The AlignedSequencesContainer class. More...

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

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

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

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

	TemplateAlignedSequenceContainer (std::shared_ptr< const Alphabet > alphabet)
	Build a new empty container with the specified alphabet. More...

	TemplateAlignedSequenceContainer (const TemplateAlignedSequenceContainer< SequenceType, SiteType > &asc)
	Copy constructor. More...

	TemplateAlignedSequenceContainer (const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)
	Convert any SiteContainer object into a AlignedSequenceContainer object. More...

	TemplateAlignedSequenceContainer (const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)
	Try to coerce a SequenceContainer object into an AlignedSequenceContainer object. More...

TemplateAlignedSequenceContainer &	operator= (const TemplateAlignedSequenceContainer< SequenceType, SiteType > &asc)

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

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

virtual	~TemplateAlignedSequenceContainer ()

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...

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

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

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

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

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

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

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

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

virtual void	clearComments ()=0

void	clearComments () override

The Clonable interface.
TemplateAlignedSequenceContainer< SequenceType, SiteType > *	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	deleteSites (size_t sitePosition, size_t length) override
	Remove a continuous range of sites in 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	clear () override
	Delete all data in the container. More...

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

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

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

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

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

Redefinition of VectorSequenceContainer methods, to check for sequence lengths.
void	setSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr) override
	Replace a sequence in the container. More...

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

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

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

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

The SequenceContainer interface.
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	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, const std::string &sequenceKey, int state) const override
	Get the value of a state at a given position. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Protected Member Functions
bool	checkSize_ (const Sequence &sequenceRef)
	Check sequence's size before insertion in sequence container. More...

virtual SequenceType &	sequence_ (size_t sequencePosition)

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

Protected Attributes
VectorMappedContainer< SequenceType >	sequenceVectorMap_

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

Comments	comments_

Private Attributes
VectorPositionedContainer< SiteType >	siteVector_

std::vector< int >	coordinates_

size_t	length_

Detailed Description

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

The AlignedSequencesContainer class.

This class inherits from the VectorSequenceContainer and add site access. Sequence addition methods are re-defined to check for sequence lengths. Sequence access is in , and site access in , where is the number of sequences in the container.

Sites are built on the fly when needed, otherwise they are only nullptr

See VectorSiteContainer for an alternative implementation.

See also: VectorSequenceContainer, Sequence, Site, VectorSiteContainer

Definition at line 39 of file AlignedSequenceContainer.h.

Constructor & Destructor Documentation

◆ TemplateAlignedSequenceContainer() [1/5]

template<class SequenceType , class SiteType >

bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer	(	std::shared_ptr< const Alphabet >	alphabet,
		std::vector< std::unique_ptr< Sequence >>	vs
	)

inline

Build a container with pointers to sequence objects.

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

Parameters

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

Definition at line 60 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::reindexSites(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

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

◆ TemplateAlignedSequenceContainer() [2/5]

template<class SequenceType , class SiteType >

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

inline

Build a new empty container with the specified alphabet.

Parameters

alphabet The alphabet of the container.

Definition at line 88 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::reindexSites().

◆ TemplateAlignedSequenceContainer() [3/5]

template<class SequenceType , class SiteType >

bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer ( const TemplateAlignedSequenceContainer< SequenceType, SiteType > & asc )

inline

Copy constructor.

Parameters

asc	The container to copy.

Definition at line 103 of file AlignedSequenceContainer.h.

◆ TemplateAlignedSequenceContainer() [4/5]

template<class SequenceType , class SiteType >

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

inline

Convert any SiteContainer object into a AlignedSequenceContainer object.

Parameters

sc	The container to copy.

Definition at line 115 of file AlignedSequenceContainer.h.

◆ TemplateAlignedSequenceContainer() [5/5]

template<class SequenceType , class SiteType >

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

inline

Try to coerce a SequenceContainer object into an AlignedSequenceContainer object.

Sequences in osc will be considered aligned, and have the same number of sites.

Parameters

sc	The ordered container to coerce.

Exceptions

SequenceNotAlignedException If sequences in sc do not have the same length.

Definition at line 130 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::addSequence(), bpp::Commentable::getComments(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::reindexSites(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), bpp::SimpleCommentable::setComments(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ ~TemplateAlignedSequenceContainer()

template<class SequenceType , class SiteType >

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

inlinevirtual

Definition at line 193 of file AlignedSequenceContainer.h.

