#include <Bpp/PopGen/MultilocusGenotype.h>

Collaboration diagram for bpp::MultilocusGenotype:

Public Member Functions
	MultilocusGenotype (size_t loci_number)
	Build a MultilocusGenotype linked to an AnalyzedLoci object. More...

	MultilocusGenotype (const MultilocusGenotype &genotype)
	Copy constructor. More...

	~MultilocusGenotype ()
	Destroy a MultilocusGenotype. More...

void	setMonolocusGenotype (size_t locus_position, const MonolocusGenotype &monogen)
	Set a MonolocusGenotype. More...

void	setMonolocusGenotypeByAlleleKey (size_t locus_position, const std::vector< size_t > &allele_keys)
	Set a MonolocusGenotype by allele keys. More...

void	setMonolocusGenotypeByAlleleId (size_t locus_position, const std::vector< std::string > &allele_id, const LocusInfo &locus_info)
	Set a MonolocusGenotype by allele id. More...

void	setMonolocusGenotypeAsMissing (size_t locus_position)
	Set a MonolocusGenotype as missing data. More...

bool	isMonolocusGenotypeMissing (size_t locus_position) const
	Tell if a MonolocusGenotype is a missing data. More...

const MonolocusGenotype &	getMonolocusGenotype (size_t locus_position) const
	Get a MonolocusGenotype. More...

size_t	size () const
	Count the number of loci. More...

size_t	countNonMissingLoci () const
	Count the number of non missing MonolocusGenotype. More...

size_t	countHomozygousLoci () const
	Count the number of homozygous MonolocusGenotype. More...

size_t	countHeterozygousLoci () const
	Count the number of heterozygous MonolocusGenotype. More...

Private Attributes
std::vector< MonolocusGenotype * >	loci_

Detailed Description

The MultilocusGenotype class.

This is a MonolocusGenotype container.

Author: Sylvain Gaillard

Definition at line 65 of file MultilocusGenotype.h.

Constructor & Destructor Documentation

◆ MultilocusGenotype() [1/2]

MultilocusGenotype::MultilocusGenotype ( size_t loci_number )

Build a MultilocusGenotype linked to an AnalyzedLoci object.

Exceptions

BadIntegerException if loci_number < 1.

Definition at line 47 of file MultilocusGenotype.cpp.

References loci_.

◆ MultilocusGenotype() [2/2]

MultilocusGenotype::MultilocusGenotype ( const MultilocusGenotype & genotype )

Copy constructor.

Definition at line 59 of file MultilocusGenotype.cpp.

References bpp::Clonable::clone(), getMonolocusGenotype(), isMonolocusGenotypeMissing(), loci_, and size().

◆ ~MultilocusGenotype()

MultilocusGenotype::~MultilocusGenotype ( )

Destroy a MultilocusGenotype.

Definition at line 72 of file MultilocusGenotype.cpp.

References loci_.

Member Function Documentation

◆ countHeterozygousLoci()

size_t MultilocusGenotype::countHeterozygousLoci ( ) const

Count the number of heterozygous MonolocusGenotype.

Definition at line 188 of file MultilocusGenotype.cpp.

References count(), and loci_.

◆ countHomozygousLoci()

size_t MultilocusGenotype::countHomozygousLoci ( ) const

Count the number of homozygous MonolocusGenotype.

Definition at line 172 of file MultilocusGenotype.cpp.

References count(), and loci_.

◆ countNonMissingLoci()

size_t MultilocusGenotype::countNonMissingLoci ( ) const

Count the number of non missing MonolocusGenotype.

Definition at line 161 of file MultilocusGenotype.cpp.

References count(), and loci_.

◆ getMonolocusGenotype()

const MonolocusGenotype & MultilocusGenotype::getMonolocusGenotype ( size_t locus_position ) const

Get a MonolocusGenotype.

Definition at line 149 of file MultilocusGenotype.cpp.

References loci_.

Referenced by bpp::MultilocusGenotypeStatistics::countBiAllelicForGroups(), bpp::MultilocusGenotypeStatistics::countHeterozygousForGroups(), bpp::MultilocusGenotypeStatistics::getAllelesMapForGroups(), bpp::MultilocusGenotypeStatistics::getHeterozygousFrqForGroups(), MultilocusGenotype(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupMonoG(), bpp::PolymorphismMultiGContainerTools::permutMonoG(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ isMonolocusGenotypeMissing()

bool MultilocusGenotype::isMonolocusGenotypeMissing ( size_t locus_position ) const

Tell if a MonolocusGenotype is a missing data.

