Partial implementation of the SequenceContainer interface. More...

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

Inheritance diagram for bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >:

Collaboration diagram for bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >:

Public Member Functions
	AbstractTemplateSequenceContainer (std::shared_ptr< const Alphabet > alphabet)
	This constructor initializes the alphabet pointer. More...

	AbstractTemplateSequenceContainer (std::shared_ptr< const Alphabet > alphabet, const Comments &comments)
	This constructor initializes the alphabet pointer and the comments field. More...

	AbstractTemplateSequenceContainer (const AbstractTemplateSequenceContainer< SequenceType, HashType > &sc)

AbstractTemplateSequenceContainer &	operator= (const AbstractTemplateSequenceContainer< SequenceType, HashType > &sc)

	AbstractTemplateSequenceContainer (const TemplateSequenceContainerInterface< SequenceType, HashType > &sc)
	Copy constructor from any SequenceContainer object. More...

AbstractTemplateSequenceContainer &	operator= (const TemplateSequenceContainerInterface< SequenceType, HashType > &sc)
	Assignation operator from any SequenceContainer object. More...

virtual	~AbstractTemplateSequenceContainer ()

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 TemplateSequenceContainerInterface< SequenceType, std::string > *	createEmptyContainer () const override=0
	Return a copy of this container, but with no data inside. More...

TemplateSequenceDataInterface< std::string > *	clone () const override=0

virtual size_t	getNumberOfSequences () const=0
	Get the number of sequences in the container. More...

virtual std::vector< std::string >	getSequenceKeys () const=0

virtual void	setSequenceKeys (const std::vector< std::string > &sequenceKeys)=0
	Reset all sequence keys. More...

virtual double	getStateValueAt (size_t sitePosition, const std::string &sequenceKey, int state) const=0
	Get the value of a state at a given position. More...

virtual double	getStateValueAt (size_t sitePosition, size_t sequencePosition, int state) const=0
	Get value of a state at a given position. More...

virtual double	operator() (size_t sitePosition, const std::string &sequenceKey, int state) const=0
	Get the value of a state at a given position. More...

virtual double	operator() (size_t sitePosition, size_t sequencePosition, int state) const=0
	Get the value of a state at a given position. More...

virtual void	clear ()=0
	Delete all data in the container. More...

virtual bool	hasSequence (const std::string &sequenceKey) const=0
	Check if a certain key is associated to a sequence in the container. More...

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

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

virtual void	clearComments ()=0

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

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

void	clearComments () override

Access by key
virtual const SequenceType &	sequence (const std::string &sequenceKey) const override=0
	Retrieve a sequence object from the container. More...

virtual void	setSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0
	Replace a sequence in the container. More...

virtual void	addSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0
	Add a sequence to the container. More...

virtual std::unique_ptr< SequenceType >	removeSequence (const std::string &sequenceKey)=0
	Remove a sequence from the container. More...

virtual const SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t sitePosition) const=0
	Get the content of the dataset at a specific position (sequence key, site position). More...

virtual SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t sitePosition)=0
	Get the content of the dataset at a specific position (sequence key, site position). More...

Access by position
virtual const SequenceType &	sequence (size_t sequencePosition) const override=0
	Retrieve a sequence object from the container. More...

virtual void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr)=0
	Replace a sequence in the container. More...

virtual void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const std::string &sequenceKey)=0
	Replace a sequence in the container. More...

virtual std::unique_ptr< SequenceType >	removeSequence (size_t sequencePosition)=0
	Remove a sequence from the container. More...

virtual const SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t sitePosition) const=0
	Get the content of the dataset at a specific position (sequence position, site position). More...

virtual SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t sitePosition)=0
	Get the content of the dataset at a specific position (sequence position, site position). More...

virtual void	insertSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const std::string &sequenceKey)=0
	Insert a sequence in the container. More...

Access by key
virtual void	deleteSequence (const std::string &sequenceKey)=0
	Remove and delete a sequence from the container. More...

Access by position
virtual void	deleteSequence (size_t sequencePosition)=0
	Remove and delete a sequence from the container. More...

Index management
Position to key and key to position.
virtual const std::string &	sequenceKey (size_t sequencePosition) const=0
	Get the key associated to a given sequence. More...

virtual size_t	getSequencePosition (const std::string &sequenceKey) const=0
	Get the position of a sequence with a given key in the container. More...

