bpp-seq-omics  2.4.1
Classes | Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::SiteFrequencySpectrumMafStatistics Class Reference

Compute the Site Frequency Spectrum of a maf block. More...

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

+ Inheritance diagram for bpp::SiteFrequencySpectrumMafStatistics:
+ Collaboration diagram for bpp::SiteFrequencySpectrumMafStatistics:

Classes

class  Categorizer
 

Public Member Functions

 SiteFrequencySpectrumMafStatistics (const Alphabet *alphabet, const std::vector< double > &bounds, const std::vector< std::string > &ingroup, const std::string outgroup="")
 
 SiteFrequencySpectrumMafStatistics (const SiteFrequencySpectrumMafStatistics &stats)
 
SiteFrequencySpectrumMafStatistics & operator= (const SiteFrequencySpectrumMafStatistics &stats)
 
virtual ~SiteFrequencySpectrumMafStatistics ()
 
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_
 
Categorizer categorizer_
 
std::vector< unsigned int > counts_
 
std::string outgroup_
 
std::vector< std::string > species_
 
bool noSpeciesMeansAllSpecies_
 

Detailed Description

Compute the Site Frequency Spectrum of a maf block.

If no outgroup is provided, the ancestral states are considered as unknown and the unfolded spectrum is computed, so that 10000 and 11110 sites are treated equally.

Definition at line 478 of file MafStatistics.h.

Constructor & Destructor Documentation

◆ SiteFrequencySpectrumMafStatistics() [1/2]

bpp::SiteFrequencySpectrumMafStatistics::SiteFrequencySpectrumMafStatistics ( const Alphabet *  alphabet,
const std::vector< double > &  bounds,
const std::vector< std::string > &  ingroup,
const std::string  outgroup = "" 
)
inline

Definition at line 515 of file MafStatistics.h.

◆ SiteFrequencySpectrumMafStatistics() [2/2]

bpp::SiteFrequencySpectrumMafStatistics::SiteFrequencySpectrumMafStatistics ( const SiteFrequencySpectrumMafStatistics &  stats)
inline

Definition at line 524 of file MafStatistics.h.

◆ ~SiteFrequencySpectrumMafStatistics()

virtual bpp::SiteFrequencySpectrumMafStatistics::~SiteFrequencySpectrumMafStatistics ( )
inlinevirtual

Definition at line 543 of file MafStatistics.h.

Member Function Documentation

◆ compute()

void SiteFrequencySpectrumMafStatistics::compute ( const MafBlock &  block)
virtual

Implements bpp::MafStatistics.

Definition at line 156 of file MafStatistics.cpp.

References alphabet_, categorizer_, count(), counts_, bpp::SiteFrequencySpectrumMafStatistics::Categorizer::getCategory(), bpp::SiteFrequencySpectrumMafStatistics::Categorizer::getNumberOfCategories(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getSequenceForSpecies(), bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::MafBlock::hasSequenceForSpecies(), bpp::Alphabet::isGap(), bpp::Alphabet::isUnresolved(), outgroup_, bpp::AbstractMafStatistics::result_, bpp::MafStatisticsResult::setValue(), bpp::Site::size(), and bpp::TextTools::toString().

◆ getFullName()

std::string bpp::SiteFrequencySpectrumMafStatistics::getFullName ( ) const
inlinevirtual

Implements bpp::MafStatistics.

Definition at line 547 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::SiteFrequencySpectrumMafStatistics::getShortName ( ) const
inlinevirtual

Implements bpp::MafStatistics.

Definition at line 546 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(), compute(), bpp::FourSpeciesPatternCountsMafStatistics::compute(), bpp::SiteMafStatistics::compute(), and bpp::SequenceDiversityMafStatistics::compute().

◆ getSupportedTags()

vector< string > SiteFrequencySpectrumMafStatistics::getSupportedTags ( ) const
virtual
Returns
A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 144 of file MafStatistics.cpp.

References categorizer_, bpp::SiteFrequencySpectrumMafStatistics::Categorizer::getNumberOfCategories(), and bpp::TextTools::toString().

◆ operator=()

SiteFrequencySpectrumMafStatistics& bpp::SiteFrequencySpectrumMafStatistics::operator= ( const SiteFrequencySpectrumMafStatistics &  stats)
inline

Definition at line 533 of file MafStatistics.h.

References alphabet_, categorizer_, counts_, and outgroup_.

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::SiteFrequencySpectrumMafStatistics::alphabet_
private

Definition at line 509 of file MafStatistics.h.

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

◆ categorizer_

Categorizer bpp::SiteFrequencySpectrumMafStatistics::categorizer_
private

Definition at line 510 of file MafStatistics.h.

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

◆ counts_

std::vector<unsigned int> bpp::SiteFrequencySpectrumMafStatistics::counts_
private

Definition at line 511 of file MafStatistics.h.

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

◆ noSpeciesMeansAllSpecies_

bool bpp::AbstractSpeciesSelectionMafStatistics::noSpeciesMeansAllSpecies_
privateinherited

Definition at line 382 of file MafStatistics.h.

◆ outgroup_

std::string bpp::SiteFrequencySpectrumMafStatistics::outgroup_
private

Definition at line 512 of file MafStatistics.h.

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

◆ result_

MafStatisticsResult bpp::AbstractMafStatistics::result_
protectedinherited

Definition at line 234 of file MafStatistics.h.

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

The documentation for this class was generated from the following files: