IndexOutOfBoundsException

if locus_position is out of bounds.

Definition at line 12 of file AnalyzedLoci.cpp.

References bpp::LocusInfo::clone().

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

Member Data Documentation

loci_

std::vector<std::unique_ptr<LocusInfo> > bpp::AnalyzedLoci::loci_

private

Definition at line 33 of file AnalyzedLoci.h.

Referenced by AnalyzedLoci(), getNumberOfLoci(), and operator=().

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

• Bpp/PopGen/DataSet/AnalyzedLoci.h
• Bpp/PopGen/DataSet/AnalyzedLoci.cpp