bpp::SequenceDiversityMafStatistics Class Reference

Provide estimates of sequence diversity. More...

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

Inheritance diagram for bpp::SequenceDiversityMafStatistics:

Collaboration diagram for bpp::SequenceDiversityMafStatistics:

Public Member Functions
	SequenceDiversityMafStatistics (const std::vector< std::string > &ingroup)
virtual	~SequenceDiversityMafStatistics ()
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_

Static Private Member Functions
static std::vector< int >	getPatterns_ (const SiteContainer &sites)

Detailed Description

Provide estimates of sequence diversity.

• Number of segregating sites
• Watterson's theta (per site)

Only fully resolved sites are analyzed (no gap, no generic character).

Definition at line 662 of file MafStatistics.h.

Constructor & Destructor Documentation

SequenceDiversityMafStatistics()

bpp::SequenceDiversityMafStatistics::SequenceDiversityMafStatistics ( const std::vector< std::string > &  ingroup )

inline

Definition at line 667 of file MafStatistics.h.

~SequenceDiversityMafStatistics()

virtual bpp::SequenceDiversityMafStatistics::~SequenceDiversityMafStatistics ( )

inlinevirtual

Definition at line 672 of file MafStatistics.h.

Member Function Documentation

compute()

void SequenceDiversityMafStatistics::compute ( const MafBlock &  block )

virtual

Implements bpp::MafStatistics.

Definition at line 451 of file MafStatistics.cpp.

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

getFullName()

std::string bpp::SequenceDiversityMafStatistics::getFullName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 676 of file MafStatistics.h.

getPatterns_()

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

staticprivate

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::SequenceDiversityMafStatistics::getShortName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 675 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(), bpp::FourSpeciesPatternCountsMafStatistics::compute(), bpp::SiteMafStatistics::compute(), and compute().

getSupportedTags()

vector< string > SequenceDiversityMafStatistics::getSupportedTags ( ) const

virtual

Returns

A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 443 of file MafStatistics.cpp.

Member Data Documentation

result_

MafStatisticsResult bpp::AbstractMafStatistics::result_

protectedinherited

Definition at line 232 of file MafStatistics.h.

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

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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