bpp::SiteMafStatistics Class Reference

Compute a few site statistics in a maf block. More...

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

Inheritance diagram for bpp::SiteMafStatistics:

Collaboration diagram for bpp::SiteMafStatistics:

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

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

Detailed Description

Compute a few site statistics in a maf block.

Computed statistics include:

• Number of sites without gaps
• Number of complete sites (no gap, no unresolved)
• Number of complete sites with only one state (constant sites)
• Number of complete biallelic sites
• Number of complete triallelic sites
• Number of complete Quadriallelic sites
• Number of parsimony informative sites

Definition at line 624 of file MafStatistics.h.

Constructor & Destructor Documentation

SiteMafStatistics()

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

inline

Definition at line 629 of file MafStatistics.h.

~SiteMafStatistics()

virtual bpp::SiteMafStatistics::~SiteMafStatistics ( )

inlinevirtual

Definition at line 634 of file MafStatistics.h.

Member Function Documentation

compute()

void SiteMafStatistics::compute ( const MafBlock &  block )

virtual

Implements bpp::MafStatistics.

Definition at line 315 of file MafStatistics.cpp.

References bpp::SiteTools::getCounts(), bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::SiteTools::hasGap(), bpp::SiteTools::isComplete(), bpp::SiteTools::isParsimonyInformativeSite(), bpp::AbstractMafStatistics::result_, and bpp::MafStatisticsResult::setValue().

getFullName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 638 of file MafStatistics.h.

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::SiteMafStatistics::getShortName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 637 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(), compute(), and bpp::SequenceDiversityMafStatistics::compute().

getSupportedTags()

vector< string > SiteMafStatistics::getSupportedTags ( ) const

virtual

Returns

A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 302 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(), compute(), bpp::PolymorphismMafStatistics::compute(), bpp::SequenceDiversityMafStatistics::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