The SiteContainer interface. More...

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

Inheritance diagram for bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >:

Collaboration diagram for bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >:

Public Member Functions
	TemplateSiteContainerInterface ()

virtual	~TemplateSiteContainerInterface ()

TemplateSiteContainerInterface< SiteType, SequenceType, HashType > *	clone () const override=0

TemplateSiteContainerInterface< SiteType, SequenceType, HashType > *	createEmptyContainer () const override=0
	Return a copy of this container, but with no data inside. More...

virtual const SiteType &	site (size_t sitePosition) const override=0
	Get a site from the container. More...

virtual void	setSite (size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true)=0
	Set a site in the container. More...

virtual void	addSite (std::unique_ptr< SiteType > &site, bool checkCoordinate)=0
	Add a site in the container. More...

virtual void	addSite (std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate)=0
	Add a site in the container. More...

virtual std::unique_ptr< SiteType >	removeSite (size_t sitePosition)=0
	Remove a site from the container. More...

virtual void	deleteSite (size_t sitePosition)=0
	Delete a site from the container. More...

virtual void	deleteSites (size_t sitePosition, size_t length) override=0
	Remove a continuous range of sites in the container. More...

virtual size_t	getNumberOfSites () const override=0
	Get the number of aligned positions in the container. More...

virtual void	reindexSites () override=0
	Set all coordinate attributes. More...

virtual Vint	getSiteCoordinates () const=0
	Get all coordinates of sites. More...

virtual void	setSiteCoordinates (const Vint &vCoordinates)=0
	Set all coordinates of sites. More...

virtual const Alphabet &	alphabet () const =0
	Get the container's alphabet. More...

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get a pointer toward the container's alphabet. More...

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

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

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

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

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

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

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

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

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

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

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

virtual void	clearComments ()=0

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

virtual void	deleteSequence (const HashType &sequenceKey)=0
	Remove and delete a sequence from the container. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Detailed Description

template<class SiteType, class SequenceType, class HashType>
class bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >

The SiteContainer interface.

Container implementing the SiteContainer interface deal with aligned sequences. This interface provides methods to retrieve, add or set sites in the alignment. As for SequenceContainers, the maintenance of Sites is up to the container.

Definition at line 26 of file SiteContainer.h.

Constructor & Destructor Documentation

◆ TemplateSiteContainerInterface()

template<class SiteType , class SequenceType , class HashType >

bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::TemplateSiteContainerInterface ( )

inline

Definition at line 31 of file SiteContainer.h.

◆ ~TemplateSiteContainerInterface()

template<class SiteType , class SequenceType , class HashType >

virtual bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::~TemplateSiteContainerInterface ( )

inlinevirtual

Definition at line 32 of file SiteContainer.h.

Member Function Documentation

◆ addSequence()

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.

◆ addSite() [1/2]

template<class SiteType , class SequenceType , class HashType >

virtual void bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::addSite	(	std::unique_ptr< SiteType > &	site,
		bool	checkCoordinate
	)

pure virtual

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.

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

Referenced by bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::merge(), and bpp::SiteContainerTools::sampleSites().

◆ addSite() [2/2]

template<class SiteType , class SequenceType , class HashType >

virtual void bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::addSite	(	std::unique_ptr< SiteType > &	site,
		size_t	sitePosition,
		bool	checkCoordinate
	)

pure virtual

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.

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

◆ alphabet()

template<class HashType = std::string>

virtual const Alphabet& bpp::TemplateSequenceDataInterface< HashType >::alphabet ( ) const

pure virtualinherited

Get the container's alphabet.

Returns: The alphabet associated to this container.

Implemented in bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >, and bpp::AbstractTemplateSequenceContainer< Sequence, std::string >.

Referenced by bpp::SiteContainerTools::resolveDottedAlignment().

◆ clear()

template<class HashType = std::string>

virtual void bpp::TemplateSequenceDataInterface< HashType >::clear ( )

pure virtualinherited

Delete all data in the container.

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

◆ clearComments()

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

◆ clone()

template<class SiteType , class SequenceType , class HashType >

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

overridepure virtual

Implements bpp::TemplateAlignmentDataInterface< HashType >.

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

◆ createEmptyContainer()

template<class SiteType , class SequenceType , class HashType >

TemplateSiteContainerInterface<SiteType, SequenceType, HashType>* bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::createEmptyContainer ( ) const

overridepure virtual

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

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

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

Implements bpp::TemplateSequenceContainerInterface< SequenceType, HashType >.

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

Referenced by bpp::SiteContainerTools::merge().

◆ deleteSequence() [1/2]

template<class HashType = std::string>

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

pure virtualinherited

Remove and delete a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

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

◆ deleteSequence() [2/2]

template<class HashType = std::string>

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

pure virtualinherited

Remove and delete a sequence from the container.

Parameters

sequencePosition The position of the sequence.

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

◆ deleteSite()

template<class SiteType , class SequenceType , class HashType >

virtual void bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::deleteSite ( size_t sitePosition )

pure virtual

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.

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

Referenced by bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), and bpp::SiteContainerTools::removeSitesWithStopCodon().

◆ deleteSites()

template<class SiteType , class SequenceType , class HashType >

virtual void bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::deleteSites	(	size_t	sitePosition,
		size_t	length
	)

overridepure virtual

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::TemplateAlignmentDataInterface< HashType >.

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

Referenced by bpp::SiteContainerTools::removeGapOnlySites(), and bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites().

◆ getAlphabet()

template<class HashType = std::string>

virtual std::shared_ptr<const Alphabet> bpp::TemplateSequenceDataInterface< HashType >::getAlphabet ( ) const

pure virtualinherited

Get a pointer toward the container's alphabet.

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

Implemented in bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >, and bpp::AbstractTemplateSequenceContainer< Sequence, std::string >.

◆ getComments()

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().

◆ getNumberOfSequences()

template<class HashType = std::string>

virtual size_t bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences ( ) const

pure virtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

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

◆ getNumberOfSites()

template<class SiteType , class SequenceType , class HashType >

virtual size_t bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::getNumberOfSites ( ) const

overridepure virtual

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

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

◆ getSequenceComments()

template<class HashType = std::string>

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

pure virtualinherited

Returns: a vector with all sequence comments.

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

Referenced by bpp::CompressedVectorSiteContainer::operator=().

◆ getSequenceKeys()

template<class HashType = std::string>

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

pure virtualinherited

Returns: a vector with all sequence keys.

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

◆ getSequenceNames()

template<class HashType = std::string>

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

pure virtualinherited

Returns: a vector with all sequence names.

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

Referenced by bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::SiteContainerTools::getSitesWithoutStopCodon(), bpp::CompressedVectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapSites(), bpp::SequenceApplicationTools::restrictSelectedSequencesByName(), bpp::SiteContainerTools::sampleSites(), bpp::Stockholm::writeAlignment(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequences(), and bpp::Phylip::writeSequential().

◆ getSequencePosition()

template<class HashType = std::string>

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

pure virtualinherited

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

Parameters

sequenceKey The key to which the sequence is associated.

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

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

◆ getSiteCoordinates()

virtual Vint bpp::TemplateAlignmentDataInterface< HashType >::getSiteCoordinates ( ) const

pure virtualinherited

Get all coordinates of sites.

Returns: A vector with all site coordinates.

◆ getStateValueAt() [1/2]

template<class HashType = std::string>

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

pure virtualinherited

Get the value of a state at a given position.

Parameters

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

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

◆ getStateValueAt() [2/2]

template<class HashType = std::string>

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

pure virtualinherited

Get value of a state at a given position.

Parameters

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

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

◆ hasSequence()

template<class HashType = std::string>

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

pure virtualinherited

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

Parameters

sequenceKey The key to which the sequence is associated.

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

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

Referenced by bpp::SequenceContainerTools::getSelectedSequences().

◆ insertSequence()

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.

◆ operator()() [1/2]

template<class HashType = std::string>

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

pure virtualinherited

Get the value of a state at a given position.

Same as getValueAt.

Parameters

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

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

◆ operator()() [2/2]

template<class HashType = std::string>

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

pure virtualinherited

Get the value of a state at a given position.

Same as getValueAt.

Parameters

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

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

◆ reindexSites()

template<class SiteType , class SequenceType , class HashType >

virtual void bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::reindexSites ( )

overridepure virtual

Set all coordinate attributes.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

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

◆ removeSequence() [1/2]

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.

◆ removeSequence() [2/2]

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

pure virtualinherited

Remove a sequence from the container.

Parameters

sequencePosition The position of the sequence.

◆ removeSite()

template<class SiteType , class SequenceType , class HashType >

virtual std::unique_ptr<SiteType> bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::removeSite ( size_t sitePosition )

pure virtual

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.

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

◆ sequence() [1/4]

template<class HashType = std::string>

virtual const CoreSequenceInterface& bpp::TemplateSequenceDataInterface< HashType >::sequence ( const HashType & sequenceKey ) const

pure 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::TemplateSequenceContainerInterface< SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateSequenceContainerInterface< SequenceType, HashType >.

◆ sequence() [2/4]

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.

Implements bpp::TemplateSequenceDataInterface< HashType >.

◆ sequence() [3/4]

template<class HashType = std::string>

virtual const CoreSequenceInterface& bpp::TemplateSequenceDataInterface< HashType >::sequence ( size_t sequencePosition ) const

pure virtualinherited

Retrieve a sequence object from the container.

Parameters

sequencePosition The position of the sequence.

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

Implemented in bpp::TemplateSequenceContainerInterface< SequenceType, HashType >, bpp::TemplateSequenceContainerInterface< SequenceType, HashType >, bpp::TemplateSequenceContainerInterface< SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ sequence() [4/4]

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

overridepure virtualinherited

Retrieve a sequence object from the container.

Parameters

sequencePosition The position of the sequence.

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

Implements bpp::TemplateSequenceDataInterface< HashType >.

◆ sequenceKey()

template<class HashType = std::string>

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

pure virtualinherited

Get the key associated to a given sequence.

Parameters

sequencePosition The position of the sequence in the container.

Returns: The key to which the sequence is associated.

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

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

◆ setComments()

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

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SimpleCommentable.

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

◆ setSequence() [1/3]

virtual void bpp::TemplateSequenceContainerInterface< SequenceType, 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.

◆ setSequence() [2/3]

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.

◆ setSequence() [3/3]

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.

◆ setSequenceKeys()

template<class HashType = std::string>

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

pure virtualinherited

Reset all sequence keys.

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

◆ setSequenceNames()

template<class HashType = std::string>

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

pure virtualinherited

Batch-set all sequence names.

Parameters

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

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

Referenced by bpp::SiteContainerTools::getSelectedSites(), and bpp::SiteContainerTools::sampleSites().

◆ setSite()

template<class SiteType , class SequenceType , class HashType >

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

pure virtual

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.

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

Referenced by bpp::SiteContainerTools::changeGapsToUnknownCharacters(), and bpp::SiteContainerTools::changeUnresolvedCharactersToGaps().

◆ setSiteCoordinates()

virtual void bpp::TemplateAlignmentDataInterface< HashType >::setSiteCoordinates ( const Vint & vCoordinates )

pure virtualinherited

Set all coordinates of sites.

Parameters

vCoordinates A vector with all site coordinates.

◆ site()

template<class SiteType , class SequenceType , class HashType >

virtual const SiteType& bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::site ( size_t sitePosition ) const

overridepure virtual

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::TemplateAlignmentDataInterface< HashType >.

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

◆ valueAt() [1/4]

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.

◆ valueAt() [2/4]

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.

◆ valueAt() [3/4]

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

pure virtualinherited

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

Parameters

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

Returns: The element at the given position.

◆ valueAt() [4/4]

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

pure virtualinherited

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

Parameters

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

Returns: The element at the given position.

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

Bpp/Seq/Container/SiteContainer.h

Public Member Functions

Detailed Description

template<class SiteType, class SequenceType, class HashType> class bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >

Constructor & Destructor Documentation

◆ TemplateSiteContainerInterface()

◆ ~TemplateSiteContainerInterface()

Member Function Documentation

◆ addSequence()

◆ addSite() [1/2]

◆ addSite() [2/2]

◆ alphabet()

◆ clear()

◆ clearComments()

◆ clone()

◆ createEmptyContainer()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ deleteSite()

◆ deleteSites()

◆ getAlphabet()

◆ getComments()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getSequenceComments()

◆ getSequenceKeys()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSiteCoordinates()

◆ getStateValueAt() [1/2]

◆ getStateValueAt() [2/2]

◆ hasSequence()

◆ insertSequence()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ reindexSites()

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ removeSite()

◆ sequence() [1/4]

◆ sequence() [2/4]

◆ sequence() [3/4]

◆ sequence() [4/4]

◆ sequenceKey()

◆ setComments()

◆ setSequence() [1/3]

◆ setSequence() [2/3]

◆ setSequence() [3/3]

◆ setSequenceKeys()

◆ setSequenceNames()

◆ setSite()

◆ setSiteCoordinates()

◆ site()

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

template<class SiteType, class SequenceType, class HashType>
class bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >