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

Collaboration diagram for bpp::Group:

Public Member Functions
	Group (size_t group_id)
	Build a void new Group. More...

	Group (const Group &group)
	Copy constructor. More...

	Group (const Group &group, size_t group_id)
	A duplication constructor with new Group Id. More...

	~Group ()
	Destroy an Group. More...

Group &	operator= (const Group &group)
	The assignation operator =. More...

void	setGroupId (size_t group_id)
	Set the id of the Group. More...

const std::string &	getGroupName () const
	Get the name of the Group. More...

void	setGroupName (const std::string &group_name)
	Set the name of the Group. More...

size_t	getGroupId () const
	Get the id of the Group. More...

void	addIndividual (const Individual &ind)
	Add an Individual. More...

void	addEmptyIndividual (const std::string &individual_id)
	Add an empty Individual to the Group. More...

size_t	getNumberOfIndividuals () const
	Get the number of Individual in the Group. More...

size_t	getMaxNumberOfSequences () const
	Get the maximum number of sequence. More...

size_t	getIndividualPosition (const std::string &individual_id) const
	Get the position of an Individual. More...

const Individual &	getIndividualById (const std::string &individual_id) const
	Get a reference to an Individual. More...

const Individual &	getIndividualAtPosition (size_t individual_position) const
	Get a reference to an Individual by its position. More...

std::unique_ptr< Individual >	removeIndividualById (const std::string &individual_id)
	Remove an Individual from the Group. More...

std::unique_ptr< Individual >	removeIndividualAtPosition (size_t individual_position)
	Remove an Individual from the Group. More...

void	deleteIndividualById (const std::string &individual_id)
	Delete an Individual from the Group. More...

void	deleteIndividualAtPosition (size_t individual_position)
	Delete an Individual from the Group. More...

void	clear ()
	Clear the Group. More...

void	setIndividualSexAtPosition (size_t individual_position, const unsigned short sex)
	Set the sex of an Individual. More...

unsigned short	getIndividualSexAtPosition (size_t individual_position) const
	Get the sex of an Individual. More...

void	setIndividualDateAtPosition (size_t individual_position, const Date &date)
	Set the date of an Individual. More...

const Date &	getIndividualDateAtPosition (size_t individual_position) const
	Get the date of an Individual. More...

void	setIndividualCoordAtPosition (size_t individual_position, const Point2D< double > &coord)
	Set the coordinates of an Individual. More...

const Point2D< double > &	getIndividualCoordAtPosition (size_t individual_position) const
	Get the coordinates of an Individual. More...

void	setIndividualLocalityAtPosition (size_t individual_position, const Locality< double > *locality)
	Set the locality of an Individual. More...

const Locality< double > &	getIndividualLocalityAtPosition (size_t individual_position) const
	Get the locality of an Individual. More...

void	addIndividualSequenceAtPosition (size_t individual_position, size_t sequence_position, const Sequence &sequence)
	Add a sequence to an Individual. More...

const Sequence &	getIndividualSequenceByName (size_t individual_position, const std::string &sequence_name) const
	Get a sequence of an Individual. More...

const Sequence &	getIndividualSequenceAtPosition (size_t individual_position, size_t sequence_position) const
	Get a sequence of an Individual. More...

void	deleteIndividualSequenceByName (size_t individual_position, const std::string &sequence_name)
	Delete a sequence of an Individual. More...

void	deleteIndividualSequenceAtPosition (size_t individual_position, size_t sequence_position)
	Delete a sequence of an Individual. More...

bool	hasIndividualSequences (size_t individual_position) const
	Tell if the Individual has some sequences. More...

std::vector< std::string >	getIndividualSequencesNames (size_t individual_position) const
	Get the sequences' names from an Individual. More...

size_t	getIndividualSequencePosition (size_t individual_position, const std::string &sequence_name) const
	Get the position of a sequence in an Individual. More...

size_t	getIndividualNumberOfSequences (size_t individual_position) const
	Get the number of sequences in an Individual. More...

void	setIndividualSequences (size_t individual_position, const MapSequenceContainer &msc)
	Set all the sequences by copying an OrderedSequenceContainer. More...

void	setIndividualGenotype (size_t individual_position, const MultilocusGenotype &genotype)
	Set the genotype of an Individual. More...

