A sequence class which is used to store data from MAF files. More...

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

Inheritance diagram for bpp::MafSequence:

Collaboration diagram for bpp::MafSequence:

Public Member Functions
	MafSequence ()

	MafSequence (const std::string &name, const std::string &sequence, bool parseName=true)

	MafSequence (const std::string &name, const std::string &sequence, size_t begin, char strand, size_t srcSize, bool parseName=true)

MafSequence *	clone () const

	~MafSequence ()

bool	hasCoordinates () const

void	removeCoordinates ()

size_t	start () const throw (Exception)

size_t	stop () const

Range< size_t >	getRange (bool origin=true) const

void	setName (const std::string &name)

const std::string &	getSpecies () const

const std::string &	getChromosome () const

char	getStrand () const

size_t	getGenomicSize () const

size_t	getSrcSize () const

void	setStart (size_t begin)

void	setChromosome (const std::string &chr)

void	setSpecies (const std::string &species)

void	setStrand (char s)

void	setSrcSize (size_t srcSize)

std::string	getDescription () const

MafSequence *	subSequence (size_t startAt, size_t length) const
	Extract a sub-sequence. More...

Static Public Member Functions
static void	splitNameIntoSpeciesAndChromosome (const std::string &name, std::string &species, std::string &chr)

Private Member Functions
void	beforeSequenceChanged (const SymbolListEditionEvent &event)

void	afterSequenceChanged (const SymbolListEditionEvent &event)

void	beforeSequenceInserted (const SymbolListInsertionEvent &event)

void	afterSequenceInserted (const SymbolListInsertionEvent &event)

void	beforeSequenceDeleted (const SymbolListDeletionEvent &event)

void	afterSequenceDeleted (const SymbolListDeletionEvent &event)

void	beforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)

void	afterSequenceSubstituted (const SymbolListSubstitutionEvent &event)

Private Attributes
bool	hasCoordinates_

size_t	begin_

std::string	species_

std::string	chromosome_

char	strand_

size_t	size_

size_t	srcSize_

Detailed Description

A sequence class which is used to store data from MAF files.

It extends the SequenceWithAnnotation class to store MAF-specific features, like the chromosome position. The sequence is its own listener, and recomputes its "genomic" site by using the SequenceTools::getNumberOfSites function when a content modification is performed. Tags like begin and stop, hovever, have to be set by hand.

A MAF sequence is necessarily a DNA sequence.

Definition at line 62 of file MafSequence.h.

Constructor & Destructor Documentation

◆ MafSequence() [1/3]

bpp::MafSequence::MafSequence ( )

inline

Definition at line 75 of file MafSequence.h.

References size_.

Referenced by clone().

◆ MafSequence() [2/3]

bpp::MafSequence::MafSequence	(	const std::string &	name,
		const std::string &	sequence,
		bool	parseName = `true`
	)

inline

Definition at line 81 of file MafSequence.h.

References chromosome_, size_, species_, and splitNameIntoSpeciesAndChromosome().

◆ MafSequence() [3/3]

bpp::MafSequence::MafSequence	(	const std::string &	name,
		const std::string &	sequence,
		size_t	begin,
		char	strand,
		size_t	srcSize,
		bool	parseName = `true`
	)

inline

Definition at line 89 of file MafSequence.h.

References chromosome_, size_, species_, and splitNameIntoSpeciesAndChromosome().

◆ ~MafSequence()

bpp::MafSequence::~MafSequence ( )

inline

Definition at line 99 of file MafSequence.h.

Member Function Documentation

◆ afterSequenceChanged()

void bpp::MafSequence::afterSequenceChanged ( const SymbolListEditionEvent & event )

inlineprivate

Definition at line 191 of file MafSequence.h.

References size_.

◆ afterSequenceDeleted()

void bpp::MafSequence::afterSequenceDeleted ( const SymbolListDeletionEvent & event )

inlineprivate

Definition at line 195 of file MafSequence.h.

References size_.

◆ afterSequenceInserted()

void bpp::MafSequence::afterSequenceInserted ( const SymbolListInsertionEvent & event )

inlineprivate

Definition at line 193 of file MafSequence.h.

References size_.

◆ afterSequenceSubstituted()

void bpp::MafSequence::afterSequenceSubstituted ( const SymbolListSubstitutionEvent & event )

inlineprivate

Definition at line 197 of file MafSequence.h.

◆ beforeSequenceChanged()

void bpp::MafSequence::beforeSequenceChanged ( const SymbolListEditionEvent & event )

inlineprivate

Definition at line 190 of file MafSequence.h.

◆ beforeSequenceDeleted()

void bpp::MafSequence::beforeSequenceDeleted ( const SymbolListDeletionEvent & event )

inlineprivate

Definition at line 194 of file MafSequence.h.

◆ beforeSequenceInserted()

void bpp::MafSequence::beforeSequenceInserted ( const SymbolListInsertionEvent & event )

inlineprivate

Definition at line 192 of file MafSequence.h.

◆ beforeSequenceSubstituted()

void bpp::MafSequence::beforeSequenceSubstituted ( const SymbolListSubstitutionEvent & event )

inlineprivate

Definition at line 196 of file MafSequence.h.

◆ clone()

MafSequence* bpp::MafSequence::clone ( ) const

inline

Definition at line 97 of file MafSequence.h.

References MafSequence().

◆ getChromosome()

const std::string& bpp::MafSequence::getChromosome ( ) const

inline

Definition at line 154 of file MafSequence.h.

References chromosome_.

Referenced by bpp::ConcatenateMafIterator::analyseCurrentBlock_(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::FeatureExtractor::analyseCurrentBlock_(), bpp::BlockMergerMafIterator::analyseCurrentBlock_(), bpp::CsvStatisticsOutputIterationListener::iterationMoves(), bpp::OutputAlignmentMafIterator::writeBlock(), and bpp::VcfOutputMafIterator::writeBlock_().

◆ getDescription()

std::string bpp::MafSequence::getDescription ( ) const

inline

Definition at line 178 of file MafSequence.h.

References hasCoordinates_, start(), stop(), and strand_.

Referenced by bpp::ConcatenateMafIterator::analyseCurrentBlock_(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), and bpp::BlockMergerMafIterator::analyseCurrentBlock_().

◆ getGenomicSize()

size_t bpp::MafSequence::getGenomicSize ( ) const

inline

Definition at line 158 of file MafSequence.h.

References size_.

Referenced by bpp::MafParser::analyseCurrentBlock_(), and bpp::OutputMafIterator::writeBlock().

◆ getRange()

Range<size_t> bpp::MafSequence::getRange ( bool origin = true ) const

inline

Returns: A range with cooridinates from this sequence.

Parameters

origin Tell if coorinates according to original sequence should be used. If 'yes' and the sequence is on the negative strand, the returned rang will be computed as [SrcSize-Stop, SrcSize-Start[

Definition at line 121 of file MafSequence.h.

References hasCoordinates_, srcSize_, start(), stop(), and strand_.

Referenced by bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), and bpp::FeatureExtractor::analyseCurrentBlock_().