The VectorSequenceContainer class. More...

#include <Bpp/Seq/Container/VectorSequenceContainer.h>

Inheritance diagram for bpp::TemplateVectorSequenceContainer< SequenceType >:

Collaboration diagram for bpp::TemplateVectorSequenceContainer< SequenceType >:

Public Member Functions
	TemplateVectorSequenceContainer (std::shared_ptr< const Alphabet > alphabet, std::vector< std::unique_ptr< SequenceType >> &vs)
	Build a container with pointers to sequence objects. More...

	TemplateVectorSequenceContainer (std::shared_ptr< const Alphabet > alphabet)
	Build an empty container that will contain sequences of a particular alphabet. More...

TemplateVectorSequenceContainer &	operator= (const TemplateVectorSequenceContainer &vsc)
	Assign from a VectorSequenceContainer. More...

TemplateVectorSequenceContainer &	operator= (const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)
	Copy from a SequenceContainer. More...

virtual	~TemplateVectorSequenceContainer ()

void	clear () override
	Delete all data in the container. More...

virtual void	addSequence (std::unique_ptr< SequenceType > &sequencePtr)
	Add a sequence to the container, using its name as a key. More...

const Alphabet &	alphabet () const override
	Get the container's alphabet. More...

std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get a pointer toward the container's alphabet. More...

virtual const Comments &	getComments () const =0
	Get the comments. More...

const Comments &	getComments () const override
	Get the comments. More...

virtual void	setComments (const Comments &comments)=0
	Set the comments. More...

void	setComments (const Comments &comments) override
	Set the comments. More...

virtual void	clearComments ()=0

void	clearComments () override

Copy constructors:
	TemplateVectorSequenceContainer (const TemplateVectorSequenceContainer< SequenceType > &vsc)
	Copy from a VectorSequenceContainer. More...

	TemplateVectorSequenceContainer (const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)
	Copy from a SequenceContainer. More...

The Clonable interface.
TemplateVectorSequenceContainer< SequenceType > *	clone () const override

The SequenceContainer interface.
TemplateVectorSequenceContainer< SequenceType > *	createEmptyContainer () const override
	Return a copy of this container, but with no data inside. More...

double	getStateValueAt (size_t sitePosition, const std::string &sequenceKey, int state) const override
	Get the value of a state at a given position. More...

double	operator() (size_t sitePosition, const std::string &sequenceKey, int state) const override
	Get the value of a state at a given position. More...

double	getStateValueAt (size_t sitePosition, size_t sequencePosition, int state) const override
	Get value of a state at a given position. More...

double	operator() (size_t sitePosition, size_t sequencePosition, int state) const override
	Get the value of a state at a given position. More...

size_t	getNumberOfSequences () const override
	Get the number of sequences in the container. More...

std::vector< std::string >	getSequenceKeys () const override

void	setSequenceKeys (const std::vector< std::string > &sequenceKeys) override
	Reset all sequence keys. More...

const std::string &	sequenceKey (size_t sequencePosition) const override
	Get the key associated to a given sequence. More...

size_t	getSequencePosition (const std::string &sequenceKey) const override
	Get the position of a sequence with a given key in the container. More...

const SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t elementPosition) const override
	Get the content of the dataset at a specific position (sequence key, site position). More...

SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t elementPosition) override
	Get the content of the dataset at a specific position (sequence key, site position). More...

const SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t elementPosition) const override
	Get the content of the dataset at a specific position (sequence position, site position). More...

SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t elementPosition) override
	Get the content of the dataset at a specific position (sequence position, site position). More...

bool	hasSequence (const std::string &sequenceKey) const override
	Check if a certain key is associated to a sequence in the container. More...

const SequenceType &	sequence (const std::string &sequenceKey) const override
	Retrieve a sequence object from the container. More...

void	setSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr) override
	Replace a sequence in the container. More...

void	addSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr) override
	Add a sequence to the container. More...

std::unique_ptr< SequenceType >	removeSequence (const std::string &sequenceKey) override
	Remove a sequence from the container. More...

void	deleteSequence (const std::string &sequenceKey) override
	Remove and delete a sequence from the container. More...

