bpp::BasicSequenceFeature Class Reference

A very simple implementation of the SequenceFeature class. More...

#include <Bpp/Seq/Feature/SequenceFeature.h>

Inheritance diagram for bpp::BasicSequenceFeature:

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Collaboration diagram for bpp::BasicSequenceFeature:

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List of all members.

Public Member Functions
	BasicSequenceFeature (const std::string &id, const std::string &seqId, const std::string &source, const std::string &type, unsigned int start, unsigned int end, bool negStrand, double score=-1)
virtual BasicSequenceFeature *	clone () const
const std::string &	getId () const
const std::string &	getSequenceId () const
const std::string &	getSource () const
const std::string &	getType () const
const unsigned int &	getStart () const
const unsigned int &	getEnd () const
bool	isNegativeStrand () const
const double &	getScore () const
const std::string &	getAttribute (const std::string &attribute) const
std::string &	getAttribute (const std::string &attribute)
void	setAttribute (const std::string &attribute, const std::string &value)
	Set the value of an attribute.
SeqRange	getRange () const
Static Public Attributes
static const std::string	NO_ATTRIBUTE_SET = ""
Protected Attributes
std::string	id_
std::string	sequenceId_
std::string	source_
std::string	type_
unsigned int	start_
unsigned int	end_
bool	negStrand_
double	score_
std::map< std::string, std::string >	attributes_

Detailed Description

A very simple implementation of the SequenceFeature class.

It uses a hash map for storing attributes.

Definition at line 181 of file SequenceFeature.h.

Constructor & Destructor Documentation

bpp::BasicSequenceFeature::BasicSequenceFeature	(	const std::string &	id,
		const std::string &	seqId,
		const std::string &	source,
		const std::string &	type,
		unsigned int	start,
		unsigned int	end,
		bool	negStrand,
		double	score = `-1`
	)			`[inline]`

Definition at line 196 of file SequenceFeature.h.

Referenced by clone().

Member Function Documentation

virtual BasicSequenceFeature* bpp::BasicSequenceFeature::clone ( ) const [inline, virtual]

Implements bpp::SequenceFeature.

Definition at line 210 of file SequenceFeature.h.

References BasicSequenceFeature().

std::string& bpp::BasicSequenceFeature::getAttribute ( const std::string & attribute ) [inline, virtual]

Parameters:

attribute

The name of the attribute to retrieve.

Returns:: The attribute with specified name.

Implements bpp::SequenceFeature.

Definition at line 230 of file SequenceFeature.h.

References attributes_.

const std::string& bpp::BasicSequenceFeature::getAttribute ( const std::string & attribute ) const [inline, virtual]

Parameters:

attribute

The name of the attribute to retrieve.

Returns:: The attribute with specified name (read only).

Implements bpp::SequenceFeature.

Definition at line 222 of file SequenceFeature.h.

References attributes_, and bpp::SequenceFeature::NO_ATTRIBUTE_SET.

const unsigned int& bpp::BasicSequenceFeature::getEnd ( ) const [inline, virtual]

Returns:: The ending position of the feature, 0-based, excluded.

Implements bpp::SequenceFeature.

Definition at line 218 of file SequenceFeature.h.

References end_.

const std::string& bpp::BasicSequenceFeature::getId ( ) const [inline, virtual]

Returns:: The id of this feature.

Implements bpp::SequenceFeature.

Definition at line 213 of file SequenceFeature.h.

References id_.

SeqRange bpp::BasicSequenceFeature::getRange ( ) const [inline, virtual]

Returns:: Coordinates as a Range object.

Implements bpp::SequenceFeature.

Definition at line 238 of file SequenceFeature.h.

References end_, negStrand_, and start_.

const double& bpp::BasicSequenceFeature::getScore ( ) const [inline, virtual]

Returns:: The score associated to the feature (eg, an E-value or a P-value).

Implements bpp::SequenceFeature.

Definition at line 220 of file SequenceFeature.h.

References score_.

const std::string& bpp::BasicSequenceFeature::getSequenceId ( ) const [inline, virtual]

Returns:: The id of the sequence on which this feature is based.

Implements bpp::SequenceFeature.

Definition at line 214 of file SequenceFeature.h.

References sequenceId_.

Referenced by bpp::GffFeatureReader::getFeaturesOfSequence().

const std::string& bpp::BasicSequenceFeature::getSource ( ) const [inline, virtual]

Returns:: A text intended to describe the algorithm or procedure used to generate the feature.

Implements bpp::SequenceFeature.

Definition at line 215 of file SequenceFeature.h.

References source_.

const unsigned int& bpp::BasicSequenceFeature::getStart ( ) const [inline, virtual]

Returns:: The starting position of the feature, 0-based, included.

Implements bpp::SequenceFeature.

Definition at line 217 of file SequenceFeature.h.

References start_.

const std::string& bpp::BasicSequenceFeature::getType ( ) const [inline, virtual]

Returns:: A text describing the type of feature. Depending on the format, it can be restricted (for example, mRNA), or any text can be supplied (for example TFXX binding site).

Implements bpp::SequenceFeature.

Definition at line 216 of file SequenceFeature.h.

References type_.

Referenced by bpp::GffFeatureReader::getFeaturesOfType().

bool bpp::BasicSequenceFeature::isNegativeStrand ( ) const [inline, virtual]