#include <Bpp/PopGen/Individual.h>

Collaboration diagram for bpp::Individual:

Public Member Functions
	Individual ()
	Build a void new Individual.
	Individual (const std::string &id)
	Build a new Individual with an identifier.
	Individual (const std::string &id, const Date &date, const Point2D< double > &coord, Locality< double > *locality, const unsigned short sex)
	Build a new Individual with parameters.
	Individual (const Individual &ind)
	The Individual copy constructor.
virtual	~Individual ()
	Destroy an Individual.
Individual &	operator= (const Individual &ind)
	The Individual copy operator.
void	setId (const std::string &id)
	Set the id of the Individual.
const std::string &	getId () const
	Get the id of the Individual.
void	setSex (const unsigned short sex)
	Set the sex of the Individual.
unsigned short	getSex () const
	Get the sex of the Individual.
void	setDate (const Date &date)
	Set the date of the Individual.
const Date &	getDate () const throw (NullPointerException)
	Get the date of the Individual.
bool	hasDate () const
	Tell if this Individual has a date.
void	setCoord (const Point2D< double > &coord)
	Set the coodinates of the Individual.
void	setCoord (const double x, const double y)
	Set the coordinates of the Individual.
const Point2D< double > &	getCoord () const throw (NullPointerException)
	Get the coordinates of the Induvidual.
bool	hasCoord () const
	Tell if this Individual has coordinates.
void	setX (const double x) throw (NullPointerException)
	Set the X coordinate of the Individual.
void	setY (const double y) throw (NullPointerException)
	Set the Y coordinate of th Individual.
double	getX () const throw (NullPointerException)
	Get the X coordinate of the Individual.
double	getY () const throw (NullPointerException)
	Get the Y coordinate of the Individual.
void	setLocality (const Locality< double > *locality)
	Set the locality of the Individual.
const Locality< double > *	getLocality () const throw (NullPointerException)
	Get the locality of the Individual.
bool	hasLocality () const
	Tell if this Individual has a locality.
void	addSequence (size_t sequence_key, const Sequence &sequence) throw (Exception)
	Add a sequence to the Individual.
const Sequence &	getSequenceByName (const std::string &sequence_name) const throw (Exception)
	Get a sequence by its name.
const Sequence &	getSequenceAtPosition (const size_t sequence_position) const throw (Exception)
	Get a sequence by its position.
void	deleteSequenceByName (const std::string &sequence_name) throw (Exception)
	Delete a sequence.
void	deleteSequenceAtPosition (size_t sequence_position) throw (Exception)
	Delete a sequence.
bool	hasSequences () const
	Tell if the Individual has some sequences.
bool	hasSequenceAtPosition (size_t position) const
	Tell if the Individual has a sequence at a given position.
const Alphabet *	getSequenceAlphabet () const throw (NullPointerException)
	Return the alphabet of the sequences.
std::vector< std::string >	getSequencesNames () const throw (NullPointerException)
	Get the sequences' names.
std::vector< size_t >	getSequencesPositions () const throw (NullPointerException)
	Get the sequences' positions.
size_t	getSequencePosition (const std::string &sequence_name) const throw (Exception)
	Get the position of a sequence.
size_t	getNumberOfSequences () const
	Get the number of sequences.
void	setSequences (const MapSequenceContainer &msc)
	Set all the sequences with a MapSequenceContainer.
const OrderedSequenceContainer &	getSequences () const throw (NullPointerException)
	Get a reference to the sequence container.
void	setGenotype (const MultilocusGenotype &genotype)
	Set a genotype.
void	initGenotype (size_t loci_number) throw (Exception)
	Init the genotype.
const MultilocusGenotype &	getGenotype () const throw (NullPointerException)
	Get the genotype.
void	deleteGenotype ()
	Delete the genotype of the individual.
bool	hasGenotype () const
	Tell if the Individual has a MultilocusGenotype.
void	setMonolocusGenotype (size_t locus_position, const MonolocusGenotype &monogen) throw (Exception)
	Set a MonolocusGenotype.
void	setMonolocusGenotypeByAlleleKey (size_t locus_position, const std::vector< size_t > allele_keys) throw (Exception)
	Set a MonolocusGenotype.
void	setMonolocusGenotypeByAlleleId (size_t locus_position, const std::vector< std::string > allele_id, const LocusInfo &locus_info) throw (Exception)
	Set a MonolocusGenotype.
const MonolocusGenotype &	getMonolocusGenotype (size_t locus_position) throw (Exception)
	Get a MonolocusGenotype.
size_t	countNonMissingLoci () const throw (NullPointerException)
	Count the number of non missing MonolocusGenotype.
size_t	countHomozygousLoci () const throw (NullPointerException)
	Count the number of homozygous MonolocusGenotype.
size_t	countHeterozygousLoci () const throw (NullPointerException)
	Count the number of heterozygous MonolocusGenotype.
Protected Attributes
std::string	id_
unsigned short	sex_
std::auto_ptr< Date >	date_
std::auto_ptr< Point2D< double > >	coord_
const Locality< double > *	locality_
std::auto_ptr < MapSequenceContainer >	sequences_
std::auto_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 75 of file Individual.h.