void	deleteSequence (size_t sequencePosition) override
	Remove and delete a sequence from the container. More...

const SequenceType &	sequence (size_t sequencePosition) const override
	Retrieve a sequence object from the container. More...

void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr) override
	Replace a sequence in the container. More...

void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const std::string &sequenceKey) override
	Replace a sequence in the container. More...

void	insertSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const std::string &sequenceKey) override
	Insert a sequence in the container. More...

std::unique_ptr< SequenceType >	removeSequence (size_t sequencePosition) override
	Remove a sequence from the container. More...

std::vector< std::string >	getSequenceNames () const override

void	setSequenceNames (const std::vector< std::string > &names, bool updateKeys) override
	Batch-set all sequence names. More...

std::vector< Comments >	getSequenceComments () const override

Protected Member Functions
virtual SequenceType &	sequence_ (size_t sequencePosition)

virtual SequenceType &	sequence_ (const std::string &sequenceKey)
	getSequence with given key More...

Protected Attributes
VectorMappedContainer< SequenceType >	sequenceVectorMap_

std::shared_ptr< const Alphabet >	alphabet_
	The container's alphabet. More...

Comments	comments_

Detailed Description

template<class SequenceType>
class bpp::TemplateVectorSequenceContainer< SequenceType >

The VectorSequenceContainer class.

This is the simplest implementation of the SequenceContainer interface. std::shared_ptr<Sequence> are stored in a std::vector, as well as in a std::map.

Definition at line 30 of file VectorSequenceContainer.h.

Constructor & Destructor Documentation

◆ TemplateVectorSequenceContainer() [1/4]

template<class SequenceType >

bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer	(	std::shared_ptr< const Alphabet >	alphabet,
		std::vector< std::unique_ptr< SequenceType >> &	vs
	)

inline

Build a container with pointers to sequence objects.

The keys of the map are set to the names of the sequences.

Parameters

alphabet	The alphabet of the container.
vs	A vector of smart pointers toward sequence objects.

Definition at line 45 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence().

◆ TemplateVectorSequenceContainer() [2/4]

template<class SequenceType >

bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer ( std::shared_ptr< const Alphabet > alphabet )

inline

Build an empty container that will contain sequences of a particular alphabet.

Parameters

alphabet The alphabet of the container.

Definition at line 62 of file VectorSequenceContainer.h.

◆ TemplateVectorSequenceContainer() [3/4]

template<class SequenceType >

bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer ( const TemplateVectorSequenceContainer< SequenceType > & vsc )

inline

Copy from a VectorSequenceContainer.

Parameters

vsc	The VectorSequenceContainer to copy into this container.

Definition at line 78 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

◆ TemplateVectorSequenceContainer() [4/4]

template<class SequenceType >

bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer ( const TemplateSequenceContainerInterface< SequenceType, std::string > & sc )

inline

Copy from a SequenceContainer.

Parameters

sc	The SequenceContainer to copy into this container.

Definition at line 97 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence(), bpp::Commentable::getComments(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), bpp::TemplateSequenceDataInterface< HashType >::sequenceKey(), and bpp::SimpleCommentable::setComments().

◆ ~TemplateVectorSequenceContainer()

template<class SequenceType >

virtual bpp::TemplateVectorSequenceContainer< SequenceType >::~TemplateVectorSequenceContainer ( )

inlinevirtual

Definition at line 150 of file VectorSequenceContainer.h.

Member Function Documentation

◆ addSequence() [1/2]

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence	(	const std::string &	sequenceKey,
		std::unique_ptr< SequenceType > &	sequencePtr
	)

inlineoverridevirtual

Add a sequence to the container.

Similar to setSequence, with the exception that an Exception will be raised in case of an existing key. Existing sequences will not be updated, only new ones will be appended.

Parameters

sequenceKey	The key to which the sequence is associated.
sequencePtr	The sequence to add.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 264 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::appendObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::addSequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), and bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer().

◆ addSequence() [2/2]

template<class SequenceType >

virtual void bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence ( std::unique_ptr< SequenceType > & sequencePtr )

inlinevirtual

Add a sequence to the container, using its name as a key.

