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_
std::string	suffix_

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

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

Detailed Description

Provide estimates of sequence diversity.

• Number of segregating sites
• Watterson's theta (per site)
• Tajima's pi (average pairwise differences)
• Tajima's D

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

Definition at line 693 of file MafStatistics.h.

Constructor & Destructor Documentation

SequenceDiversityMafStatistics()

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

inline

Definition at line 698 of file MafStatistics.h.

~SequenceDiversityMafStatistics()

virtual bpp::SequenceDiversityMafStatistics::~SequenceDiversityMafStatistics ( )

inlinevirtual

Definition at line 703 of file MafStatistics.h.

Member Function Documentation

compute()

void SequenceDiversityMafStatistics::compute ( const MafBlock &  block )

virtual

Implements bpp::MafStatistics.

Definition at line 481 of file MafStatistics.cpp.

References bpp::SiteContainerTools::computeSimilarity(), bpp::SiteContainerTools::getCompleteSites(), bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::SiteTools::isComplete(), bpp::SiteTools::isConstant(), bpp::AbstractMafStatistics::result_, bpp::MafStatisticsResult::setValue(), and bpp::SiteContainerTools::SIMILARITY_NOGAP.

getFullName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 707 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 241 of file MafStatistics.h.

References bpp::AbstractMafStatistics::result_.

getShortName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 706 of file MafStatistics.h.

getSiteContainer_()

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

protectedinherited

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 compute().

getSupportedTags()

vector< string > SequenceDiversityMafStatistics::getSupportedTags ( ) const

virtual

Returns

A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 471 of file MafStatistics.cpp.

Member Data Documentation

noSpeciesMeansAllSpecies_

bool bpp::AbstractSpeciesSelectionMafStatistics::noSpeciesMeansAllSpecies_

privateinherited

Definition at line 382 of file MafStatistics.h.

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(), bpp::PolymorphismMafStatistics::compute(), compute(), and bpp::AbstractMafStatistics::getResult().

species_

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

privateinherited

Definition at line 381 of file MafStatistics.h.

suffix_

std::string bpp::AbstractSpeciesSelectionMafStatistics::suffix_

protectedinherited

Definition at line 385 of file MafStatistics.h.

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

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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