A low memory, yet restricted, version of the VectorSiteContainer class. More...

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

Inheritance diagram for bpp::CompressedVectorSiteContainer:

Collaboration diagram for bpp::CompressedVectorSiteContainer:

Public Member Functions
	CompressedVectorSiteContainer (std::vector< std::unique_ptr< Site >> &vs, std::shared_ptr< const Alphabet > &alphabet)
	Build a new container from a set of sites. More...

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

	CompressedVectorSiteContainer (const std::vector< std::string > &names, std::shared_ptr< const Alphabet > &alphabet)
	Build a new empty container with specified sequence names. More...

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

	CompressedVectorSiteContainer (const CompressedVectorSiteContainer &vsc)

	CompressedVectorSiteContainer (const SiteContainerInterface &sc)

CompressedVectorSiteContainer &	operator= (const CompressedVectorSiteContainer &vsc)

CompressedVectorSiteContainer &	operator= (const SiteContainerInterface &sc)

virtual	~CompressedVectorSiteContainer ()

size_t	getNumberOfUniqueSites () const

void	setSequence (size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey) override

void	setSequence (size_t sequencePosition, std::unique_ptr< Sequence > &sequence) override

void	setSequence (const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence) override

void	addSequence (const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence) override

void	insertSequence (size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey) override

const int &	valueAt (const std::string &sequenceKey, size_t sitePosition) const override

int &	valueAt (const std::string &sequenceKey, size_t sitePosition) override

const int &	valueAt (size_t sequencePosition, size_t sitePosition) const override
	Get the content of the dataset at a specific position (sequence position, site position). More...

int &	valueAt (size_t sequencePosition, size_t sitePosition) override
	Get the content of the dataset at a specific position (sequence position, site position). More...

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

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

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

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

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

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

virtual void	clearComments ()=0

void	clearComments () override

The Clonable interface.
CompressedVectorSiteContainer *	clone () const override

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

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

std::unique_ptr< Site >	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< Site > &site, bool checkCoordinate=false) override
	Add a site in the container. More...

void	addSite (std::unique_ptr< Site > &site, size_t sitePosition, bool checkCoordinate=false) 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 &coordinates) override
	Set all coordinates of sites. More...

The SequenceContainer interface.
const Sequence &	sequence (size_t sequenceIndex) const override
	Retrieve a sequence object from the container. More...

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

bool	hasSequence (const std::string &name) 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...

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

std::unique_ptr< Sequence >	removeSequence (const std::string &sequenceKey) override

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...

CompressedVectorSiteContainer *	createEmptyContainer () const override
	Return a copy of this container, but with no data inside. More...

SequenceData methods.
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...

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

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

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

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

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

Access by position
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 HashType &sequenceKey)=0
	Replace a sequence in the container. More...

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

Protected Member Functions
Site &	getSite_ (size_t sitePosition)

size_t	getSiteIndex_ (const Site &site)

Protected Attributes
VectorPositionedContainer< Site >	siteContainer_

VectorMappedContainer< Sequence >	sequenceContainer_

std::vector< std::string >	sequenceNames_

std::vector< Comments >	sequenceComments_

std::vector< size_t >	index_

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

Comments	comments_

Detailed Description

A low memory, yet restricted, version of the VectorSiteContainer class.

This implementation is very similar to VectorSiteContainer, but identical sites are stored only once, which significantly reduces memory usage in the case of containers where the number of sites is large compared to the number of sequences. site access is as fast as in the standard VectorSiteContainer class, but site addition takes more time, as the new site must be first compared to the existing set. A major restriction of this container is that you can't add or remove sequences. The number of sequences is fixed after the first site has been added.

Warning: Since the data is compressed, the sites given as input are modified. The major practical consequence is that the 'position' attribute of sites will be lost. Instead, the position will correspond to the position in the compressed container. In addition, this container may lead to unexpected behavior if used with derived classes of Site.

See also: Sequence, Site, VectorSiteContainer

Definition at line 41 of file CompressedVectorSiteContainer.h.

Constructor & Destructor Documentation

◆ CompressedVectorSiteContainer() [1/6]

CompressedVectorSiteContainer::CompressedVectorSiteContainer	(	std::vector< std::unique_ptr< Site >> &	vs,
		std::shared_ptr< const Alphabet > &	alphabet
	)

Build a new container from a set of sites.

Parameters

vs	A std::vector of sites.
alphabet	The common alphabet for all sites.

Exceptions

Exception If sites differ in size or in alphabet.

Class constructors:

Definition at line 16 of file CompressedVectorSiteContainer.cpp.

References addSite(), sequenceContainer_, sequenceNames_, site(), and bpp::TextTools::toString().

Referenced by clone(), and createEmptyContainer().

◆ CompressedVectorSiteContainer() [2/6]

CompressedVectorSiteContainer::CompressedVectorSiteContainer	(	size_t	size,
		std::shared_ptr< const Alphabet > &	alphabet
	)

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 45 of file CompressedVectorSiteContainer.cpp.

References sequenceContainer_, sequenceNames_, and bpp::TextTools::toString().

◆ CompressedVectorSiteContainer() [3/6]

CompressedVectorSiteContainer::CompressedVectorSiteContainer	(	const std::vector< std::string > &	names,
		std::shared_ptr< const Alphabet > &	alphabet
	)

Build a new empty container with specified sequence names.

Parameters

names	Sequence names. This will set the number of sequences in the container.
alphabet	The alphabet for this container.

Definition at line 65 of file CompressedVectorSiteContainer.cpp.

References sequenceContainer_, sequenceNames_, and bpp::TextTools::toString().

◆ CompressedVectorSiteContainer() [4/6]

CompressedVectorSiteContainer::CompressedVectorSiteContainer ( std::shared_ptr< const Alphabet > & alphabet )

Build a new empty container.

Parameters

alphabet The alphabet for this container.

Definition at line 86 of file CompressedVectorSiteContainer.cpp.

◆ CompressedVectorSiteContainer() [5/6]

CompressedVectorSiteContainer::CompressedVectorSiteContainer ( const CompressedVectorSiteContainer & vsc )

Definition at line 97 of file CompressedVectorSiteContainer.cpp.

References sequenceContainer_, sequenceNames_, and siteContainer_.

◆ CompressedVectorSiteContainer() [6/6]

CompressedVectorSiteContainer::CompressedVectorSiteContainer ( const SiteContainerInterface & sc )

Definition at line 120 of file CompressedVectorSiteContainer.cpp.

References addSite(), bpp::Site::clone(), bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::getNumberOfSites(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceNames(), sequenceContainer_, and bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::site().

◆ ~CompressedVectorSiteContainer()

virtual bpp::CompressedVectorSiteContainer::~CompressedVectorSiteContainer ( )

inlinevirtual

Definition at line 97 of file CompressedVectorSiteContainer.h.

References clear().

Member Function Documentation

◆ addSequence() [1/2]

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

virtual void bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence	(	const HashType &	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 >.

Referenced by bpp::SequenceContainerTools::append(), bpp::Pasta::appendAlignmentFromStream(), bpp::Clustal::appendAlignmentFromStream(), bpp::DCSE::appendAlignmentFromStream(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::GenBank::appendSequencesFromStream(), bpp::Fasta::appendSequencesFromStream(), bpp::Mase::appendSequencesFromStream(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SequenceContainerTools::mergeByKey(), bpp::Phylip::readInterleaved(), and bpp::Phylip::readSequential().

◆ addSequence() [2/2]

void bpp::CompressedVectorSiteContainer::addSequence	(	const std::string &	sequenceKey,
		std::unique_ptr< Sequence > &	sequence
	)

inlineoverride

Definition at line 285 of file CompressedVectorSiteContainer.h.