Parameters

sequencePtr A unique_ptr to the sequence to add.

Definition at line 371 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence().

◆ alphabet()

const Alphabet& bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::alphabet ( ) const

inlineoverridevirtualinherited

Get the container's alphabet.

Returns: The alphabet associated to this container.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 95 of file AbstractSequenceContainer.h.

◆ clear()

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::clear ( )

inlineoverridevirtual

Delete all data in the container.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 152 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::clear(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::clear(), and bpp::TemplateVectorSequenceContainer< SequenceType >::operator=().

◆ clearComments() [1/2]

void bpp::SimpleCommentable::clearComments ( )

inlineoverridevirtualinherited

Implements bpp::Commentable.

Definition at line 88 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

◆ clearComments() [2/2]

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

◆ clone()

template<class SequenceType >

TemplateVectorSequenceContainer<SequenceType>* bpp::TemplateVectorSequenceContainer< SequenceType >::clone ( ) const

inlineoverridevirtual

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 163 of file VectorSequenceContainer.h.

◆ createEmptyContainer()

template<class SequenceType >

TemplateVectorSequenceContainer<SequenceType>* bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer ( ) const

inlineoverridevirtual

Return a copy of this container, but with no data inside.

This method creates a new SequencedContainer object. The class of this container depends on the class implementing this interface.

Returns: A new empty container, with the same alphabet as this one.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 176 of file VectorSequenceContainer.h.

References bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::SimpleCommentable::getComments(), and bpp::SimpleCommentable::setComments().

◆ deleteSequence() [1/2]

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::deleteSequence ( const std::string & sequenceKey )

inlineoverridevirtual

Remove and delete a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 280 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::deleteObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ deleteSequence() [2/2]

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::deleteSequence ( size_t sequencePosition )

inlineoverridevirtual

Remove and delete a sequence from the container.

Parameters

sequencePosition The position of the sequence.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 285 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::deleteObject(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet ( ) const

inlineoverridevirtualinherited

Get a pointer toward the container's alphabet.

Returns: A pointer toward the alphabet associated to this container.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 101 of file AbstractSequenceContainer.h.

◆ getComments() [1/2]

virtual const Comments& bpp::Commentable::getComments ( ) const

pure virtualinherited

Get the comments.

Returns: The comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Mase::appendSequencesFromStream(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractCoreSequence::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

◆ getComments() [2/2]

const Comments& bpp::SimpleCommentable::getComments ( ) const

inlineoverridevirtualinherited

Get the comments.

Returns: The comments.

Implements bpp::Commentable.

Definition at line 79 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::createEmptyContainer(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getNumberOfSequences()

template<class SequenceType >

size_t bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences ( ) const

inlineoverridevirtual

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 204 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::getSize(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ getSequenceComments()

template<class SequenceType >

std::vector<Comments> bpp::TemplateVectorSequenceContainer< SequenceType >::getSequenceComments ( ) const

inlineoverridevirtual

Returns: a vector with all sequence comments.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 352 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequence().

◆ getSequenceKeys()

template<class SequenceType >

std::vector<std::string> bpp::TemplateVectorSequenceContainer< SequenceType >::getSequenceKeys ( ) const

inlineoverridevirtual

Returns: a vector with all sequence keys.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 209 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::getObjectNames(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ getSequenceNames()

template<class SequenceType >

std::vector<std::string> bpp::TemplateVectorSequenceContainer< SequenceType >::getSequenceNames ( ) const

inlineoverridevirtual

Returns: a vector with all sequence names.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 327 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequence().

◆ getSequencePosition()

template<class SequenceType >

size_t bpp::TemplateVectorSequenceContainer< SequenceType >::getSequencePosition ( const std::string & sequenceKey ) const

inlineoverridevirtual

Get the position of a sequence with a given key in the container.

Parameters

sequenceKey The key to which the sequence is associated.

Returns: The position of the sequence with name 'name', if it exists.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 224 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::getObjectPosition(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence().

