bpp-popgen  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 PolymorphismMultiGContainer permutMultiG (const PolymorphismMultiGContainer &pmgc)
 Permut the MultilocusGenotype in the whole PolymorphismMultiGContainer. More...
 
static PolymorphismMultiGContainer permutMonoG (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the MonolocusGenotype. More...
 
static PolymorphismMultiGContainer permutIntraGroupMonoG (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the MonolocusGenotype between individuals in the same group. More...
 
static PolymorphismMultiGContainer permutAlleles (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the Alleles. More...
 
static PolymorphismMultiGContainer permutIntraGroupAlleles (const PolymorphismMultiGContainer &pmgc, const std::set< size_t > &groups)
 Permut the Alleles between individuals in the same group. More...
 
static 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 61 of file PolymorphismMultiGContainerTools.h.

Member Function Documentation

◆ extractGroups()

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

Definition at line 348 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::PolymorphismMultiGContainer::getMultilocusGenotype(), bpp::PolymorphismMultiGContainer::setGroupName(), and bpp::PolymorphismMultiGContainer::size().

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

◆ permutAlleles()

PolymorphismMultiGContainer PolymorphismMultiGContainerTools::permutAlleles ( 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 197 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::MonolocusGenotype::getAlleleIndex(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::MultilocusGenotype::getMonolocusGenotype(), bpp::PolymorphismMultiGContainer::getMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::MultilocusGenotype::isMonolocusGenotypeMissing(), bpp::PolymorphismMultiGContainer::setGroupName(), bpp::MultilocusGenotype::setMonolocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

◆ permutIntraGroupAlleles()

PolymorphismMultiGContainer PolymorphismMultiGContainerTools::permutIntraGroupAlleles ( 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 263 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::MonolocusGenotype::getAlleleIndex(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::MultilocusGenotype::getMonolocusGenotype(), bpp::PolymorphismMultiGContainer::getMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::MultilocusGenotype::isMonolocusGenotypeMissing(), bpp::PolymorphismMultiGContainer::setGroupName(), bpp::MultilocusGenotype::setMonolocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

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

◆ permutIntraGroupMonoG()

PolymorphismMultiGContainer PolymorphismMultiGContainerTools::permutIntraGroupMonoG ( 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 127 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::MultilocusGenotype::getMonolocusGenotype(), bpp::PolymorphismMultiGContainer::getMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::PolymorphismMultiGContainer::setGroupName(), bpp::MultilocusGenotype::setMonolocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

◆ permutMonoG()

PolymorphismMultiGContainer PolymorphismMultiGContainerTools::permutMonoG ( 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 69 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::addMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getAllGroupsIds(), bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::getGroupName(), bpp::MultilocusGenotype::getMonolocusGenotype(), bpp::PolymorphismMultiGContainer::getMultilocusGenotype(), bpp::PolymorphismMultiGContainer::getNumberOfLoci(), bpp::PolymorphismMultiGContainer::setGroupName(), bpp::MultilocusGenotype::setMonolocusGenotype(), and bpp::PolymorphismMultiGContainer::size().

◆ permutMultiG()

PolymorphismMultiGContainer PolymorphismMultiGContainerTools::permutMultiG ( const PolymorphismMultiGContainer &  pmgc)
static

Permut the MultilocusGenotype in the whole PolymorphismMultiGContainer.

Parameters
pmgcThe PolymorphismMultiGContainer to permut.
Returns
A permuted PolymorphismMultiGContainer.

Definition at line 49 of file PolymorphismMultiGContainerTools.cpp.

References bpp::PolymorphismMultiGContainer::getGroupId(), bpp::PolymorphismMultiGContainer::setGroupId(), and bpp::PolymorphismMultiGContainer::size().

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

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