bpp::CharacterCountsMafStatistics Class Reference

Compute the base frequencies of a maf block. More...

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

Inheritance diagram for bpp::CharacterCountsMafStatistics:

Collaboration diagram for bpp::CharacterCountsMafStatistics:

Public Member Functions
	CharacterCountsMafStatistics (const Alphabet *alphabet, const std::vector< std::string > &species, const std::string suffix)
	CharacterCountsMafStatistics (const CharacterCountsMafStatistics &stats)
CharacterCountsMafStatistics &	operator= (const CharacterCountsMafStatistics &stats)
virtual	~CharacterCountsMafStatistics ()
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< std::string >	species_
bool	noSpeciesMeansAllSpecies_

Detailed Description

Compute the base frequencies of a maf block.

For each block, provides the following numbers (with their corresponding tags):

• A: total counts of A
• C: total counts of C
• G: total counts of G
• T [or U]: total counts of T/U
• Gap: total counts of gaps
• Unresolved: total counts of unresolved characters The sum of all characters should equal BlockSize x BlockLength

Definition at line 436 of file MafStatistics.h.

Constructor & Destructor Documentation

CharacterCountsMafStatistics() [1/2]

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

inline

Definition at line 444 of file MafStatistics.h.

CharacterCountsMafStatistics() [2/2]

bpp::CharacterCountsMafStatistics::CharacterCountsMafStatistics ( const CharacterCountsMafStatistics &  stats )

inline

Definition at line 449 of file MafStatistics.h.

~CharacterCountsMafStatistics()

virtual bpp::CharacterCountsMafStatistics::~CharacterCountsMafStatistics ( )

inlinevirtual

Definition at line 461 of file MafStatistics.h.

Member Function Documentation

compute()

void CharacterCountsMafStatistics::compute ( const MafBlock &  block )

virtual

Implements bpp::MafStatistics.

Definition at line 127 of file MafStatistics.cpp.

References alphabet_, bpp::SequenceContainerTools::getCounts(), bpp::Alphabet::getGapCharacterCode(), bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::Alphabet::getSize(), bpp::Alphabet::intToChar(), bpp::Alphabet::isUnresolved(), bpp::AbstractMafStatistics::result_, and bpp::MafStatisticsResult::setValue().

getFullName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 465 of file MafStatistics.h.

References bpp::AbstractSpeciesSelectionMafStatistics::suffix_.

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::CharacterCountsMafStatistics::getShortName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 464 of file MafStatistics.h.

References bpp::AbstractSpeciesSelectionMafStatistics::suffix_.

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 compute(), bpp::SiteFrequencySpectrumMafStatistics::compute(), bpp::FourSpeciesPatternCountsMafStatistics::compute(), bpp::SiteMafStatistics::compute(), and bpp::SequenceDiversityMafStatistics::compute().

getSupportedTags()

vector< string > CharacterCountsMafStatistics::getSupportedTags ( ) const

virtual

Returns

A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 115 of file MafStatistics.cpp.

References alphabet_, bpp::Alphabet::getSize(), and bpp::Alphabet::intToChar().

operator=()

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

inline

Definition at line 454 of file MafStatistics.h.

References alphabet_.

Member Data Documentation

alphabet_

const Alphabet* bpp::CharacterCountsMafStatistics::alphabet_

private

Definition at line 441 of file MafStatistics.h.

Referenced by compute(), getSupportedTags(), 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 compute(), bpp::SiteFrequencySpectrumMafStatistics::compute(), bpp::FourSpeciesPatternCountsMafStatistics::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 getFullName(), and 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