◆ getStateValueAt() [1/2]

template<class SequenceType >

double bpp::TemplateVectorSequenceContainer< SequenceType >::getStateValueAt	(	size_t	sitePosition,
		const std::string &	sequenceKey,
		int	state
	)		const

inlineoverridevirtual

Get the value of a state at a given position.

Parameters

sitePosition	index of the site
sequenceKey	key of the sequence in the container
state	state in the alphabet

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 184 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

◆ getStateValueAt() [2/2]

template<class SequenceType >

double bpp::TemplateVectorSequenceContainer< SequenceType >::getStateValueAt	(	size_t	sitePosition,
		size_t	sequencePosition,
		int	state
	)		const

inlineoverridevirtual

Get value of a state at a given position.

Parameters

sitePosition	index of the site
sequencePosition	index of the sequence in the container
state	state in the alphabet

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 194 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence().

◆ hasSequence()

template<class SequenceType >

bool bpp::TemplateVectorSequenceContainer< SequenceType >::hasSequence ( const std::string & sequenceKey ) const

inlineoverridevirtual

Check if a certain key is associated to a sequence in the container.

Parameters

sequenceKey The key to which the sequence is associated.

Returns: True if the key was found in the contained.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 249 of file VectorSequenceContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ insertSequence()

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::insertSequence	(	size_t	sequencePosition,
		std::unique_ptr< SequenceType > &	sequencePtr,
		const std::string &	sequenceKey
	)

inlineoverridevirtual

Insert a sequence in the container.

Parameters

sequencePosition	The position of the sequence.
sequencePtr	The sequence to add.
sequenceKey	The new key of the sequence.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 311 of file VectorSequenceContainer.h.

References bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::VectorMappedContainer< T >::insertObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::insertSequence().

◆ operator()() [1/2]

template<class SequenceType >

double bpp::TemplateVectorSequenceContainer< SequenceType >::operator()	(	size_t	sitePosition,
		const std::string &	sequenceKey,
		int	state
	)		const

inlineoverridevirtual

Get the value of a state at a given position.

Same as getValueAt.

Parameters

sitePosition	index of the site
sequenceKey	key of the sequence in the container
state	state in the alphabet

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 189 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

◆ operator()() [2/2]

template<class SequenceType >

double bpp::TemplateVectorSequenceContainer< SequenceType >::operator()	(	size_t	sitePosition,
		size_t	sequencePosition,
		int	state
	)		const

inlineoverridevirtual

Get the value of a state at a given position.

Same as getValueAt.

Parameters

sitePosition	index of the site
sequencePosition	index of the sequence in the container
state	state in the alphabet

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 199 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence().

◆ operator=() [1/2]

template<class SequenceType >

TemplateVectorSequenceContainer& bpp::TemplateVectorSequenceContainer< SequenceType >::operator= ( const TemplateSequenceContainerInterface< SequenceType, std::string > & sc )

inline

Copy from a SequenceContainer.

Parameters

sc	The SequenceContainer to copy into this container.

Definition at line 136 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::clear(), bpp::Commentable::getComments(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), bpp::TemplateSequenceDataInterface< HashType >::sequenceKey(), and bpp::SimpleCommentable::setComments().

◆ operator=() [2/2]

template<class SequenceType >

TemplateVectorSequenceContainer& bpp::TemplateVectorSequenceContainer< SequenceType >::operator= ( const TemplateVectorSequenceContainer< SequenceType > & vsc )

inline

Assign from a VectorSequenceContainer.

Parameters

vsc	The VectorSequenceContainer to copy into this container.

Definition at line 118 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::clear(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::operator=().

◆ removeSequence() [1/2]

template<class SequenceType >

std::unique_ptr<SequenceType> bpp::TemplateVectorSequenceContainer< SequenceType >::removeSequence ( const std::string & sequenceKey )

inlineoverridevirtual

Remove a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 273 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::removeObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ removeSequence() [2/2]

template<class SequenceType >

std::unique_ptr<SequenceType> bpp::TemplateVectorSequenceContainer< SequenceType >::removeSequence ( size_t sequencePosition )

inlineoverridevirtual

Remove a sequence from the container.

