bpp-seq-omics  2.4.1
Public Member Functions | Protected Member Functions | Protected Attributes | Static Private Member Functions | Private Attributes | List of all members
bpp::PolymorphismMafStatistics Class Reference

Counts number of polymorphic / fixed sites in two populations. More...

#include <Bpp/Seq/Io/Maf/MafStatistics.h>

+ Inheritance diagram for bpp::PolymorphismMafStatistics:
+ Collaboration diagram for bpp::PolymorphismMafStatistics:

Public Member Functions

 PolymorphismMafStatistics (const std::vector< std::vector< std::string > > &species)
 
virtual ~PolymorphismMafStatistics ()
 
std::string getShortName () const
 
std::string getFullName () const
 
void compute (const MafBlock &block)
 
std::vector< std::string > getSupportedTags () const
 
const MafStatisticsResult & getResult () const
 

Protected Member Functions

std::vector< SiteContainer * > getSiteContainers_ (const MafBlock &block)
 

Protected Attributes

MafStatisticsResult result_
 

Static Private Member Functions

static std::vector< int > getPatterns_ (const SiteContainer &sites)
 

Private Attributes

std::vector< std::vector< std::string > > species_
 

Detailed Description

Counts number of polymorphic / fixed sites in two populations.

The two populations are defined as two distinct sets of species. The following counts are computed and returned:

  • P: number of sites polymorphic in both populations
  • F: number of sites fixed in both populations
  • FF: number of sites fixed in both populations, but with distinct states
  • PF / FP: number of sites polymorphic in one species and fixed in the other.
  • X: unresolved (because of gap or generic character)
  • FX / PX / XF / XP: unresolved in one population

Definition at line 656 of file MafStatistics.h.

Constructor & Destructor Documentation

◆ PolymorphismMafStatistics()

bpp::PolymorphismMafStatistics::PolymorphismMafStatistics ( const std::vector< std::vector< std::string > > &  species)
inline

Definition at line 661 of file MafStatistics.h.

◆ ~PolymorphismMafStatistics()

virtual bpp::PolymorphismMafStatistics::~PolymorphismMafStatistics ( )
inlinevirtual

Definition at line 669 of file MafStatistics.h.

Member Function Documentation

◆ compute()

void PolymorphismMafStatistics::compute ( const MafBlock &  block)
virtual

Implements bpp::MafStatistics.

Definition at line 388 of file MafStatistics.cpp.

References bpp::MafBlock::getNumberOfSites(), getPatterns_(), bpp::AbstractSpeciesMultipleSelectionMafStatistics::getSiteContainers_(), bpp::AbstractMafStatistics::result_, and bpp::MafStatisticsResult::setValue().

◆ getFullName()

std::string bpp::PolymorphismMafStatistics::getFullName ( ) const
inlinevirtual

Implements bpp::MafStatistics.

Definition at line 673 of file MafStatistics.h.

◆ getPatterns_()

vector< int > PolymorphismMafStatistics::getPatterns_ ( const SiteContainer &  sites)
staticprivate

Definition at line 370 of file MafStatistics.cpp.

References bpp::SiteContainer::getNumberOfSites(), bpp::SiteContainer::getSite(), bpp::SiteTools::isComplete(), and bpp::SiteTools::isConstant().

Referenced by compute().

◆ getResult()

const MafStatisticsResult& bpp::AbstractMafStatistics::getResult ( ) const
inlinevirtualinherited

Implements bpp::MafStatistics.

Definition at line 241 of file MafStatistics.h.

References bpp::AbstractMafStatistics::result_.

◆ getShortName()

std::string bpp::PolymorphismMafStatistics::getShortName ( ) const
inlinevirtual

Implements bpp::MafStatistics.

Definition at line 672 of file MafStatistics.h.

◆ getSiteContainers_()

vector< SiteContainer * > AbstractSpeciesMultipleSelectionMafStatistics::getSiteContainers_ ( const MafBlock &  block)
protectedinherited

Definition at line 97 of file MafStatistics.cpp.

References bpp::VectorSiteContainer::addSequence(), bpp::MafBlock::getAlignment(), bpp::AlignedSequenceContainer::getAlphabet(), bpp::MafBlock::getSequencesForSpecies(), bpp::MafBlock::hasSequenceForSpecies(), and bpp::AbstractSpeciesMultipleSelectionMafStatistics::species_.

Referenced by compute().

◆ getSupportedTags()

vector< string > PolymorphismMafStatistics::getSupportedTags ( ) const
virtual
Returns
A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 354 of file MafStatistics.cpp.

Member Data Documentation

◆ result_

MafStatisticsResult bpp::AbstractMafStatistics::result_
protectedinherited

Definition at line 234 of file MafStatistics.h.

Referenced by bpp::CharacterCountsMafStatistics::compute(), bpp::SiteFrequencySpectrumMafStatistics::compute(), bpp::FourSpeciesPatternCountsMafStatistics::compute(), bpp::SiteMafStatistics::compute(), compute(), bpp::SequenceDiversityMafStatistics::compute(), and bpp::AbstractMafStatistics::getResult().

◆ species_

std::vector< std::vector<std::string> > bpp::AbstractSpeciesMultipleSelectionMafStatistics::species_
privateinherited

Definition at line 412 of file MafStatistics.h.

Referenced by bpp::AbstractSpeciesMultipleSelectionMafStatistics::AbstractSpeciesMultipleSelectionMafStatistics(), and bpp::AbstractSpeciesMultipleSelectionMafStatistics::getSiteContainers_().

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