Constructor & Destructor Documentation

Individual::Individual ( )

Build a void new Individual.

Definition at line 47 of file Individual.cpp.

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

Build a new Individual with an identifier.

Definition at line 55 of file Individual.cpp.

Individual::Individual	(	const std::string &	id,
		const Date &	date,
		const Point2D< double > &	coord,
		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 63 of file Individual.cpp.

Individual::Individual ( const Individual & ind )

The Individual copy constructor.

Definition at line 76 of file Individual.cpp.

References genotype_, getCoord(), getDate(), getGenotype(), getLocality(), getSequences(), hasGenotype(), setCoord(), setDate(), setLocality(), and setSequences().

Individual::~Individual ( ) [virtual]

Destroy an Individual.

Definition at line 113 of file Individual.cpp.

Member Function Documentation

void Individual::addSequence	(	size_t	sequence_key,
		const Sequence &	sequence
	)		throw (Exception)

Add a sequence to the Individual.

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

Parameters:

sequence_key	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 298 of file Individual.cpp.

References bpp::AlphabetMismatchException::getAlphabets(), bpp::TextTools::toString(), and bpp::Exception::what().

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

size_t Individual::countHeterozygousLoci ( ) const throw (NullPointerException)

Count the number of heterozygous MonolocusGenotype.

Exceptions:

NullPointerException if there is no genotype defined.

Definition at line 624 of file Individual.cpp.

References genotype_, and hasGenotype().

size_t Individual::countHomozygousLoci ( ) const throw (NullPointerException)

Count the number of homozygous MonolocusGenotype.

Exceptions:

NullPointerException if there is no genotype defined.

Definition at line 615 of file Individual.cpp.

References genotype_, and hasGenotype().

size_t Individual::countNonMissingLoci ( ) const throw (NullPointerException)

Count the number of non missing MonolocusGenotype.

Exceptions:

NullPointerException if there is no genotype defined.

Definition at line 606 of file Individual.cpp.

References genotype_, and hasGenotype().

void Individual::deleteGenotype ( )

Delete the genotype of the individual.

Definition at line 520 of file Individual.cpp.

References genotype_.

void Individual::deleteSequenceAtPosition ( size_t sequence_position ) throw (Exception)

Delete a sequence.

Parameters:

sequence_position The position of the sequence.

Exceptions:

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

Definition at line 373 of file Individual.cpp.

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

void Individual::deleteSequenceByName ( const std::string & sequence_name ) throw (Exception)

Delete a sequence.

Parameters:

sequence_name The name of the sequence.

Exceptions:

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

Definition at line 357 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

const Point2D< double > & Individual::getCoord ( ) const throw (NullPointerException)

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 215 of file Individual.cpp.

References coord_, and hasCoord().

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

const Date & Individual::getDate ( ) const throw (NullPointerException)

Get the date of the Individual.

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

Definition at line 183 of file Individual.cpp.

References date_, and hasDate().

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

const MultilocusGenotype & Individual::getGenotype ( ) const throw (NullPointerException)

Get the genotype.

Definition at line 511 of file Individual.cpp.

References genotype_, and hasGenotype().

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

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 146 of file Individual.h.

References id_.

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

const Locality< double > * Individual::getLocality ( ) const throw (NullPointerException)

Get the locality of the Individual.

Returns:: A pointer to the Locality of the Individual.

Definition at line 280 of file Individual.cpp.

References hasLocality(), and locality_.

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

const MonolocusGenotype & Individual::getMonolocusGenotype ( size_t locus_position ) throw (Exception)

Get a MonolocusGenotype.

Exceptions:

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locus_position excedes the number of loci.

Definition at line 590 of file Individual.cpp.

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

size_t Individual::getNumberOfSequences ( ) const

Get the number of sequences.

Definition at line 461 of file Individual.cpp.

References sequences_.

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

const Alphabet * Individual::getSequenceAlphabet ( ) const throw (NullPointerException)

Return the alphabet of the sequences.

Exceptions:

NullPointerException if there is no sequence container defined.

Definition at line 452 of file Individual.cpp.

References sequences_.

const Sequence & Individual::getSequenceAtPosition ( const size_t sequence_position ) const throw (Exception)

Get a sequence by its position.

Parameters:

sequence_position 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 340 of file Individual.cpp.

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

Referenced by bpp::DataSet::getPolymorphismSequenceContainer(), and bpp::PopgenlibIO::write().

const Sequence & Individual::getSequenceByName ( const std::string & sequence_name ) const throw (Exception)

Get a sequence by its name.

Parameters:

sequence_name 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 323 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

size_t Individual::getSequencePosition ( const std::string & sequence_name ) const throw (Exception)

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 413 of file Individual.cpp.

