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

Collaboration diagram for bpp::DataSet:

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

	~DataSet ()
	Destroy a DataSet. More...

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

DataSet &	operator= (const DataSet &ds)

void	addLocality (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...

const Locality< double > &	getLocalityAtPosition (size_t locality_position) const
	Get a Locality by locality_position. More...

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

void	deleteLocalityAtPosition (size_t locality_position)
	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 group_position) const
	Get a group by position. More...

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

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

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

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

const Individual *	getIndividualAtPositionFromGroup (size_t group_position, size_t individual_position) const
	Get an Individual from a Group. More...

const Individual *	getIndividualByIdFromGroup (size_t group_position, const std::string &individual_id) const
	Get an Individual from a Group. More...

void	deleteIndividualAtPositionFromGroup (size_t group_position, size_t individual_position)
	Delete an Individual from a group. More...

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

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

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

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

const Date *	getIndividualDateInGroup (size_t group_position, size_t individual_position) const
	Get the Date of an Individual in a Group. More...

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

const Point2D< double > *	getIndividualCoordInGroup (size_t group_position, size_t individual_position) const
	Get the coordinate of an Individual in a Group. More...

void	setIndividualLocalityInGroupByName (size_t group_position, size_t individual_position, const std::string &locality_name)
	Set the Locality of an Individual in a Group. More...

const Locality< double > *	getIndividualLocalityInGroup (size_t group_position, size_t individual_position) const
	Get the Locality of an Individual in a Group. More...

void	addIndividualSequenceInGroup (size_t group_position, size_t individual_position, size_t sequence_position, const Sequence &sequence)
	Add a Sequence to an Individual in a Group. More...

const Sequence &	getIndividualSequenceByNameInGroup (size_t group_position, size_t individual_position, const std::string &sequence_name) const
	Get a Sequence from an Individual of a Group. More...

const Sequence &	getIndividualSequenceAtPositionInGroup (size_t group_position, size_t individual_position, size_t sequence_position) const
	Get a Sequence from an Individual of a Group. More...

void	deleteIndividualSequenceByNameInGroup (size_t group_position, size_t individual_position, const std::string &sequence_name)
	Delete a Sequence of an Individual of a Group. More...

void	deleteIndividualSequenceAtPositionInGroup (size_t group_position, size_t individual_position, size_t sequence_position)
	Delete a Sequence of an Individual of a Group. More...

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

size_t	getIndividualSequencePositionInGroup (size_t group_position, size_t individual_position, const std::string &sequence_name) const
	Get the position of a Sequence in an Individual of a Group. More...

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

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

void	initIndividualGenotypeInGroup (size_t group_position, size_t individual_position)
	Initialyze the genotype of an Individual in a Group. More...

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

void	setIndividualMonolocusGenotypeInGroup (size_t group_position, size_t individual_position, size_t locus_position, const MonolocusGenotype &monogen)
	Set a MonolocusGenotype of an Individual from a group. More...

void	setIndividualMonolocusGenotypeByAlleleKeyInGroup (size_t group_position, size_t individual_position, size_t locus_position, const std::vector< size_t > allele_keys)
	Set a MonolocusGenotype of an Individual from a group. More...

void	setIndividualMonolocusGenotypeByAlleleIdInGroup (size_t group_position, size_t individual_position, size_t locus_position, const std::vector< std::string > allele_id)
	Set a MonolocusGenotype of an Individual from a group. More...

const MonolocusGenotype *	getIndividualMonolocusGenotypeInGroup (size_t group_position, size_t individual_position, size_t locus_position) const
	Get a MonolocusGenotype from an Individual of a Group. More...

void	setAlphabet (const Alphabet *alpha)
	Set the alphabet of the AnalyzedSequences. More...

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

const Alphabet *	getAlphabet () const
	Get 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 number_of_loci)
	Initialize the AnalyzedLoci for number of loci. More...

const AnalyzedLoci *	getAnalyzedLoci () 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...