Access sequence names
virtual std::vector< std::string >	getSequenceNames () const=0

virtual void	setSequenceNames (const std::vector< std::string > &names, bool updateKeys)=0
	Batch-set all sequence names. More...

virtual std::vector< Comments >	getSequenceComments () const=0

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

Comments	comments_

Detailed Description

template<class SequenceType, class HashType = std::string>
class bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >

Partial implementation of the SequenceContainer interface.

This abstract class provides an alphabet and comments, with associated methods.

Definition at line 23 of file AbstractSequenceContainer.h.

Constructor & Destructor Documentation

◆ AbstractTemplateSequenceContainer() [1/4]

template<class SequenceType , class HashType = std::string>

bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::AbstractTemplateSequenceContainer ( std::shared_ptr< const Alphabet > alphabet )

inline

This constructor initializes the alphabet pointer.

This constructor is to be called by constructors of derived classes.

Parameters

alphabet The alphabet to be associated to this container.

Definition at line 41 of file AbstractSequenceContainer.h.

◆ AbstractTemplateSequenceContainer() [2/4]

template<class SequenceType , class HashType = std::string>

bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::AbstractTemplateSequenceContainer	(	std::shared_ptr< const Alphabet >	alphabet,
		const Comments &	comments
	)

inline

This constructor initializes the alphabet pointer and the comments field.

This constructor is to be called by constructors of derived classes.

Parameters

alphabet	The alphabet to be associated to this container.
comments	General comments to be associated to this container.

Definition at line 53 of file AbstractSequenceContainer.h.

◆ AbstractTemplateSequenceContainer() [3/4]

template<class SequenceType , class HashType = std::string>

bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::AbstractTemplateSequenceContainer ( const AbstractTemplateSequenceContainer< SequenceType, HashType > & sc )

inline

Definition at line 58 of file AbstractSequenceContainer.h.

◆ AbstractTemplateSequenceContainer() [4/4]

template<class SequenceType , class HashType = std::string>

bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::AbstractTemplateSequenceContainer ( const TemplateSequenceContainerInterface< SequenceType, HashType > & sc )

inline

Copy constructor from any SequenceContainer object.

Parameters

sc	Another sequence container.

Definition at line 74 of file AbstractSequenceContainer.h.

◆ ~AbstractTemplateSequenceContainer()

template<class SequenceType , class HashType = std::string>

virtual bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::~AbstractTemplateSequenceContainer ( )

inlinevirtual

Definition at line 92 of file AbstractSequenceContainer.h.

Member Function Documentation

◆ addSequence()

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >.

◆ alphabet()

template<class SequenceType , class HashType = std::string>

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

inlineoverridevirtual

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.

References bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::alphabet_.

◆ clear()

virtual void bpp::TemplateSequenceDataInterface< std::string >::clear ( )

pure virtualinherited

Delete all data in the container.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ 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()

TemplateSequenceDataInterface<std::string >* bpp::TemplateSequenceDataInterface< std::string >::clone ( ) const

overridepure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateAlignmentDataInterface< HashType >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ createEmptyContainer()

virtual TemplateSequenceContainerInterface<SequenceType, std::string >* bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::createEmptyContainer ( ) const

overridepure virtualinherited

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::TemplateSequenceDataInterface< std::string >.

Implemented in bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ deleteSequence() [1/2]

virtual void bpp::TemplateSequenceDataInterface< std::string >::deleteSequence ( const std::string & sequenceKey )

pure virtualinherited

Remove and delete a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ deleteSequence() [2/2]

virtual void bpp::TemplateSequenceDataInterface< std::string >::deleteSequence ( size_t sequencePosition )

pure virtualinherited

Remove and delete a sequence from the container.

Parameters

sequencePosition The position of the sequence.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getAlphabet()

template<class SequenceType , class HashType = std::string>

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

inlineoverridevirtual

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.

References bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::alphabet_.

◆ 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()

virtual size_t bpp::TemplateSequenceDataInterface< std::string >::getNumberOfSequences ( ) const

pure virtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequenceComments()

virtual std::vector<Comments> bpp::TemplateSequenceDataInterface< std::string >::getSequenceComments ( ) const

pure virtualinherited

Returns: a vector with all sequence comments.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequenceKeys()

virtual std::vector<std::string > bpp::TemplateSequenceDataInterface< std::string >::getSequenceKeys ( ) const

pure virtualinherited

Returns: a vector with all sequence keys.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequenceNames()

virtual std::vector<std::string> bpp::TemplateSequenceDataInterface< std::string >::getSequenceNames ( ) const

pure virtualinherited

Returns: a vector with all sequence names.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequencePosition()

virtual size_t bpp::TemplateSequenceDataInterface< std::string >::getSequencePosition ( const std::string & sequenceKey ) const

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getStateValueAt() [1/2]

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

pure virtualinherited

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

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getStateValueAt() [2/2]

virtual double bpp::TemplateSequenceDataInterface< std::string >::getStateValueAt	(	size_t	sitePosition,
		size_t	sequencePosition,
		int	state
	)		const

pure virtualinherited

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

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ hasSequence()

virtual bool bpp::TemplateSequenceDataInterface< std::string >::hasSequence ( const std::string & sequenceKey ) const

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ insertSequence()

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >.

◆ operator()() [1/2]

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

pure virtualinherited

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

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ operator()() [2/2]

virtual double bpp::TemplateSequenceDataInterface< std::string >::operator()	(	size_t	sitePosition,
		size_t	sequencePosition,
		int	state
	)		const

pure virtualinherited

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

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ operator=() [1/2]

template<class SequenceType , class HashType = std::string>

AbstractTemplateSequenceContainer& bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator= ( const AbstractTemplateSequenceContainer< SequenceType, HashType > & sc )

inline

Definition at line 62 of file AbstractSequenceContainer.h.

References bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::alphabet_, and bpp::SimpleCommentable::operator=().

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

◆ operator=() [2/2]

template<class SequenceType , class HashType = std::string>

AbstractTemplateSequenceContainer& bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator= ( const TemplateSequenceContainerInterface< SequenceType, HashType > & sc )

inline

Assignation operator from any SequenceContainer object.

Parameters

sc	Another sequence container.

Definition at line 84 of file AbstractSequenceContainer.h.

References bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::alphabet_, bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::Commentable::getComments(), and bpp::SimpleCommentable::setComments().

◆ removeSequence() [1/2]

virtual std::unique_ptr<SequenceType> bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::removeSequence ( const std::string & sequenceKey )

pure virtualinherited

Remove a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ removeSequence() [2/2]

virtual std::unique_ptr<SequenceType> bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::removeSequence ( size_t sequencePosition )

pure virtualinherited

Remove a sequence from the container.

Parameters

sequencePosition The position of the sequence.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ sequence() [1/2]

virtual const SequenceType& bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::sequence ( const std::string & sequenceKey ) const

overridepure virtualinherited

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::TemplateSequenceDataInterface< std::string >.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ sequence() [2/2]

virtual const SequenceType& bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::sequence ( size_t sequencePosition ) const

overridepure virtualinherited

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::TemplateSequenceDataInterface< std::string >.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ sequenceKey()

virtual const std::string & bpp::TemplateSequenceDataInterface< std::string >::sequenceKey ( size_t sequencePosition ) const

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ 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]

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >.

◆ setSequence() [2/3]

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >.

◆ setSequence() [3/3]

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >.

◆ setSequenceKeys()

virtual void bpp::TemplateSequenceDataInterface< std::string >::setSequenceKeys ( const std::vector< std::string > & sequenceKeys )

pure virtualinherited

Reset all sequence keys.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ setSequenceNames()

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ valueAt() [1/4]

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ valueAt() [2/4]

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

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ valueAt() [3/4]

virtual const SequenceType::ElementType& bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::valueAt	(	size_t	sequencePosition,
		size_t	sitePosition
	)		const

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, and bpp::TemplateVectorSequenceContainer< SequenceType >.

◆ valueAt() [4/4]

virtual SequenceType::ElementType& bpp::TemplateSequenceContainerInterface< SequenceType, std::string >::valueAt	(	size_t	sequencePosition,
		size_t	sitePosition
	)

pure virtualinherited

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.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

Member Data Documentation

◆ alphabet_

template<class SequenceType , class HashType = std::string>

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

protected

The container's alphabet.

Definition at line 31 of file AbstractSequenceContainer.h.

Referenced by bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::alphabet(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::getAlphabet(), and bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=().

◆ 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().

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

Bpp/Seq/Container/AbstractSequenceContainer.h

Public Member Functions

Protected Attributes

Detailed Description

template<class SequenceType, class HashType = std::string> class bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >

Constructor & Destructor Documentation

◆ AbstractTemplateSequenceContainer() [1/4]

◆ AbstractTemplateSequenceContainer() [2/4]

◆ AbstractTemplateSequenceContainer() [3/4]

◆ AbstractTemplateSequenceContainer() [4/4]

◆ ~AbstractTemplateSequenceContainer()

Member Function Documentation

◆ addSequence()

◆ 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]

◆ 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_

template<class SequenceType, class HashType = std::string>
class bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >