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

MafStatisticsResult result_
 

Private Attributes

const Alphabet * alphabet_
 

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 380 of file MafStatistics.h.

Constructor & Destructor Documentation

◆ CharacterCountsMafStatistics() [1/2]

bpp::CharacterCountsMafStatistics::CharacterCountsMafStatistics ( const Alphabet *  alphabet)
inline

Definition at line 387 of file MafStatistics.h.

◆ CharacterCountsMafStatistics() [2/2]

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

Definition at line 388 of file MafStatistics.h.

◆ ~CharacterCountsMafStatistics()

virtual bpp::CharacterCountsMafStatistics::~CharacterCountsMafStatistics ( )
inlinevirtual

Definition at line 396 of file MafStatistics.h.

Member Function Documentation

◆ compute()

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

Implements bpp::MafStatistics.

Definition at line 79 of file MafStatistics.cpp.

References bpp::MafBlock::getAlignment().

◆ getFullName()

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

Implements bpp::MafStatistics.

Definition at line 400 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::CharacterCountsMafStatistics::getShortName ( ) const
inlinevirtual

Implements bpp::MafStatistics.

Definition at line 399 of file MafStatistics.h.

◆ getSupportedTags()

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

Implements bpp::MafStatistics.

Definition at line 67 of file MafStatistics.cpp.

◆ operator=()

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

Definition at line 390 of file MafStatistics.h.

References alphabet_.

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::CharacterCountsMafStatistics::alphabet_
private

Definition at line 384 of file MafStatistics.h.

Referenced by operator=().

◆ result_

MafStatisticsResult bpp::AbstractMafStatistics::result_
protectedinherited

Definition at line 232 of file MafStatistics.h.

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

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