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

Collaboration diagram for bpp::DataSet:

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

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

	DataSet (const DataSet &ds)
	Copy constructor. More...

DataSet &	operator= (const DataSet &ds)

void	addLocality (const Locality< double > &locality)
	Add a locality to the DataSet. More...

size_t	getLocalityPosition (const std::string &name) const
	Get the position of a locality in the container. More...

std::shared_ptr< const Locality< double > >	getLocalityAtPosition (size_t localityPosition) const
	Get a Locality by localityPosition. More...

const Locality< double > &	localityAtPosition (size_t localityPosition) const
	Get a Locality by localityPosition. More...

std::shared_ptr< const Locality< double > >	getLocalityByName (const std::string &name) const
	Get a Locality by name. More...

const Locality< double > &	localityByName (const std::string &name) const
	Get a Locality by name. More...

void	deleteLocalityAtPosition (size_t localityPosition)
	Delete a Locality from the DataSet. More...

void	deleteLocalityByName (const std::string &name)
	Delete a Locality from the DataSet. More...

size_t	getNumberOfLocalities () const
	Get the number of Localities. More...

bool	hasLocality () const
	Tell if there is at least one locality. More...

void	addGroup (const Group &group)
	Add a Group to the DataSet. More...

void	addEmptyGroup (size_t group_id)
	Add an empty Group to the DataSet. More...

const Group &	getGroupById (size_t group_id) const
	Get a group by identifier. More...

size_t	getGroupPosition (size_t group_id) const
	Get the position of a Group. More...

std::string	getGroupName (size_t group_id) const
	Get the name of a Group. If the name is an empty string it just returns the group_id. More...

void	setGroupName (size_t group_id, const std::string &group_name) const
	set the name of a Group. More...

const Group &	getGroupAtPosition (size_t groupPosition) const
	Get a group by position. More...

void	deleteGroupAtPosition (size_t groupPosition)
	Delete a Group from the DataSet. More...

size_t	getNumberOfGroups () const
	Get the number of Groups. More...

void	mergeTwoGroups (size_t source_id, size_t target_id)
	Merge two groups. More...

void	mergeGroups (std::vector< size_t > &group_ids)
	Merge some Groups in one. More...

void	splitGroup (size_t group_id, std::vector< size_t > individuals_selection)
	Split a group in two. More...

void	addIndividualToGroup (size_t groupPosition, const Individual &individual)
	Add an Individual to a Group. More...

void	addEmptyIndividualToGroup (size_t groupPosition, const std::string &individual_id)
	Add an empty Individual to a Group. More...

size_t	getNumberOfIndividualsInGroup (size_t groupPosition) const
	Get the number of Individuals in a Group. More...

size_t	getIndividualPositionInGroup (size_t groupPosition, const std::string &individual_id) const
	Get the position of an Individual in a Group. More...

const Individual &	getIndividualAtPositionFromGroup (size_t groupPosition, size_t individualPosition) const
	Get an Individual from a Group. More...

const Individual &	getIndividualByIdFromGroup (size_t groupPosition, const std::string &individualId) const
	Get an Individual from a Group. More...

void	deleteIndividualAtPositionFromGroup (size_t groupPosition, size_t individualPosition)
	Delete an Individual from a group. More...

void	deleteIndividualByIdFromGroup (size_t groupPosition, const std::string &individualId)
	Delete an Individual from a group. More...

void	setIndividualSexInGroup (size_t groupPosition, size_t individualPosition, const unsigned short sex)
	Set the sex of an Individual in a Group. More...

unsigned short	getIndividualSexInGroup (size_t groupPosition, size_t individualPosition) const
	Get the sex of an Individual in a Group. More...

void	setIndividualDateInGroup (size_t groupPosition, size_t individualPosition, const Date &date)
	Set the Date of an Individual in a Group. More...

const Date &	individualDateInGroup (size_t groupPosition, size_t individualPosition) const
	Get the Date of an Individual in a Group. More...

void	setIndividualCoordInGroup (size_t groupPosition, size_t individualPosition, const Point2D< double > &coord)
	Set the coordinates of an Individual in a Group. More...

const Point2D< double > &	individualCoordInGroup (size_t groupPosition, size_t individualPosition) const
	Get the coordinate of an Individual in a Group. More...

void	setIndividualLocalityInGroupByName (size_t groupPosition, size_t individualPosition, const std::string &localityName)
	Set the Locality of an Individual in a Group. More...

std::shared_ptr< const Locality< double > >	getIndividualLocalityInGroup (size_t groupPosition, size_t individualPosition) const
	Get the Locality of an Individual in a Group. More...

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

const Sequence &	getIndividualSequenceByNameInGroup (size_t groupPosition, size_t individualPosition, const std::string &sequenceName) const
	Get a Sequence from an Individual of a Group. More...

const Sequence &	getIndividualSequenceAtPositionInGroup (size_t groupPosition, size_t individualPosition, size_t sequencePosition) const
	Get a Sequence from an Individual of a Group. More...

void	deleteIndividualSequenceByNameInGroup (size_t groupPosition, size_t individualPosition, const std::string &sequenceName)
	Delete a Sequence of an Individual of a Group. More...

void	deleteIndividualSequenceAtPositionInGroup (size_t groupPosition, size_t individualPosition, size_t sequencePosition)
	Delete a Sequence of an Individual of a Group. More...

std::vector< std::string >	getIndividualSequencesNamesInGroup (size_t groupPosition, size_t individualPosition) const
	Get the Sequences' names from an Individual of a Group. More...

size_t	getIndividualSequencePositionInGroup (size_t groupPosition, size_t individualPosition, const std::string &sequenceName) const
	Get the position of a Sequence in an Individual of a Group. More...

size_t	getIndividualNumberOfSequencesInGroup (size_t groupPosition, size_t individualPosition) const
	Get the number of Sequences in an Individual of a Group. More...

void	setIndividualGenotypeInGroup (size_t groupPosition, size_t individualPosition, const MultilocusGenotype &genotype)
	Set the MultilocusGenotype of an Individual in a Group. More...

void	initIndividualGenotypeInGroup (size_t groupPosition, size_t individualPosition)
	Initialize the genotype of an Individual in a Group. More...

void	deleteIndividualGenotypeInGroup (size_t groupPosition, size_t individualPosition)
	Delete the MultilocusGenotype of an Individual from a Group. More...

void	setIndividualMonolocusGenotypeInGroup (size_t groupPosition, size_t individualPosition, size_t locusPosition, const MonolocusGenotypeInterface &monogen)
	Set a MonolocusGenotype of an Individual from a group. More...

void	setIndividualMonolocusGenotypeByAlleleKeyInGroup (size_t groupPosition, size_t individualPosition, size_t locusPosition, const std::vector< size_t > alleleKeys)
	Set a MonolocusGenotype of an Individual from a group. More...

void	setIndividualMonolocusGenotypeByAlleleIdInGroup (size_t groupPosition, size_t individualPosition, size_t locusPosition, const std::vector< std::string > alleleId)
	Set a MonolocusGenotype of an Individual from a group. More...

const MonolocusGenotypeInterface &	getIndividualMonolocusGenotypeInGroup (size_t groupPosition, size_t individualPosition, size_t locusPosition) const
	Get a MonolocusGenotype from an Individual of a Group. More...

void	setAlphabet (std::shared_ptr< const Alphabet > alpha)
	Set the alphabet of the AnalyzedSequences. More...

void	setAlphabet (const std::string &alphaType)
	Set the alphabet of the AnalyzedSequences by its type.. More...

std::shared_ptr< const Alphabet >	getAlphabet () const
	Get a pointer toward the alphabet if there is sequence data. More...

const Alphabet &	alphabet () const
	Get a reference toward the alphabet if there is sequence data. More...

std::string	getAlphabetType () const
	Get the alphabet type as a string. More...

void	setAnalyzedLoci (const AnalyzedLoci &analyzedLoci)
	Set the AnalyzedLoci to the DataSet. More...

void	initAnalyzedLoci (size_t numberOfLoci)
	Initialize the AnalyzedLoci for number of loci. More...

const AnalyzedLoci &	analyzedLoci () const
	Get the AnalyzedLoci if there is one. More...

void	deleteAnalyzedLoci ()
	Delete the AnalyzedLoci. More...

void	setLocusInfo (size_t locus_position, const LocusInfo &locus)
	Set a LocusInfo. More...

const LocusInfo &	getLocusInfoByName (const std::string &locus_name) const
	Get a LocusInfo by its name. More...

const LocusInfo &	getLocusInfoAtPosition (size_t locus_position) const
	Get a LocusInfo by its position. More...

void	addAlleleInfoByLocusName (const std::string &locus_name, const AlleleInfo &allele)
	Add an AlleleInfo to a LocusInfo. More...

void	addAlleleInfoByLocusPosition (size_t locus_position, const AlleleInfo &allele)
	Add an AlleleInfo to a LocusInfo. More...

size_t	getNumberOfLoci () const
	Get the number of loci. More...

size_t	getPloidyByLocusName (const std::string &locus_name) const
	Get the ploidy of a locus. More...

size_t	getPloidyByLocusPosition (size_t locus_position) const
	Get the ploidy of a locus. More...

std::unique_ptr< PolymorphismMultiGContainer >	getPolymorphismMultiGContainer () const
	Get a PolymorphismMultiGContainer with all allelic data of the DataSet. More...

std::unique_ptr< PolymorphismMultiGContainer >	getPolymorphismMultiGContainer (const std::map< size_t, std::vector< size_t >> &selection) const
	Get a PolymorphismMultiGContainer from a selection of groups and individuals. More...

std::unique_ptr< PolymorphismSequenceContainer >	getPolymorphismSequenceContainer (const std::map< size_t, std::vector< size_t >> &selection, size_t sequence_position) const
	Get a PolymorphismSequenceContainer from a selection of groups and individuals. More...

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

bool	hasAlleleicData () const
	Tell if there is alelelic data. More...

Private Attributes
std::unique_ptr< AnalyzedLoci >	analyzedLoci_

std::shared_ptr< const Alphabet >	sequenceAlphabet_

std::vector< std::shared_ptr< Locality< double > > >	localities_

std::vector< std::unique_ptr< Group > >	groups_

Detailed Description

The DataSet class.

A DataSet the object that manage every data on which one can compute some statistics.

Author: Sylvain Gaillard

Definition at line 36 of file DataSet.h.

Constructor & Destructor Documentation

◆ DataSet() [1/2]

bpp::DataSet::DataSet ( )

inline

Build a new void DataSet.

Definition at line 49 of file DataSet.h.

◆ ~DataSet()

virtual bpp::DataSet::~DataSet ( )

virtualdefault

Destroy a DataSet.

◆ DataSet() [2/2]

DataSet::DataSet ( const DataSet & ds )

Copy constructor.

Definition at line 13 of file DataSet.cpp.

References analyzedLoci_, groups_, and localities_.

Member Function Documentation

◆ addAlleleInfoByLocusName()

void DataSet::addAlleleInfoByLocusName	(	const std::string &	locus_name,
		const AlleleInfo &	allele
	)

Add an AlleleInfo to a LocusInfo.

Definition at line 1050 of file DataSet.cpp.

References analyzedLoci_, bpp::BadIdentifierException::getIdentifier(), and bpp::LocusNotFoundException::getIdentifier().

◆ addAlleleInfoByLocusPosition()

void DataSet::addAlleleInfoByLocusPosition	(	size_t	locus_position,
		const AlleleInfo &	allele
	)

Add an AlleleInfo to a LocusInfo.

Definition at line 1070 of file DataSet.cpp.

References analyzedLoci_, bpp::IndexOutOfBoundsException::getBounds(), and bpp::BadIdentifierException::getIdentifier().

Referenced by bpp::PopgenlibIO::parseIndividual_(), and bpp::Genepop::read().

◆ addEmptyGroup()

void DataSet::addEmptyGroup ( size_t group_id )

Add an empty Group to the DataSet.

Definition at line 166 of file DataSet.cpp.

References groups_.

Referenced by bpp::PopgenlibIO::parseIndividual_(), bpp::GeneMapperCsvExport::read(), bpp::Genepop::read(), and bpp::Genetix::read().

◆ addEmptyIndividualToGroup()

void DataSet::addEmptyIndividualToGroup	(	size_t	groupPosition,
		const std::string &	individual_id
	)

Add an empty Individual to a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
BadIdentifierException	if the individual's id is already in use.

Definition at line 374 of file DataSet.cpp.

References bpp::BadIdentifierException::getIdentifier(), getNumberOfGroups(), and groups_.

Referenced by bpp::Genepop::read(), and bpp::Genetix::read().

◆ addGroup()

void DataSet::addGroup ( const Group & group )

Add a Group to the DataSet.

Parameters

group A pointer to the Group to add.

Definition at line 154 of file DataSet.cpp.

References bpp::Group::getGroupId(), and groups_.

Referenced by splitGroup().

◆ addIndividualSequenceInGroup()

void DataSet::addIndividualSequenceInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence
	)

Add a Sequence to an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
AlphabetMismatchException	if the sequence's alphabet doesn't match the container's alphabet.
BadIdentifierException	if the sequence's name is already in use.

Definition at line 623 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), bpp::AlphabetMismatchException::getFirstAlphabet(), bpp::BadIdentifierException::getIdentifier(), getNumberOfGroups(), bpp::AlphabetMismatchException::getSecondAlphabet(), groups_, and setAlphabet().

◆ addIndividualToGroup()

void DataSet::addIndividualToGroup	(	size_t	groupPosition,
		const Individual &	individual
	)

Add an Individual to a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
BadIdentifierException	if the individual's id is already in use.

Definition at line 356 of file DataSet.cpp.

References bpp::BadIdentifierException::getIdentifier(), getNumberOfGroups(), bpp::Individual::getSequenceAlphabet(), groups_, bpp::Individual::hasSequences(), and setAlphabet().

Referenced by bpp::PopgenlibIO::parseIndividual_(), and bpp::GeneMapperCsvExport::read().

◆ addLocality()

void DataSet::addLocality ( const Locality< double > & locality )

Add a locality to the DataSet.

Parameters

locality A Locality object.

Exceptions

BadIdentifierException if the locality's name already exists.

Definition at line 60 of file DataSet.cpp.

References bpp::Locality< T >::getName(), and localities_.

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

◆ alphabet()

const Alphabet& bpp::DataSet::alphabet ( ) const

inline

Get a reference toward the alphabet if there is sequence data.

Exceptions

NullPointerException if there is no sequence data.

Definition at line 573 of file DataSet.h.

References sequenceAlphabet_.

◆ analyzedLoci()

const AnalyzedLoci& bpp::DataSet::analyzedLoci ( ) const

inline

Get the AnalyzedLoci if there is one.

Exceptions

NullPointerException if there is no AnalyzedLoci.

Definition at line 621 of file DataSet.h.

References analyzedLoci_.

Referenced by bpp::GeneMapperCsvExport::read(), setAnalyzedLoci(), and bpp::DarwinVarSingle::write().

◆ deleteAnalyzedLoci()

void bpp::DataSet::deleteAnalyzedLoci ( )

inline

Delete the AnalyzedLoci.

Definition at line 631 of file DataSet.h.

References analyzedLoci_.

◆ deleteGroupAtPosition()

void DataSet::deleteGroupAtPosition ( size_t groupPosition )

Delete a Group from the DataSet.

Exceptions

IndexOutOfBoundsException if groupPosition exceeds the number of groups.

Definition at line 242 of file DataSet.cpp.

References groups_.

Referenced by mergeGroups(), and mergeTwoGroups().

◆ deleteIndividualAtPositionFromGroup()

void DataSet::deleteIndividualAtPositionFromGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)

Delete an Individual from a group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 447 of file DataSet.cpp.

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

◆ deleteIndividualByIdFromGroup()

void DataSet::deleteIndividualByIdFromGroup	(	size_t	groupPosition,
		const std::string &	individualId
	)

Delete an Individual from a group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndividualNotFoundException	if individual_id is not found.

Definition at line 463 of file DataSet.cpp.

References bpp::IndividualNotFoundException::getIdentifier(), getNumberOfGroups(), and groups_.

◆ deleteIndividualGenotypeInGroup()

void DataSet::deleteIndividualGenotypeInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)

Delete the MultilocusGenotype of an Individual from a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 856 of file DataSet.cpp.

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

◆ deleteIndividualSequenceAtPositionInGroup()

void DataSet::deleteIndividualSequenceAtPositionInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	sequencePosition
	)

Delete a Sequence of an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_position is not found.

Definition at line 724 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), groups_, and bpp::IndexOutOfBoundsException::what().