Exceptions

IndexOutOfBoundsException if locus_position excedes the number of loci.

Definition at line 142 of file MultilocusGenotype.cpp.

References loci_.

Referenced by bpp::MultilocusGenotypeStatistics::countBiAllelicForGroups(), bpp::MultilocusGenotypeStatistics::countHeterozygousForGroups(), bpp::MultilocusGenotypeStatistics::countNonMissingForGroups(), bpp::MultilocusGenotypeStatistics::getAllelesMapForGroups(), bpp::MultilocusGenotypeStatistics::getHeterozygousFrqForGroups(), MultilocusGenotype(), bpp::PolymorphismMultiGContainerTools::permutAlleles(), bpp::PolymorphismMultiGContainerTools::permutIntraGroupAlleles(), bpp::DarwinVarSingle::write(), and bpp::PopgenlibIO::write().

◆ setMonolocusGenotype()

void MultilocusGenotype::setMonolocusGenotype	(	size_t	locus_position,
		const MonolocusGenotype &	monogen
	)

Set a MonolocusGenotype.

Definition at line 83 of file MultilocusGenotype.cpp.

References bpp::Clonable::clone(), and loci_.

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

◆ setMonolocusGenotypeAsMissing()

void MultilocusGenotype::setMonolocusGenotypeAsMissing ( size_t locus_position )

Set a MonolocusGenotype as missing data.

Exceptions

IndexOutOfBoundsException if locus_position excedes the number of loci.

Definition at line 133 of file MultilocusGenotype.cpp.

References loci_.

◆ setMonolocusGenotypeByAlleleId()

void MultilocusGenotype::setMonolocusGenotypeByAlleleId	(	size_t	locus_position,
		const std::vector< std::string > &	allele_id,
		const LocusInfo &	locus_info
	)

Set a MonolocusGenotype by allele id.

Exceptions

IndexOutOfBoundsException	if locus_position excedes the number of loci.
AlleleNotFoundException	if at least one of the id is not found in the LocusInfo.

Definition at line 108 of file MultilocusGenotype.cpp.

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

◆ setMonolocusGenotypeByAlleleKey()

void MultilocusGenotype::setMonolocusGenotypeByAlleleKey	(	size_t	locus_position,
		const std::vector< size_t > &	allele_keys
	)

Set a MonolocusGenotype by allele keys.

Exceptions

IndexOutOfBoundsException	if locus_position excedes the number of loci.
Exception	if there is no key in allele_keys.

Definition at line 93 of file MultilocusGenotype.cpp.

References bpp::MonolocusGenotypeTools::buildMonolocusGenotypeByAlleleKey(), loci_, and setMonolocusGenotype().

Referenced by setMonolocusGenotypeByAlleleId().

◆ size()

size_t MultilocusGenotype::size ( ) const

Count the number of loci.

Return the size of _loci.

Definition at line 156 of file MultilocusGenotype.cpp.

References loci_.

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

Member Data Documentation

◆ loci_

std::vector<MonolocusGenotype*> bpp::MultilocusGenotype::loci_

private

Definition at line 68 of file MultilocusGenotype.h.

Referenced by countHeterozygousLoci(), countHomozygousLoci(), countNonMissingLoci(), getMonolocusGenotype(), isMonolocusGenotypeMissing(), MultilocusGenotype(), setMonolocusGenotype(), setMonolocusGenotypeAsMissing(), setMonolocusGenotypeByAlleleKey(), size(), and ~MultilocusGenotype().

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

Bpp/PopGen/MultilocusGenotype.h
Bpp/PopGen/MultilocusGenotype.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MultilocusGenotype() [1/2]

◆ MultilocusGenotype() [2/2]

◆ ~MultilocusGenotype()

Member Function Documentation

◆ countHeterozygousLoci()

◆ countHomozygousLoci()

◆ countNonMissingLoci()

◆ getMonolocusGenotype()

◆ isMonolocusGenotypeMissing()

◆ setMonolocusGenotype()

◆ setMonolocusGenotypeAsMissing()

◆ setMonolocusGenotypeByAlleleId()

◆ setMonolocusGenotypeByAlleleKey()

◆ size()

Member Data Documentation

◆ loci_