bpp-seq-omics  2.4.1
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::AbstractSpeciesSelectionMafStatistics Class Referenceabstract

Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner. More...

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

+ Inheritance diagram for bpp::AbstractSpeciesSelectionMafStatistics:
+ Collaboration diagram for bpp::AbstractSpeciesSelectionMafStatistics:

Public Member Functions

 AbstractSpeciesSelectionMafStatistics (const std::vector< std::string > &species, bool noSpeciesMeansAllSpecies=false, const std::string &suffix="")
 
virtual std::string getShortName () const =0
 
virtual std::string getFullName () const =0
 
virtual const MafStatisticsResult & getResult () const =0
 
virtual void compute (const MafBlock &block)=0
 
virtual std::vector< std::string > getSupportedTags () const =0
 

Protected Member Functions

SiteContainer * getSiteContainer_ (const MafBlock &block)
 

Protected Attributes

std::string suffix_
 

Private Attributes

std::vector< std::string > species_
 
bool noSpeciesMeansAllSpecies_
 

Detailed Description

Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner.

This class stores a selection of species and create for each block the corresponding SiteContainer instance.

Definition at line 377 of file MafStatistics.h.

Constructor & Destructor Documentation

◆ AbstractSpeciesSelectionMafStatistics()

bpp::AbstractSpeciesSelectionMafStatistics::AbstractSpeciesSelectionMafStatistics ( const std::vector< std::string > &  species,
bool  noSpeciesMeansAllSpecies = false,
const std::string &  suffix = "" 
)
inline

Definition at line 388 of file MafStatistics.h.

Member Function Documentation

◆ compute()

virtual void bpp::MafStatistics::compute ( const MafBlock &  block)
pure virtualinherited

Implemented in bpp::SequenceDiversityMafStatistics, bpp::PolymorphismMafStatistics, bpp::SiteMafStatistics, bpp::FourSpeciesPatternCountsMafStatistics, bpp::SiteFrequencySpectrumMafStatistics, bpp::CharacterCountsMafStatistics, bpp::AlignmentScoreMafStatistics, bpp::SequenceLengthMafStatistics, bpp::BlockLengthMafStatistics, bpp::BlockSizeMafStatistics, and bpp::PairwiseDivergenceMafStatistics.

◆ getFullName()

virtual std::string bpp::MafStatistics::getFullName ( ) const
pure virtualinherited

Implemented in bpp::SequenceDiversityMafStatistics, bpp::PolymorphismMafStatistics, bpp::SiteMafStatistics, bpp::FourSpeciesPatternCountsMafStatistics, bpp::SiteFrequencySpectrumMafStatistics, bpp::CharacterCountsMafStatistics, bpp::AlignmentScoreMafStatistics, bpp::SequenceLengthMafStatistics, bpp::BlockLengthMafStatistics, bpp::BlockSizeMafStatistics, and bpp::PairwiseDivergenceMafStatistics.

◆ getResult()

virtual const MafStatisticsResult& bpp::MafStatistics::getResult ( ) const
pure virtualinherited

Implemented in bpp::AbstractMafStatisticsSimple, and bpp::AbstractMafStatistics.

◆ getShortName()

virtual std::string bpp::MafStatistics::getShortName ( ) const
pure virtualinherited

Implemented in bpp::SequenceDiversityMafStatistics, bpp::PolymorphismMafStatistics, bpp::SiteMafStatistics, bpp::FourSpeciesPatternCountsMafStatistics, bpp::SiteFrequencySpectrumMafStatistics, bpp::CharacterCountsMafStatistics, bpp::AlignmentScoreMafStatistics, bpp::SequenceLengthMafStatistics, bpp::BlockLengthMafStatistics, bpp::BlockSizeMafStatistics, and bpp::PairwiseDivergenceMafStatistics.

◆ getSiteContainer_()

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

Definition at line 68 of file MafStatistics.cpp.

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

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

◆ getSupportedTags()

virtual std::vector<std::string> bpp::MafStatistics::getSupportedTags ( ) const
pure virtualinherited
Returns
A vector with all available tags.

Implemented in bpp::SequenceDiversityMafStatistics, bpp::PolymorphismMafStatistics, bpp::SiteMafStatistics, bpp::FourSpeciesPatternCountsMafStatistics, bpp::SiteFrequencySpectrumMafStatistics, bpp::CharacterCountsMafStatistics, and bpp::AbstractMafStatisticsSimple.

Member Data Documentation

◆ noSpeciesMeansAllSpecies_

bool bpp::AbstractSpeciesSelectionMafStatistics::noSpeciesMeansAllSpecies_
private

Definition at line 382 of file MafStatistics.h.

◆ species_

std::vector<std::string> bpp::AbstractSpeciesSelectionMafStatistics::species_
private

Definition at line 381 of file MafStatistics.h.

◆ suffix_

std::string bpp::AbstractSpeciesSelectionMafStatistics::suffix_
protected

Definition at line 385 of file MafStatistics.h.

Referenced by bpp::CharacterCountsMafStatistics::getFullName(), and bpp::CharacterCountsMafStatistics::getShortName().

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