◆ deleteIndividualSequenceByNameInGroup()

void DataSet::deleteIndividualSequenceByNameInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const std::string &	sequenceName
	)

Delete a Sequence of an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 700 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), bpp::SequenceNotFoundException::getSequenceId(), and groups_.

◆ deleteLocalityAtPosition()

void DataSet::deleteLocalityAtPosition ( size_t localityPosition )

Delete a Locality from the DataSet.

Exceptions

IndexOutOfBoundsException if locality_position exceeds the number of Locality.

Definition at line 130 of file DataSet.cpp.

References localities_.

Referenced by deleteLocalityByName().

◆ deleteLocalityByName()

void DataSet::deleteLocalityByName ( const std::string & name )

Delete a Locality from the DataSet.

Exceptions

LocalityNotFoundException if the locality's name is not found.

Definition at line 139 of file DataSet.cpp.

References deleteLocalityAtPosition(), and getLocalityPosition().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::DataSet::getAlphabet ( ) const

inline

Get a pointer toward the alphabet if there is sequence data.

Exceptions

NullPointerException if there is no sequence data.

Definition at line 561 of file DataSet.h.

References sequenceAlphabet_.

Referenced by getPolymorphismSequenceContainer(), and bpp::PopgenlibIO::read().

◆ getAlphabetType()

std::string bpp::DataSet::getAlphabetType ( ) const

inline

Get the alphabet type as a string.

Exceptions

NullPointerException if there is no sequence data.

Definition at line 585 of file DataSet.h.

References sequenceAlphabet_.

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

◆ getGroupAtPosition()

const Group & DataSet::getGroupAtPosition ( size_t groupPosition ) const

Get a group by position.

Exceptions

IndexOutOfBoundsException if groupPosition exceeds the number of groups.

Definition at line 233 of file DataSet.cpp.

References groups_.

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

◆ getGroupById()

const Group & DataSet::getGroupById ( size_t group_id ) const

Get a group by identifier.

Definition at line 178 of file DataSet.cpp.

References groups_.

Referenced by getGroupName(), mergeGroups(), and mergeTwoGroups().

◆ getGroupName()

string DataSet::getGroupName ( size_t group_id ) const

Get the name of a Group. If the name is an empty string it just returns the group_id.

Exceptions

GroupNotFoundException if the group_id is not found.

Definition at line 193 of file DataSet.cpp.

References getGroupById(), bpp::Group::getGroupName(), and bpp::TextTools::toString().

◆ getGroupPosition()

size_t DataSet::getGroupPosition ( size_t group_id ) const

Get the position of a Group.

Exceptions

GroupNotFoundException if the group_id is not found.

Definition at line 221 of file DataSet.cpp.

References groups_.

Referenced by getPolymorphismMultiGContainer(), getPolymorphismSequenceContainer(), mergeGroups(), mergeTwoGroups(), bpp::PopgenlibIO::parseIndividual_(), bpp::GeneMapperCsvExport::read(), bpp::Genepop::read(), and splitGroup().

◆ getIndividualAtPositionFromGroup()

const Individual & DataSet::getIndividualAtPositionFromGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get an Individual from a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 415 of file DataSet.cpp.

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

Referenced by getPolymorphismMultiGContainer(), getPolymorphismSequenceContainer(), bpp::DarwinDon::write(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getIndividualByIdFromGroup()

const Individual & DataSet::getIndividualByIdFromGroup	(	size_t	groupPosition,
		const std::string &	individualId
	)		const

Get an Individual from a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndividualNotFoundException	if individual_id is not found.

Definition at line 431 of file DataSet.cpp.

References bpp::IndividualNotFoundException::getIdentifier(), getNumberOfGroups(), and groups_.

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

◆ getIndividualLocalityInGroup()

shared_ptr< const Locality< double > > DataSet::getIndividualLocalityInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get the Locality of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no locality.

Definition at line 603 of file DataSet.cpp.

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

◆ getIndividualMonolocusGenotypeInGroup()

const MonolocusGenotypeInterface & DataSet::getIndividualMonolocusGenotypeInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	locusPosition
	)		const

Get a MonolocusGenotype from an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position exceeds the number of locus.
AlleleNotFoundException	if at least one of the id is not found.

Definition at line 957 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), groups_, and bpp::IndexOutOfBoundsException::what().

◆ getIndividualNumberOfSequencesInGroup()

size_t DataSet::getIndividualNumberOfSequencesInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get the number of Sequences in an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.

Definition at line 792 of file DataSet.cpp.

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

◆ getIndividualPositionInGroup()

size_t DataSet::getIndividualPositionInGroup	(	size_t	groupPosition,
		const std::string &	individual_id
	)		const

Get the position of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndividualNotFoundException	if individual_id is not found.

Definition at line 399 of file DataSet.cpp.

References bpp::IndividualNotFoundException::getIdentifier(), getNumberOfGroups(), and groups_.

Referenced by bpp::GeneMapperCsvExport::read(), and bpp::Genepop::read().

◆ getIndividualSequenceAtPositionInGroup()

const Sequence & DataSet::getIndividualSequenceAtPositionInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	sequencePosition
	)		const

Get a Sequence from an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_position is not found.

Definition at line 676 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), groups_, and bpp::IndexOutOfBoundsException::what().

◆ getIndividualSequenceByNameInGroup()

const Sequence & DataSet::getIndividualSequenceByNameInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const std::string &	sequenceName
	)		const

Get a Sequence from an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_name is not found.
BadIntegerException	if sequence_position is already in use.

Definition at line 652 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), bpp::SequenceNotFoundException::getSequenceId(), and groups_.

◆ getIndividualSequencePositionInGroup()

size_t DataSet::getIndividualSequencePositionInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const std::string &	sequenceName
	)		const

Get the position of a Sequence in an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 768 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), bpp::SequenceNotFoundException::getSequenceId(), and groups_.