PolymorphismMultiGContainer *	getPolymorphismMultiGContainer () const
	Get a PolymorphismMultiGContainer with all allelic data of the DataSet. More...

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

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
AnalyzedLoci *	analyzedLoci_

AnalyzedSequences *	analyzedSequences_

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

std::vector< 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 72 of file DataSet.h.

Constructor & Destructor Documentation

◆ DataSet() [1/2]

DataSet::DataSet ( )

Build a new void DataSet.

Definition at line 48 of file DataSet.cpp.

◆ ~DataSet()

DataSet::~DataSet ( )

Destroy a DataSet.

Definition at line 98 of file DataSet.cpp.

References analyzedLoci_, analyzedSequences_, getNumberOfGroups(), getNumberOfLocalities(), groups_, and localities_.

◆ DataSet() [2/2]

DataSet::DataSet ( const DataSet & ds )

Copy constructor.

Definition at line 55 of file DataSet.cpp.

References analyzedLoci_, analyzedSequences_, 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 1162 of file DataSet.cpp.

References bpp::AnalyzedLoci::addAlleleInfoByLocusName(), 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 1182 of file DataSet.cpp.

References bpp::AnalyzedLoci::addAlleleInfoByLocusPosition(), 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 217 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	group_position,
		const std::string &	individual_id
	)

Add an empty Individual to a Group.

Exceptions

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

Definition at line 423 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 205 of file DataSet.cpp.

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

Referenced by splitGroup().

◆ addIndividualSequenceInGroup()

void DataSet::addIndividualSequenceInGroup	(	size_t	group_position,
		size_t	individual_position,
		size_t	sequence_position,
		const Sequence &	sequence
	)

Add a Sequence to an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes 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 672 of file DataSet.cpp.

References bpp::Sequence::getAlphabet(), bpp::AlphabetMismatchException::getAlphabets(), bpp::IndexOutOfBoundsException::getBadIndex(), bpp::IndexOutOfBoundsException::getBounds(), bpp::BadIdentifierException::getIdentifier(), getNumberOfGroups(), groups_, and setAlphabet().

◆ addIndividualToGroup()

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

Add an Individual to a Group.

Exceptions

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

Definition at line 405 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 ( 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 119 of file DataSet.cpp.

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

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

◆ deleteAnalyzedLoci()

void DataSet::deleteAnalyzedLoci ( )

Delete the AnalyzedLoci.

Definition at line 1102 of file DataSet.cpp.

References analyzedLoci_.

Referenced by setAnalyzedLoci().

◆ deleteGroupAtPosition()

void DataSet::deleteGroupAtPosition ( size_t group_position )

Delete a Group from the DataSet.

Exceptions

IndexOutOfBoundsException if group_position excedes the number of groups.

Definition at line 290 of file DataSet.cpp.

References groups_.

Referenced by mergeGroups(), and mergeTwoGroups().

◆ deleteIndividualAtPositionFromGroup()

void DataSet::deleteIndividualAtPositionFromGroup	(	size_t	group_position,
		size_t	individual_position
	)

Delete an Individual from a group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 496 of file DataSet.cpp.

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

◆ deleteIndividualByIdFromGroup()

void DataSet::deleteIndividualByIdFromGroup	(	size_t	group_position,
		const std::string &	individual_id
	)

Delete an Individual from a group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndividualNotFoundException	if individual_id is not found.

Definition at line 512 of file DataSet.cpp.

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

◆ deleteIndividualGenotypeInGroup()

void DataSet::deleteIndividualGenotypeInGroup	(	size_t	group_position,
		size_t	individual_position
	)

Delete the MultilocusGenotype of an Individual from a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 905 of file DataSet.cpp.

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

◆ deleteIndividualSequenceAtPositionInGroup()

void DataSet::deleteIndividualSequenceAtPositionInGroup	(	size_t	group_position,
		size_t	individual_position,
		size_t	sequence_position
	)

Delete a Sequence of an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_position is not found.

