The PolymorphismMultiGContainer class. More...

#include <Bpp/PopGen/PolymorphismMultiGContainer.h>

Collaboration diagram for bpp::PolymorphismMultiGContainer:

Public Member Functions
	PolymorphismMultiGContainer ()
	Build a new PolymorphismMultilocusGenotypeContainer. More...

	PolymorphismMultiGContainer (const PolymorphismMultiGContainer &pmgc)
	The copy constructor. More...

	~PolymorphismMultiGContainer ()
	Destroy a PolymorphismMultilocusGenotypeContainer. More...

PolymorphismMultiGContainer &	operator= (const PolymorphismMultiGContainer &pmgc)
	The assignation operator=. More...

void	addMultilocusGenotype (const MultilocusGenotype &mg, size_t group)
	Add a MultilocusGenotype to the container. More...

const MultilocusGenotype *	getMultilocusGenotype (size_t position) const
	Get a MultilocusGenotype at a position. More...

MultilocusGenotype *	removeMultilocusGenotype (size_t position)
	Remove a MultilocusGenotype. More...

void	deleteMultilocusGenotype (size_t position)
	Delete a MultilocusGenotype. More...

bool	isAligned () const
	Tell if the MultilocusGenotypes are aligned (i.e. same size). More...

size_t	getNumberOfLoci () const
	Get the number of loci if the MultilocusGenotypes are aligned. More...

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

void	setGroupId (size_t position, size_t group_id)
	Set the Group id of a MultilocusGenotype. More...

std::set< size_t >	getAllGroupsIds () const
	Get the groups' ids. More...

std::vector< std::string >	getAllGroupsNames () const
	Get the groups names or ids if not available. More...

bool	groupExists (size_t group) const
	Tell if a group exists. More...

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

size_t	getGroupSize (size_t group) const
	Get group size. More...

std::string	getGroupName (size_t group_id) const
	Get the group name for a given group id or just the id if not available juste return it's id. More...

void	setGroupName (size_t group_id, std::string name)
	Set the name for the given group id. More...

void	addGroupName (size_t group_id, std::string name)
	Inserts a name for the given group id. More...

size_t	getLocusGroupSize (size_t group, size_t locus_position) const
	Get the size of a group for a given locus. More...

size_t	size () const
	Get the number of MultilocusGenotype. More...

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

Private Attributes
std::vector< MultilocusGenotype * >	multilocusGenotypes_

std::vector< size_t >	groups_

std::map< size_t, std::string >	groups_names_

Detailed Description

The PolymorphismMultiGContainer class.

This class is a container of MultilocusGenotype.

Author: Sylvain Gaillard

Definition at line 67 of file PolymorphismMultiGContainer.h.

Constructor & Destructor Documentation

◆ PolymorphismMultiGContainer() [1/2]

PolymorphismMultiGContainer::PolymorphismMultiGContainer ( )

Build a new PolymorphismMultilocusGenotypeContainer.

Definition at line 47 of file PolymorphismMultiGContainer.cpp.

◆ PolymorphismMultiGContainer() [2/2]

PolymorphismMultiGContainer::PolymorphismMultiGContainer ( const PolymorphismMultiGContainer & pmgc )

The copy constructor.

Definition at line 51 of file PolymorphismMultiGContainer.cpp.

References getAllGroupsIds(), getGroupId(), getGroupName(), getMultilocusGenotype(), groups_, groups_names_, multilocusGenotypes_, and size().

◆ ~PolymorphismMultiGContainer()

PolymorphismMultiGContainer::~PolymorphismMultiGContainer ( )

Destroy a PolymorphismMultilocusGenotypeContainer.

Definition at line 71 of file PolymorphismMultiGContainer.cpp.

References clear().

Member Function Documentation

◆ addGroupName()

void PolymorphismMultiGContainer::addGroupName	(	size_t	group_id,
		std::string	name
	)

Inserts a name for the given group id.

Definition at line 276 of file PolymorphismMultiGContainer.cpp.

References groups_names_.

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

◆ addMultilocusGenotype()

void PolymorphismMultiGContainer::addMultilocusGenotype	(	const MultilocusGenotype &	mg,
		size_t	group
	)

Add a MultilocusGenotype to the container.

Definition at line 99 of file PolymorphismMultiGContainer.cpp.

References groups_, groups_names_, and multilocusGenotypes_.

Referenced by bpp::PolymorphismMultiGContainerTools::extractGroups(), bpp::DataSet::getPolymorphismMultiGContainer(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), and bpp::PolymorphismMultiGContainerTools::permutMonoG().

◆ clear()

void PolymorphismMultiGContainer::clear ( )

Clear the container.

Definition at line 311 of file PolymorphismMultiGContainer.cpp.

References groups_, groups_names_, and multilocusGenotypes_.

Referenced by operator=(), and ~PolymorphismMultiGContainer().

◆ deleteMultilocusGenotype()

void PolymorphismMultiGContainer::deleteMultilocusGenotype ( size_t position )

Delete a MultilocusGenotype.

Exceptions

IndexOutOfBoundsException if position excedes the size of the container.

Definition at line 134 of file PolymorphismMultiGContainer.cpp.

References groups_, multilocusGenotypes_, and size().

◆ getAllGroupsIds()

std::set< size_t > PolymorphismMultiGContainer::getAllGroupsIds ( ) const

Get the groups' ids.

Definition at line 189 of file PolymorphismMultiGContainer.cpp.

References groups_, and size().

Referenced by bpp::PolymorphismMultiGContainerTools::extractGroups(), getNumberOfGroups(), operator=(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), bpp::PolymorphismMultiGContainerTools::permutMonoG(), and PolymorphismMultiGContainer().

◆ getAllGroupsNames()

std::vector< std::string > PolymorphismMultiGContainer::getAllGroupsNames ( ) const

Get the groups names or ids if not available.

Definition at line 201 of file PolymorphismMultiGContainer.cpp.

References groups_names_, and bpp::TextTools::toString().

Referenced by bpp::MultilocusGenotypeStatistics::getDistanceMatrix().

◆ getGroupId()

size_t PolymorphismMultiGContainer::getGroupId ( size_t position ) const

Get the Group id of a MultilocusGenotype.

Exceptions

IndexOutOfBoundsException if position excedes the size of the container.

Definition at line 171 of file PolymorphismMultiGContainer.cpp.

References groups_, and size().

Referenced by bpp::MultilocusGenotypeStatistics::countBiAllelicForGroups(), bpp::MultilocusGenotypeStatistics::countHeterozygousForGroups(), bpp::MultilocusGenotypeStatistics::countNonMissingForGroups(), bpp::PolymorphismMultiGContainerTools::extractGroups(), bpp::MultilocusGenotypeStatistics::getAllelesMapForGroups(), bpp::MultilocusGenotypeStatistics::getHeterozygousFrqForGroups(), operator=(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), bpp::PolymorphismMultiGContainerTools::permutMonoG(), bpp::PolymorphismMultiGContainerTools::permutMultiG(), and PolymorphismMultiGContainer().

◆ getGroupName()

std::string PolymorphismMultiGContainer::getGroupName ( size_t group_id ) const

Get the group name for a given group id or just the id if not available juste return it's id.

Definition at line 251 of file PolymorphismMultiGContainer.cpp.

References groups_names_, and bpp::TextTools::toString().

Referenced by bpp::PolymorphismMultiGContainerTools::extractGroups(), operator=(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), bpp::PolymorphismMultiGContainerTools::permutMonoG(), and PolymorphismMultiGContainer().

◆ getGroupSize()

size_t PolymorphismMultiGContainer::getGroupSize ( size_t group ) const

Get group size.

Definition at line 238 of file PolymorphismMultiGContainer.cpp.

References groups_, and size().

