A simple ensemble of sequence features. More...

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

Collaboration diagram for bpp::SequenceFeatureSet:

Public Member Functions
	SequenceFeatureSet ()

virtual	~SequenceFeatureSet ()

	SequenceFeatureSet (const SequenceFeatureSet &sfs)

SequenceFeatureSet &	operator= (const SequenceFeatureSet &sfs)

void	clear ()
	Delete all features in this set. More...

const SequenceFeature &	getFeature (size_t i) const

const SequenceFeature &	operator[] (size_t i) const

size_t	getNumberOfFeatures () const

bool	isEmpty () const

void	addFeature (const SequenceFeature &feature)
	Add a feature to the container. The feature will be copied and the copy owned by the container. More...

std::set< std::string >	getSequences () const

std::set< std::string >	getTypes () const

void	fillRangeCollection (RangeCollection< size_t > &coords) const
	Get all coordinates of features. All ranges are added to a RangeCollection container, as SeqRange objects. More...

void	fillRangeCollectionForSequence (const std::string &seqId, RangeCollection< size_t > &coords) const
	Get all coordinates of features for a given source. All ranges are added to a RangeCollection container, as SeqRange objects. More...

SequenceFeatureSet *	getSubsetForType (const std::string &type) const

SequenceFeatureSet *	getSubsetForTypes (const std::vector< std::string > &types) const

SequenceFeatureSet *	getSubsetForSequence (const std::string &id) const

SequenceFeatureSet *	getSubsetForSequences (const std::vector< std::string > &ids) const

SequenceFeatureSet *	getSubsetForRange (const SeqRange &range, bool complete) const

Private Attributes
std::vector< SequenceFeature * >	features_

Detailed Description

A simple ensemble of sequence features.

This class is at a draft stage, and further improvements are expected, notably to allow proper indexation, nested features, etc.

For now, it is mostly a vector of feature object, stored as pointers. A few functions are provided for convenience.

Author: Julien Dutheil

Definition at line 417 of file SequenceFeature.h.

Constructor & Destructor Documentation

◆ SequenceFeatureSet() [1/2]

bpp::SequenceFeatureSet::SequenceFeatureSet ( )

inline

Definition at line 423 of file SequenceFeature.h.

Referenced by getSubsetForRange(), getSubsetForSequence(), getSubsetForSequences(), getSubsetForType(), and getSubsetForTypes().

◆ ~SequenceFeatureSet()

virtual bpp::SequenceFeatureSet::~SequenceFeatureSet ( )

inlinevirtual

Definition at line 425 of file SequenceFeature.h.

References clear().

◆ SequenceFeatureSet() [2/2]

bpp::SequenceFeatureSet::SequenceFeatureSet ( const SequenceFeatureSet & sfs )

inline

Definition at line 427 of file SequenceFeature.h.

References features_.

Member Function Documentation

◆ addFeature()

void bpp::SequenceFeatureSet::addFeature ( const SequenceFeature & feature )

inline

Add a feature to the container. The feature will be copied and the copy owned by the container.

Parameters

feature The feature to add to the container.

Definition at line 493 of file SequenceFeature.h.

References bpp::SequenceFeature::clone(), and features_.

Referenced by bpp::BedGraphFeatureReader::getAllFeatures(), bpp::GffFeatureReader::getAllFeatures(), bpp::GtfFeatureReader::getAllFeatures(), bpp::BedGraphFeatureReader::getFeaturesOfSequence(), bpp::GffFeatureReader::getFeaturesOfSequence(), bpp::GtfFeatureReader::getFeaturesOfSequence(), bpp::BedGraphFeatureReader::getFeaturesOfType(), bpp::GffFeatureReader::getFeaturesOfType(), bpp::GtfFeatureReader::getFeaturesOfType(), bpp::SequenceFeatureTools::getOrfs(), getSubsetForRange(), getSubsetForSequence(), getSubsetForSequences(), getSubsetForType(), and getSubsetForTypes().

◆ clear()

void bpp::SequenceFeatureSet::clear ( )

inline

Delete all features in this set.

Definition at line 451 of file SequenceFeature.h.

References features_.

Referenced by operator=(), and ~SequenceFeatureSet().

◆ fillRangeCollection()

void bpp::SequenceFeatureSet::fillRangeCollection ( RangeCollection< size_t > & coords ) const

inline

Get all coordinates of features. All ranges are added to a RangeCollection container, as SeqRange objects.

Parameters

coords [out] a container where to add the coordinates of each feature.

Definition at line 528 of file SequenceFeature.h.

References bpp::RangeCollection< class >::addRange(), and features_.

◆ fillRangeCollectionForSequence()

void bpp::SequenceFeatureSet::fillRangeCollectionForSequence	(	const std::string &	seqId,
		RangeCollection< size_t > &	coords
	)		const

inline

Get all coordinates of features for a given source. All ranges are added to a RangeCollection container, as SeqRange objects.

Parameters

seqId	The name of the sequence id to consider.
coords	[out] a container where to add the coordinates of each feature.

Definition at line 542 of file SequenceFeature.h.

References bpp::RangeCollection< class >::addRange(), and features_.

Referenced by bpp::FeatureExtractorMafIterator::FeatureExtractorMafIterator(), and bpp::FeatureFilterMafIterator::FeatureFilterMafIterator().

