bpp-seq-omics  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::FourSpeciesPatternCountsMafStatistics Class Reference

Compute the frequency of site patterns for a quadruplet of species. More...

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

+ Inheritance diagram for bpp::FourSpeciesPatternCountsMafStatistics:
+ Collaboration diagram for bpp::FourSpeciesPatternCountsMafStatistics:

Public Member Functions

 FourSpeciesPatternCountsMafStatistics (const Alphabet *alphabet, const std::vector< std::string > &species)
 
 FourSpeciesPatternCountsMafStatistics (const FourSpeciesPatternCountsMafStatistics &stats)
 
FourSpeciesPatternCountsMafStatistics & operator= (const FourSpeciesPatternCountsMafStatistics &stats)
 
virtual ~FourSpeciesPatternCountsMafStatistics ()
 
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

SiteContainer * getSiteContainer_ (const MafBlock &block)
 

Protected Attributes

MafStatisticsResult result_
 

Private Attributes

const Alphabet * alphabet_
 
std::vector< unsigned int > counts_
 

Detailed Description

Compute the frequency of site patterns for a quadruplet of species.

Only parsimony informative sites are categorized. Species: A B C D P1 1 1 0 0 P2 0 1 1 0 P3 1 0 1 0 Sites with more than two states are ignored, as well as sites containing gaps or unresolved characters.

Definition at line 538 of file MafStatistics.h.

Constructor & Destructor Documentation

◆ FourSpeciesPatternCountsMafStatistics() [1/2]

bpp::FourSpeciesPatternCountsMafStatistics::FourSpeciesPatternCountsMafStatistics ( const Alphabet *  alphabet,
const std::vector< std::string > &  species 
)
inline

Definition at line 547 of file MafStatistics.h.

◆ FourSpeciesPatternCountsMafStatistics() [2/2]

bpp::FourSpeciesPatternCountsMafStatistics::FourSpeciesPatternCountsMafStatistics ( const FourSpeciesPatternCountsMafStatistics &  stats)
inline

Definition at line 561 of file MafStatistics.h.

◆ ~FourSpeciesPatternCountsMafStatistics()

virtual bpp::FourSpeciesPatternCountsMafStatistics::~FourSpeciesPatternCountsMafStatistics ( )
inlinevirtual

Definition at line 576 of file MafStatistics.h.

Member Function Documentation

◆ compute()

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

Implements bpp::MafStatistics.

Definition at line 259 of file MafStatistics.cpp.

References counts_, bpp::MafBlock::getNumberOfSites(), bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::AbstractMafStatistics::result_, and bpp::MafStatisticsResult::setValue().

◆ getFullName()

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

Implements bpp::MafStatistics.

Definition at line 580 of file MafStatistics.h.

◆ getResult()

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

Implements bpp::MafStatistics.

Definition at line 239 of file MafStatistics.h.

References bpp::AbstractMafStatistics::result_.

◆ getShortName()

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

Implements bpp::MafStatistics.

Definition at line 579 of file MafStatistics.h.

◆ getSiteContainer_()

SiteContainer * AbstractSpeciesSelectionMafStatistics::getSiteContainer_ ( const MafBlock &  block)
protectedinherited

Definition at line 95 of file MafStatistics.cpp.

References bpp::MafBlock::getAlignment(), bpp::MafBlock::getSequencesForSpecies(), and bpp::MafBlock::hasSequenceForSpecies().

Referenced by bpp::SiteFrequencySpectrumMafStatistics::compute(), compute(), bpp::SiteMafStatistics::compute(), and bpp::SequenceDiversityMafStatistics::compute().

◆ getSupportedTags()

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

Implements bpp::MafStatistics.

Definition at line 249 of file MafStatistics.cpp.

◆ operator=()

FourSpeciesPatternCountsMafStatistics& bpp::FourSpeciesPatternCountsMafStatistics::operator= ( const FourSpeciesPatternCountsMafStatistics &  stats)
inline

Definition at line 568 of file MafStatistics.h.

References alphabet_, and counts_.

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::FourSpeciesPatternCountsMafStatistics::alphabet_
private

Definition at line 543 of file MafStatistics.h.

Referenced by operator=().

◆ counts_

std::vector<unsigned int> bpp::FourSpeciesPatternCountsMafStatistics::counts_
private

Definition at line 544 of file MafStatistics.h.

Referenced by compute(), and operator=().

◆ result_

MafStatisticsResult bpp::AbstractMafStatistics::result_
protectedinherited

Definition at line 232 of file MafStatistics.h.

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

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