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

Collaboration diagram for bpp::AnalyzedLoci:

Public Member Functions
	AnalyzedLoci (size_t number_of_loci)
	Build a void AnalyzedLoci with a specific number of loci. More...

	AnalyzedLoci (const AnalyzedLoci &analyzed_loci)
	Copy constructor. More...

	~AnalyzedLoci ()
	Destroy the AnalyzedLoci. More...

void	setLocusInfo (size_t locus_position, const LocusInfo &locus)
	Set a LocusInfo. More...

size_t	getLocusInfoPosition (const std::string &locus_name) const
	Get the position of a LocusInfo. More...

const LocusInfo &	getLocusInfoByName (const std::string &locus_name) const
	Get a LocusInfo by name. More...

const LocusInfo &	getLocusInfoAtPosition (size_t locus_position) const
	Get a LocusInfo by its position. More...

void	addAlleleInfoByLocusName (const std::string &locus_name, const AlleleInfo &allele)
	Add an AlleleInfo to a LocusInfo by LocusInfo name. More...

void	addAlleleInfoByLocusPosition (size_t locus_position, 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 &locus_name) const
	Get the ploidy of a locus by name. More...

unsigned int	getPloidyByLocusPosition (size_t locus_position) const
	Get the ploidy of a locus by its position. More...

Private Attributes
std::vector< LocusInfo * >	loci_

Detailed Description

The AnalyzedLoci class.

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

Author: Sylvain Gaillard

Definition at line 64 of file AnalyzedLoci.h.

Constructor & Destructor Documentation

◆ AnalyzedLoci() [1/2]

AnalyzedLoci::AnalyzedLoci ( size_t number_of_loci )

Build a void AnalyzedLoci with a specific number of loci.

Definition at line 47 of file AnalyzedLoci.cpp.

References loci_.

◆ AnalyzedLoci() [2/2]

AnalyzedLoci::AnalyzedLoci ( const AnalyzedLoci & analyzed_loci )

Copy constructor.

Definition at line 57 of file AnalyzedLoci.cpp.

References getLocusInfoAtPosition(), getNumberOfLoci(), and loci_.

◆ ~AnalyzedLoci()

AnalyzedLoci::~AnalyzedLoci ( )

Destroy the AnalyzedLoci.

Definition at line 67 of file AnalyzedLoci.cpp.

References loci_.

Member Function Documentation

◆ addAlleleInfoByLocusName()

void AnalyzedLoci::addAlleleInfoByLocusName	(	const std::string &	locus_name,
		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 131 of file AnalyzedLoci.cpp.

References bpp::BadIdentifierException::getIdentifier(), and loci_.

Referenced by bpp::DataSet::addAlleleInfoByLocusName(), and bpp::GeneMapperCsvExport::read().

◆ addAlleleInfoByLocusPosition()

void AnalyzedLoci::addAlleleInfoByLocusPosition	(	size_t	locus_position,
		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 157 of file AnalyzedLoci.cpp.

References bpp::BadIdentifierException::getIdentifier(), and loci_.

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

◆ getLocusInfoAtPosition()

const LocusInfo & AnalyzedLoci::getLocusInfoAtPosition ( size_t locus_position ) const

Get a LocusInfo by its position.

Exceptions

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

Definition at line 117 of file AnalyzedLoci.cpp.

References loci_.

Referenced by AnalyzedLoci(), and bpp::DataSet::getLocusInfoAtPosition().

◆ getLocusInfoByName()

const LocusInfo & AnalyzedLoci::getLocusInfoByName ( const std::string & locus_name ) const

Get a LocusInfo by name.

Exceptions

BadIdentifierException if locus_name is not found.

Definition at line 103 of file AnalyzedLoci.cpp.

References loci_.

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

◆ getLocusInfoPosition()

size_t AnalyzedLoci::getLocusInfoPosition ( const std::string & locus_name ) const

Get the position of a LocusInfo.

Exceptions

BadIdentifierException if locus_name is not found.

Definition at line 90 of file AnalyzedLoci.cpp.

References loci_.

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

◆ getNumberOfAlleles()

std::vector< size_t > AnalyzedLoci::getNumberOfAlleles ( ) const

Get the number of alleles at each locus.

Definition at line 178 of file AnalyzedLoci.cpp.

References loci_.

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

◆ getNumberOfLoci()

size_t bpp::AnalyzedLoci::getNumberOfLoci ( ) const

inline

Get the number of loci.

Definition at line 138 of file AnalyzedLoci.h.

References loci_.

Referenced by AnalyzedLoci(), bpp::DataSet::getNumberOfLoci(), and bpp::DataSet::setLocusInfo().

◆ getPloidyByLocusName()

unsigned int AnalyzedLoci::getPloidyByLocusName ( const std::string & locus_name ) const

Get the ploidy of a locus by name.

Exceptions

LocusNotFoundException if locus_name is not found.

Definition at line 190 of file AnalyzedLoci.cpp.

References loci_.

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

◆ getPloidyByLocusPosition()

unsigned int AnalyzedLoci::getPloidyByLocusPosition ( size_t locus_position ) const

Get the ploidy of a locus by its position.

Exceptions

IndexOutOfBoundsException if locus_position is out of bounds.

Definition at line 203 of file AnalyzedLoci.cpp.

References loci_.

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

◆ setLocusInfo()

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

Set a LocusInfo.

Exceptions

IndexOutOfBoundsException if locus_position is out of bounds.

Definition at line 77 of file AnalyzedLoci.cpp.

References loci_.

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

Member Data Documentation

◆ loci_

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

private

Definition at line 67 of file AnalyzedLoci.h.

Referenced by addAlleleInfoByLocusName(), addAlleleInfoByLocusPosition(), AnalyzedLoci(), getLocusInfoAtPosition(), getLocusInfoByName(), getLocusInfoPosition(), getNumberOfAlleles(), getNumberOfLoci(), getPloidyByLocusName(), getPloidyByLocusPosition(), setLocusInfo(), and ~AnalyzedLoci().

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

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AnalyzedLoci() [1/2]

◆ AnalyzedLoci() [2/2]

◆ ~AnalyzedLoci()

Member Function Documentation

◆ addAlleleInfoByLocusName()

◆ addAlleleInfoByLocusPosition()

◆ getLocusInfoAtPosition()

◆ getLocusInfoByName()

◆ getLocusInfoPosition()

◆ getNumberOfAlleles()

◆ getNumberOfLoci()

◆ getPloidyByLocusName()

◆ getPloidyByLocusPosition()

◆ setLocusInfo()

Member Data Documentation

◆ loci_