◆ getLocusGroupSize()

size_t PolymorphismMultiGContainer::getLocusGroupSize	(	size_t	group,
		size_t	locus_position
	)		const

Get the size of a group for a given locus.

Definition at line 284 of file PolymorphismMultiGContainer.cpp.

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

Referenced by bpp::MultilocusGenotypeStatistics::getVarianceComponents(), bpp::MultilocusGenotypeStatistics::getWCMultilocusFis(), and bpp::MultilocusGenotypeStatistics::getWCMultilocusFst().

◆ getMultilocusGenotype()

const MultilocusGenotype * PolymorphismMultiGContainer::getMultilocusGenotype ( size_t position ) const

Get a MultilocusGenotype at a position.

Exceptions

IndexOutOfBoundsException if position excedes the size of the container.

Definition at line 113 of file PolymorphismMultiGContainer.cpp.

References multilocusGenotypes_, and size().

Referenced by bpp::MultilocusGenotypeStatistics::countBiAllelicForGroups(), bpp::MultilocusGenotypeStatistics::countHeterozygousForGroups(), bpp::MultilocusGenotypeStatistics::countNonMissingForGroups(), bpp::PolymorphismMultiGContainerTools::extractGroups(), bpp::MultilocusGenotypeStatistics::getAllelesMapForGroups(), bpp::MultilocusGenotypeStatistics::getHeterozygousFrqForGroups(), operator=(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), bpp::PolymorphismMultiGContainerTools::permutMonoG(), and PolymorphismMultiGContainer().

◆ getNumberOfGroups()

size_t PolymorphismMultiGContainer::getNumberOfGroups ( ) const

Get the number of groups.

Definition at line 231 of file PolymorphismMultiGContainer.cpp.

References getAllGroupsIds().

◆ getNumberOfLoci()

size_t PolymorphismMultiGContainer::getNumberOfLoci ( ) const

Get the number of loci if the MultilocusGenotypes are aligned.

Exceptions

Exception if MultilocusGenotypes are not aligned.

Definition at line 160 of file PolymorphismMultiGContainer.cpp.

References isAligned(), multilocusGenotypes_, and size().

Referenced by bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), and bpp::PolymorphismMultiGContainerTools::permutMonoG().

◆ groupExists()

bool PolymorphismMultiGContainer::groupExists ( size_t group ) const

Tell if a group exists.

Definition at line 219 of file PolymorphismMultiGContainer.cpp.

References groups_, and size().

◆ isAligned()

bool PolymorphismMultiGContainer::isAligned ( ) const

Tell if the MultilocusGenotypes are aligned (i.e. same size).

Definition at line 145 of file PolymorphismMultiGContainer.cpp.

References multilocusGenotypes_, and size().

Referenced by getNumberOfLoci().

◆ operator=()

PolymorphismMultiGContainer & PolymorphismMultiGContainer::operator= ( const PolymorphismMultiGContainer & pmgc )

The assignation operator=.

Definition at line 78 of file PolymorphismMultiGContainer.cpp.

References clear(), getAllGroupsIds(), getGroupId(), getGroupName(), getMultilocusGenotype(), groups_, groups_names_, multilocusGenotypes_, and size().

◆ removeMultilocusGenotype()

MultilocusGenotype * PolymorphismMultiGContainer::removeMultilocusGenotype ( size_t position )

Remove a MultilocusGenotype.

Exceptions

IndexOutOfBoundsException if position excedes the size of the container.

Definition at line 122 of file PolymorphismMultiGContainer.cpp.

References groups_, multilocusGenotypes_, and size().

◆ setGroupId()

void PolymorphismMultiGContainer::setGroupId	(	size_t	position,
		size_t	group_id
	)

Set the Group id of a MultilocusGenotype.

Exceptions

IndexOutOfBoundsException if position excedes the size of the container.

Definition at line 180 of file PolymorphismMultiGContainer.cpp.

References groups_, and size().

Referenced by bpp::PolymorphismMultiGContainerTools::permutMultiG().

