The VectorSiteContainer class. More...

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

Inheritance diagram for bpp::TemplateVectorSiteContainer< SiteType, SequenceType >:

Collaboration diagram for bpp::TemplateVectorSiteContainer< SiteType, SequenceType >:

Public Member Functions
	TemplateVectorSiteContainer (std::vector< std::unique_ptr< SiteType >> &vs, std::shared_ptr< const Alphabet > alphabet, bool checkPositions=true)
	Build a new container from a set of sites. More...

	TemplateVectorSiteContainer (size_t size, std::shared_ptr< const Alphabet > alphabet)
	Build a new empty container with specified size. More...

	TemplateVectorSiteContainer (const std::vector< std::string > &sequenceKeys, std::shared_ptr< const Alphabet > alphabet, bool useKeysAsNames=true)
	Build a new empty container with specified sequence keys. More...

	TemplateVectorSiteContainer (std::shared_ptr< const Alphabet > alphabet)
	Build a new empty container. More...

	TemplateVectorSiteContainer (const TemplateVectorSiteContainer< SiteType, SequenceType > &vsc)

	TemplateVectorSiteContainer (const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)

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

TemplateVectorSiteContainer< SiteType, SequenceType > &	operator= (const TemplateVectorSiteContainer< SiteType, SequenceType > &vsc)

TemplateVectorSiteContainer< SiteType, SequenceType > &	operator= (const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)

TemplateVectorSiteContainer< SiteType, SequenceType > &	operator= (const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)

virtual	~TemplateVectorSiteContainer ()

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

The Clonable interface.
TemplateVectorSiteContainer< SiteType, SequenceType > *	clone () const override

The SiteContainer interface implementation:
const SiteType &	site (size_t sitePosition) const override
	Get a site from the container. More...

void	setSite (size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override
	Set a site in the container. More...

std::unique_ptr< SiteType >	removeSite (size_t sitePosition) override
	Remove a site from the container. More...

void	deleteSite (size_t sitePosition) override
	Delete a site from the container. More...

void	addSite (std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override
	Add a site in the container. More...

void	addSite (std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate=true) override
	Add a site in the container. More...

void	deleteSites (size_t sitePosition, size_t length) override
	Remove a continuous range of sites in the container. More...

size_t	getNumberOfSites () const override
	Get the number of aligned positions in the container. More...

void	reindexSites () override
	Set all coordinate attributes. More...

Vint	getSiteCoordinates () const override
	Get all coordinates of sites. More...

void	setSiteCoordinates (const Vint &vCoordinates) override
	Set all coordinates of sites. More...

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

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

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

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

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

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

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

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

TemplateVectorSiteContainer< SiteType, SequenceType > *	createEmptyContainer () const override
	Return a copy of this container, but with no data inside. More...

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

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

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

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

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

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

Protected Member Functions
SiteType &	site_ (size_t sitePosition)

void	realloc_ (size_t n)

Protected Attributes
VectorPositionedContainer< SiteType >	siteContainer_

VectorMappedContainer< SequenceType >	sequenceContainer_

std::vector< std::string >	sequenceNames_

std::vector< Comments >	sequenceComments_

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

Comments	comments_

Detailed Description

template<class SiteType, class SequenceType>
class bpp::TemplateVectorSiteContainer< SiteType, SequenceType >

The VectorSiteContainer class.

Sites are stored in a std::vector of pointers. Site access is hence in , and sequence access in , where is the number of sites in the container.

Sequences are built & stored on the fly, with a cache for time efficiency.

See VectorSequenceContainer for an alternative implementation.

See also: Sequence, Site, AlignedSequenceContainer

Definition at line 41 of file VectorSiteContainer.h.

Constructor & Destructor Documentation

◆ TemplateVectorSiteContainer() [1/7]

template<class SiteType , class SequenceType >

bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::TemplateVectorSiteContainer	(	std::vector< std::unique_ptr< SiteType >> &	vs,
		std::shared_ptr< const Alphabet >	alphabet,
		bool	checkPositions = `true`
	)

inline

Build a new container from a set of sites.

Parameters

vs	A std::vector of sites.
alphabet	The common alphabet for all sites.
checkPositions	Check for the redundancy of site position tag. This may turn to be very time consuming!

Exceptions

Exception If sites differ in size or in alphabet.

Definition at line 60 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::VectorMappedContainer< T >::appendObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TextTools::toString().

◆ TemplateVectorSiteContainer() [2/7]

template<class SiteType , class SequenceType >

bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::TemplateVectorSiteContainer	(	size_t	size,
		std::shared_ptr< const Alphabet >	alphabet
	)

inline

Build a new empty container with specified size.

Parameters

size	Number of sequences in the container.
alphabet	The alphabet for this container.

Definition at line 94 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::appendObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TextTools::toString().

◆ TemplateVectorSiteContainer() [3/7]

template<class SiteType , class SequenceType >

bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::TemplateVectorSiteContainer	(	const std::vector< std::string > &	sequenceKeys,
		std::shared_ptr< const Alphabet >	alphabet,
		bool	useKeysAsNames = `true`
	)

inline

Build a new empty container with specified sequence keys.

Parameters

sequenceKeys	Sequence keys. This will set the number of sequences in the container.
alphabet	The alphabet for this container.
useKeysAsNames	If yes, the sequence keys will also be used as sequence names (default). Otherwise, sequence names will be set to Seq_1, Seq_2, etc.

Definition at line 118 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::appendObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TextTools::toString().

◆ TemplateVectorSiteContainer() [4/7]

template<class SiteType , class SequenceType >

bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::TemplateVectorSiteContainer ( std::shared_ptr< const Alphabet > alphabet )

inline

Build a new empty container.

Parameters

alphabet The alphabet for this container.

Definition at line 155 of file VectorSiteContainer.h.

◆ TemplateVectorSiteContainer() [5/7]

template<class SiteType , class SequenceType >

bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::TemplateVectorSiteContainer ( const TemplateVectorSiteContainer< SiteType, SequenceType > & vsc )

inline

Definition at line 164 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::VectorMappedContainer< T >::appendObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequenceKeys(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ TemplateVectorSiteContainer() [6/7]

template<class SiteType , class SequenceType >

bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::TemplateVectorSiteContainer ( const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > & sc )

inline

Definition at line 184 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::VectorMappedContainer< T >::appendObject(), bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::getNumberOfSites(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceKeys(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::site().

◆ TemplateVectorSiteContainer() [7/7]

template<class SiteType , class SequenceType >

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

inline

Definition at line 203 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSequence(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceKeys(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::reindexSites(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

◆ ~TemplateVectorSiteContainer()

template<class SiteType , class SequenceType >

virtual bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::~TemplateVectorSiteContainer ( )

inlinevirtual

Definition at line 274 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear().

Member Function Documentation

◆ addSequence()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 731 of file VectorSiteContainer.h.

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

◆ addSite() [1/2]

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite	(	std::unique_ptr< SiteType > &	site,
		bool	checkCoordinate = `true`
	)

inlineoverridevirtual

Add a site in the container.

Parameters

site	The site to add.
checkCoordinate	Look if the coordinate of the new site match a coordinate attribute in the container.

Exceptions

Exception If the specified site does not exists or is not correct.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 355 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::appendObject(), bpp::VectorPositionedContainer< T >::appendObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::VectorMappedContainer< T >::nullify(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_, and bpp::TextTools::toString().

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

◆ addSite() [2/2]

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite	(	std::unique_ptr< SiteType > &	site,
		size_t	sitePosition,
		bool	checkCoordinate = `true`
	)

inlineoverridevirtual

Add a site in the container.

Parameters

site	The site to add.
sitePosition	The coordinate where to insert the site.
checkCoordinate	Look if the coordinate of the new site match a coordinate attribute in the container.