void	initIndividualGenotype (size_t individual_position, size_t loci_number)
	Initialyze the genotype of an Individual. More...

void	deleteIndividualGenotype (size_t individual_position)
	Delete the genotype of an Individual. More...

bool	hasIndividualGenotype (size_t individual_position) const
	Tell if an Individual has a genotype. More...

void	setIndividualMonolocusGenotype (size_t individual_position, size_t locus_position, const MonolocusGenotype &monogen)
	Set a MonolocusGenotype of an Individual. More...

void	setIndividualMonolocusGenotypeByAlleleKey (size_t individual_position, size_t locus_position, const std::vector< size_t > &allele_keys)
	Set a MonolocusGenotype of an Individual. More...

void	setIndividualMonolocusGenotypeByAlleleId (size_t individual_position, size_t locus_position, const std::vector< std::string > &allele_id, const LocusInfo &locus_info)
	Set a MonolocusGenotype of an Individual. More...

const MonolocusGenotype &	getIndividualMonolocusGenotype (size_t individual_position, size_t locus_position) const
	Get a MonolocusGenotype of an Individual. More...

bool	hasSequenceData () const
	Tell if at least one individual has at least one sequence. More...

const Alphabet *	getAlphabet () const
	Get the alphabet used for the sequences. More...

size_t	getGroupSizeForLocus (size_t locus_position) const
	Get the number of individual that have a data at the specified locus. More...

size_t	getGroupSizeForSequence (size_t sequence_position) const
	Get the number of individual that have a sequence at the specified position. More...

Protected Attributes
size_t	id_

std::string	name_

std::vector< Individual * >	individuals_

Detailed Description

The Group class.

A Group is an ensemble of Individuals with some statistics like the average allele number.

Author: Sylvain Gaillard

Definition at line 70 of file Group.h.

Constructor & Destructor Documentation

◆ Group() [1/3]

Group::Group ( size_t group_id )

Build a void new Group.

Definition at line 47 of file Group.cpp.

◆ Group() [2/3]

Group::Group ( const Group & group )

Copy constructor.

If you need to use a copy constructor in a DataSet context, use the one which specify a new Group Id.

Definition at line 51 of file Group.cpp.

References addIndividual(), getIndividualAtPosition(), and getNumberOfIndividuals().

◆ Group() [3/3]

Group::Group	(	const Group &	group,
		size_t	group_id
	)

A duplication constructor with new Group Id.

Definition at line 62 of file Group.cpp.

References addIndividual(), getIndividualAtPosition(), and getNumberOfIndividuals().

◆ ~Group()

Group::~Group ( )

Destroy an Group.

Definition at line 74 of file Group.cpp.

Member Function Documentation

◆ addEmptyIndividual()

void Group::addEmptyIndividual ( const std::string & individual_id )

Add an empty Individual to the Group.

Exceptions

BadIdentifierException if individual_id is already in use.

Definition at line 110 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ addIndividual()

void Group::addIndividual ( const Individual & ind )

Add an Individual.

Add an Individual to the group.

Parameters

ind	The Individual to add to the Group.

Exceptions

BadIdentifierException if individual's identifier is already in use.

Definition at line 98 of file Group.cpp.

References bpp::Individual::getId(), getIndividualPosition(), and individuals_.

Referenced by Group(), operator=(), and bpp::DataSet::splitGroup().

◆ addIndividualSequenceAtPosition()

void Group::addIndividualSequenceAtPosition	(	size_t	individual_position,
		size_t	sequence_position,
		const Sequence &	sequence
	)

Add a sequence to an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
AlphabetMismatchException	if the sequence's alphabet doesn't match the container's alphabet.
BadIdentifierException	if the sequence's name is already in use.
BadIntegerException	if sequence_position is already in use.

Definition at line 303 of file Group.cpp.

References bpp::AlphabetMismatchException::getAlphabets(), bpp::BadIdentifierException::getIdentifier(), getNumberOfIndividuals(), and individuals_.

◆ clear()

void Group::clear ( )

Clear the Group.

Delete all the Individuals of the group.

Definition at line 178 of file Group.cpp.

References individuals_.