Definition at line 773 of file DataSet.cpp.

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

◆ deleteIndividualSequenceByNameInGroup()

void DataSet::deleteIndividualSequenceByNameInGroup	(	size_t	group_position,
		size_t	individual_position,
		const std::string &	sequence_name
	)

Delete a Sequence of an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 749 of file DataSet.cpp.

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

◆ deleteLocalityAtPosition()

void DataSet::deleteLocalityAtPosition ( size_t locality_position )

Delete a Locality from the DataSet.

Exceptions

IndexOutOfBoundsException if locality_position excedes the number of Locality.

Definition at line 166 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 176 of file DataSet.cpp.

References deleteLocalityAtPosition(), and getLocalityPosition().

◆ getAlphabet()

const Alphabet * DataSet::getAlphabet ( ) const

Get the alphabet if there is sequence data.

Exceptions

NullPointerException if there is no sequence data.

Definition at line 1046 of file DataSet.cpp.

References analyzedSequences_, and bpp::AnalyzedSequences::getAlphabet().

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

◆ getAlphabetType()

std::string DataSet::getAlphabetType ( ) const

Get the alphabet type as a string.

Exceptions

NullPointerException if there is no sequence data.

Definition at line 1055 of file DataSet.cpp.

References analyzedSequences_, and bpp::AnalyzedSequences::getAlphabetType().

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

◆ getAnalyzedLoci()

const AnalyzedLoci * DataSet::getAnalyzedLoci ( ) const

Get the AnalyzedLoci if there is one.

Exceptions

NullPointerException if there is no AnalyzedLoci.

Definition at line 1093 of file DataSet.cpp.

References analyzedLoci_.

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

◆ getGroupAtPosition()

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

Get a group by position.

Exceptions

IndexOutOfBoundsException if group_position excedes the number of groups.

Definition at line 281 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 229 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 241 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 269 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	group_position,
		size_t	individual_position
	)		const

Get an Individual from a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 464 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	group_position,
		const std::string &	individual_id
	)		const

Get an Individual from a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndividualNotFoundException	if individual_id is not found.

Definition at line 480 of file DataSet.cpp.

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

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

◆ getIndividualCoordInGroup()

const Point2D< double > * DataSet::getIndividualCoordInGroup	(	size_t	group_position,
		size_t	individual_position
	)		const

Get the coordinate of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no coordinate.

Definition at line 612 of file DataSet.cpp.

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

◆ getIndividualDateInGroup()

const Date * DataSet::getIndividualDateInGroup	(	size_t	group_position,
		size_t	individual_position
	)		const

Get the Date of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no date.

Definition at line 576 of file DataSet.cpp.

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

◆ getIndividualLocalityInGroup()

const Locality< double > * DataSet::getIndividualLocalityInGroup	(	size_t	group_position,
		size_t	individual_position
	)		const

Get the Locality of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no locality.

Definition at line 652 of file DataSet.cpp.

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

◆ getIndividualMonolocusGenotypeInGroup()

const MonolocusGenotype * DataSet::getIndividualMonolocusGenotypeInGroup	(	size_t	group_position,
		size_t	individual_position,
		size_t	locus_position
	)		const

Get a MonolocusGenotype from an Individual of a Group.

Exceptions

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

Definition at line 1002 of file DataSet.cpp.

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

◆ getIndividualNumberOfSequencesInGroup()

size_t DataSet::getIndividualNumberOfSequencesInGroup	(	size_t	group_position,
		size_t	individual_position
	)		const

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

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no sequences.

Definition at line 841 of file DataSet.cpp.

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

◆ getIndividualPositionInGroup()

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

Get the position of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndividualNotFoundException	if individual_id is not found.

Definition at line 448 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	group_position,
		size_t	individual_position,
		size_t	sequence_position
	)		const

Get a Sequence from an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_position is not found.