◆ setGroupName()

void PolymorphismMultiGContainer::setGroupName	(	size_t	group_id,
		std::string	name
	)

Set the name for the given group id.

Definition at line 264 of file PolymorphismMultiGContainer.cpp.

References groups_names_.

Referenced by bpp::PolymorphismMultiGContainerTools::extractGroups(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), and bpp::PolymorphismMultiGContainerTools::permutMonoG().

◆ size()

size_t PolymorphismMultiGContainer::size ( ) const

Get the number of MultilocusGenotype.

Definition at line 304 of file PolymorphismMultiGContainer.cpp.

References multilocusGenotypes_.

Referenced by bpp::MultilocusGenotypeStatistics::countBiAllelicForGroups(), bpp::MultilocusGenotypeStatistics::countHeterozygousForGroups(), bpp::MultilocusGenotypeStatistics::countNonMissingForGroups(), deleteMultilocusGenotype(), bpp::PolymorphismMultiGContainerTools::extractGroups(), bpp::MultilocusGenotypeStatistics::getAllelesMapForGroups(), getAllGroupsIds(), getGroupId(), getGroupSize(), bpp::MultilocusGenotypeStatistics::getHeterozygousFrqForGroups(), getLocusGroupSize(), getMultilocusGenotype(), getNumberOfLoci(), groupExists(), isAligned(), operator=(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), bpp::PolymorphismMultiGContainerTools::permutMonoG(), bpp::PolymorphismMultiGContainerTools::permutMultiG(), PolymorphismMultiGContainer(), removeMultilocusGenotype(), and setGroupId().

Member Data Documentation

◆ groups_

std::vector<size_t> bpp::PolymorphismMultiGContainer::groups_

private

Definition at line 71 of file PolymorphismMultiGContainer.h.

Referenced by addMultilocusGenotype(), clear(), deleteMultilocusGenotype(), getAllGroupsIds(), getGroupId(), getGroupSize(), getLocusGroupSize(), groupExists(), operator=(), PolymorphismMultiGContainer(), removeMultilocusGenotype(), and setGroupId().

◆ groups_names_

std::map<size_t, std::string> bpp::PolymorphismMultiGContainer::groups_names_

private

Definition at line 72 of file PolymorphismMultiGContainer.h.

Referenced by addGroupName(), addMultilocusGenotype(), clear(), getAllGroupsNames(), getGroupName(), operator=(), PolymorphismMultiGContainer(), and setGroupName().

◆ multilocusGenotypes_

std::vector<MultilocusGenotype*> bpp::PolymorphismMultiGContainer::multilocusGenotypes_

private

Definition at line 70 of file PolymorphismMultiGContainer.h.

Referenced by addMultilocusGenotype(), clear(), deleteMultilocusGenotype(), getLocusGroupSize(), getMultilocusGenotype(), getNumberOfLoci(), isAligned(), operator=(), PolymorphismMultiGContainer(), removeMultilocusGenotype(), and size().

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

Bpp/PopGen/PolymorphismMultiGContainer.h
Bpp/PopGen/PolymorphismMultiGContainer.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PolymorphismMultiGContainer() [1/2]

◆ PolymorphismMultiGContainer() [2/2]

◆ ~PolymorphismMultiGContainer()

Member Function Documentation

◆ addGroupName()

◆ addMultilocusGenotype()

◆ clear()

◆ deleteMultilocusGenotype()

◆ getAllGroupsIds()

◆ getAllGroupsNames()

◆ getGroupId()

◆ getGroupName()

◆ getGroupSize()

◆ getLocusGroupSize()

◆ getMultilocusGenotype()

◆ getNumberOfGroups()

◆ getNumberOfLoci()

◆ groupExists()

◆ isAligned()

◆ operator=()

◆ removeMultilocusGenotype()

◆ setGroupId()

◆ setGroupName()

◆ size()

Member Data Documentation

◆ groups_

◆ groups_names_

◆ multilocusGenotypes_