Exceptions

Exception If the specified site does not exists or is not correct.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 398 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::appendObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::VectorPositionedContainer< T >::insertObject(), bpp::VectorMappedContainer< T >::nullify(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_, and bpp::TextTools::toString().

◆ 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 SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear ( )

inlineoverridevirtual

Delete all data in the container.

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

Definition at line 634 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::clear(), bpp::VectorPositionedContainer< T >::clear(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

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

◆ 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 SiteType , class SequenceType >

TemplateVectorSiteContainer<SiteType, SequenceType>* bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clone ( ) const

inlineoverridevirtual

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 285 of file VectorSiteContainer.h.

◆ createEmptyContainer()

template<class SiteType , class SequenceType >

TemplateVectorSiteContainer<SiteType, SequenceType>* bpp::TemplateVectorSiteContainer< SiteType, 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::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 642 of file VectorSiteContainer.h.

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

◆ deleteSequence() [1/2]

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 585 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

◆ deleteSequence() [2/2]

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 570 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::deleteObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSequence().

◆ deleteSite()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSite ( size_t sitePosition )

inlineoverridevirtual

Delete a site from the container.

The site is deleted (ie the container is shortened).

Parameters

sitePosition The position of the site in the container.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 347 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::deleteObject(), bpp::VectorMappedContainer< T >::nullify(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ deleteSites()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSites	(	size_t	sitePosition,
		size_t	length
	)

inlineoverridevirtual

Remove a continuous range of sites in the container.

Parameters

sitePosition	The position of the first site in the container.
length	The length of the region to delete, starting at pposition sitePosition.

Exceptions

IndexOutOfBoundsException If the specified range is not valid.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 444 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::deleteObjects(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ 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 SiteType , class SequenceType >

size_t bpp::TemplateVectorSiteContainer< SiteType, 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 592 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getNumberOfObjects(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_.

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::insertSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequenceNames(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSite().

◆ getNumberOfSites()

template<class SiteType , class SequenceType >

size_t bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites ( ) const

inlineoverridevirtual

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 449 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ getSequenceComments()

template<class SiteType , class SequenceType >

std::vector<Comments> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequenceComments ( ) const

inlineoverridevirtual

Returns: a vector with all sequence comments.

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

Definition at line 629 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_.

◆ getSequenceKeys()

template<class SiteType , class SequenceType >

std::vector<std::string> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequenceKeys ( ) const

inlineoverridevirtual

Returns: a vector with all sequence keys.

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

Definition at line 597 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getObjectNames(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_.

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

◆ getSequenceNames()

template<class SiteType , class SequenceType >

std::vector<std::string> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequenceNames ( ) const

inlineoverridevirtual

Returns: a vector with all sequence names.

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

Definition at line 612 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_.

◆ getSequencePosition()

template<class SiteType , class SequenceType >

size_t bpp::TemplateVectorSiteContainer< SiteType, 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 497 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getObjectPosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getStateValueAt(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::operator()(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::valueAt().

◆ getSiteCoordinates()

template<class SiteType , class SequenceType >

Vint bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSiteCoordinates ( ) const

inlineoverridevirtual

Get all coordinates of sites.

Returns: A vector with all site coordinates.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

Definition at line 462 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ getStateValueAt() [1/2]

template<class SiteType , class SequenceType >

double bpp::TemplateVectorSiteContainer< SiteType, 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 675 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ getStateValueAt() [2/2]

template<class SiteType , class SequenceType >

double bpp::TemplateVectorSiteContainer< SiteType, 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 685 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ hasSequence()

template<class SiteType , class SequenceType >

bool bpp::TemplateVectorSiteContainer< SiteType, 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 491 of file VectorSiteContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

◆ insertSequence()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 762 of file VectorSiteContainer.h.