Parameters

sequencePosition The position of the sequence.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 319 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::removeObject(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ sequence() [1/2]

template<class SequenceType >

const SequenceType& bpp::TemplateVectorSequenceContainer< SequenceType >::sequence ( const std::string & sequenceKey ) const

inlineoverridevirtual

Retrieve a sequence object from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Returns: A reference toward the Sequence with corresponding name.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 254 of file VectorSequenceContainer.h.

References bpp::MappedNamedContainer< T >::getObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ sequence() [2/2]

template<class SequenceType >

const SequenceType& bpp::TemplateVectorSequenceContainer< SequenceType >::sequence ( size_t sequencePosition ) const

inlineoverridevirtual

Retrieve a sequence object from the container.

Parameters

sequencePosition The position of the sequence.

Returns: A reference toward the Sequence object with corresponding name.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 290 of file VectorSequenceContainer.h.

References bpp::MappedNamedContainer< T >::getObject(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ sequence_() [1/2]

template<class SequenceType >

virtual SequenceType& bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_ ( const std::string & sequenceKey )

inlineprotectedvirtual

getSequence with given key

Definition at line 387 of file VectorSequenceContainer.h.

References bpp::MappedNamedContainer< T >::object(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ sequence_() [2/2]

template<class SequenceType >

virtual SequenceType& bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_ ( size_t sequencePosition )

inlineprotectedvirtual

Definition at line 377 of file VectorSequenceContainer.h.

References bpp::MappedNamedContainer< T >::object(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ sequenceKey()

template<class SequenceType >

const std::string& bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey ( size_t sequencePosition ) const

inlineoverridevirtual

Get the key associated to a given sequence.

Parameters

sequencePosition The position of the sequence in the container.

Returns: The key to which the sequence is associated.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 219 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::getObjectName(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ setComments() [1/2]

void bpp::SimpleCommentable::setComments ( const Comments & comments )

inlineoverridevirtualinherited

Set the comments.

Parameters

comments The new comments.

Implements bpp::Commentable.

Definition at line 86 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), and bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer().

◆ setComments() [2/2]

virtual void bpp::Commentable::setComments ( const Comments & comments )

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Pasta::appendAlignmentFromStream(), bpp::Clustal::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), and bpp::Mase::appendSequencesFromStream().

◆ setSequence() [1/3]

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence	(	const std::string &	sequenceKey,
		std::unique_ptr< SequenceType > &	sequencePtr
	)

inlineoverridevirtual

Replace a sequence in the container.

If a sequence is found with the given key, it will be updated with the new one. If no sequence with the given key is found, the new sequence will be added to the container.

Parameters

sequenceKey	The key to which the sequence is associated.
sequencePtr	The sequence to set.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 259 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::getSequencePosition(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::setSequence().

◆ setSequence() [2/3]

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence	(	size_t	sequencePosition,
		std::unique_ptr< SequenceType > &	sequencePtr
	)

inlineoverridevirtual

Replace a sequence in the container.

The original key associated to the sequence will be kept.

Parameters

sequencePosition	The position of the sequence.
sequencePtr	The sequence to add.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 295 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::addObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ setSequence() [3/3]

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence	(	size_t	sequencePosition,
		std::unique_ptr< SequenceType > &	sequencePtr,
		const std::string &	sequenceKey
	)

inlineoverridevirtual

Replace a sequence in the container.

The original key associated to the sequence will be kept.

Parameters

sequencePosition	The position of the sequence.
sequencePtr	The sequence to add.
sequenceKey	The new key of the sequence.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 303 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< T >::addObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_.

◆ setSequenceKeys()

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::setSequenceKeys ( const std::vector< std::string > & sequenceKeys )

inlineoverridevirtual

Reset all sequence keys.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 214 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_, and bpp::VectorMappedContainer< T >::setObjectNames().

◆ setSequenceNames()

template<class SequenceType >

void bpp::TemplateVectorSequenceContainer< SequenceType >::setSequenceNames	(	const std::vector< std::string > &	names,
		bool	updateKeys
	)

inlineoverridevirtual

Batch-set all sequence names.

Parameters

names	A vector of sequence names. Must be the same size as the number of sequences in the container, otherwise a DimensionException is thrown.
updateKeys	Tell whether the keys of the sequences should be updated with the new sequence names.

