bpp-seq-omics  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
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_
 

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 parsimony informative sites

Definition at line 595 of file MafStatistics.h.

Constructor & Destructor Documentation

◆ SiteMafStatistics()

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

Definition at line 600 of file MafStatistics.h.

◆ ~SiteMafStatistics()

virtual bpp::SiteMafStatistics::~SiteMafStatistics ( )
inlinevirtual

Definition at line 605 of file MafStatistics.h.

Member Function Documentation

◆ compute()

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

Implements bpp::MafStatistics.

Definition at line 305 of file MafStatistics.cpp.

References bpp::AbstractSpeciesSelectionMafStatistics::getSiteContainer_(), bpp::AbstractMafStatistics::result_, and bpp::MafStatisticsResult::setValue().

◆ getFullName()

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

Implements bpp::MafStatistics.

Definition at line 609 of file MafStatistics.h.

◆ getResult()

const MafStatisticsResult& bpp::AbstractMafStatistics::getResult ( ) const
inlinevirtualinherited

Implements bpp::MafStatistics.

Definition at line 239 of file MafStatistics.h.

References bpp::AbstractMafStatistics::result_.

◆ getShortName()

std::string bpp::SiteMafStatistics::getShortName ( ) const
inlinevirtual

Implements bpp::MafStatistics.

Definition at line 608 of file MafStatistics.h.

◆ getSiteContainer_()

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

Definition at line 95 of file MafStatistics.cpp.

References bpp::MafBlock::getAlignment(), bpp::MafBlock::getSequencesForSpecies(), and bpp::MafBlock::hasSequenceForSpecies().

Referenced by 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 296 of file MafStatistics.cpp.

Member Data Documentation

◆ result_

MafStatisticsResult bpp::AbstractMafStatistics::result_
protectedinherited

Definition at line 232 of file MafStatistics.h.

Referenced by bpp::SiteFrequencySpectrumMafStatistics::compute(), bpp::FourSpeciesPatternCountsMafStatistics::compute(), compute(), bpp::PolymorphismMafStatistics::compute(), bpp::SequenceDiversityMafStatistics::compute(), and bpp::AbstractMafStatistics::getResult().

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