bpp::SequenceFeatureSet Class Reference

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
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	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::vector< std::string > &types) 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 361 of file SequenceFeature.h.

Constructor & Destructor Documentation

SequenceFeatureSet() [1/2]

bpp::SequenceFeatureSet::SequenceFeatureSet ( )

inline

Definition at line 367 of file SequenceFeature.h.

Referenced by getSubsetForType().

~SequenceFeatureSet()

virtual bpp::SequenceFeatureSet::~SequenceFeatureSet ( )

inlinevirtual

Definition at line 369 of file SequenceFeature.h.

References clear().

SequenceFeatureSet() [2/2]

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

inline

Definition at line 371 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 432 of file SequenceFeature.h.

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

Referenced by bpp::GtfFeatureReader::getFeaturesOfSequence(), bpp::GffFeatureReader::getFeaturesOfSequence(), bpp::GtfFeatureReader::getFeaturesOfType(), bpp::GffFeatureReader::getFeaturesOfType(), bpp::SequenceFeatureTools::getOrfs(), and getSubsetForType().

clear()

void bpp::SequenceFeatureSet::clear ( )

inline

Delete all features in this set.

Definition at line 395 of file SequenceFeature.h.

References features_.

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

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 468 of file SequenceFeature.h.

References features_.

Referenced by bpp::FeatureExtractor::FeatureExtractor(), 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 409 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 425 of file SequenceFeature.h.

References features_.

Referenced by 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 439 of file SequenceFeature.h.

References features_.

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

getSubsetForType()

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

inline

Parameters

types

The feature type.

Returns

A new set with all features of a given type.

Definition at line 482 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 452 of file SequenceFeature.h.

References features_.

operator=()

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

inline

Definition at line 380 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 418 of file SequenceFeature.h.

References features_.

Member Data Documentation

features_

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

private

Definition at line 364 of file SequenceFeature.h.

Referenced by addFeature(), clear(), fillRangeCollectionForSequence(), getFeature(), getNumberOfFeatures(), getSequences(), getSubsetForType(), getTypes(), operator=(), operator[](), and SequenceFeatureSet().

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

• Bpp/Seq/Feature/SequenceFeature.h