◆ addSite() [1/2]

void CompressedVectorSiteContainer::addSite	(	std::unique_ptr< Site > &	site,
		bool	checkCoordinate = `false`
	)

overridevirtual

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< Site, Sequence, std::string >.

Definition at line 331 of file CompressedVectorSiteContainer.cpp.

References bpp::AbstractTemplateSequenceContainer< Sequence, std::string >::getAlphabet(), bpp::AbstractTemplateSymbolList< T >::getAlphabet(), getNumberOfSequences(), getNumberOfUniqueSites(), getSiteIndex_(), index_, sequenceComments_, sequenceContainer_, sequenceNames_, site(), siteContainer_, bpp::AbstractTemplateSymbolList< T >::size(), and bpp::TextTools::toString().

Referenced by CompressedVectorSiteContainer(), and operator=().

◆ addSite() [2/2]

void CompressedVectorSiteContainer::addSite	(	std::unique_ptr< Site > &	site,
		size_t	sitePosition,
		bool	checkCoordinate = `false`
	)

overridevirtual

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< Site, Sequence, std::string >.

Definition at line 374 of file CompressedVectorSiteContainer.cpp.

References bpp::AbstractTemplateSequenceContainer< Sequence, std::string >::getAlphabet(), bpp::AbstractTemplateSymbolList< T >::getAlphabet(), getNumberOfSequences(), getNumberOfSites(), getNumberOfUniqueSites(), getSiteIndex_(), index_, sequenceComments_, sequenceContainer_, sequenceNames_, site(), siteContainer_, bpp::AbstractTemplateSymbolList< T >::size(), and bpp::TextTools::toString().

◆ alphabet()

const Alphabet& bpp::AbstractTemplateSequenceContainer< Sequence , 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()

void bpp::CompressedVectorSiteContainer::clear ( )

inlineoverridevirtual

Delete all data in the container.

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

Definition at line 248 of file CompressedVectorSiteContainer.h.

References index_, sequenceComments_, sequenceContainer_, sequenceNames_, and siteContainer_.

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

◆ 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()

CompressedVectorSiteContainer* bpp::CompressedVectorSiteContainer::clone ( ) const

inlineoverridevirtual

Implements bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >.

Definition at line 105 of file CompressedVectorSiteContainer.h.

References CompressedVectorSiteContainer().

◆ createEmptyContainer()

CompressedVectorSiteContainer* bpp::CompressedVectorSiteContainer::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< Site, Sequence, std::string >.

Definition at line 257 of file CompressedVectorSiteContainer.h.

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

◆ deleteSequence() [1/2]

void bpp::CompressedVectorSiteContainer::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 200 of file CompressedVectorSiteContainer.h.

◆ deleteSequence() [2/2]

void bpp::CompressedVectorSiteContainer::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 194 of file CompressedVectorSiteContainer.h.

◆ deleteSite()

void CompressedVectorSiteContainer::deleteSite ( size_t sitePosition )

overridevirtual

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< Site, Sequence, std::string >.

Definition at line 309 of file CompressedVectorSiteContainer.cpp.

References getNumberOfSites(), and removeSite().

Referenced by deleteSites().

◆ deleteSites()

void CompressedVectorSiteContainer::deleteSites	(	size_t	sitePosition,
		size_t	length
	)

overridevirtual

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< Site, Sequence, std::string >.

Definition at line 320 of file CompressedVectorSiteContainer.cpp.

References deleteSite().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSequenceContainer< Sequence , 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(), 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()

size_t bpp::CompressedVectorSiteContainer::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 206 of file CompressedVectorSiteContainer.h.

References sequenceContainer_.

Referenced by addSite(), sequence(), setSequenceNames(), and setSite().

◆ getNumberOfSites()

size_t bpp::CompressedVectorSiteContainer::getNumberOfSites ( ) const

inlineoverridevirtual

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

Implements bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >.

