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

Inheritance diagram for bpp::Group:

Collaboration diagram for bpp::Group:

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

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

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

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

virtual	~Group ()=default
	Destroy a Group. More...

Group *	clone () const override

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

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

void	setGroupName (const std::string &groupName)
	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 &individualId)
	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 &individualId) const
	Get the position of an Individual. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

void	setIndividualLocalityAtPosition (size_t individualPosition, std::shared_ptr< const Locality< double >> locality)
	Set the locality of an Individual. More...

std::shared_ptr< const Locality< double > >	getIndividualLocalityAtPosition (size_t individualPosition) const
	Get the locality of an Individual. More...

void	addIndividualSequenceAtPosition (size_t individualPosition, size_t sequencePosition, std::unique_ptr< Sequence > &sequence)
	Add a sequence to an Individual. More...

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

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

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

void	deleteIndividualSequenceAtPosition (size_t individualPosition, size_t sequencePosition)
	Delete a sequence of an Individual. More...

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

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

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

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

void	setIndividualSequences (size_t individualPosition, const SequenceContainerInterface &sc)
	Set all the sequences by copying an OrderedSequenceContainer. More...

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

void	initIndividualGenotype (size_t individualPosition, size_t loci_number)
	Initialize the genotype of an Individual. More...

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

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

void	setIndividualMonolocusGenotype (size_t individualPosition, size_t locusPosition, const MonolocusGenotypeInterface &monogen)
	Set a MonolocusGenotype of an Individual. More...

void	setIndividualMonolocusGenotypeByAlleleKey (size_t individualPosition, size_t locusPosition, const std::vector< size_t > &alleleKeys)
	Set a MonolocusGenotype of an Individual. More...

void	setIndividualMonolocusGenotypeByAlleleId (size_t individualPosition, size_t locusPosition, const std::vector< std::string > &alleleId, const LocusInfo &locusInfo)
	Set a MonolocusGenotype of an Individual. More...

const MonolocusGenotypeInterface &	getIndividualMonolocusGenotype (size_t individualPosition, size_t locusPosition) const
	Get a MonolocusGenotype of an Individual. More...

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

std::shared_ptr< const Alphabet >	getAlphabet () const
	Get the alphabet used for the sequences. More...

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

size_t	getGroupSizeForSequence (size_t sequencePosition) 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< std::unique_ptr< Individual > >	individuals_

Detailed Description

The Group class.

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

Author: Sylvain Gaillard

Definition at line 34 of file Group.h.

Constructor & Destructor Documentation

◆ Group() [1/3]

bpp::Group::Group ( size_t groupId )

inline

Build a void new Group.

Definition at line 47 of file Group.h.

Referenced by clone().

◆ Group() [2/3]

bpp::Group::Group ( const Group & group )

inline

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 59 of file Group.h.

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

◆ Group() [3/3]

bpp::Group::Group	(	const Group &	group,
		size_t	groupId
	)

inline

A duplication constructor with new Group Id.

Definition at line 88 of file Group.h.

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

◆ ~Group()

virtual bpp::Group::~Group ( )

virtualdefault

Destroy a Group.

Member Function Documentation

◆ addEmptyIndividual()

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

Add an empty Individual to the Group.

Exceptions

BadIdentifierException if individualId is already in use.

Definition at line 24 of file Group.cpp.

◆ 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 12 of file Group.cpp.

References bpp::Individual::getId().

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

◆ addIndividualSequenceAtPosition()

void Group::addIndividualSequenceAtPosition	(	size_t	individualPosition,
		size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence
	)

Add a sequence to an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds 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 sequencePosition is already in use.

Definition at line 203 of file Group.cpp.

References bpp::AlphabetMismatchException::getFirstAlphabet(), bpp::BadIdentifierException::getIdentifier(), and bpp::AlphabetMismatchException::getSecondAlphabet().

◆ clear()

void bpp::Group::clear ( )

inline

Clear the Group.

Delete all the Individuals of the group.

Definition at line 245 of file Group.h.

References individuals_.

◆ clone()

Group* bpp::Group::clone ( ) const

inlineoverridevirtual

Implements bpp::Clonable.

Definition at line 105 of file Group.h.

References Group().

◆ deleteIndividualAtPosition()

void Group::deleteIndividualAtPosition ( size_t individualPosition )

Delete an Individual from the Group.

Parameters

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

Free the memory by calling the destructor of the Individual.