◆ getIndividualSequencesNamesInGroup()

std::vector< std::string > DataSet::getIndividualSequencesNamesInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get the Sequences' names from an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no sequences.

Definition at line 748 of file DataSet.cpp.

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

◆ getIndividualSexInGroup()

unsigned short DataSet::getIndividualSexInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get the sex of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 495 of file DataSet.cpp.

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

◆ getLocalityAtPosition()

shared_ptr< const Locality< double > > DataSet::getLocalityAtPosition ( size_t localityPosition ) const

Get a Locality by localityPosition.

Returns: A const pointer to the locality matching the locality_position.

Parameters

localityPosition The position of the Locality in the DataSet.

Exceptions

IndexOutOfBoundsException if locality_position exceeds the number of locality of the DataSet.

Definition at line 84 of file DataSet.cpp.

References localities_.

Referenced by getLocalityByName().

◆ getLocalityByName()

shared_ptr< const Locality< double > > DataSet::getLocalityByName ( const std::string & name ) const

Get a Locality by name.

Exceptions

LocalityNotFoundException if the locality's name is not found.

Definition at line 102 of file DataSet.cpp.

References getLocalityAtPosition(), and getLocalityPosition().

Referenced by bpp::PopgenlibIO::parseIndividual_(), and setIndividualLocalityInGroupByName().

◆ getLocalityPosition()

size_t DataSet::getLocalityPosition ( const std::string & name ) const

Get the position of a locality in the container.

Returns: The locality_position (position) of the Locality.

Parameters

name	The locality's name to find.

Exceptions

LocalityNotFoundException if the locality's name doesn't match any name in the DataSet.

Definition at line 72 of file DataSet.cpp.

References localities_.

Referenced by deleteLocalityByName(), getLocalityByName(), and localityByName().

◆ getLocusInfoAtPosition()

const LocusInfo & DataSet::getLocusInfoAtPosition ( size_t locus_position ) const

Get a LocusInfo by its position.

Definition at line 1030 of file DataSet.cpp.

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

Referenced by bpp::PopgenlibIO::parseIndividual_(), setIndividualMonolocusGenotypeByAlleleIdInGroup(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getLocusInfoByName()

const LocusInfo & DataSet::getLocusInfoByName ( const std::string & locus_name ) const

Get a LocusInfo by its name.

Definition at line 1014 of file DataSet.cpp.

References analyzedLoci_.

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

◆ getNumberOfGroups()

size_t DataSet::getNumberOfGroups ( ) const

Get the number of Groups.

Definition at line 251 of file DataSet.cpp.

References groups_.

Referenced by addEmptyIndividualToGroup(), addIndividualSequenceInGroup(), addIndividualToGroup(), deleteIndividualAtPositionFromGroup(), deleteIndividualByIdFromGroup(), deleteIndividualGenotypeInGroup(), deleteIndividualSequenceAtPositionInGroup(), deleteIndividualSequenceByNameInGroup(), getIndividualAtPositionFromGroup(), getIndividualByIdFromGroup(), getIndividualLocalityInGroup(), getIndividualMonolocusGenotypeInGroup(), getIndividualNumberOfSequencesInGroup(), getIndividualPositionInGroup(), getIndividualSequenceAtPositionInGroup(), getIndividualSequenceByNameInGroup(), getIndividualSequencePositionInGroup(), getIndividualSequencesNamesInGroup(), getIndividualSexInGroup(), getNumberOfIndividualsInGroup(), getPolymorphismMultiGContainer(), individualCoordInGroup(), individualDateInGroup(), initIndividualGenotypeInGroup(), setIndividualCoordInGroup(), setIndividualDateInGroup(), setIndividualGenotypeInGroup(), setIndividualLocalityInGroupByName(), setIndividualMonolocusGenotypeByAlleleIdInGroup(), setIndividualMonolocusGenotypeByAlleleKeyInGroup(), setIndividualMonolocusGenotypeInGroup(), setIndividualSexInGroup(), bpp::DarwinDon::write(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getNumberOfIndividualsInGroup()

size_t DataSet::getNumberOfIndividualsInGroup ( size_t groupPosition ) const

Get the number of Individuals in a Group.

Exceptions

IndexOutOfBoundsException if groupPosition exceeds the number of groups.

Definition at line 390 of file DataSet.cpp.

References getNumberOfGroups(), and groups_.

Referenced by getPolymorphismMultiGContainer(), bpp::DarwinDon::write(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getNumberOfLocalities()

size_t bpp::DataSet::getNumberOfLocalities ( ) const

inline

Get the number of Localities.

Definition at line 138 of file DataSet.h.

References localities_.

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

◆ getNumberOfLoci()

size_t DataSet::getNumberOfLoci ( ) const

Get the number of loci.

Definition at line 1090 of file DataSet.cpp.

References analyzedLoci_.

Referenced by initIndividualGenotypeInGroup(), bpp::PopgenlibIO::parseIndividual_(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ getPloidyByLocusName()

size_t DataSet::getPloidyByLocusName ( const std::string & locus_name ) const

Get the ploidy of a locus.

Definition at line 1099 of file DataSet.cpp.

References analyzedLoci_, and bpp::LocusNotFoundException::getIdentifier().

◆ getPloidyByLocusPosition()

size_t DataSet::getPloidyByLocusPosition ( size_t locus_position ) const

Get the ploidy of a locus.

Definition at line 1115 of file DataSet.cpp.

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

◆ getPolymorphismMultiGContainer() [1/2]

unique_ptr< PolymorphismMultiGContainer > DataSet::getPolymorphismMultiGContainer ( ) const

Get a PolymorphismMultiGContainer with all allelic data of the DataSet.

Definition at line 1131 of file DataSet.cpp.

References getIndividualAtPositionFromGroup(), getNumberOfGroups(), getNumberOfIndividualsInGroup(), and groups_.

◆ getPolymorphismMultiGContainer() [2/2]

unique_ptr< PolymorphismMultiGContainer > DataSet::getPolymorphismMultiGContainer ( const std::map< size_t, std::vector< size_t >> & selection ) const

Get a PolymorphismMultiGContainer from a selection of groups and individuals.

Parameters

selection A map with groups id as keys and vector of individuals position in each group as values.

Definition at line 1153 of file DataSet.cpp.

References getGroupPosition(), getIndividualAtPositionFromGroup(), and groups_.

◆ getPolymorphismSequenceContainer()

unique_ptr< PolymorphismSequenceContainer > DataSet::getPolymorphismSequenceContainer	(	const std::map< size_t, std::vector< size_t >> &	selection,
		size_t	sequence_position
	)		const

Get a PolymorphismSequenceContainer from a selection of groups and individuals.

All the sequences are ingroup. You may change their state after created the container.

Parameters

selection	A map with groups id as keys and vector of individuals position in each group as values.
sequence_position	The position of the sequence in the individuals;

Definition at line 1191 of file DataSet.cpp.

References getAlphabet(), getGroupPosition(), and getIndividualAtPositionFromGroup().

◆ hasAlleleicData()

bool bpp::DataSet::hasAlleleicData ( ) const

inline

Tell if there is alelelic data.

Definition at line 711 of file DataSet.h.

References analyzedLoci_.

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

◆ hasLocality()

bool bpp::DataSet::hasLocality ( ) const

inline

Tell if there is at least one locality.

Definition at line 143 of file DataSet.h.

References getNumberOfLocalities().

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

◆ hasSequenceData()

bool bpp::DataSet::hasSequenceData ( ) const

inline

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

Definition at line 706 of file DataSet.h.

References sequenceAlphabet_.

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

◆ individualCoordInGroup()

const Point2D< double > & DataSet::individualCoordInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get the coordinate of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no coordinate.

Definition at line 563 of file DataSet.cpp.

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

◆ individualDateInGroup()

const Date & DataSet::individualDateInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)		const

Get the Date of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no date.

Definition at line 527 of file DataSet.cpp.

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

◆ initAnalyzedLoci()

void bpp::DataSet::initAnalyzedLoci ( size_t numberOfLoci )

inline

Initialize the AnalyzedLoci for number of loci.

Exceptions

Exception if the AnalyzedLoci has already been initialized.

Definition at line 609 of file DataSet.h.

References analyzedLoci_.

Referenced by bpp::GeneMapperCsvExport::read(), bpp::Genepop::read(), and bpp::Genetix::read().

◆ initIndividualGenotypeInGroup()

void DataSet::initIndividualGenotypeInGroup	(	size_t	groupPosition,
		size_t	individualPosition
	)

Initialize the genotype of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
BadIntegerException	if the number of loci is < 1;
NullPointerException	if analyzed_loci is NULL.
Exception	if the individual already has a genotype.

Definition at line 828 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::BadIntegerException::getBadInteger(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), getNumberOfLoci(), and groups_.

Referenced by bpp::GeneMapperCsvExport::read(), bpp::Genepop::read(), and bpp::Genetix::read().

◆ localityAtPosition()

const Locality< double > & DataSet::localityAtPosition ( size_t localityPosition ) const

Get a Locality by localityPosition.

Returns: A const pointer to the locality matching the locality_position.

Parameters

localityPosition The position of the Locality in the DataSet.

Exceptions

IndexOutOfBoundsException if locality_position exceeds the number of locality of the DataSet.

Definition at line 93 of file DataSet.cpp.

References localities_.

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

◆ localityByName()

const Locality< double > & DataSet::localityByName ( const std::string & name ) const

Get a Locality by name.

Exceptions

LocalityNotFoundException if the locality's name is not found.

Definition at line 116 of file DataSet.cpp.

References getLocalityPosition(), and localityAtPosition().

◆ mergeGroups()

void DataSet::mergeGroups ( std::vector< size_t > & group_ids )

Merge some Groups in one.

Merge all the groups which are specified in the first one (smallest identifier). When a group is merged to the first, it is deleted from the DataSet.

Parameters

group_ids A vector size_t listing the id of groups to merge.

Exceptions

IndexOutOfBoundsException if one of the int in groups exceeds the number of groups.

Definition at line 289 of file DataSet.cpp.

References deleteGroupAtPosition(), getGroupAtPosition(), getGroupById(), getGroupPosition(), bpp::Group::getIndividualAtPosition(), bpp::Group::getNumberOfIndividuals(), and groups_.

◆ mergeTwoGroups()

void DataSet::mergeTwoGroups	(	size_t	source_id,
		size_t	target_id
	)

Merge two groups.

This method merge two groups. The source group is emptied into the target and then is deleted.

Definition at line 258 of file DataSet.cpp.

References deleteGroupAtPosition(), getGroupById(), getGroupPosition(), and groups_.

◆ operator=()

DataSet & DataSet::operator= ( const DataSet & ds )

Definition at line 33 of file DataSet.cpp.

References analyzedLoci_, groups_, localities_, and sequenceAlphabet_.

◆ setAlphabet() [1/2]

void DataSet::setAlphabet ( const std::string & alphaType )

Set the alphabet of the AnalyzedSequences by its type..

Definition at line 984 of file DataSet.cpp.

References bpp::AlphabetTools::DNA_ALPHABET, bpp::AlphabetTools::PROTEIN_ALPHABET, bpp::AlphabetTools::RNA_ALPHABET, and sequenceAlphabet_.

◆ setAlphabet() [2/2]

void bpp::DataSet::setAlphabet ( std::shared_ptr< const Alphabet > alpha )

inline

Set the alphabet of the AnalyzedSequences.

Definition at line 549 of file DataSet.h.

References sequenceAlphabet_.

Referenced by addIndividualSequenceInGroup(), addIndividualToGroup(), and bpp::PopgenlibIO::parseGeneral_().

◆ setAnalyzedLoci()

void bpp::DataSet::setAnalyzedLoci ( const AnalyzedLoci & analyzedLoci )

inline

Set the AnalyzedLoci to the DataSet.

Exceptions

Exception if at least one Individual has a genotype referring to the actual AnalyzedLoci.

Definition at line 599 of file DataSet.h.

References analyzedLoci(), analyzedLoci_, and bpp::AnalyzedLoci::clone().

Referenced by bpp::GeneMapperCsvExport::read(), and bpp::PopgenlibIO::read().

◆ setGroupName()

void DataSet::setGroupName	(	size_t	group_id,
		const std::string &	group_name
	)		const

set the name of a Group.

Exceptions

GroupNotFoundException if the group_id is not found.

Definition at line 206 of file DataSet.cpp.

References groups_.

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

◆ setIndividualCoordInGroup()

void DataSet::setIndividualCoordInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const Point2D< double > &	coord
	)

Set the coordinates of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 547 of file DataSet.cpp.

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

◆ setIndividualDateInGroup()

void DataSet::setIndividualDateInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const Date &	date
	)

Set the Date of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 511 of file DataSet.cpp.

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

◆ setIndividualGenotypeInGroup()

void DataSet::setIndividualGenotypeInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const MultilocusGenotype &	genotype
	)

Set the MultilocusGenotype of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 812 of file DataSet.cpp.

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

◆ setIndividualLocalityInGroupByName()

void DataSet::setIndividualLocalityInGroupByName	(	size_t	groupPosition,
		size_t	individualPosition,
		const std::string &	localityName
	)

Set the Locality of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
LocalityNotFoundException	if locality_name is not found.

Definition at line 583 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), bpp::LocalityNotFoundException::getIdentifier(), getLocalityByName(), getNumberOfGroups(), and groups_.

◆ setIndividualMonolocusGenotypeByAlleleIdInGroup()

void DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	locusPosition,
		const std::vector< std::string >	alleleId
	)

Set a MonolocusGenotype of an Individual from a group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position exceeds the number of locus.
Exception	if there is no key in allele_keys.

Definition at line 928 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), bpp::AlleleNotFoundException::getIdentifier(), getLocusInfoAtPosition(), getNumberOfGroups(), groups_, and bpp::IndexOutOfBoundsException::what().

Referenced by bpp::Genepop::read(), and bpp::Genetix::read().

◆ setIndividualMonolocusGenotypeByAlleleKeyInGroup()

void DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	locusPosition,
		const std::vector< size_t >	alleleKeys
	)

Set a MonolocusGenotype of an Individual from a group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position exceeds the number of locus.
Exception	if the ploidy doesn't match.

Definition at line 900 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), groups_, and bpp::IndexOutOfBoundsException::what().

◆ setIndividualMonolocusGenotypeInGroup()

void DataSet::setIndividualMonolocusGenotypeInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		size_t	locusPosition,
		const MonolocusGenotypeInterface &	monogen
	)

Set a MonolocusGenotype of an Individual from a group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position exceeds the number of locus.

Definition at line 872 of file DataSet.cpp.

References bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), getNumberOfGroups(), groups_, and bpp::IndexOutOfBoundsException::what().

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

◆ setIndividualSexInGroup()

void DataSet::setIndividualSexInGroup	(	size_t	groupPosition,
		size_t	individualPosition,
		const unsigned short	sex
	)

Set the sex of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if groupPosition exceeds the number of groups.
IndexOutOfBoundsException	if individualPosition exceeds the number of individual in the group.

Definition at line 479 of file DataSet.cpp.

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

◆ setLocusInfo()

void DataSet::setLocusInfo	(	size_t	locus_position,
		const LocusInfo &	locus
	)

Set a LocusInfo.

Exceptions

NullPointerException	if there is no AnalyzedLoci to setup.
IndexOutOfBoundsException	if locus_position exceeds the total of LocusInfo of the DataSet.

Definition at line 998 of file DataSet.cpp.

References analyzedLoci_.

Referenced by bpp::Genepop::read(), and bpp::Genetix::read().

◆ splitGroup()

void DataSet::splitGroup	(	size_t	group_id,
		std::vector< size_t >	individuals_selection
	)

Split a group in two.

Parameters

group_id	The identifier of the source group.
individuals_selection	The positions of the Individuals to extract from the group to make the new group.

Exceptions

GroupNotFoundException	if the group_id is not found.
IndexOutOfBoundsException	if one position of the selection exceeds the number of individuals of the group.

Definition at line 320 of file DataSet.cpp.

References addGroup(), bpp::Group::addIndividual(), getGroupPosition(), bpp::GroupNotFoundException::getIdentifier(), and groups_.

Member Data Documentation

◆ analyzedLoci_

std::unique_ptr<AnalyzedLoci> bpp::DataSet::analyzedLoci_

private

Definition at line 39 of file DataSet.h.

Referenced by addAlleleInfoByLocusName(), addAlleleInfoByLocusPosition(), analyzedLoci(), DataSet(), deleteAnalyzedLoci(), getLocusInfoAtPosition(), getLocusInfoByName(), getNumberOfLoci(), getPloidyByLocusName(), getPloidyByLocusPosition(), hasAlleleicData(), initAnalyzedLoci(), operator=(), setAnalyzedLoci(), and setLocusInfo().