Definition at line 133 of file CompressedVectorSiteContainer.h.

References index_.

Referenced by addSite(), deleteSite(), getSiteCoordinates(), removeSite(), sequence(), setSite(), and setSiteCoordinates().

◆ getNumberOfUniqueSites()

size_t bpp::CompressedVectorSiteContainer::getNumberOfUniqueSites ( ) const

inline

Returns: The number of site instances

Definition at line 148 of file CompressedVectorSiteContainer.h.

References siteContainer_.

Referenced by addSite(), getSiteIndex_(), and setSite().

◆ getSequenceComments()

std::vector<Comments> bpp::CompressedVectorSiteContainer::getSequenceComments ( ) const

inlineoverridevirtual

Returns: a vector with all sequence comments.

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

Definition at line 243 of file CompressedVectorSiteContainer.h.

References sequenceComments_.

◆ getSequenceKeys()

std::vector<std::string> bpp::CompressedVectorSiteContainer::getSequenceKeys ( ) const

inlineoverridevirtual

Returns: a vector with all sequence keys.

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

Definition at line 211 of file CompressedVectorSiteContainer.h.

References sequenceContainer_.

◆ getSequenceNames()

std::vector<std::string> bpp::CompressedVectorSiteContainer::getSequenceNames ( ) const

inlineoverridevirtual

Returns: a vector with all sequence names.

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

Definition at line 226 of file CompressedVectorSiteContainer.h.

References sequenceNames_.

Referenced by operator=().

◆ getSequencePosition()

size_t bpp::CompressedVectorSiteContainer::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 176 of file CompressedVectorSiteContainer.h.

References sequenceContainer_, and sequenceKey().

Referenced by getStateValueAt(), operator()(), sequence(), and valueAt().

◆ getSite_()

Site& bpp::CompressedVectorSiteContainer::getSite_ ( 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 354 of file CompressedVectorSiteContainer.h.

References index_, and siteContainer_.

Referenced by reindexSites(), and setSiteCoordinates().

◆ getSiteCoordinates()

Vint CompressedVectorSiteContainer::getSiteCoordinates ( ) const

overridevirtual

Get all coordinates of sites.

Returns: A vector with all site coordinates.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

Definition at line 443 of file CompressedVectorSiteContainer.cpp.

References getNumberOfSites(), index_, and siteContainer_.

◆ getSiteIndex_()

size_t CompressedVectorSiteContainer::getSiteIndex_ ( const Site & site )

protected

Returns: The position of the site in the compressed set. If the site is not found, this will return the number of sites in the compressed set.

Definition at line 488 of file CompressedVectorSiteContainer.cpp.

References getNumberOfUniqueSites(), site(), siteContainer_, and bpp::AbstractTemplateSymbolList< T >::size().

Referenced by addSite(), and setSite().

◆ getStateValueAt() [1/2]

double bpp::CompressedVectorSiteContainer::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 324 of file CompressedVectorSiteContainer.h.

References getSequencePosition(), bpp::Site::getStateValueAt(), sequenceKey(), and site().

◆ getStateValueAt() [2/2]

double bpp::CompressedVectorSiteContainer::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 334 of file CompressedVectorSiteContainer.h.

References bpp::Site::getStateValueAt(), and site().

◆ hasSequence()

bool bpp::CompressedVectorSiteContainer::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 170 of file CompressedVectorSiteContainer.h.

References sequenceContainer_.

◆ insertSequence() [1/2]

void bpp::CompressedVectorSiteContainer::insertSequence	(	size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence,
		const std::string &	sequenceKey
	)

inlineoverride

Definition at line 291 of file CompressedVectorSiteContainer.h.

◆ insertSequence() [2/2]

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

virtual void bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::insertSequence	(	size_t	sequencePosition,
		std::unique_ptr< SequenceType > &	sequencePtr,
		const HashType &	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]

double bpp::CompressedVectorSiteContainer::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 329 of file CompressedVectorSiteContainer.h.

References getSequencePosition(), bpp::Site::getStateValueAt(), sequenceKey(), and site().

◆ operator()() [2/2]

double bpp::CompressedVectorSiteContainer::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 339 of file CompressedVectorSiteContainer.h.

References bpp::Site::getStateValueAt(), and site().

◆ operator=() [1/2]

CompressedVectorSiteContainer & CompressedVectorSiteContainer::operator= ( const CompressedVectorSiteContainer & vsc )

Definition at line 143 of file CompressedVectorSiteContainer.cpp.

References clear(), getSequenceNames(), index_, bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), sequenceComments_, sequenceContainer_, sequenceNames_, and siteContainer_.

◆ operator=() [2/2]

CompressedVectorSiteContainer & CompressedVectorSiteContainer::operator= ( const SiteContainerInterface & sc )

Definition at line 169 of file CompressedVectorSiteContainer.cpp.

References addSite(), clear(), bpp::Site::clone(), bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::getNumberOfSites(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceComments(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceNames(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), sequenceComments_, sequenceNames_, and bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::site().

◆ reindexSites()

void CompressedVectorSiteContainer::reindexSites ( )

overridevirtual

Set all coordinate attributes.

Implements bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >.

Definition at line 420 of file CompressedVectorSiteContainer.cpp.

References getSite_(), bpp::AbstractCoreSite::setCoordinate(), and siteContainer_.

◆ removeSequence() [1/3]

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

virtual std::unique_ptr<SequenceType> bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::removeSequence ( const HashType & 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 >.

Referenced by bpp::SequenceContainerTools::keepOnlySelectedSequences(), and bpp::SequenceApplicationTools::restrictSelectedSequencesByName().

◆ removeSequence() [2/3]

std::unique_ptr<Sequence> bpp::CompressedVectorSiteContainer::removeSequence ( const std::string & sequenceKey )

inlineoverride

Definition at line 188 of file CompressedVectorSiteContainer.h.

◆ removeSequence() [3/3]

std::unique_ptr<Sequence> bpp::CompressedVectorSiteContainer::removeSequence ( size_t sequencePosition )

inlineoverridevirtual

Remove a sequence from the container.

Parameters

sequencePosition The position of the sequence.

Implements bpp::TemplateSequenceContainerInterface< SequenceType, HashType >.

Definition at line 182 of file CompressedVectorSiteContainer.h.

◆ removeSite()

std::unique_ptr< Site > CompressedVectorSiteContainer::removeSite ( size_t sitePosition )

overridevirtual

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< Site, Sequence, std::string >.

Definition at line 268 of file CompressedVectorSiteContainer.cpp.

References getNumberOfSites(), index_, sequenceContainer_, and siteContainer_.

Referenced by deleteSite().

◆ sequence() [1/3]

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

virtual const SequenceType& bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence ( const HashType & 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.

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

◆ sequence() [2/3]

const Sequence& bpp::CompressedVectorSiteContainer::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::TemplateSequenceDataInterface< std::string >.

Definition at line 163 of file CompressedVectorSiteContainer.h.

References getSequencePosition(), sequence(), and sequenceKey().

◆ sequence() [3/3]

const Sequence & CompressedVectorSiteContainer::sequence ( size_t sequencePosition ) const

overridevirtual

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, HashType >.

Definition at line 456 of file CompressedVectorSiteContainer.cpp.

References bpp::AbstractTemplateSequenceContainer< Sequence, std::string >::getAlphabet(), getNumberOfSequences(), getNumberOfSites(), index_, sequenceComments_, sequenceContainer_, sequenceKey(), sequenceNames_, and siteContainer_.

Referenced by sequence().

◆ sequenceKey()

const std::string& bpp::CompressedVectorSiteContainer::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 221 of file CompressedVectorSiteContainer.h.

References sequenceContainer_.

Referenced by getSequencePosition(), getStateValueAt(), operator()(), sequence(), and valueAt().

◆ 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 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() [1/6]

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

virtual void bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::setSequence	(	const HashType &	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() [2/6]

void bpp::CompressedVectorSiteContainer::setSequence	(	const std::string &	sequenceKey,
		std::unique_ptr< Sequence > &	sequence
	)

inlineoverride

Definition at line 279 of file CompressedVectorSiteContainer.h.

◆ setSequence() [3/6]

void bpp::CompressedVectorSiteContainer::setSequence	(	size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence
	)

inlineoverride

Definition at line 273 of file CompressedVectorSiteContainer.h.

◆ setSequence() [4/6]

void bpp::CompressedVectorSiteContainer::setSequence	(	size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence,
		const std::string &	sequenceKey
	)

inlineoverride

Definition at line 267 of file CompressedVectorSiteContainer.h.

◆ setSequence() [5/6]

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

virtual void bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::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() [6/6]

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

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

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

inlineoverridevirtual

Reset all sequence keys.

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

Definition at line 216 of file CompressedVectorSiteContainer.h.

References sequenceContainer_.

Referenced by setSequenceNames().

◆ setSequenceNames()

void bpp::CompressedVectorSiteContainer::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 231 of file CompressedVectorSiteContainer.h.

References getNumberOfSequences(), sequenceContainer_, sequenceNames_, and setSequenceKeys().

◆ setSite()

void CompressedVectorSiteContainer::setSite	(	size_t	sitePosition,
		std::unique_ptr< Site > &	site,
		bool	checkCoordinate = `true`
	)

overridevirtual

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< Site, Sequence, std::string >.

Definition at line 189 of file CompressedVectorSiteContainer.cpp.

References bpp::AbstractTemplateSequenceContainer< Sequence, std::string >::getAlphabet(), bpp::AbstractTemplateSymbolList< T >::getAlphabet(), getNumberOfSequences(), getNumberOfSites(), getNumberOfUniqueSites(), getSiteIndex_(), index_, sequenceContainer_, site(), siteContainer_, and bpp::AbstractTemplateSymbolList< T >::size().

◆ setSiteCoordinates()

void CompressedVectorSiteContainer::setSiteCoordinates ( const Vint & vCoordinates )

overridevirtual

Set all coordinates of sites.

Parameters

vCoordinates A vector with all site coordinates.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

Definition at line 430 of file CompressedVectorSiteContainer.cpp.

References getNumberOfSites(), getSite_(), and bpp::AbstractCoreSite::setCoordinate().

◆ site()

const Site& bpp::CompressedVectorSiteContainer::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< Site, Sequence, std::string >.

Definition at line 116 of file CompressedVectorSiteContainer.h.

References index_, and siteContainer_.

Referenced by addSite(), CompressedVectorSiteContainer(), getSiteIndex_(), getStateValueAt(), operator()(), setSite(), and valueAt().

◆ valueAt() [1/6]

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

virtual const SequenceType::ElementType& bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::valueAt	(	const HashType &	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() [2/6]

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

virtual SequenceType::ElementType& bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::valueAt	(	const HashType &	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() [3/6]

const int& bpp::CompressedVectorSiteContainer::valueAt	(	const std::string &	sequenceKey,
		size_t	sitePosition
	)		const

inlineoverride

Definition at line 297 of file CompressedVectorSiteContainer.h.

References getSequencePosition(), sequenceKey(), and site().

◆ valueAt() [4/6]

int& bpp::CompressedVectorSiteContainer::valueAt	(	const std::string &	sequenceKey,
		size_t	sitePosition
	)

inlineoverride

Definition at line 302 of file CompressedVectorSiteContainer.h.

◆ valueAt() [5/6]

const int& bpp::CompressedVectorSiteContainer::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, HashType >.

Definition at line 308 of file CompressedVectorSiteContainer.h.

References site().

◆ valueAt() [6/6]

int& bpp::CompressedVectorSiteContainer::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, HashType >.

Definition at line 313 of file CompressedVectorSiteContainer.h.

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSequenceContainer< Sequence , 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().

◆ index_

std::vector<size_t> bpp::CompressedVectorSiteContainer::index_

protected

Definition at line 50 of file CompressedVectorSiteContainer.h.

Referenced by addSite(), clear(), getNumberOfSites(), getSite_(), getSiteCoordinates(), operator=(), removeSite(), sequence(), setSite(), and site().

◆ sequenceComments_

std::vector<Comments> bpp::CompressedVectorSiteContainer::sequenceComments_

protected

Definition at line 49 of file CompressedVectorSiteContainer.h.

Referenced by addSite(), clear(), getSequenceComments(), operator=(), and sequence().

◆ sequenceContainer_

VectorMappedContainer<Sequence> bpp::CompressedVectorSiteContainer::sequenceContainer_

protected

Definition at line 47 of file CompressedVectorSiteContainer.h.

Referenced by addSite(), clear(), CompressedVectorSiteContainer(), getNumberOfSequences(), getSequenceKeys(), getSequencePosition(), hasSequence(), operator=(), removeSite(), sequence(), sequenceKey(), setSequenceKeys(), setSequenceNames(), and setSite().

◆ sequenceNames_

std::vector<std::string> bpp::CompressedVectorSiteContainer::sequenceNames_

protected

Definition at line 48 of file CompressedVectorSiteContainer.h.

Referenced by addSite(), clear(), CompressedVectorSiteContainer(), getSequenceNames(), operator=(), sequence(), and setSequenceNames().

◆ siteContainer_

VectorPositionedContainer<Site> bpp::CompressedVectorSiteContainer::siteContainer_

protected

Definition at line 46 of file CompressedVectorSiteContainer.h.

Referenced by addSite(), clear(), CompressedVectorSiteContainer(), getNumberOfUniqueSites(), getSite_(), getSiteCoordinates(), getSiteIndex_(), operator=(), reindexSites(), removeSite(), sequence(), setSite(), and site().

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

Bpp/Seq/Container/CompressedVectorSiteContainer.h
Bpp/Seq/Container/CompressedVectorSiteContainer.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CompressedVectorSiteContainer() [1/6]

◆ CompressedVectorSiteContainer() [2/6]

◆ CompressedVectorSiteContainer() [3/6]

◆ CompressedVectorSiteContainer() [4/6]

◆ CompressedVectorSiteContainer() [5/6]

◆ CompressedVectorSiteContainer() [6/6]

◆ ~CompressedVectorSiteContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ 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()

◆ getNumberOfUniqueSites()

◆ getSequenceComments()

◆ getSequenceKeys()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSite_()

◆ getSiteCoordinates()

◆ getSiteIndex_()

◆ getStateValueAt() [1/2]

◆ getStateValueAt() [2/2]

◆ hasSequence()

◆ insertSequence() [1/2]

◆ insertSequence() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ reindexSites()

◆ removeSequence() [1/3]

◆ removeSequence() [2/3]

◆ removeSequence() [3/3]

◆ removeSite()

◆ sequence() [1/3]

◆ sequence() [2/3]

◆ sequence() [3/3]

◆ sequenceKey()

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setSequence() [1/6]

◆ setSequence() [2/6]

◆ setSequence() [3/6]

◆ setSequence() [4/6]

◆ setSequence() [5/6]

◆ setSequence() [6/6]

◆ setSequenceKeys()

◆ setSequenceNames()

◆ setSite()

◆ setSiteCoordinates()

◆ site()

◆ valueAt() [1/6]

◆ valueAt() [2/6]

◆ valueAt() [3/6]

◆ valueAt() [4/6]

◆ valueAt() [5/6]

◆ valueAt() [6/6]

Member Data Documentation

◆ alphabet_

◆ comments_