Definition at line 80 of file Group.cpp.

◆ deleteIndividualById()

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

Delete an Individual from the Group.

Parameters

individualId The id of the Individual to delete.

Exceptions

IndividualNotFoundException if individualId is not found.

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

Definition at line 68 of file Group.cpp.

◆ deleteIndividualGenotype()

void Group::deleteIndividualGenotype ( size_t individualPosition )

Delete the genotype of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 382 of file Group.cpp.

◆ deleteIndividualSequenceAtPosition()

void Group::deleteIndividualSequenceAtPosition	(	size_t	individualPosition,
		size_t	sequencePosition
	)

Delete a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequencePosition is not found.

Definition at line 279 of file Group.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

◆ deleteIndividualSequenceByName()

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

Delete a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds 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 261 of file Group.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

◆ getAlphabet()

shared_ptr< const Alphabet > Group::getAlphabet ( ) const

Get the alphabet used for the sequences.

Definition at line 494 of file Group.cpp.

◆ 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().

◆ 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 locusPosition ) const

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

Definition at line 504 of file Group.cpp.

References count().

◆ getGroupSizeForSequence()

size_t Group::getGroupSizeForSequence ( size_t sequencePosition ) const

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

Definition at line 515 of file Group.cpp.

References count().

◆ getIndividualAtPosition()

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

Get a reference to an Individual by its position.

Parameters

individualPosition The position of the Individual in the group.

Returns: A pointer to the Individual.

Exceptions

IndividualNotFoundException if individualId is not found.

Definition at line 102 of file Group.cpp.

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

◆ getIndividualById()

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

Get a reference to an Individual.

Parameters

individualId The id of the Individual to find.

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

Definition at line 92 of file Group.cpp.

◆ getIndividualCoordAtPosition()

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

Get the coordinates of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the individual has no coordinate.

Definition at line 168 of file Group.cpp.

◆ getIndividualDateAtPosition()

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

Get the date of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the Individual has no date.

Definition at line 147 of file Group.cpp.

◆ getIndividualLocalityAtPosition()

std::shared_ptr< const Locality< double > > Group::getIndividualLocalityAtPosition ( size_t individualPosition ) const

Get the locality of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the individual has no locality.

Definition at line 189 of file Group.cpp.

◆ getIndividualMonolocusGenotype()

const MonolocusGenotypeInterface & Group::getIndividualMonolocusGenotype	(	size_t	individualPosition,
		size_t	locusPosition
	)		const

Get a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locusPosition exceeds the number of locus.

Definition at line 464 of file Group.cpp.

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

◆ getIndividualNumberOfSequences()

size_t Group::getIndividualNumberOfSequences ( size_t individualPosition ) const

Get the number of sequences in an Individual.

Exceptions

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

Definition at line 336 of file Group.cpp.

◆ getIndividualPosition()

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

Get the position of an Individual.

Exceptions

IndividualNotFoundException if individualId is not found.

Definition at line 34 of file Group.cpp.

◆ getIndividualSequenceAtPosition()

const Sequence & Group::getIndividualSequenceAtPosition	(	size_t	individualPosition,
		size_t	sequencePosition
	)		const

Get a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if there is no sequence container defined in the individual.
SequenceNotFoundException	if sequencePosition is not found.

Definition at line 243 of file Group.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

◆ getIndividualSequenceByName()

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

Get a sequence of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds 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 225 of file Group.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

◆ getIndividualSequencePosition()

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

Get the position of a sequence in an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds 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 318 of file Group.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

◆ getIndividualSequencesNames()

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

Get the sequences' names from an Individual.

Exceptions

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

Definition at line 304 of file Group.cpp.

◆ getIndividualSexAtPosition()

unsigned short Group::getIndividualSexAtPosition ( size_t individualPosition ) const

Get the sex of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 133 of file Group.cpp.

◆ getMaxNumberOfSequences()

size_t Group::getMaxNumberOfSequences ( ) const

Get the maximum number of sequence.

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

Definition at line 109 of file Group.cpp.

◆ getNumberOfIndividuals()

size_t bpp::Group::getNumberOfIndividuals ( ) const

inline

Get the number of Individual in the Group.

Returns: An integer as the number of Individual.

Definition at line 158 of file Group.h.

References individuals_.

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

◆ hasIndividualGenotype()

bool Group::hasIndividualGenotype ( size_t individualPosition ) const

Tell if an Individual has a genotype.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 389 of file Group.cpp.

◆ hasIndividualSequences()

bool Group::hasIndividualSequences ( size_t individualPosition ) const

Tell if the Individual has some sequences.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 297 of file Group.cpp.

◆ hasSequenceData()

bool Group::hasSequenceData ( ) const

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

Definition at line 484 of file Group.cpp.

◆ initIndividualGenotype()

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

Initialize the genotype of an Individual.

Exceptions

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

Definition at line 364 of file Group.cpp.

References bpp::BadIntegerException::getBadInteger().

◆ operator=()

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

inline

The assignation operator =.

Definition at line 73 of file Group.h.

References addIndividual(), getIndividualAtPosition(), getNumberOfIndividuals(), id_, individuals_, and name_.

◆ removeIndividualAtPosition()

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

Remove an Individual from the Group.

Parameters

individualPosition 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 59 of file Group.cpp.

◆ removeIndividualById()

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

Remove an Individual from the Group.

Parameters

individualId The id of the Individual to remove.

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

Exceptions

IndividualNotFoundException if individualId is not found.

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

Definition at line 44 of file Group.cpp.

◆ setGroupId()

void bpp::Group::setGroupId ( size_t groupId )

inline

Set the id of the Group.

Parameters

groupId The id of the Group as an size_t.

Definition at line 113 of file Group.h.

References id_.

◆ setGroupName()

void bpp::Group::setGroupName ( const std::string & groupName )

inline

Set the name of the Group.

Parameters

groupName Name of the Group as string.

Definition at line 127 of file Group.h.

References name_.

◆ setIndividualCoordAtPosition()

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

Set the coordinates of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 161 of file Group.cpp.

◆ setIndividualDateAtPosition()

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

Set the date of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 140 of file Group.cpp.

◆ setIndividualGenotype()

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

Set the genotype of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 357 of file Group.cpp.

◆ setIndividualLocalityAtPosition()

void Group::setIndividualLocalityAtPosition	(	size_t	individualPosition,
		std::shared_ptr< const Locality< double >>	locality
	)

Set the locality of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 182 of file Group.cpp.

◆ setIndividualMonolocusGenotype()

void Group::setIndividualMonolocusGenotype	(	size_t	individualPosition,
		size_t	locusPosition,
		const MonolocusGenotypeInterface &	monogen
	)

Set a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locusPosition exceeds the number of locus.

Definition at line 396 of file Group.cpp.

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

◆ setIndividualMonolocusGenotypeByAlleleId()

void Group::setIndividualMonolocusGenotypeByAlleleId	(	size_t	individualPosition,
		size_t	locusPosition,
		const std::vector< std::string > &	alleleId,
		const LocusInfo &	locusInfo
	)

Set a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locusPosition exceeds the number of locus.
AlleleNotFoundException	if at least one id is not found in locus_info.

Definition at line 442 of file Group.cpp.

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

◆ setIndividualMonolocusGenotypeByAlleleKey()

void Group::setIndividualMonolocusGenotypeByAlleleKey	(	size_t	individualPosition,
		size_t	locusPosition,
		const std::vector< size_t > &	alleleKeys
	)

Set a MonolocusGenotype of an Individual.

Exceptions

IndexOutOfBoundsException	if individualPosition exceeds the number of individuals.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locusPosition exceeds the number of locus.
Exception	if there is no key in allele_keys.

Definition at line 417 of file Group.cpp.

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

◆ setIndividualSequences()

void Group::setIndividualSequences	(	size_t	individualPosition,
		const SequenceContainerInterface &	sc
	)

Set all the sequences by copying an OrderedSequenceContainer.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 350 of file Group.cpp.

◆ setIndividualSexAtPosition()

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

Set the sex of an Individual.

Exceptions

IndexOutOfBoundsException if individualPosition exceeds the number of individuals.

Definition at line 126 of file Group.cpp.

Member Data Documentation

◆ id_

size_t bpp::Group::id_

protected

Definition at line 38 of file Group.h.

Referenced by getGroupId(), operator=(), and setGroupId().

◆ individuals_

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

protected

Definition at line 40 of file Group.h.

Referenced by clear(), getNumberOfIndividuals(), and operator=().

◆ name_

std::string bpp::Group::name_

protected

Definition at line 39 of file Group.h.

Referenced by getGroupName(), operator=(), 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()

◆ clone()

◆ 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_