bpp::SequenceLengthMafStatistics Class Reference

Retrieve the sequence length (number of nucleotides) for a given species in a maf block. More...

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

Inheritance diagram for bpp::SequenceLengthMafStatistics:

Collaboration diagram for bpp::SequenceLengthMafStatistics:

Public Member Functions
	SequenceLengthMafStatistics (const std::string &species)
	~SequenceLengthMafStatistics ()
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	species_

Detailed Description

Retrieve the sequence length (number of nucleotides) for a given species in a maf block.

If no sequence is found for the current block, 0 is returned. If several sequences are found for a given species, an exception is thrown.

Definition at line 327 of file MafStatistics.h.

Constructor & Destructor Documentation

SequenceLengthMafStatistics()

bpp::SequenceLengthMafStatistics::SequenceLengthMafStatistics ( const std::string &  species )

inline

Definition at line 334 of file MafStatistics.h.

~SequenceLengthMafStatistics()

bpp::SequenceLengthMafStatistics::~SequenceLengthMafStatistics ( )

inline

Definition at line 335 of file MafStatistics.h.

Member Function Documentation

compute()

void bpp::SequenceLengthMafStatistics::compute ( const MafBlock &  block )

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 340 of file MafStatistics.h.

References bpp::SequenceTools::getNumberOfSites(), bpp::MafBlock::getSequencesForSpecies(), bpp::AbstractMafStatisticsSimple::result_, bpp::SimpleMafStatisticsResult::setValue(), and species_.

getFullName()

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

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 339 of file MafStatistics.h.

References species_.

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::SequenceLengthMafStatistics::getShortName ( ) const

inlinevirtual

Implements bpp::MafStatistics.

Definition at line 338 of file MafStatistics.h.

References species_.

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(), compute(), bpp::AlignmentScoreMafStatistics::compute(), bpp::AbstractMafStatisticsSimple::getResult(), and bpp::AbstractMafStatisticsSimple::getSupportedTags().

species_

std::string bpp::SequenceLengthMafStatistics::species_

private

Definition at line 331 of file MafStatistics.h.

Referenced by compute(), getFullName(), and getShortName().

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

• Bpp/Seq/Io/Maf/MafStatistics.h