Definition at line 725 of file DataSet.cpp.

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

◆ getIndividualSequenceByNameInGroup()

const Sequence & DataSet::getIndividualSequenceByNameInGroup	(	size_t	group_position,
		size_t	individual_position,
		const std::string &	sequence_name
	)		const

Get a Sequence from an Individual of a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes 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 701 of file DataSet.cpp.

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

◆ getIndividualSequencePositionInGroup()

size_t DataSet::getIndividualSequencePositionInGroup	(	size_t	group_position,
		size_t	individual_position,
		const std::string &	sequence_name
	)		const

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

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no sequences.
SequenceNotFoundException	if sequence_name is not found.

Definition at line 817 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	group_position,
		size_t	individual_position
	)		const

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

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no sequences.

Definition at line 797 of file DataSet.cpp.

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

◆ getIndividualSexInGroup()

unsigned short DataSet::getIndividualSexInGroup	(	size_t	group_position,
		size_t	individual_position
	)		const

Get the sex of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 544 of file DataSet.cpp.

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

◆ getLocalityAtPosition()

const Locality< double > & DataSet::getLocalityAtPosition ( size_t locality_position ) const

Get a Locality by locality_position.

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

Parameters

locality_position The position of the Locality in the DataSet.

Exceptions

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

Definition at line 143 of file DataSet.cpp.

References localities_.

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

◆ getLocalityByName()

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 152 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 131 of file DataSet.cpp.

References localities_.

Referenced by deleteLocalityByName(), and getLocalityByName().

◆ getLocusInfoAtPosition()

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

Get a LocusInfo by its position.

Definition at line 1142 of file DataSet.cpp.

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

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 1126 of file DataSet.cpp.

References analyzedLoci_, and bpp::AnalyzedLoci::getLocusInfoByName().

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

◆ getNumberOfGroups()

size_t DataSet::getNumberOfGroups ( ) const

Get the number of Groups.

Definition at line 300 of file DataSet.cpp.

References groups_.

◆ getNumberOfIndividualsInGroup()

size_t DataSet::getNumberOfIndividualsInGroup ( size_t group_position ) const

Get the number of Individuals in a Group.

Exceptions

IndexOutOfBoundsException if group_position excedes the number of groups.

Definition at line 439 of file DataSet.cpp.

References getNumberOfGroups(), and groups_.

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

◆ getNumberOfLocalities()

size_t DataSet::getNumberOfLocalities ( ) const

Get the number of Localities.

Definition at line 190 of file DataSet.cpp.

References localities_.

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

◆ getNumberOfLoci()

size_t DataSet::getNumberOfLoci ( ) const

Get the number of loci.

Definition at line 1202 of file DataSet.cpp.

References analyzedLoci_, and bpp::AnalyzedLoci::getNumberOfLoci().

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 1211 of file DataSet.cpp.

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

◆ getPloidyByLocusPosition()

size_t DataSet::getPloidyByLocusPosition ( size_t locus_position ) const

Get the ploidy of a locus.

Definition at line 1227 of file DataSet.cpp.

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

◆ getPolymorphismMultiGContainer() [1/2]

PolymorphismMultiGContainer * DataSet::getPolymorphismMultiGContainer ( ) const

Get a PolymorphismMultiGContainer with all allelic data of the DataSet.

Definition at line 1245 of file DataSet.cpp.

References bpp::PolymorphismMultiGContainer::addGroupName(), bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::Individual::getGenotype(), getIndividualAtPositionFromGroup(), getNumberOfGroups(), getNumberOfIndividualsInGroup(), groups_, and bpp::Individual::hasGenotype().

◆ getPolymorphismMultiGContainer() [2/2]

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 1268 of file DataSet.cpp.

References bpp::PolymorphismMultiGContainer::addGroupName(), bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::Individual::getGenotype(), getGroupPosition(), getIndividualAtPositionFromGroup(), groups_, and bpp::Individual::hasGenotype().

