bpp-popgen3  3.0.0
Static Public Member Functions | List of all members
bpp::PolymorphismMultiGContainerTools Class Reference

Tools for PolymorphismMultiGContainer. More...

#include <Bpp/PopGen/PolymorphismMultiGContainerTools.h>

Static Public Member Functions

static std::unique_ptr< PolymorphismMultiGContainer > permuteMultiG (const PolymorphismMultiGContainer &pmgc)
 Permut the MultilocusGenotype in the whole PolymorphismMultiGContainer. More...
 
static std::unique_ptr< PolymorphismMultiGContainer > permuteMonoG (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the MonolocusGenotype. More...
 
static std::unique_ptr< PolymorphismMultiGContainer > permuteIntraGroupMonoG (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the MonolocusGenotype between individuals in the same group. More...
 
static std::unique_ptr< PolymorphismMultiGContainer > permuteAlleles (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the Alleles. More...
 
static std::unique_ptr< PolymorphismMultiGContainer > permuteIntraGroupAlleles (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the Alleles between individuals in the same group. More...
 
static std::unique_ptr< PolymorphismMultiGContainer > extractGroups (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 

Detailed Description

Tools for PolymorphismMultiGContainer.

Provides static methods for permutations.

Author
Sylvain Gaillard

Definition at line 25 of file PolymorphismMultiGContainerTools.h.

Member Function Documentation

◆ extractGroups()

unique_ptr< PolymorphismMultiGContainer > PolymorphismMultiGContainerTools::extractGroups ( const PolymorphismMultiGContainer &  pmgc,
const std::set< size_t > &  groups 
)
static

Definition at line 318 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::PolymorphismMultiGContainer::multilocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

Referenced by bpp::MultilocusGenotypeStatistics::getWCMultilocusFisAndPerm(), and bpp::MultilocusGenotypeStatistics::getWCMultilocusFstAndPerm().

◆ permuteAlleles()

unique_ptr< PolymorphismMultiGContainer > PolymorphismMultiGContainerTools::permuteAlleles ( const PolymorphismMultiGContainer &  pmgc,
const std::set< size_t > &  groups 
)
static

Permut the Alleles.

Permut the alleles in one or several groups breaking the links between them.

Parameters
pmgcThe PolymorphismMultiGContainer to permut.
groupsThe groups ids between which the MonolocusGenotypes will be permuted.
Returns
A permuted PolymorphismMultiGContainer.

Definition at line 164 of file PolymorphismMultiGContainerTools.cpp.

References bpp::MonolocusGenotypeInterface::getAlleleIndex(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::MultilocusGenotype::isMonolocusGenotypeMissing(), bpp::MultilocusGenotype::monolocusGenotype(), bpp::PolymorphismMultiGContainer::multilocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

◆ permuteIntraGroupAlleles()

unique_ptr< PolymorphismMultiGContainer > PolymorphismMultiGContainerTools::permuteIntraGroupAlleles ( const PolymorphismMultiGContainer &  pmgc,
const std::set< size_t > &  groups 
)
static

Permut the Alleles between individuals in the same group.

Permut the alleles in one or several groups

Parameters
pmgcThe PolymorphismMultiGContainer to permut.
groupsThe groups ids between which the MonolocusGenotypes will be permuted.
Returns
A permuted PolymorphismMultiGContainer.

Definition at line 231 of file PolymorphismMultiGContainerTools.cpp.

References bpp::MonolocusGenotypeInterface::getAlleleIndex(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::MultilocusGenotype::isMonolocusGenotypeMissing(), bpp::MultilocusGenotype::monolocusGenotype(), bpp::PolymorphismMultiGContainer::multilocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

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

◆ permuteIntraGroupMonoG()

unique_ptr< PolymorphismMultiGContainer > PolymorphismMultiGContainerTools::permuteIntraGroupMonoG ( const PolymorphismMultiGContainer &  pmgc,
const std::set< size_t > &  groups 
)
static

Permut the MonolocusGenotype between individuals in the same group.

Permut the MonolocusGenotypes for a set of groups. The idiv for the other groups are kept intact

Parameters
pmgcThe PolymorphismMultiGContainer to permut.
groupsThe groups ids for which the MonolocusGenotypes will be permuted.
Returns
A permuted PolymorphismMultiGContainer.

Definition at line 93 of file PolymorphismMultiGContainerTools.cpp.

References bpp::MonolocusGenotypeInterface::clone(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::MultilocusGenotype::monolocusGenotype(), bpp::PolymorphismMultiGContainer::multilocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

◆ permuteMonoG()

unique_ptr< PolymorphismMultiGContainer > PolymorphismMultiGContainerTools::permuteMonoG ( const PolymorphismMultiGContainer &  pmgc,
const std::set< size_t > &  groups 
)
static

Permut the MonolocusGenotype.

Permut the MonolocusGenotypes in one or several groups breaking the links between them.

Parameters
pmgcThe PolymorphismMultiGContainer to permut.
groupsThe groups ids between which the MonolocusGenotypes will be permuted.
Returns
A permuted PolymorphismMultiGContainer.

Definition at line 34 of file PolymorphismMultiGContainerTools.cpp.

References bpp::MonolocusGenotypeInterface::clone(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::MultilocusGenotype::monolocusGenotype(), bpp::PolymorphismMultiGContainer::multilocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

◆ permuteMultiG()

unique_ptr< PolymorphismMultiGContainer > PolymorphismMultiGContainerTools::permuteMultiG ( const PolymorphismMultiGContainer &  pmgc)
static

Permut the MultilocusGenotype in the whole PolymorphismMultiGContainer.

Parameters
pmgcThe PolymorphismMultiGContainer to permut.
Returns
A permuted PolymorphismMultiGContainer.

Definition at line 15 of file PolymorphismMultiGContainerTools.cpp.

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

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