References bpp::SequenceNotFoundException::getSequenceId(), and bpp::TextTools::toInt().

const OrderedSequenceContainer & Individual::getSequences ( ) const throw (NullPointerException)

Get a reference to the sequence container.

Exceptions:

NullPointerException if there is no sequence container defined.

Definition at line 477 of file Individual.cpp.

References sequences_.

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

std::vector< std::string > Individual::getSequencesNames ( ) const throw (NullPointerException)

Get the sequences' 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 389 of file Individual.cpp.

References sequences_.

std::vector< size_t > Individual::getSequencesPositions ( ) const throw (NullPointerException)

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 398 of file Individual.cpp.

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

Referenced by hasSequenceAtPosition().

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 160 of file Individual.h.

References sex_.

Referenced by operator=().

double Individual::getX ( ) const throw (NullPointerException)

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 252 of file Individual.cpp.

References coord_, and hasCoord().

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

double Individual::getY ( ) const throw (NullPointerException)

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 262 of file Individual.cpp.

References coord_, and hasCoord().

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

bool Individual::hasCoord ( ) const

Tell if this Individual has coordinates.

Definition at line 225 of file Individual.cpp.

References coord_.

Referenced by getCoord(), getX(), getY(), and bpp::PopgenlibIO::write().

bool Individual::hasDate ( ) const

Tell if this Individual has a date.

Definition at line 193 of file Individual.cpp.

References date_.

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

bool Individual::hasGenotype ( ) const

Tell if the Individual has a MultilocusGenotype.

Definition at line 527 of file Individual.cpp.

References genotype_.

Referenced by countHeterozygousLoci(), countHomozygousLoci(), countNonMissingLoci(), getGenotype(), bpp::DataSet::getPolymorphismMultiGContainer(), Individual(), operator=(), and bpp::PopgenlibIO::write().

bool Individual::hasLocality ( ) const

Tell if this Individual has a locality.

Definition at line 290 of file Individual.cpp.

References locality_.

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

bool Individual::hasSequenceAtPosition ( size_t position ) const

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

Definition at line 436 of file Individual.cpp.

References getSequencesPositions(), and hasSequences().

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

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 429 of file Individual.cpp.

References getNumberOfSequences().

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

void Individual::initGenotype ( size_t loci_number ) throw (Exception)

Init the genotype.

Exceptions:

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

Definition at line 495 of file Individual.cpp.

References bpp::BadIntegerException::getBadInteger().

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

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

The Individual copy operator.

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

Definition at line 117 of file Individual.cpp.

References coord_, date_, genotype_, getCoord(), getDate(), getGenotype(), getId(), getLocality(), getSequences(), getSex(), hasGenotype(), locality_, sequences_, setCoord(), setDate(), setId(), setLocality(), setSequences(), and setSex().

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

Set the coodinates of the Individual.

Parameters:

coord A Point2D object.

Definition at line 201 of file Individual.cpp.

References coord_.

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

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 208 of file Individual.cpp.

References coord_.

void Individual::setDate ( const Date & date )

Set the date of the Individual.

Parameters:

date	The date as a Date object.

Definition at line 176 of file Individual.cpp.

References date_.

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

void Individual::setGenotype ( const MultilocusGenotype & genotype )

Set a genotype.

Parameters:

genotype The MultilocusGenotype which will be copied.

Definition at line 488 of file Individual.cpp.

References genotype_.

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 160 of file Individual.cpp.

References id_.

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

void Individual::setLocality ( const Locality< double > * locality )

Set the locality of the Individual.

Parameters:

locality A pointer to a Locality object.

Definition at line 273 of file Individual.cpp.

References locality_.

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

void Individual::setMonolocusGenotype	(	size_t	locus_position,
		const MonolocusGenotype &	monogen
	)		throw (Exception)

Set a MonolocusGenotype.

Exceptions:

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locus_position excedes the number of loci.

Definition at line 534 of file Individual.cpp.

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

void Individual::setMonolocusGenotypeByAlleleId	(	size_t	locus_position,
		const std::vector< std::string >	allele_id,
		const LocusInfo &	locus_info
	)		throw (Exception)

Set a MonolocusGenotype.

Exceptions:

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

Definition at line 570 of file Individual.cpp.

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

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

void Individual::setMonolocusGenotypeByAlleleKey	(	size_t	locus_position,
		const std::vector< size_t >	allele_keys
	)		throw (Exception)

Set a MonolocusGenotype.

Exceptions:

NullPointerException	if there is no genotype defined.
IndexOutOfBoundsException	if locus_position excedes the number of loci.
Exception	if there is no key in allele_keys.

Definition at line 550 of file Individual.cpp.

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

void Individual::setSequences ( const MapSequenceContainer & msc )

Set all the sequences with a MapSequenceContainer.

Definition at line 470 of file Individual.cpp.

References sequences_.

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

void Individual::setSex ( const unsigned short sex )

Set the sex of the Individual.

Parameters: