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 const size_t	size () const

virtual bool	isStranded () const =0

virtual bool	isNegativeStrand () const =0

virtual void	invert ()=0

virtual SeqRange	getRange () const =0

virtual bool	isEmpty () const

virtual bool	isPoint () const

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

virtual bool	overlap (const SeqRange &range) const =0

virtual bool	includes (const SeqRange &range) const =0

virtual bool	isIncludedIn (const SeqRange &range) 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 136 of file SequenceFeature.h.

Member Function Documentation

◆ clone()

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

pure virtual

Implements bpp::Clonable.

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::BedGraphFeatureReader::toString(), and 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 size(), bpp::BedGraphFeatureReader::toString(), and 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(), bpp::BedGraphFeatureReader::toString(), 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 size(), bpp::BedGraphFeatureReader::toString(), and 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().

◆ includes()

virtual bool bpp::SequenceFeature::includes ( const SeqRange & range ) const

pure virtual

Returns: True if the feature fully contains the given range.

Implemented in bpp::BasicSequenceFeature.

◆ invert()

virtual void bpp::SequenceFeature::invert ( )

pure virtual

Change the orientation of the feature.

Implemented in bpp::BasicSequenceFeature.

◆ isEmpty()

virtual bool bpp::SequenceFeature::isEmpty ( ) const

inlinevirtual

Returns: Check if the feature is empty (start == end)

Definition at line 222 of file SequenceFeature.h.

References size().

◆ isIncludedIn()

virtual bool bpp::SequenceFeature::isIncludedIn ( const SeqRange & range ) const

pure virtual

Returns: True if the feature is fully contained in the given range.

Implemented in bpp::BasicSequenceFeature.

◆ isNegativeStrand()

virtual bool bpp::SequenceFeature::isNegativeStrand ( ) const

pure virtual

Returns: True if the sequence is coded on the negative strand. False if it is on the positive one or unknown.

Implemented in bpp::BasicSequenceFeature.

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

◆ isPoint()

virtual bool bpp::SequenceFeature::isPoint ( ) const

inlinevirtual

Returns: Check if the feature is a point annotation (start + 1 == end)

Definition at line 227 of file SequenceFeature.h.

References size().

◆ isStranded()

virtual bool bpp::SequenceFeature::isStranded ( ) const

pure virtual

Returns: True if the feature is stranded.

Implemented in bpp::BasicSequenceFeature.

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

◆ overlap() [1/2]

virtual bool bpp::SequenceFeature::overlap ( const SeqRange & range ) const

pure virtual

Returns: True if the feature overlap with the given range (non-null intersection).

Implemented in bpp::BasicSequenceFeature.

◆ overlap() [2/2]

virtual bool bpp::SequenceFeature::overlap ( const SequenceFeature & feat ) const

pure virtual

Returns: True if the features overlap.

Implemented in bpp::BasicSequenceFeature.

◆ removeAttribute()

virtual void bpp::SequenceFeature::removeAttribute ( const std::string & attribute )

pure virtual

Parameters

attribute The name of the attribute to be removed.

Implemented in bpp::BasicSequenceFeature.

◆ setAttribute()

virtual void bpp::SequenceFeature::setAttribute	(	const std::string &	attribute,
		const std::string &	value
	)

pure virtual

Set the value of an attribute.

Parameters

attribute	The name of the attribute to set.
value	The value of the attribute to set.

Implemented in bpp::BasicSequenceFeature.

◆ setId()

virtual void bpp::SequenceFeature::setId ( const std::string & id )

pure virtual

Parameters

id	A std::string representing the id.

Implemented in bpp::BasicSequenceFeature.

◆ setScore()

virtual void bpp::SequenceFeature::setScore ( double score )

pure virtual

Parameters

score A double representing the score of this feature.

Implemented in bpp::BasicSequenceFeature.

◆ setSequenceId()

virtual void bpp::SequenceFeature::setSequenceId ( const std::string & id )

pure virtual

Parameters

id	A std::string representing the id of the reference.

Implemented in bpp::BasicSequenceFeature.

◆ setSource()

virtual void bpp::SequenceFeature::setSource ( const std::string & source )

pure virtual

Parameters

source A std::string representing the source of the feature.

Implemented in bpp::BasicSequenceFeature.

◆ setType()

virtual void bpp::SequenceFeature::setType ( const std::string & type )

pure virtual

Parameters

type	A std::string representing the type of this feature.

Implemented in bpp::BasicSequenceFeature.

◆ size()

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

inlinevirtual

Returns: The size of the feature.

Definition at line 195 of file SequenceFeature.h.

References getEnd(), and getStart().

Referenced by isEmpty(), and isPoint().

Member Data Documentation

◆ NO_ATTRIBUTE_SET

const std::string SequenceFeature::NO_ATTRIBUTE_SET = ""

static

Definition at line 140 of file SequenceFeature.h.

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

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

Bpp/Seq/Feature/SequenceFeature.h
Bpp/Seq/Feature/SequenceFeature.cpp

Public Member Functions

Static Public Attributes

Detailed Description

Member Function Documentation

◆ clone()

◆ getAttribute() [1/2]

◆ getAttribute() [2/2]

◆ getAttributeList()

◆ getEnd()

◆ getId()

◆ getRange()

◆ getScore()

◆ getSequenceId()

◆ getSource()

◆ getStart()

◆ getType()

◆ includes()

◆ invert()

◆ isEmpty()

◆ isIncludedIn()

◆ isNegativeStrand()

◆ isPoint()

◆ isStranded()

◆ overlap() [1/2]

◆ overlap() [2/2]

◆ removeAttribute()

◆ setAttribute()

◆ setId()

◆ setScore()

◆ setSequenceId()

◆ setSource()

◆ setType()

◆ size()

Member Data Documentation

◆ NO_ATTRIBUTE_SET