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

Collaboration diagram for bpp::Individual:

Public Member Functions
	Individual ()
	Build a void new Individual. More...

	Individual (const std::string &id)
	Build a new Individual with an identifier. More...

	Individual (const std::string &id, const Date &date, const Point2D< double > &coord, std::shared_ptr< Locality< double >> locality, const unsigned short sex)
	Build a new Individual with parameters. More...

	Individual (const Individual &ind)
	The Individual copy constructor. More...

virtual	~Individual ()
	Destroy an Individual. More...

Individual &	operator= (const Individual &ind)
	The Individual copy operator. More...

void	setId (const std::string &id)
	Set the id of the Individual. More...

const std::string &	getId () const
	Get the id of the Individual. More...

void	setSex (const unsigned short sex)
	Set the sex of the Individual. More...

unsigned short	getSex () const
	Get the sex of the Individual. More...

void	setDate (const Date &date)
	Set the date of the Individual. More...

const Date &	date () const
	Get the date of the Individual. More...

bool	hasDate () const
	Tell if this Individual has a date. More...

void	setCoord (const Point2D< double > &coord)
	Set the coordinates of the Individual. More...

void	setCoord (const double x, const double y)
	Set the coordinates of the Individual. More...

const Point2D< double > &	coord () const
	Get the coordinates of the Induvidual. More...

bool	hasCoord () const
	Tell if this Individual has coordinates. More...

void	setX (const double x)
	Set the X coordinate of the Individual. More...

void	setY (const double y)
	Set the Y coordinate of th Individual. More...

double	getX () const
	Get the X coordinate of the Individual. More...

double	getY () const
	Get the Y coordinate of the Individual. More...

void	setLocality (std::shared_ptr< const Locality< double >> locality)
	Set the locality of the Individual. More...

std::shared_ptr< const Locality< double > >	getLocality () const
	Get the locality of the Individual. More...

const Locality< double > &	locality () const
	Get the locality of the Individual. More...

bool	hasLocality () const
	Tell if this Individual has a locality. More...

void	addSequence (size_t sequenceKey, std::unique_ptr< Sequence > &sequence)
	Add a sequence to the Individual. More...

const Sequence &	sequenceByName (const std::string &sequenceName) const
	Get a sequence from its name. More...

const Sequence &	sequenceAtPosition (size_t sequencePosition) const
	Get a sequence by its position. More...

void	deleteSequenceByName (const std::string &sequenceName)
	Delete a sequence. More...

void	deleteSequenceAtPosition (size_t sequencePosition)
	Delete a sequence. More...

bool	hasSequences () const
	Tell if the Individual has some sequences. More...

bool	hasSequenceAtPosition (size_t position) const
	Tell if the Individual has a sequence at a given position. More...

std::shared_ptr< const Alphabet >	getSequenceAlphabet () const
	Return the alphabet of the sequences. More...

const Alphabet &	sequenceAlphabet () const
	Return the alphabet of the sequences. More...

std::vector< std::string >	getSequenceNames () const
	Get the sequence names. More...

std::vector< size_t >	getSequencePositions () const
	Get the sequences' positions. More...

size_t	getSequencePosition (const std::string &sequenceKey) const
	Get the position of a sequence. More...

size_t	getNumberOfSequences () const
	Get the number of sequences. More...

void	setSequences (const SequenceContainerInterface &sc)
	Set all the sequences with a SequenceContainer. The container will be copied. More...

const SequenceContainerInterface &	sequences () const
	Get a reference to the sequence container. More...

void	setGenotype (const MultilocusGenotype &genotype)
	Set a genotype. More...

void	initGenotype (size_t lociNumber)
	Init the genotype. More...

const MultilocusGenotype &	getGenotype () const
	Get the genotype. More...

void	deleteGenotype ()
	Delete the genotype of the individual. More...

bool	hasGenotype () const
	Tell if the Individual has a MultilocusGenotype. More...

void	setMonolocusGenotype (size_t locusPosition, const MonolocusGenotypeInterface &monogen)
	Set a MonolocusGenotype. More...

void	setMonolocusGenotypeByAlleleKey (size_t locusPosition, const std::vector< size_t > alleleKeys)
	Set a MonolocusGenotype. More...

void	setMonolocusGenotypeByAlleleId (size_t locusPosition, const std::vector< std::string > alleleId, const LocusInfo &locusInfo)
	Set a MonolocusGenotype. More...

const MonolocusGenotypeInterface &	getMonolocusGenotype (size_t locusPosition)
	Get a MonolocusGenotype. More...

size_t	countNonMissingLoci () const
	Count the number of non missing MonolocusGenotype. More...

size_t	countHomozygousLoci () const
	Count the number of homozygous MonolocusGenotype. More...

size_t	countHeterozygousLoci () const
	Count the number of heterozygous MonolocusGenotype. More...

Protected Attributes
std::string	id_

unsigned short	sex_

std::unique_ptr< Date >	date_

std::unique_ptr< Point2D< double > >	coord_

std::shared_ptr< const Locality< double > >	locality_

std::unique_ptr< VectorSequenceContainer >	sequences_

std::unique_ptr< MultilocusGenotype >	genotype_

Detailed Description

The Individual class.

This class is designed to store data on a single individual. This individual has only one sequence for each locus ... no information about diploid sequence data. See the no more in use MultiSeqIndividual documentation for an alternative.

Author: Sylvain Gaillard

Definition at line 39 of file Individual.h.

Constructor & Destructor Documentation

◆ Individual() [1/4]

Individual::Individual ( )

Build a void new Individual.

Definition at line 12 of file Individual.cpp.

◆ Individual() [2/4]

Individual::Individual ( const std::string & id )

Build a new Individual with an identifier.

Definition at line 21 of file Individual.cpp.

◆ Individual() [3/4]

Individual::Individual	(	const std::string &	id,
		const Date &	date,
		const Point2D< double > &	coord,
		std::shared_ptr< Locality< double >>	locality,
		const unsigned short	sex
	)

Build a new Individual with parameters.

Parameters

id	The id of the Individual as a string.
date	The date of the Individual as a Date object.
coord	The coordinates of the Individual as a Point2D object.
locality	The locality of the Individual as a pointer to a Locality object.
sex	The sex of the Individual as an unsigned short.

Definition at line 29 of file Individual.cpp.

◆ Individual() [4/4]

Individual::Individual ( const Individual & ind )

The Individual copy constructor.

Definition at line 42 of file Individual.cpp.

References coord(), date(), genotype_, getGenotype(), hasGenotype(), sequences(), setCoord(), setDate(), and setSequences().

◆ ~Individual()

Individual::~Individual ( )

virtual

Destroy an Individual.

Definition at line 74 of file Individual.cpp.

Member Function Documentation

◆ addSequence()

void Individual::addSequence	(	size_t	sequenceKey,
		std::unique_ptr< Sequence > &	sequence
	)

Add a sequence to the Individual.

Creates the sequence container when adding the first sequence. Otherwise add the sequence to the end of the sequence container.

Parameters

sequenceKey	the place where the sequence will be put.
sequence	The sequence to add.

Exceptions

AlphabetMismatchException	if the sequence's alphabet doesn't match the container's alphabet.
BadIdentifierException	if sequence's name is already in use.
BadIntegerException	if sequence_position is already in use.

Definition at line 254 of file Individual.cpp.

References bpp::AlphabetMismatchException::getFirstAlphabet(), bpp::AlphabetMismatchException::getSecondAlphabet(), sequences_, bpp::TextTools::toString(), and bpp::Exception::what().

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

◆ coord()

const Point2D< double > & Individual::coord ( ) const

Get the coordinates of the Induvidual.

Returns: A pointer toward a Point2D object if the Individual has coordinates. Otherwise throw a NullPointerException.

Definition at line 176 of file Individual.cpp.

References coord_, and hasCoord().

Referenced by Individual(), operator=(), and setCoord().

◆ countHeterozygousLoci()

size_t Individual::countHeterozygousLoci ( ) const

Count the number of heterozygous MonolocusGenotype.

Exceptions

NullPointerException if there is no genotype defined.

Definition at line 556 of file Individual.cpp.

References genotype_, and hasGenotype().

◆ countHomozygousLoci()

size_t Individual::countHomozygousLoci ( ) const

Count the number of homozygous MonolocusGenotype.

Exceptions

NullPointerException if there is no genotype defined.

Definition at line 547 of file Individual.cpp.

References genotype_, and hasGenotype().

◆ countNonMissingLoci()

size_t Individual::countNonMissingLoci ( ) const

Count the number of non missing MonolocusGenotype.

Exceptions

NullPointerException if there is no genotype defined.

Definition at line 538 of file Individual.cpp.

References genotype_, and hasGenotype().

◆ date()

const Date & Individual::date ( ) const

Get the date of the Individual.

Returns: A reference toward a Date object if the Individual has a date. Otherwise throw a NullPointerException.

Definition at line 144 of file Individual.cpp.

References date_, and hasDate().

Referenced by Individual(), operator=(), and setDate().

◆ deleteGenotype()

void Individual::deleteGenotype ( )

Delete the genotype of the individual.

Definition at line 450 of file Individual.cpp.

References genotype_.

◆ deleteSequenceAtPosition()

void Individual::deleteSequenceAtPosition ( size_t sequencePosition )

Delete a sequence.

Parameters

sequencePosition The position of the sequence.

Exceptions

NullPointerException	if there is no sequence container defined.
SequenceNotFoundException	if sequence_postion is not found.

Definition at line 328 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId(), sequences_, and bpp::TextTools::toString().

◆ deleteSequenceByName()

void Individual::deleteSequenceByName ( const std::string & sequenceName )

Delete a sequence.

Parameters

sequenceName The name of the sequence.

Exceptions

NullPointerException	if there is no sequence container defined.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 311 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId(), sequences_, and bpp::VectorTools::which().

◆ getGenotype()

const MultilocusGenotype & Individual::getGenotype ( ) const

Get the genotype.

Definition at line 441 of file Individual.cpp.

References genotype_, and hasGenotype().

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

◆ getId()

const std::string& bpp::Individual::getId ( ) const

inline

Get the id of the Individual.

Returns: The id of the Individual as a string.

Definition at line 110 of file Individual.h.

References id_.

Referenced by bpp::Group::addIndividual(), operator=(), bpp::PopgenlibIO::parseIndividual_(), bpp::DarwinDon::write(), and bpp::PopgenlibIO::write().

◆ getLocality()

shared_ptr< const Locality< double > > Individual::getLocality ( ) const

Get the locality of the Individual.

Returns: A pointer to the Locality of the Individual.

Definition at line 233 of file Individual.cpp.

References hasLocality(), and locality_.

Referenced by operator=().

◆ getMonolocusGenotype()

const MonolocusGenotypeInterface & Individual::getMonolocusGenotype ( size_t locusPosition )

Get a MonolocusGenotype.

Exceptions

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locusPosition exceeds the number of loci.

Definition at line 522 of file Individual.cpp.

References genotype_, bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), and hasGenotype().

◆ getNumberOfSequences()

size_t bpp::Individual::getNumberOfSequences ( ) const

inline

Get the number of sequences.

Definition at line 353 of file Individual.h.

References sequences_.

Referenced by hasSequences().

◆ getSequenceAlphabet()

shared_ptr< const Alphabet > Individual::getSequenceAlphabet ( ) const

Return the alphabet of the sequences.

Exceptions

NullPointerException if there is no sequence container defined.

Definition at line 398 of file Individual.cpp.

References sequences_.

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

◆ getSequenceNames()

std::vector<std::string> bpp::Individual::getSequenceNames ( ) const

inline

Get the sequence names.

Returns: All the sequences' names of the individual in a vector of string.

Exceptions

NullPointerException if there is no sequence container defined.

Definition at line 327 of file Individual.h.

References sequences_.

◆ getSequencePosition()

size_t Individual::getSequencePosition ( const std::string & sequenceKey ) const

Get the position of a sequence.

Exceptions

NullPointerException	if there is no sequence container defined.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 359 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId(), and sequences_.

◆ getSequencePositions()

std::vector< size_t > Individual::getSequencePositions ( ) const

Get the sequences' positions.

Returns: All the positions where a sequence is found.

Exceptions

NullPointerException if there is no sequence container defined.

Definition at line 344 of file Individual.cpp.

References sequences_, and bpp::TextTools::toInt().

Referenced by hasSequenceAtPosition().

◆ getSex()

unsigned short bpp::Individual::getSex ( ) const

inline

Get the sex of the Individual.

Returns: The sex of the Individual as an unsigned short.

Definition at line 124 of file Individual.h.

References sex_.

Referenced by operator=().

◆ getX()

double Individual::getX ( ) const

Get the X coordinate of the Individual.

Returns: The X coordinate as a double if the Individual has coordinates. Otherwise throw a NullPointerException.

Definition at line 213 of file Individual.cpp.

References coord_, and hasCoord().

◆ getY()

double Individual::getY ( ) const

Get the Y coordinate of the Individual.

Returns: The Y coordinate as a double if the Individual has coordinates. Otherwise throw a NullPointerException.

Definition at line 223 of file Individual.cpp.

References coord_, and hasCoord().

◆ hasCoord()

bool Individual::hasCoord ( ) const

Tell if this Individual has coordinates.

Definition at line 186 of file Individual.cpp.

References coord_.

Referenced by coord(), getX(), getY(), setX(), and setY().

◆ hasDate()

bool Individual::hasDate ( ) const

Tell if this Individual has a date.

Definition at line 154 of file Individual.cpp.

References date_.

Referenced by date().

◆ hasGenotype()

bool Individual::hasGenotype ( ) const

Tell if the Individual has a MultilocusGenotype.

Definition at line 457 of file Individual.cpp.

References genotype_.

Referenced by countHeterozygousLoci(), countHomozygousLoci(), countNonMissingLoci(), getGenotype(), getMonolocusGenotype(), Individual(), initGenotype(), operator=(), setMonolocusGenotype(), setMonolocusGenotypeByAlleleId(), and setMonolocusGenotypeByAlleleKey().

◆ hasLocality()

bool bpp::Individual::hasLocality ( ) const

inline

Tell if this Individual has a locality.

Definition at line 237 of file Individual.h.

References locality_.

Referenced by getLocality(), and locality().

◆ hasSequenceAtPosition()

bool Individual::hasSequenceAtPosition ( size_t position ) const

Tell if the Individual has a sequence at a given position.

Definition at line 382 of file Individual.cpp.

References getSequencePositions(), and hasSequences().

◆ hasSequences()

bool Individual::hasSequences ( ) const

Tell if the Individual has some sequences.

Returns: TRUE if the individual has at least one sequence.; FALSE if the container is empty or undifined.

Definition at line 375 of file Individual.cpp.

References getNumberOfSequences().

Referenced by bpp::DataSet::addIndividualToGroup(), and hasSequenceAtPosition().

◆ initGenotype()

void Individual::initGenotype ( size_t lociNumber )

Init the genotype.

Exceptions

Exception	if the Individual already has a Genotype.
BadIntegerException	if loci_number < 1.

Definition at line 425 of file Individual.cpp.

References genotype_, bpp::BadIntegerException::getBadInteger(), and hasGenotype().

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

◆ locality()

const Locality< double > & Individual::locality ( ) const

Get the locality of the Individual.

Returns: A pointer to the Locality of the Individual.

Definition at line 243 of file Individual.cpp.

References hasLocality(), and locality_.

Referenced by setLocality().

◆ operator=()

Individual & Individual::operator= ( const Individual & ind )

The Individual copy operator.

Returns: A ref toward the assigned Individual. Make a copy of each attribute of the Individual.

Definition at line 78 of file Individual.cpp.

References coord(), coord_, date(), date_, genotype_, getGenotype(), getId(), getLocality(), getSex(), hasGenotype(), locality_, sequences(), sequences_, setCoord(), setDate(), setId(), setLocality(), setSequences(), and setSex().

◆ sequenceAlphabet()

const Alphabet & Individual::sequenceAlphabet ( ) const

Return the alphabet of the sequences.

Exceptions

NullPointerException if there is no sequence container defined.

Definition at line 407 of file Individual.cpp.

References sequences_.

◆ sequenceAtPosition()

const Sequence & Individual::sequenceAtPosition ( size_t sequencePosition ) const

Get a sequence by its position.

Parameters

sequencePosition The position of the sequence in the sequence set.

Returns: A reference to the sequence.

Exceptions

NullPointerException	if there is no sequence container defined.
SequenceNotFoundException	if sequence_position is not found (i.e. missing data or not used).

Definition at line 295 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId(), sequences_, and bpp::TextTools::toString().

◆ sequenceByName()

const Sequence & Individual::sequenceByName ( const std::string & sequenceName ) const

Get a sequence from its name.

Parameters

sequenceName The name of the sequence.

Returns: A reference to the sequence.

Exceptions

NullPointerException	if there is no sequence container defined.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 278 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId(), sequences_, and bpp::VectorTools::which().

◆ sequences()

const SequenceContainerInterface& bpp::Individual::sequences ( ) const

inline

Get a reference to the sequence container.

Exceptions

NullPointerException if there is no sequence container defined.

Definition at line 372 of file Individual.h.

References sequences_.

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

◆ setCoord() [1/2]

void Individual::setCoord	(	const double	x,
		const double	y
	)

Set the coordinates of the Individual.

Parameters

x	The X coordinate as a double.
y	The Y coordinate as a double.

Definition at line 169 of file Individual.cpp.

References coord_.

◆ setCoord() [2/2]

void Individual::setCoord ( const Point2D< double > & coord )

Set the coordinates of the Individual.

Parameters

coord A Point2D object.

Definition at line 162 of file Individual.cpp.

References coord(), and coord_.

Referenced by Individual(), operator=(), and bpp::PopgenlibIO::parseIndividual_().

◆ setDate()

void Individual::setDate ( const Date & date )

Set the date of the Individual.

Parameters

date	The date as a Date object.

Definition at line 137 of file Individual.cpp.

References date(), and date_.

Referenced by Individual(), operator=(), and bpp::PopgenlibIO::parseIndividual_().

◆ setGenotype()

void Individual::setGenotype ( const MultilocusGenotype & genotype )

Set a genotype.

Parameters

genotype The MultilocusGenotype which will be copied.

Definition at line 418 of file Individual.cpp.

References genotype_.

◆ setId()

void Individual::setId ( const std::string & id )

Set the id of the Individual.

Parameters

id	The id of the Individual as a string.

Definition at line 121 of file Individual.cpp.

References id_.

Referenced by operator=(), and bpp::PopgenlibIO::parseIndividual_().

◆ setLocality()

void bpp::Individual::setLocality ( std::shared_ptr< const Locality< double >> locality )

inline

Set the locality of the Individual.

Parameters

locality A pointer to a Locality object.

Definition at line 215 of file Individual.h.

References locality(), and locality_.

Referenced by operator=(), and bpp::PopgenlibIO::parseIndividual_().

◆ setMonolocusGenotype()

void Individual::setMonolocusGenotype	(	size_t	locusPosition,
		const MonolocusGenotypeInterface &	monogen
	)

Set a MonolocusGenotype.

Exceptions

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locusPosition exceeds the number of loci.

Definition at line 464 of file Individual.cpp.

References genotype_, bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), and hasGenotype().

◆ setMonolocusGenotypeByAlleleId()

void Individual::setMonolocusGenotypeByAlleleId	(	size_t	locusPosition,
		const std::vector< std::string >	alleleId,
		const LocusInfo &	locusInfo
	)

Set a MonolocusGenotype.

Exceptions

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locusPosition exceeds the number of loci.
AlleleNotFoundException	if at least one the id is not found in the LocusInfo.

Definition at line 502 of file Individual.cpp.

References genotype_, bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), bpp::AlleleNotFoundException::getIdentifier(), and hasGenotype().

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

◆ setMonolocusGenotypeByAlleleKey()

void Individual::setMonolocusGenotypeByAlleleKey	(	size_t	locusPosition,
		const std::vector< size_t >	alleleKeys
	)

Set a MonolocusGenotype.

Exceptions

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locusPosition exceeds the number of loci.
Exception	if there is no key in alleleKeys.

Definition at line 482 of file Individual.cpp.

References genotype_, bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), and hasGenotype().

◆ setSequences()

void bpp::Individual::setSequences ( const SequenceContainerInterface & sc )

inline

Set all the sequences with a SequenceContainer. The container will be copied.

Definition at line 362 of file Individual.h.

References sequences_.

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

◆ setSex()

void Individual::setSex ( const unsigned short sex )

Set the sex of the Individual.

Parameters

sex	An unsigned short coding for the sex.

Definition at line 129 of file Individual.cpp.

References sex_.

Referenced by operator=().

◆ setX()

void Individual::setX ( const double x )

Set the X coordinate of the Individual.

Parameters

x	The X coordinate as a double.

Set the X coordinate if the Individual has coordinates. Otherwise throw a NullPointerException.

Definition at line 193 of file Individual.cpp.

References coord_, and hasCoord().

◆ setY()

void Individual::setY ( const double y )

Set the Y coordinate of th Individual.

Parameters

y	The Y coordinate as a double.

Set the Y coordinate if the Individual has coordinates. Otherwise throw a NullPointerException.

Definition at line 203 of file Individual.cpp.

References coord_, and hasCoord().

Member Data Documentation

◆ coord_

std::unique_ptr<Point2D<double> > bpp::Individual::coord_

protected

Definition at line 45 of file Individual.h.

Referenced by coord(), getX(), getY(), hasCoord(), operator=(), setCoord(), setX(), and setY().

◆ date_

std::unique_ptr<Date> bpp::Individual::date_

protected

Definition at line 44 of file Individual.h.

Referenced by date(), hasDate(), operator=(), and setDate().

◆ genotype_

std::unique_ptr<MultilocusGenotype> bpp::Individual::genotype_

protected

Definition at line 48 of file Individual.h.

Referenced by countHeterozygousLoci(), countHomozygousLoci(), countNonMissingLoci(), deleteGenotype(), getGenotype(), getMonolocusGenotype(), hasGenotype(), Individual(), initGenotype(), operator=(), setGenotype(), setMonolocusGenotype(), setMonolocusGenotypeByAlleleId(), and setMonolocusGenotypeByAlleleKey().

◆ id_

std::string bpp::Individual::id_

protected

Definition at line 42 of file Individual.h.

Referenced by getId(), and setId().

◆ locality_

std::shared_ptr<const Locality<double> > bpp::Individual::locality_

protected

Definition at line 46 of file Individual.h.

Referenced by getLocality(), hasLocality(), locality(), operator=(), and setLocality().

◆ sequences_

std::unique_ptr<VectorSequenceContainer> bpp::Individual::sequences_

protected

Definition at line 47 of file Individual.h.

Referenced by addSequence(), deleteSequenceAtPosition(), deleteSequenceByName(), getNumberOfSequences(), getSequenceAlphabet(), getSequenceNames(), getSequencePosition(), getSequencePositions(), operator=(), sequenceAlphabet(), sequenceAtPosition(), sequenceByName(), sequences(), and setSequences().

◆ sex_

unsigned short bpp::Individual::sex_

protected

Definition at line 43 of file Individual.h.

Referenced by getSex(), and setSex().

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

Bpp/PopGen/DataSet/Individual.h
Bpp/PopGen/DataSet/Individual.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Individual() [1/4]

◆ Individual() [2/4]

◆ Individual() [3/4]

◆ Individual() [4/4]

◆ ~Individual()

Member Function Documentation

◆ addSequence()

◆ coord()

◆ countHeterozygousLoci()

◆ countHomozygousLoci()

◆ countNonMissingLoci()

◆ date()

◆ deleteGenotype()

◆ deleteSequenceAtPosition()

◆ deleteSequenceByName()

◆ getGenotype()

◆ getId()

◆ getLocality()

◆ getMonolocusGenotype()

◆ getNumberOfSequences()

◆ getSequenceAlphabet()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSequencePositions()

◆ getSex()

◆ getX()

◆ getY()

◆ hasCoord()

◆ hasDate()

◆ hasGenotype()

◆ hasLocality()

◆ hasSequenceAtPosition()

◆ hasSequences()

◆ initGenotype()

◆ locality()

◆ operator=()

◆ sequenceAlphabet()

◆ sequenceAtPosition()

◆ sequenceByName()

◆ sequences()

◆ setCoord() [1/2]

◆ setCoord() [2/2]

◆ setDate()

◆ setGenotype()

◆ setId()

◆ setLocality()

◆ setMonolocusGenotype()

◆ setMonolocusGenotypeByAlleleId()

◆ setMonolocusGenotypeByAlleleKey()

◆ setSequences()

◆ setSex()

◆ setX()

◆ setY()

Member Data Documentation

◆ coord_

◆ date_

◆ genotype_

◆ id_

◆ locality_

◆ sequences_

◆ sex_