◆ operator()() [1/2]

template<class SiteType , class SequenceType >

double bpp::TemplateVectorSiteContainer< SiteType, 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 680 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ operator()() [2/2]

template<class SiteType , class SequenceType >

double bpp::TemplateVectorSiteContainer< SiteType, 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 690 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ operator=() [1/3]

template<class SiteType , class SequenceType >

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

inline

Definition at line 258 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceKeys(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::reindexSites(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

◆ operator=() [2/3]

template<class SiteType , class SequenceType >

TemplateVectorSiteContainer<SiteType, SequenceType>& bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::operator= ( const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > & sc )

inline

Definition at line 236 of file VectorSiteContainer.h.

◆ operator=() [3/3]

template<class SiteType , class SequenceType >

TemplateVectorSiteContainer<SiteType, SequenceType>& bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::operator= ( const TemplateVectorSiteContainer< SiteType, SequenceType > & vsc )

inline

Definition at line 219 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ realloc_()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::realloc_ ( size_t n )

inlineprotected

Definition at line 807 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::reindexSites().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSequence().

◆ reindexSites()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::reindexSites ( )

inlineoverridevirtual

Set all coordinate attributes.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 454 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

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

◆ removeSequence() [1/2]

template<class SiteType , class SequenceType >

std::unique_ptr<SequenceType> bpp::TemplateVectorSiteContainer< SiteType, 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 563 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

◆ removeSequence() [2/2]

template<class SiteType , class SequenceType >

std::unique_ptr<SequenceType> bpp::TemplateVectorSiteContainer< SiteType, 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 544 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::VectorMappedContainer< T >::removeObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSequence().

◆ removeSite()

template<class SiteType , class SequenceType >

std::unique_ptr<SiteType> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSite ( size_t sitePosition )

inlineoverridevirtual

Remove a site from the container.

The site is deleted (ie the container is shortened) and a pointer toward it is returned.

Parameters

sitePosition The position of the site in the container.

Returns: A pointer toward the given site in the alignment.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 337 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::nullify(), bpp::VectorPositionedContainer< T >::removeObject(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ sequence() [1/2]

template<class SiteType , class SequenceType >

const SequenceType& bpp::TemplateVectorSiteContainer< SiteType, 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 503 of file VectorSiteContainer.h.

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

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::insertSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequence().

◆ sequence() [2/2]

template<class SiteType , class SequenceType >

const SequenceType& bpp::TemplateVectorSiteContainer< SiteType, 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 509 of file VectorSiteContainer.h.

◆ sequenceKey()

template<class SiteType , class SequenceType >

const std::string& bpp::TemplateVectorSiteContainer< SiteType, 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 607 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getObjectName(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_.

◆ 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 SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 696 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey().

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

◆ setSequence() [2/3]

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 703 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getObjectName(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequence().

◆ setSequence() [3/3]

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 709 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::addObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

◆ setSequenceKeys()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequenceKeys ( const std::vector< std::string > & sequenceKeys )

inlineoverridevirtual

Reset all sequence keys.

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

Definition at line 602 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::VectorMappedContainer< T >::setObjectNames().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequenceNames().

◆ setSequenceNames()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, 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 617 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSequences(), bpp::VectorMappedContainer< T >::nullify(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequenceKeys().

◆ setSite()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSite	(	size_t	sitePosition,
		std::unique_ptr< SiteType > &	site,
		bool	checkCoordinate = `true`
	)

inlineoverridevirtual

Set a site in the container.

Parameters

sitePosition	The position of the site in the container.
site	The site to set.
checkCoordinate	Look if the coordinate of the new site match a coordinate attribute in the container.

Exceptions

Exception If the specified site does not exists or is not correct.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 301 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::addObject(), bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::VectorMappedContainer< T >::nullify(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ setSiteCoordinates()

template<class SiteType , class SequenceType >

void bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSiteCoordinates ( const Vint & vCoordinates )

inlineoverridevirtual

Set all coordinates of sites.

Parameters

vCoordinates A vector with all site coordinates.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

Definition at line 472 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

◆ site()

template<class SiteType , class SequenceType >

const SiteType& bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site ( size_t sitePosition ) const

inlineoverridevirtual

Get a site from the container.

Parameters

sitePosition The position of the site in the container.

Returns: A site object corresponding to site i in the alignment.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >.

Definition at line 296 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::getObject(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ site_()

template<class SiteType , class SequenceType >

SiteType& bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_ ( size_t sitePosition )

inlineprotected

Get a non-const reference to a site in the container. It is a convenient short-cut for use within the class only, as this can potentially mess up the data.

Parameters

sitePosition the index of the site to retrieve.

Returns: A reference to the selected site.

Definition at line 801 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::getObject(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_.

◆ valueAt() [1/4]

template<class SiteType , class SequenceType >

const SequenceType::ElementType& bpp::TemplateVectorSiteContainer< SiteType, 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 650 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ valueAt() [2/4]

template<class SiteType , class SequenceType >

SequenceType::ElementType& bpp::TemplateVectorSiteContainer< SiteType, 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 655 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::getObjectName(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

◆ valueAt() [3/4]

template<class SiteType , class SequenceType >

const SequenceType::ElementType& bpp::TemplateVectorSiteContainer< SiteType, 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 663 of file VectorSiteContainer.h.

References bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site().

◆ valueAt() [4/4]

template<class SiteType , class SequenceType >

SequenceType::ElementType& bpp::TemplateVectorSiteContainer< SiteType, 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 668 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::getObjectName(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_, and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

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().

◆ sequenceComments_

template<class SiteType , class SequenceType >

std::vector<Comments> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceComments_

protected

Definition at line 49 of file VectorSiteContainer.h.

◆ sequenceContainer_

template<class SiteType , class SequenceType >

VectorMappedContainer<SequenceType> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceContainer_

protected

Definition at line 47 of file VectorSiteContainer.h.

◆ sequenceNames_

template<class SiteType , class SequenceType >

std::vector<std::string> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceNames_

protected

Definition at line 48 of file VectorSiteContainer.h.

◆ siteContainer_

template<class SiteType , class SequenceType >

VectorPositionedContainer<SiteType> bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::siteContainer_

protected

Definition at line 46 of file VectorSiteContainer.h.

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSites(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSites(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

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

Bpp/Seq/Container/VectorSiteContainer.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<class SiteType, class SequenceType> class bpp::TemplateVectorSiteContainer< SiteType, SequenceType >

Constructor & Destructor Documentation

◆ TemplateVectorSiteContainer() [1/7]

◆ TemplateVectorSiteContainer() [2/7]

◆ TemplateVectorSiteContainer() [3/7]

◆ TemplateVectorSiteContainer() [4/7]

◆ TemplateVectorSiteContainer() [5/7]

◆ TemplateVectorSiteContainer() [6/7]

◆ TemplateVectorSiteContainer() [7/7]

◆ ~TemplateVectorSiteContainer()

Member Function Documentation

◆ addSequence()

◆ addSite() [1/2]

◆ addSite() [2/2]

◆ alphabet()

◆ clear()

◆ clearComments() [1/2]

◆ clearComments() [2/2]

◆ clone()

◆ createEmptyContainer()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ deleteSite()

◆ deleteSites()

◆ getAlphabet()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getSequenceComments()

◆ getSequenceKeys()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSiteCoordinates()

◆ getStateValueAt() [1/2]

◆ getStateValueAt() [2/2]

◆ hasSequence()

◆ insertSequence()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ realloc_()

◆ reindexSites()

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ removeSite()

◆ sequence() [1/2]

◆ sequence() [2/2]

◆ sequenceKey()

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setSequence() [1/3]

◆ setSequence() [2/3]

◆ setSequence() [3/3]

◆ setSequenceKeys()

◆ setSequenceNames()

◆ setSite()

◆ setSiteCoordinates()

◆ site()

◆ site_()

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ alphabet_

◆ comments_

◆ sequenceComments_

◆ sequenceContainer_

◆ sequenceNames_

◆ siteContainer_

template<class SiteType, class SequenceType>
class bpp::TemplateVectorSiteContainer< SiteType, SequenceType >