◆ deleteIndividualAtPosition()

void Group::deleteIndividualAtPosition ( size_t individual_position )

Delete an Individual from the Group.

Parameters

individual_position The position in the Group of the Individual to delete.

Free the memory by calling the destructor of the Individual.

Definition at line 166 of file Group.cpp.

References getNumberOfIndividuals(), and removeIndividualAtPosition().

◆ deleteIndividualById()

void Group::deleteIndividualById ( const std::string & individual_id )

Delete an Individual from the Group.

Parameters

individual_id The id of the Individual to delete.

Exceptions

IndividualNotFoundException if individual_id is not found.

Search an Individual in the Group by cheking the id and delete it if it is foundi and free the memory by calling the destructor of the Individual.

Definition at line 154 of file Group.cpp.

References removeIndividualById().

◆ deleteIndividualGenotype()

void Group::deleteIndividualGenotype ( size_t individual_position )

Delete the genotype of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 482 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ deleteIndividualSequenceAtPosition()

void Group::deleteIndividualSequenceAtPosition	(	size_t	individual_position,
		size_t	sequence_position
	)

Delete a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequence_position is not found.

Definition at line 379 of file Group.cpp.

References getNumberOfIndividuals(), bpp::SequenceNotFoundException::getSequenceId(), and individuals_.

◆ deleteIndividualSequenceByName()

void Group::deleteIndividualSequenceByName	(	size_t	individual_position,
		const std::string &	sequence_name
	)

Delete a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 361 of file Group.cpp.

References getNumberOfIndividuals(), bpp::SequenceNotFoundException::getSequenceId(), and individuals_.

◆ getAlphabet()

const Alphabet * Group::getAlphabet ( ) const

Get the alphabet used for the sequences.

Definition at line 586 of file Group.cpp.

References getNumberOfIndividuals(), hasIndividualSequences(), and individuals_.

◆ getGroupId()

size_t bpp::Group::getGroupId ( ) const

inline

Get the id of the Group.

Returns: The id of the Group as an size_t.

Definition at line 134 of file Group.h.

References id_.

Referenced by bpp::DataSet::addGroup(), and operator=().

◆ getGroupName()

const std::string& bpp::Group::getGroupName ( ) const

inline

Get the name of the Group.

Returns: The name of the Group as a string.

Definition at line 120 of file Group.h.

References name_.

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

◆ getGroupSizeForLocus()

size_t Group::getGroupSizeForLocus ( size_t locus_position ) const

Get the number of individual that have a data at the specified locus.

Definition at line 596 of file Group.cpp.

References count(), and individuals_.

◆ getGroupSizeForSequence()

size_t Group::getGroupSizeForSequence ( size_t sequence_position ) const

Get the number of individual that have a sequence at the specified position.

Definition at line 607 of file Group.cpp.

References count(), and individuals_.

◆ getIndividualAtPosition()

const Individual & Group::getIndividualAtPosition ( size_t individual_position ) const

Get a reference to an Individual by its position.

Parameters

individual_position The position of the Individual in the group.

Returns: A pointer to the Individual.

Exceptions

IndividualNotFoundException if individual_id is not found.

Definition at line 197 of file Group.cpp.

References individuals_.

Referenced by getIndividualById(), Group(), bpp::DataSet::mergeGroups(), and operator=().

◆ getIndividualById()

const Individual & Group::getIndividualById ( const std::string & individual_id ) const

Get a reference to an Individual.

Parameters

individual_id The id of the Individual to find.

Returns: A pointer to the Individual or NULL if the Individual is not found.

Definition at line 187 of file Group.cpp.

References getIndividualAtPosition(), and individuals_.

◆ getIndividualCoordAtPosition()

const Point2D< double > & Group::getIndividualCoordAtPosition ( size_t individual_position ) const

Get the coordinates of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the individual has no coordinate.

Definition at line 268 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getIndividualDateAtPosition()

const Date & Group::getIndividualDateAtPosition ( size_t individual_position ) const

Get the date of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the Individual has no date.

Definition at line 247 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getIndividualLocalityAtPosition()

const Locality< double > & Group::getIndividualLocalityAtPosition ( size_t individual_position ) const

Get the locality of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the individual has no locality.