◆ getFeature()

const SequenceFeature& bpp::SequenceFeatureSet::getFeature ( size_t i ) const

inline

Parameters

i	The index of the feature.

Returns: A reference toward the feature.

Definition at line 465 of file SequenceFeature.h.

References features_.

◆ getNumberOfFeatures()

size_t bpp::SequenceFeatureSet::getNumberOfFeatures ( ) const

inline

Returns: The number of features in this set.

Definition at line 481 of file SequenceFeature.h.

References features_.

Referenced by bpp::BedGraphFeatureReader::toString(), and bpp::GffFeatureReader::toString().

◆ getSequences()

std::set<std::string> bpp::SequenceFeatureSet::getSequences ( ) const

inline

Returns: A set containing all sequences ids in this set.

Definition at line 500 of file SequenceFeature.h.

References features_.

Referenced by bpp::CoordinateTranslatorMafIterator::CoordinateTranslatorMafIterator(), bpp::FeatureExtractorMafIterator::FeatureExtractorMafIterator(), and bpp::FeatureFilterMafIterator::FeatureFilterMafIterator().

◆ getSubsetForRange()

SequenceFeatureSet* bpp::SequenceFeatureSet::getSubsetForRange	(	const SeqRange &	range,
		bool	complete
	)		const

inline

Parameters

range	The range of features to look for.
complete	If true, only return features fully included in the given range. Otherwise returns features overlapping with the range.

Returns: A new set with all features included in the given range.

Definition at line 622 of file SequenceFeature.h.

References addFeature(), features_, and SequenceFeatureSet().

◆ getSubsetForSequence()

SequenceFeatureSet* bpp::SequenceFeatureSet::getSubsetForSequence ( const std::string & id ) const

inline

Parameters

id	The sequence id to look for.

Returns: A new set with all features for a given sequence id.

Definition at line 588 of file SequenceFeature.h.

References addFeature(), features_, and SequenceFeatureSet().

Referenced by bpp::CoordinateTranslatorMafIterator::CoordinateTranslatorMafIterator().

◆ getSubsetForSequences()

SequenceFeatureSet* bpp::SequenceFeatureSet::getSubsetForSequences ( const std::vector< std::string > & ids ) const

inline

Parameters

ids	The sequence ids to look for.

Returns: A new set with all features of given sequence ids.

Definition at line 604 of file SequenceFeature.h.

References addFeature(), features_, and SequenceFeatureSet().

◆ getSubsetForType()

SequenceFeatureSet* bpp::SequenceFeatureSet::getSubsetForType ( const std::string & type ) const

inline

Parameters

type	The feature type.

Returns: A new set with all features of a given type.

Definition at line 556 of file SequenceFeature.h.

References addFeature(), features_, and SequenceFeatureSet().

◆ getSubsetForTypes()

SequenceFeatureSet* bpp::SequenceFeatureSet::getSubsetForTypes ( const std::vector< std::string > & types ) const

inline

Parameters

types The feature types.

Returns: A new set with all features of given types.

Definition at line 572 of file SequenceFeature.h.

References addFeature(), features_, and SequenceFeatureSet().

◆ getTypes()

std::set<std::string> bpp::SequenceFeatureSet::getTypes ( ) const

inline

Returns: A set containing all feature type in this set.

Definition at line 513 of file SequenceFeature.h.

References features_.

◆ isEmpty()

bool bpp::SequenceFeatureSet::isEmpty ( ) const

inline

Returns: True if the set contains no feature.

Definition at line 486 of file SequenceFeature.h.

References features_.

◆ operator=()

SequenceFeatureSet& bpp::SequenceFeatureSet::operator= ( const SequenceFeatureSet & sfs )

inline

Definition at line 436 of file SequenceFeature.h.

References clear(), and features_.

◆ operator[]()

const SequenceFeature& bpp::SequenceFeatureSet::operator[] ( size_t i ) const

inline

Parameters

i	The index of the feature.

Returns: A reference toward the feature.

See also: getFeature(size_t i)

Definition at line 474 of file SequenceFeature.h.

References features_.

Member Data Documentation

◆ features_

std::vector<SequenceFeature*> bpp::SequenceFeatureSet::features_

private

Definition at line 420 of file SequenceFeature.h.

Referenced by addFeature(), clear(), fillRangeCollection(), fillRangeCollectionForSequence(), getFeature(), getNumberOfFeatures(), getSequences(), getSubsetForRange(), getSubsetForSequence(), getSubsetForSequences(), getSubsetForType(), getSubsetForTypes(), getTypes(), isEmpty(), operator=(), operator[](), and SequenceFeatureSet().

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

Bpp/Seq/Feature/SequenceFeature.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SequenceFeatureSet() [1/2]

◆ ~SequenceFeatureSet()

◆ SequenceFeatureSet() [2/2]

Member Function Documentation

◆ addFeature()

◆ clear()

◆ fillRangeCollection()

◆ fillRangeCollectionForSequence()

◆ getFeature()

◆ getNumberOfFeatures()

◆ getSequences()

◆ getSubsetForRange()

◆ getSubsetForSequence()

◆ getSubsetForSequences()

◆ getSubsetForType()

◆ getSubsetForTypes()

◆ getTypes()

◆ isEmpty()

◆ operator=()

◆ operator[]()

Member Data Documentation

◆ features_