bpp::FourSpeciesPatternCountsMafStatistics Class Reference

Compute the frequency of site patterns for a quadruplet of species. More...

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

Inheritance diagram for bpp::FourSpeciesPatternCountsMafStatistics:

Collaboration diagram for bpp::FourSpeciesPatternCountsMafStatistics:

Public Member Functions
	FourSpeciesPatternCountsMafStatistics (const Alphabet *alphabet, const std::vector< std::string > &species)
	FourSpeciesPatternCountsMafStatistics (const FourSpeciesPatternCountsMafStatistics &stats)
FourSpeciesPatternCountsMafStatistics &	operator= (const FourSpeciesPatternCountsMafStatistics &stats)
virtual	~FourSpeciesPatternCountsMafStatistics ()
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
const Alphabet *	alphabet_
std::vector< unsigned int >	counts_
std::vector< std::string >	species_
bool	noSpeciesMeansAllSpecies_

Detailed Description

Compute the frequency of site patterns for a quadruplet of species.

Only parsimony informative sites are categorized. Species: A B C D P1 1 1 0 0 P2 0 1 1 0 P3 1 0 1 0 Sites with more than two states are ignored, as well as sites containing gaps or unresolved characters.

Definition at line 563 of file MafStatistics.h.

Constructor & Destructor Documentation

FourSpeciesPatternCountsMafStatistics() [1/2]

bpp::FourSpeciesPatternCountsMafStatistics::FourSpeciesPatternCountsMafStatistics ( const Alphabet *  alphabet, const std::vector< std::string > &  species  )

inline

Definition at line 572 of file MafStatistics.h.

References bpp::VectorTools::unique().

FourSpeciesPatternCountsMafStatistics() [2/2]

bpp::FourSpeciesPatternCountsMafStatistics::FourSpeciesPatternCountsMafStatistics ( const FourSpeciesPatternCountsMafStatistics &  stats )

inline

Definition at line 586 of file MafStatistics.h.

~FourSpeciesPatternCountsMafStatistics()

virtual bpp::FourSpeciesPatternCountsMafStatistics::~FourSpeciesPatternCountsMafStatistics ( )

inlinevirtual

Definition at line 601 of file MafStatistics.h.

Member Function Documentation

compute()

void FourSpeciesPatternCountsMafStatistics::compute ( const MafBlock &  block )

virtual

Implements bpp::MafStatistics.

Definition at line 265 of file MafStatistics.cpp.

References counts_, bpp::MafBlock::getNumberOfSites(), bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::SiteTools::isComplete(), bpp::AbstractMafStatistics::result_, and bpp::MafStatisticsResult::setValue().

getFullName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 605 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::FourSpeciesPatternCountsMafStatistics::getShortName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 604 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(), compute(), bpp::SiteMafStatistics::compute(), and bpp::SequenceDiversityMafStatistics::compute().

getSupportedTags()

vector< string > FourSpeciesPatternCountsMafStatistics::getSupportedTags ( ) const

virtual

Returns

A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 255 of file MafStatistics.cpp.

operator=()

FourSpeciesPatternCountsMafStatistics& bpp::FourSpeciesPatternCountsMafStatistics::operator= ( const FourSpeciesPatternCountsMafStatistics &  stats )

inline

Definition at line 593 of file MafStatistics.h.

References alphabet_, and counts_.

Member Data Documentation

alphabet_

const Alphabet* bpp::FourSpeciesPatternCountsMafStatistics::alphabet_

private

Definition at line 568 of file MafStatistics.h.

Referenced by operator=().

counts_

std::vector<unsigned int> bpp::FourSpeciesPatternCountsMafStatistics::counts_

private

Definition at line 569 of file MafStatistics.h.

Referenced by compute(), and operator=().

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(), compute(), bpp::SiteMafStatistics::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