bpp::PairwiseDivergenceMafStatistics Class Reference

Computes the pairwise divergence for a pair of sequences in a maf block. More...

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

Inheritance diagram for bpp::PairwiseDivergenceMafStatistics:

Collaboration diagram for bpp::PairwiseDivergenceMafStatistics:

Public Member Functions
	PairwiseDivergenceMafStatistics (const std::string &species1, const std::string &species2)
	~PairwiseDivergenceMafStatistics ()
std::string	getShortName () const
std::string	getFullName () const
void	compute (const MafBlock &block)
const SimpleMafStatisticsResult &	getResult () const
std::vector< std::string >	getSupportedTags () const

Protected Attributes
SimpleMafStatisticsResult	result_

Private Attributes
std::string	species1_
std::string	species2_

Detailed Description

Computes the pairwise divergence for a pair of sequences in a maf block.

Definition at line 265 of file MafStatistics.h.

Constructor & Destructor Documentation

PairwiseDivergenceMafStatistics()

bpp::PairwiseDivergenceMafStatistics::PairwiseDivergenceMafStatistics ( const std::string &  species1, const std::string &  species2  )

inline

Definition at line 273 of file MafStatistics.h.

~PairwiseDivergenceMafStatistics()

bpp::PairwiseDivergenceMafStatistics::~PairwiseDivergenceMafStatistics ( )

inline

Definition at line 276 of file MafStatistics.h.

Member Function Documentation

compute()

void PairwiseDivergenceMafStatistics::compute ( const MafBlock &  block )

virtual

Implements bpp::MafStatistics.

Definition at line 56 of file MafStatistics.cpp.

References bpp::SequenceTools::getPercentIdentity(), bpp::MafBlock::getSequencesForSpecies(), and bpp::NumConstants::NaN().

getFullName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 280 of file MafStatistics.h.

References species1_, and species2_.

getResult()

const SimpleMafStatisticsResult& bpp::AbstractMafStatisticsSimple::getResult ( ) const

inlinevirtualinherited

Implements bpp::MafStatistics.

Definition at line 258 of file MafStatistics.h.

References bpp::AbstractMafStatisticsSimple::result_.

getShortName()

std::string bpp::PairwiseDivergenceMafStatistics::getShortName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 279 of file MafStatistics.h.

References species1_, and species2_.

getSupportedTags()

std::vector<std::string> bpp::AbstractMafStatisticsSimple::getSupportedTags ( ) const

inlinevirtualinherited

Returns

A vector with all available tags.

Implements bpp::MafStatistics.

Definition at line 259 of file MafStatistics.h.

References bpp::MafStatisticsResult::getAvailableTags(), and bpp::AbstractMafStatisticsSimple::result_.

Member Data Documentation

result_

SimpleMafStatisticsResult bpp::AbstractMafStatisticsSimple::result_

protectedinherited

Definition at line 251 of file MafStatistics.h.

Referenced by bpp::BlockSizeMafStatistics::compute(), bpp::BlockLengthMafStatistics::compute(), bpp::SequenceLengthMafStatistics::compute(), bpp::AlignmentScoreMafStatistics::compute(), bpp::AbstractMafStatisticsSimple::getResult(), and bpp::AbstractMafStatisticsSimple::getSupportedTags().

species1_

std::string bpp::PairwiseDivergenceMafStatistics::species1_

private

Definition at line 269 of file MafStatistics.h.

Referenced by getFullName(), and getShortName().

species2_

std::string bpp::PairwiseDivergenceMafStatistics::species2_

private

Definition at line 270 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