The base interface for sequence features. More...

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

Inheritance diagram for bpp::SequenceFeature:

Collaboration diagram for bpp::SequenceFeature:

Public Member Functions
virtual SequenceFeature *	clone () const =0

virtual const std::string &	getId () const =0

virtual void	setId (const std::string &id)=0

virtual const std::string &	getSequenceId () const =0

virtual void	setSequenceId (const std::string &id)=0

virtual const std::string &	getSource () const =0

virtual void	setSource (const std::string &source)=0

virtual const std::string &	getType () const =0

virtual void	setType (const std::string &type)=0

virtual const size_t	getStart () const =0

virtual const size_t	getEnd () const =0

virtual bool	isStranded () const =0

virtual bool	isNegativeStrand () const =0

virtual void	invert ()=0

virtual SeqRange	getRange () const =0

virtual bool	overlap (const SequenceFeature &feat) const =0

virtual const double &	getScore () const =0

virtual void	setScore (double score)=0

virtual const std::string &	getAttribute (const std::string &attribute) const =0

virtual std::string &	getAttribute (const std::string &attribute)=0

virtual std::set< std::string >	getAttributeList () const =0

virtual void	setAttribute (const std::string &attribute, const std::string &value)=0
	Set the value of an attribute. More...

virtual void	removeAttribute (const std::string &attribute)=0

Static Public Attributes
static const std::string	NO_ATTRIBUTE_SET = ""

Detailed Description

The base interface for sequence features.

This interface provides the most generic information common to all features, that is:

sequence reference
procedure used to generate the information
start and end positions. Coordinates are 0-based, of type [a,b[, so that if a==b, the annotation is considered empty. A one-character annotation is then noted as start=12(included),end=13(excluded) for instance.

Subclasses inheriting this interface provide specialisations for various types of annotations. Depending on the file format of annotations, not all types of annotations may be supported.

Author: Julien Dutheil

Definition at line 126 of file SequenceFeature.h.

Member Function Documentation

◆ clone()

virtual SequenceFeature* bpp::SequenceFeature::clone ( ) const

pure virtual

Implemented in bpp::BasicSequenceFeature.

Referenced by bpp::SequenceFeatureSet::addFeature().

◆ getAttribute() [1/2]

virtual const std::string& bpp::SequenceFeature::getAttribute ( const std::string & attribute ) const

pure virtual

Parameters

attribute The name of the attribute to retrieve.

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

Implemented in bpp::BasicSequenceFeature.

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

◆ getAttribute() [2/2]

virtual std::string& bpp::SequenceFeature::getAttribute ( const std::string & attribute )

pure virtual

Parameters

attribute The name of the attribute to retrieve.

Returns: The attribute with specified name.

Implemented in bpp::BasicSequenceFeature.

◆ getAttributeList()

virtual std::set< std::string > bpp::SequenceFeature::getAttributeList ( ) const

pure virtual

Returns: The list of all attributes available.

Implemented in bpp::BasicSequenceFeature.

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

◆ getEnd()

virtual const size_t bpp::SequenceFeature::getEnd ( ) const

pure virtual

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

Implemented in bpp::BasicSequenceFeature.

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

◆ getId()

virtual const std::string& bpp::SequenceFeature::getId ( ) const

pure virtual

Returns: The id of this feature.

Implemented in bpp::BasicSequenceFeature.

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

◆ getRange()

virtual SeqRange bpp::SequenceFeature::getRange ( ) const

pure virtual

Returns: Coordinates as a Range object.

Implemented in bpp::BasicSequenceFeature.

Referenced by bpp::BasicSequenceFeature::overlap().

◆ getScore()

virtual const double& bpp::SequenceFeature::getScore ( ) const

pure virtual

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

Implemented in bpp::BasicSequenceFeature.

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

◆ getSequenceId()

virtual const std::string& bpp::SequenceFeature::getSequenceId ( ) const

pure virtual

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

Implemented in bpp::BasicSequenceFeature.

Referenced by bpp::BasicSequenceFeature::overlap(), and bpp::GffFeatureReader::toString().

◆ getSource()

virtual const std::string& bpp::SequenceFeature::getSource ( ) const

pure virtual

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

Implemented in bpp::BasicSequenceFeature.

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

◆ getStart()

virtual const size_t bpp::SequenceFeature::getStart ( ) const

pure virtual

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

Implemented in bpp::BasicSequenceFeature.

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

◆ getType()

virtual const std::string& bpp::SequenceFeature::getType ( ) const

pure 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).

Implemented in bpp::BasicSequenceFeature.

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