Definition at line 289 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getIndividualMonolocusGenotype()

const MonolocusGenotype & Group::getIndividualMonolocusGenotype	(	size_t	individual_position,
		size_t	locus_position
	)		const

Get a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position excedes the number of locus.

Definition at line 558 of file Group.cpp.

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

◆ getIndividualNumberOfSequences()

size_t Group::getIndividualNumberOfSequences ( size_t individual_position ) const

Get the number of sequences in an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.

Definition at line 436 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getIndividualPosition()

size_t Group::getIndividualPosition ( const std::string & individual_id ) const

Get the position of an Individual.

Exceptions

IndividualNotFoundException if individual_id is not found.

Definition at line 120 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

Referenced by addIndividual(), and removeIndividualById().

◆ getIndividualSequenceAtPosition()

const Sequence & Group::getIndividualSequenceAtPosition	(	size_t	individual_position,
		size_t	sequence_position
	)		const

Get a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequence_position is not found.

Definition at line 343 of file Group.cpp.

References getNumberOfIndividuals(), bpp::SequenceNotFoundException::getSequenceId(), and individuals_.

◆ getIndividualSequenceByName()

const Sequence & Group::getIndividualSequenceByName	(	size_t	individual_position,
		const std::string &	sequence_name
	)		const

Get a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 325 of file Group.cpp.

References getNumberOfIndividuals(), bpp::SequenceNotFoundException::getSequenceId(), and individuals_.

◆ getIndividualSequencePosition()

size_t Group::getIndividualSequencePosition	(	size_t	individual_position,
		const std::string &	sequence_name
	)		const

Get the position of a sequence in an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 418 of file Group.cpp.

References getNumberOfIndividuals(), bpp::SequenceNotFoundException::getSequenceId(), and individuals_.

◆ getIndividualSequencesNames()

vector< string > Group::getIndividualSequencesNames ( size_t individual_position ) const

Get the sequences' names from an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.

Definition at line 404 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getIndividualSexAtPosition()

unsigned short Group::getIndividualSexAtPosition ( size_t individual_position ) const

Get the sex of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 233 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getMaxNumberOfSequences()

size_t Group::getMaxNumberOfSequences ( ) const

Get the maximum number of sequence.

Give the value of the highest sequence key. This value is usefull to discover the missing sequences data for each individual.

Definition at line 209 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ getNumberOfIndividuals()

size_t Group::getNumberOfIndividuals ( ) const

Get the number of Individual in the Group.

Returns: An integer as the number of Individual.

Definition at line 204 of file Group.cpp.

References individuals_.

Referenced by addEmptyIndividual(), addIndividualSequenceAtPosition(), deleteIndividualAtPosition(), deleteIndividualGenotype(), deleteIndividualSequenceAtPosition(), deleteIndividualSequenceByName(), getAlphabet(), getIndividualCoordAtPosition(), getIndividualDateAtPosition(), getIndividualLocalityAtPosition(), getIndividualMonolocusGenotype(), getIndividualNumberOfSequences(), getIndividualPosition(), getIndividualSequenceAtPosition(), getIndividualSequenceByName(), getIndividualSequencePosition(), getIndividualSequencesNames(), getIndividualSexAtPosition(), getMaxNumberOfSequences(), Group(), hasIndividualGenotype(), hasIndividualSequences(), hasSequenceData(), initIndividualGenotype(), bpp::DataSet::mergeGroups(), operator=(), setIndividualCoordAtPosition(), setIndividualDateAtPosition(), setIndividualGenotype(), setIndividualLocalityAtPosition(), setIndividualMonolocusGenotype(), setIndividualMonolocusGenotypeByAlleleId(), setIndividualMonolocusGenotypeByAlleleKey(), setIndividualSequences(), and setIndividualSexAtPosition().

◆ hasIndividualGenotype()

bool Group::hasIndividualGenotype ( size_t individual_position ) const

Tell if an Individual has a genotype.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 489 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ hasIndividualSequences()

bool Group::hasIndividualSequences ( size_t individual_position ) const

Tell if the Individual has some sequences.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 397 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

Referenced by getAlphabet(), and hasSequenceData().

◆ hasSequenceData()

bool Group::hasSequenceData ( ) const

Tell if at least one individual has at least one sequence.

Definition at line 576 of file Group.cpp.

References getNumberOfIndividuals(), and hasIndividualSequences().

◆ initIndividualGenotype()

void Group::initIndividualGenotype	(	size_t	individual_position,
		size_t	loci_number
	)

Initialyze the genotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
BadIntegerException	if loci_number < 1.
Exception	if the individual already has a genotype.

Definition at line 464 of file Group.cpp.

References bpp::BadIntegerException::getBadInteger(), getNumberOfIndividuals(), and individuals_.

◆ operator=()

Group & Group::operator= ( const Group & group )

The assignation operator =.

Definition at line 78 of file Group.cpp.

References addIndividual(), getGroupId(), getIndividualAtPosition(), getNumberOfIndividuals(), and setGroupId().

◆ removeIndividualAtPosition()

std::unique_ptr< Individual > Group::removeIndividualAtPosition ( size_t individual_position )

Remove an Individual from the Group.

Parameters

individual_position The position in the Group of the Individual to remove.

Returns: An std::auto_ptr to the removed Individual.

Remove the individual at the specified position and return a pointer to this Individual.

Definition at line 145 of file Group.cpp.

References individuals_.

Referenced by deleteIndividualAtPosition().

◆ removeIndividualById()

std::unique_ptr< Individual > Group::removeIndividualById ( const std::string & individual_id )

Remove an Individual from the Group.

Parameters

individual_id The id of the Individual to remove.

Returns: An std::auto_ptr to the removed Individual.

Exceptions

IndividualNotFoundException if individual_id is not found.

Search an Individual in the Group by cheking the id and remove it if it is found then return a pointer to this Individual.

Definition at line 130 of file Group.cpp.

References getIndividualPosition(), and individuals_.

Referenced by deleteIndividualById().

◆ setGroupId()

void Group::setGroupId ( size_t group_id )

Set the id of the Group.

Parameters

group_id The id of the Group as an size_t.

Definition at line 88 of file Group.cpp.

References id_.

Referenced by operator=().

◆ setGroupName()

void Group::setGroupName ( const std::string & group_name )

Set the name of the Group.

Parameters

group_name Name of the Group as string.

Definition at line 93 of file Group.cpp.

References name_.

◆ setIndividualCoordAtPosition()

void Group::setIndividualCoordAtPosition	(	size_t	individual_position,
		const Point2D< double > &	coord
	)

Set the coordinates of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 261 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ setIndividualDateAtPosition()

void Group::setIndividualDateAtPosition	(	size_t	individual_position,
		const Date &	date
	)

Set the date of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 240 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ setIndividualGenotype()

void Group::setIndividualGenotype	(	size_t	individual_position,
		const MultilocusGenotype &	genotype
	)

Set the genotype of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 457 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ setIndividualLocalityAtPosition()

void Group::setIndividualLocalityAtPosition	(	size_t	individual_position,
		const Locality< double > *	locality
	)

Set the locality of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 282 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ setIndividualMonolocusGenotype()

void Group::setIndividualMonolocusGenotype	(	size_t	individual_position,
		size_t	locus_position,
		const MonolocusGenotype &	monogen
	)

Set a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position excedes the number of locus.

Definition at line 496 of file Group.cpp.

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

◆ setIndividualMonolocusGenotypeByAlleleId()

void Group::setIndividualMonolocusGenotypeByAlleleId	(	size_t	individual_position,
		size_t	locus_position,
		const std::vector< std::string > &	allele_id,
		const LocusInfo &	locus_info
	)

Set a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position excedes the number of locus.
AlleleNotFoundException	if at least one id is not found in locus_info.

Definition at line 536 of file Group.cpp.

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

◆ setIndividualMonolocusGenotypeByAlleleKey()

void Group::setIndividualMonolocusGenotypeByAlleleKey	(	size_t	individual_position,
		size_t	locus_position,
		const std::vector< size_t > &	allele_keys
	)

Set a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individual_position excedes the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position excedes the number of locus.
Exception	if there is no key in allele_keys.

Definition at line 514 of file Group.cpp.

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

◆ setIndividualSequences()

void Group::setIndividualSequences	(	size_t	individual_position,
		const MapSequenceContainer &	msc
	)

Set all the sequences by copying an OrderedSequenceContainer.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 450 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

◆ setIndividualSexAtPosition()

void Group::setIndividualSexAtPosition	(	size_t	individual_position,
		const unsigned short	sex
	)

Set the sex of an Individual.

Exceptions

IndexOutOfBoundsException if individual_position excedes the number of individuals.

Definition at line 226 of file Group.cpp.

References getNumberOfIndividuals(), and individuals_.

Member Data Documentation

◆ id_

size_t bpp::Group::id_

protected

Definition at line 73 of file Group.h.

Referenced by getGroupId(), and setGroupId().

◆ individuals_

std::vector<Individual*> bpp::Group::individuals_

protected

Definition at line 75 of file Group.h.

Referenced by addEmptyIndividual(), addIndividual(), addIndividualSequenceAtPosition(), clear(), deleteIndividualGenotype(), deleteIndividualSequenceAtPosition(), deleteIndividualSequenceByName(), getAlphabet(), getGroupSizeForLocus(), getGroupSizeForSequence(), getIndividualAtPosition(), getIndividualById(), getIndividualCoordAtPosition(), getIndividualDateAtPosition(), getIndividualLocalityAtPosition(), getIndividualMonolocusGenotype(), getIndividualNumberOfSequences(), getIndividualPosition(), getIndividualSequenceAtPosition(), getIndividualSequenceByName(), getIndividualSequencePosition(), getIndividualSequencesNames(), getIndividualSexAtPosition(), getMaxNumberOfSequences(), getNumberOfIndividuals(), hasIndividualGenotype(), hasIndividualSequences(), initIndividualGenotype(), removeIndividualAtPosition(), removeIndividualById(), setIndividualCoordAtPosition(), setIndividualDateAtPosition(), setIndividualGenotype(), setIndividualLocalityAtPosition(), setIndividualMonolocusGenotype(), setIndividualMonolocusGenotypeByAlleleId(), setIndividualMonolocusGenotypeByAlleleKey(), setIndividualSequences(), and setIndividualSexAtPosition().

◆ name_

std::string bpp::Group::name_

protected

Definition at line 74 of file Group.h.

Referenced by getGroupName(), and setGroupName().

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

Bpp/PopGen/DataSet/Group.h
Bpp/PopGen/DataSet/Group.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Group() [1/3]

◆ Group() [2/3]

◆ Group() [3/3]

◆ ~Group()

Member Function Documentation

◆ addEmptyIndividual()

◆ addIndividual()

◆ addIndividualSequenceAtPosition()

◆ clear()

◆ deleteIndividualAtPosition()

◆ deleteIndividualById()

◆ deleteIndividualGenotype()

◆ deleteIndividualSequenceAtPosition()

◆ deleteIndividualSequenceByName()

◆ getAlphabet()

◆ getGroupId()

◆ getGroupName()

◆ getGroupSizeForLocus()

◆ getGroupSizeForSequence()

◆ getIndividualAtPosition()

◆ getIndividualById()

◆ getIndividualCoordAtPosition()

◆ getIndividualDateAtPosition()

◆ getIndividualLocalityAtPosition()

◆ getIndividualMonolocusGenotype()

◆ getIndividualNumberOfSequences()

◆ getIndividualPosition()

◆ getIndividualSequenceAtPosition()

◆ getIndividualSequenceByName()

◆ getIndividualSequencePosition()

◆ getIndividualSequencesNames()

◆ getIndividualSexAtPosition()

◆ getMaxNumberOfSequences()

◆ getNumberOfIndividuals()

◆ hasIndividualGenotype()

◆ hasIndividualSequences()

◆ hasSequenceData()

◆ initIndividualGenotype()

◆ operator=()

◆ removeIndividualAtPosition()

◆ removeIndividualById()

◆ setGroupId()

◆ setGroupName()

◆ setIndividualCoordAtPosition()

◆ setIndividualDateAtPosition()

◆ setIndividualGenotype()

◆ setIndividualLocalityAtPosition()

◆ setIndividualMonolocusGenotype()

◆ setIndividualMonolocusGenotypeByAlleleId()

◆ setIndividualMonolocusGenotypeByAlleleKey()

◆ setIndividualSequences()

◆ setIndividualSexAtPosition()

Member Data Documentation

◆ id_

◆ individuals_

◆ name_