bpp::AbstractSpeciesSelectionMafStatistics Class Reference

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)
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)

Private Attributes
std::vector< std::string >	species_

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 411 of file MafStatistics.h.

Constructor & Destructor Documentation

AbstractSpeciesSelectionMafStatistics()

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

inline

Definition at line 418 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 95 of file MafStatistics.cpp.

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

Referenced by 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

species_

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

private

Definition at line 415 of file MafStatistics.h.

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

• Bpp/Seq/Io/Maf/MafStatistics.h
• Bpp/Seq/Io/Maf/MafStatistics.cpp