◆ groups_

std::vector<std::unique_ptr<Group> > bpp::DataSet::groups_

private

Definition at line 42 of file DataSet.h.

Referenced by addEmptyGroup(), addEmptyIndividualToGroup(), addGroup(), addIndividualSequenceInGroup(), addIndividualToGroup(), DataSet(), deleteGroupAtPosition(), deleteIndividualAtPositionFromGroup(), deleteIndividualByIdFromGroup(), deleteIndividualGenotypeInGroup(), deleteIndividualSequenceAtPositionInGroup(), deleteIndividualSequenceByNameInGroup(), getGroupAtPosition(), getGroupById(), getGroupPosition(), getIndividualAtPositionFromGroup(), getIndividualByIdFromGroup(), getIndividualLocalityInGroup(), getIndividualMonolocusGenotypeInGroup(), getIndividualNumberOfSequencesInGroup(), getIndividualPositionInGroup(), getIndividualSequenceAtPositionInGroup(), getIndividualSequenceByNameInGroup(), getIndividualSequencePositionInGroup(), getIndividualSequencesNamesInGroup(), getIndividualSexInGroup(), getNumberOfGroups(), getNumberOfIndividualsInGroup(), getPolymorphismMultiGContainer(), individualCoordInGroup(), individualDateInGroup(), initIndividualGenotypeInGroup(), mergeGroups(), mergeTwoGroups(), operator=(), setGroupName(), setIndividualCoordInGroup(), setIndividualDateInGroup(), setIndividualGenotypeInGroup(), setIndividualLocalityInGroupByName(), setIndividualMonolocusGenotypeByAlleleIdInGroup(), setIndividualMonolocusGenotypeByAlleleKeyInGroup(), setIndividualMonolocusGenotypeInGroup(), setIndividualSexInGroup(), and splitGroup().

◆ localities_

std::vector<std::shared_ptr<Locality<double> > > bpp::DataSet::localities_

private

Definition at line 41 of file DataSet.h.

Referenced by addLocality(), DataSet(), deleteLocalityAtPosition(), getLocalityAtPosition(), getLocalityPosition(), getNumberOfLocalities(), localityAtPosition(), and operator=().

◆ sequenceAlphabet_

std::shared_ptr<const Alphabet> bpp::DataSet::sequenceAlphabet_

private

Definition at line 40 of file DataSet.h.

Referenced by alphabet(), getAlphabet(), getAlphabetType(), hasSequenceData(), operator=(), and setAlphabet().

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

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DataSet() [1/2]

◆ ~DataSet()

◆ DataSet() [2/2]

Member Function Documentation

◆ addAlleleInfoByLocusName()

◆ addAlleleInfoByLocusPosition()

◆ addEmptyGroup()

◆ addEmptyIndividualToGroup()

◆ addGroup()

◆ addIndividualSequenceInGroup()

◆ addIndividualToGroup()

◆ addLocality()

◆ alphabet()

◆ analyzedLoci()

◆ deleteAnalyzedLoci()

◆ deleteGroupAtPosition()

◆ deleteIndividualAtPositionFromGroup()

◆ deleteIndividualByIdFromGroup()

◆ deleteIndividualGenotypeInGroup()

◆ deleteIndividualSequenceAtPositionInGroup()

◆ deleteIndividualSequenceByNameInGroup()

◆ deleteLocalityAtPosition()

◆ deleteLocalityByName()

◆ getAlphabet()

◆ getAlphabetType()

◆ getGroupAtPosition()

◆ getGroupById()

◆ getGroupName()

◆ getGroupPosition()

◆ getIndividualAtPositionFromGroup()

◆ getIndividualByIdFromGroup()

◆ getIndividualLocalityInGroup()

◆ getIndividualMonolocusGenotypeInGroup()

◆ getIndividualNumberOfSequencesInGroup()

◆ getIndividualPositionInGroup()

◆ getIndividualSequenceAtPositionInGroup()

◆ getIndividualSequenceByNameInGroup()

◆ getIndividualSequencePositionInGroup()

◆ getIndividualSequencesNamesInGroup()

◆ getIndividualSexInGroup()

◆ getLocalityAtPosition()

◆ getLocalityByName()

◆ getLocalityPosition()

◆ getLocusInfoAtPosition()

◆ getLocusInfoByName()

◆ getNumberOfGroups()

◆ getNumberOfIndividualsInGroup()

◆ getNumberOfLocalities()

◆ getNumberOfLoci()

◆ getPloidyByLocusName()

◆ getPloidyByLocusPosition()

◆ getPolymorphismMultiGContainer() [1/2]

◆ getPolymorphismMultiGContainer() [2/2]

◆ getPolymorphismSequenceContainer()

◆ hasAlleleicData()

◆ hasLocality()

◆ hasSequenceData()

◆ individualCoordInGroup()

◆ individualDateInGroup()

◆ initAnalyzedLoci()

◆ initIndividualGenotypeInGroup()

◆ localityAtPosition()

◆ localityByName()

◆ mergeGroups()

◆ mergeTwoGroups()

◆ operator=()

◆ setAlphabet() [1/2]

◆ setAlphabet() [2/2]

◆ setAnalyzedLoci()

◆ setGroupName()

◆ setIndividualCoordInGroup()

◆ setIndividualDateInGroup()

◆ setIndividualGenotypeInGroup()

◆ setIndividualLocalityInGroupByName()

◆ setIndividualMonolocusGenotypeByAlleleIdInGroup()

◆ setIndividualMonolocusGenotypeByAlleleKeyInGroup()