◆ getPolymorphismSequenceContainer()

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 1307 of file DataSet.cpp.

References bpp::PolymorphismSequenceContainer::addSequenceWithFrequency(), getAlphabet(), getGroupPosition(), getIndividualAtPositionFromGroup(), bpp::Sequence::getName(), bpp::Individual::getSequenceAtPosition(), bpp::Individual::hasSequenceAtPosition(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ hasAlleleicData()

bool DataSet::hasAlleleicData ( ) const

Tell if there is alelelic data.

Definition at line 1356 of file DataSet.cpp.

References analyzedLoci_.

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

◆ hasLocality()

bool DataSet::hasLocality ( ) const

Tell if there is at least one locality.

Definition at line 197 of file DataSet.cpp.

References getNumberOfLocalities().

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

◆ hasSequenceData()

bool DataSet::hasSequenceData ( ) const

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

Definition at line 1349 of file DataSet.cpp.

References analyzedSequences_.

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

◆ initAnalyzedLoci()

void DataSet::initAnalyzedLoci ( size_t number_of_loci )

Initialize the AnalyzedLoci for number of loci.

Exceptions

Exception if the AnalyzedLoci has already been initialyzed.

Definition at line 1084 of file DataSet.cpp.

References analyzedLoci_.

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

◆ initIndividualGenotypeInGroup()

void DataSet::initIndividualGenotypeInGroup	(	size_t	group_position,
		size_t	individual_position
	)

Initialyze the genotype of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes 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 877 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().

◆ 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 excedes the number of groups.

Definition at line 338 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 methode merge two groups. The source group is emptied into the target and then is deleted.

Definition at line 307 of file DataSet.cpp.

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

◆ operator=()

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

Definition at line 78 of file DataSet.cpp.

References analyzedLoci_, analyzedSequences_, groups_, and localities_.

◆ setAlphabet() [1/2]

void DataSet::setAlphabet ( const Alphabet * alpha )

Set the alphabet of the AnalyzedSequences.

Definition at line 1028 of file DataSet.cpp.

References analyzedSequences_, and bpp::AnalyzedSequences::setAlphabet().

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

◆ setAlphabet() [2/2]

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

Set the alphabet of the AnalyzedSequences by its type..

Definition at line 1037 of file DataSet.cpp.

References analyzedSequences_, and bpp::AnalyzedSequences::setAlphabet().

◆ setAnalyzedLoci()

void DataSet::setAnalyzedLoci ( const AnalyzedLoci & analyzedLoci )

Set the AnalyzedLoci to the DataSet.

Exceptions

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

Definition at line 1066 of file DataSet.cpp.

References analyzedLoci_, and deleteAnalyzedLoci().

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 254 of file DataSet.cpp.

References groups_.

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

◆ setIndividualCoordInGroup()

void DataSet::setIndividualCoordInGroup	(	size_t	group_position,
		size_t	individual_position,
		const Point2D< double > &	coord
	)

Set the coordinates of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 596 of file DataSet.cpp.

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

◆ setIndividualDateInGroup()

void DataSet::setIndividualDateInGroup	(	size_t	group_position,
		size_t	individual_position,
		const Date &	date
	)

Set the Date of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 560 of file DataSet.cpp.

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

◆ setIndividualGenotypeInGroup()

void DataSet::setIndividualGenotypeInGroup	(	size_t	group_position,
		size_t	individual_position,
		const MultilocusGenotype &	genotype
	)

Set the MultilocusGenotype of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 861 of file DataSet.cpp.

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

◆ setIndividualLocalityInGroupByName()

void DataSet::setIndividualLocalityInGroupByName	(	size_t	group_position,
		size_t	individual_position,
		const std::string &	locality_name
	)

Set the Locality of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
LocalityNotFoundException	if locality_name is not found.

Definition at line 632 of file DataSet.cpp.

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

◆ setIndividualMonolocusGenotypeByAlleleIdInGroup()

void DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup	(	size_t	group_position,
		size_t	individual_position,
		size_t	locus_position,
		const std::vector< std::string >	allele_id
	)

Set a MonolocusGenotype of an Individual from a group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
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 973 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	group_position,
		size_t	individual_position,
		size_t	locus_position,
		const std::vector< size_t >	allele_keys
	)

Set a MonolocusGenotype of an Individual from a group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position excedes the number of locus.
Exception	if the ploidy doesn't match.

Definition at line 945 of file DataSet.cpp.

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

◆ setIndividualMonolocusGenotypeInGroup()

void DataSet::setIndividualMonolocusGenotypeInGroup	(	size_t	group_position,
		size_t	individual_position,
		size_t	locus_position,
		const MonolocusGenotype &	monogen
	)

Set a MonolocusGenotype of an Individual from a group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.
NullPointerException	if the individual has no genotype.
IndexOutOfBoundsException	if locus_position excedes the number of locus.

Definition at line 921 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	group_position,
		size_t	individual_position,
		const unsigned short	sex
	)

Set the sex of an Individual in a Group.

Exceptions

IndexOutOfBoundsException	if group_position excedes the number of groups.
IndexOutOfBoundsException	if individual_position excedes the number of individual in the group.

Definition at line 528 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 excedes the total of LocusInfo of the DataSet.

Definition at line 1110 of file DataSet.cpp.

References analyzedLoci_, bpp::AnalyzedLoci::getNumberOfLoci(), and bpp::AnalyzedLoci::setLocusInfo().

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 excedes the number of individuals of the group.

Definition at line 369 of file DataSet.cpp.

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

Member Data Documentation

◆ analyzedLoci_

AnalyzedLoci* bpp::DataSet::analyzedLoci_

private

Definition at line 75 of file DataSet.h.

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

◆ analyzedSequences_

AnalyzedSequences* bpp::DataSet::analyzedSequences_

private

Definition at line 76 of file DataSet.h.

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

◆ groups_

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

private

Definition at line 78 of file DataSet.h.

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

◆ localities_

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

private

Definition at line 77 of file DataSet.h.

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

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()

◆ deleteAnalyzedLoci()

◆ deleteGroupAtPosition()

◆ deleteIndividualAtPositionFromGroup()

◆ deleteIndividualByIdFromGroup()

◆ deleteIndividualGenotypeInGroup()

◆ deleteIndividualSequenceAtPositionInGroup()

◆ deleteIndividualSequenceByNameInGroup()

◆ deleteLocalityAtPosition()

◆ deleteLocalityByName()

◆ getAlphabet()

◆ getAlphabetType()

◆ getAnalyzedLoci()

◆ getGroupAtPosition()

◆ getGroupById()

◆ getGroupName()

◆ getGroupPosition()

◆ getIndividualAtPositionFromGroup()

◆ getIndividualByIdFromGroup()

◆ getIndividualCoordInGroup()

◆ getIndividualDateInGroup()

◆ 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()

◆ initAnalyzedLoci()

◆ initIndividualGenotypeInGroup()

◆ mergeGroups()

◆ mergeTwoGroups()

◆ operator=()

◆ setAlphabet() [1/2]

◆ setAlphabet() [2/2]

◆ setAnalyzedLoci()

◆ setGroupName()

◆ setIndividualCoordInGroup()

◆ setIndividualDateInGroup()

◆ setIndividualGenotypeInGroup()

◆ setIndividualLocalityInGroupByName()

◆ setIndividualMonolocusGenotypeByAlleleIdInGroup()

◆ setIndividualMonolocusGenotypeByAlleleKeyInGroup()

◆ setIndividualMonolocusGenotypeInGroup()

◆ setIndividualSexInGroup()

◆ setLocusInfo()