Implements bpp::TemplateSequenceDataInterface< std::string >.

Definition at line 338 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_, and bpp::VectorMappedContainer< T >::setObjectNames().

◆ valueAt() [1/4]

template<class SequenceType >

const SequenceType::ElementType& bpp::TemplateVectorSequenceContainer< SequenceType >::valueAt	(	const std::string &	sequenceKey,
		size_t	sitePosition
	)		const

inlineoverridevirtual

Get the content of the dataset at a specific position (sequence key, site position).

Parameters

sequenceKey	key of the sequence in the container
sitePosition	index of the site

Returns: The element at the given position.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 229 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

◆ valueAt() [2/4]

template<class SequenceType >

SequenceType::ElementType& bpp::TemplateVectorSequenceContainer< SequenceType >::valueAt	(	const std::string &	sequenceKey,
		size_t	sitePosition
	)

inlineoverridevirtual

Get the content of the dataset at a specific position (sequence key, site position).

Parameters

sequenceKey	key of the sequence in the container
sitePosition	index of the site

Returns: The element at the given position.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 234 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), and bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey().

◆ valueAt() [3/4]

template<class SequenceType >

const SequenceType::ElementType& bpp::TemplateVectorSequenceContainer< SequenceType >::valueAt	(	size_t	sequencePosition,
		size_t	sitePosition
	)		const

inlineoverridevirtual

Get the content of the dataset at a specific position (sequence position, site position).

Parameters

sequencePosition	index of the sequence in the container
sitePosition	index of the site

Returns: The element at the given position.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 239 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence().

◆ valueAt() [4/4]

template<class SequenceType >

SequenceType::ElementType& bpp::TemplateVectorSequenceContainer< SequenceType >::valueAt	(	size_t	sequencePosition,
		size_t	sitePosition
	)

inlineoverridevirtual

Get the content of the dataset at a specific position (sequence position, site position).

Parameters

sequencePosition	index of the sequence in the container
sitePosition	index of the site

Returns: The element at the given position.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, std::string >.

Definition at line 244 of file VectorSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::alphabet_

protectedinherited

The container's alphabet.

Definition at line 31 of file AbstractSequenceContainer.h.

◆ comments_

Comments bpp::SimpleCommentable::comments_

protectedinherited

Definition at line 50 of file Commentable.h.

Referenced by bpp::SimpleCommentable::clearComments(), bpp::SimpleCommentable::getComments(), bpp::SimpleCommentable::operator=(), and bpp::SimpleCommentable::setComments().

◆ sequenceVectorMap_

template<class SequenceType >

VectorMappedContainer<SequenceType> bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceVectorMap_

protected

Definition at line 34 of file VectorSequenceContainer.h.

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

Bpp/Seq/Container/VectorSequenceContainer.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<class SequenceType> class bpp::TemplateVectorSequenceContainer< SequenceType >

Constructor & Destructor Documentation

◆ TemplateVectorSequenceContainer() [1/4]

◆ TemplateVectorSequenceContainer() [2/4]

◆ TemplateVectorSequenceContainer() [3/4]

◆ TemplateVectorSequenceContainer() [4/4]

◆ ~TemplateVectorSequenceContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ alphabet()

◆ clear()

◆ clearComments() [1/2]

◆ clearComments() [2/2]

◆ clone()

◆ createEmptyContainer()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ getAlphabet()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getNumberOfSequences()

◆ getSequenceComments()

◆ getSequenceKeys()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getStateValueAt() [1/2]

◆ getStateValueAt() [2/2]

◆ hasSequence()

◆ insertSequence()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ sequence() [1/2]

◆ sequence() [2/2]

◆ sequence_() [1/2]

◆ sequence_() [2/2]

◆ sequenceKey()

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setSequence() [1/3]

◆ setSequence() [2/3]

◆ setSequence() [3/3]

◆ setSequenceKeys()

◆ setSequenceNames()

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ alphabet_

◆ comments_

◆ sequenceVectorMap_

template<class SequenceType>
class bpp::TemplateVectorSequenceContainer< SequenceType >