bpp::AnalyzedLoci Class Reference

The AnalyzedLoci class. More...

#include <Bpp/PopGen/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) throw (IndexOutOfBoundsException)
	Set a LocusInfo. More...
size_t	getLocusInfoPosition (const std::string &locus_name) const throw (BadIdentifierException)
	Get the position of a LocusInfo. More...
const LocusInfo &	getLocusInfoByName (const std::string &locus_name) const throw (BadIdentifierException)
	Get a LocusInfo by name. More...
const LocusInfo &	getLocusInfoAtPosition (size_t locus_position) const throw (Exception)
	Get a LocusInfo by its position. More...
void	addAlleleInfoByLocusName (const std::string &locus_name, const AlleleInfo &allele) throw (Exception)
	Add an AlleleInfo to a LocusInfo by LocusInfo name. More...
void	addAlleleInfoByLocusPosition (size_t locus_position, const AlleleInfo &allele) throw (Exception)
	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 throw (LocusNotFoundException)
	Get the ploidy of a locus by name. More...
unsigned int	getPloidyByLocusPosition (size_t locus_position) const throw (IndexOutOfBoundsException)
	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
	)
throw	(	Exception
	)

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 135 of file AnalyzedLoci.cpp.

References bpp::BadIdentifierException::getIdentifier().

addAlleleInfoByLocusPosition()

void AnalyzedLoci::addAlleleInfoByLocusPosition	(	size_t	locus_position,
		const AlleleInfo &	allele
	)
throw	(	Exception
	)

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 162 of file AnalyzedLoci.cpp.

References bpp::BadIdentifierException::getIdentifier().

getLocusInfoAtPosition()

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

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 120 of file AnalyzedLoci.cpp.

Referenced by AnalyzedLoci().

getLocusInfoByName()

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

Get a LocusInfo by name.

Exceptions

BadIdentifierException

if locus_name is not found.

Definition at line 105 of file AnalyzedLoci.cpp.

getLocusInfoPosition()

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

Get the position of a LocusInfo.

Exceptions

BadIdentifierException

if locus_name is not found.

Definition at line 91 of file AnalyzedLoci.cpp.

getNumberOfAlleles()

std::vector< size_t > AnalyzedLoci::getNumberOfAlleles

(

)

const

Get the number of alleles at each locus.

Definition at line 184 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 144 of file AnalyzedLoci.h.

References loci_.

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

getPloidyByLocusName()

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

Get the ploidy of a locus by name.

Exceptions

LocusNotFoundException

if locus_name is not found.

Definition at line 196 of file AnalyzedLoci.cpp.

getPloidyByLocusPosition()

unsigned int AnalyzedLoci::getPloidyByLocusPosition	(	size_t	locus_position	)	const
throw	(	IndexOutOfBoundsException
	)

Get the ploidy of a locus by its position.

Exceptions

IndexOutOfBoundsException

if locus_position is out of bounds.

Definition at line 210 of file AnalyzedLoci.cpp.

setLocusInfo()

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

Set a LocusInfo.

Exceptions

IndexOutOfBoundsException

if locus_position is out of bounds.

Definition at line 77 of file AnalyzedLoci.cpp.

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

Member Data Documentation

loci_

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

private

Definition at line 67 of file AnalyzedLoci.h.

Referenced by AnalyzedLoci(), getNumberOfAlleles(), getNumberOfLoci(), and ~AnalyzedLoci().

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

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