Member Function Documentation

◆ addSequence() [1/2]

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 475 of file AlignedSequenceContainer.h.

References bpp::TemplateVectorSequenceContainer< SequenceType >::addSequence(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::reindexSites(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

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

◆ addSequence() [2/2]

template<class SequenceType >

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

inlinevirtualinherited

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

Parameters

sequencePtr A unique_ptr to the sequence to add.

Definition at line 371 of file VectorSequenceContainer.h.

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

◆ addSite() [1/2]

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 341 of file AlignedSequenceContainer.h.

References bpp::VectorPositionedContainer< T >::appendObject(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::site(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ addSite() [2/2]

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 376 of file AlignedSequenceContainer.h.

◆ 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.

◆ checkSize_()

template<class SequenceType , class SiteType >

bool bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_ ( const Sequence & sequenceRef )

inlineprotected

Check sequence's size before insertion in sequence container.

Parameters

sequenceRef The sequence to check.

Returns: True if sequence length = number of sites in container.

Definition at line 573 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, and bpp::AbstractTemplateSymbolList< T >::size().

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

◆ clear()

template<class SequenceType , class SiteType >

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

inlineoverridevirtual

Delete all data in the container.

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

Definition at line 414 of file AlignedSequenceContainer.h.

References bpp::VectorPositionedContainer< T >::clear(), bpp::TemplateVectorSequenceContainer< SequenceType >::clear(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ clearComments() [1/2]

void bpp::SimpleCommentable::clearComments ( )

inlineoverridevirtualinherited

Implements bpp::Commentable.

Definition at line 88 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

◆ clearComments() [2/2]

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

◆ clone()

template<class SequenceType , class SiteType >

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

inlineoverridevirtual

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

Definition at line 201 of file AlignedSequenceContainer.h.

◆ createEmptyContainer()

template<class SequenceType , class SiteType >

TemplateAlignedSequenceContainer* bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 422 of file AlignedSequenceContainer.h.

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

◆ deleteSequence() [1/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Remove and delete a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

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

Definition at line 280 of file VectorSequenceContainer.h.

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

◆ deleteSequence() [2/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Remove and delete a sequence from the container.

Parameters

sequencePosition The position of the sequence.

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

Definition at line 285 of file VectorSequenceContainer.h.

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

◆ deleteSite()

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 300 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::VectorPositionedContainer< T >::deleteObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ deleteSites()

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 320 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::VectorPositionedContainer< T >::deleteObjects(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ getAlphabet()

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

inlineoverridevirtualinherited

Get a pointer toward the container's alphabet.

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

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

Definition at line 101 of file AbstractSequenceContainer.h.

◆ getComments() [1/2]

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

pure virtualinherited

Get the comments.

Returns: The comments.

Implemented in bpp::SimpleCommentable.

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

◆ getComments() [2/2]

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

inlineoverridevirtualinherited

Get the comments.

Returns: The comments.

Implements bpp::Commentable.

Definition at line 79 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

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

◆ getNumberOfSequences()

template<class SequenceType >

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

inlineoverridevirtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

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

Definition at line 204 of file VectorSequenceContainer.h.

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

◆ getNumberOfSites()

template<class SequenceType , class SiteType >

size_t bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 431 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_.

◆ getSequenceComments()

template<class SequenceType >

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

inlineoverridevirtualinherited

Returns: a vector with all sequence comments.

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

Definition at line 352 of file VectorSequenceContainer.h.

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

◆ getSequenceKeys()

template<class SequenceType >

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

inlineoverridevirtualinherited

Returns: a vector with all sequence keys.

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

Definition at line 209 of file VectorSequenceContainer.h.

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

◆ getSequenceNames()

template<class SequenceType >

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

inlineoverridevirtualinherited

Returns: a vector with all sequence names.

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

Definition at line 327 of file VectorSequenceContainer.h.

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

◆ getSequencePosition()

template<class SequenceType >

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

inlineoverridevirtualinherited

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

Parameters

sequenceKey The key to which the sequence is associated.

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

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

Definition at line 224 of file VectorSequenceContainer.h.

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

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

◆ getSiteCoordinates()

template<class SequenceType , class SiteType >

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

inlineoverridevirtual

Get all coordinates of sites.

Returns: A vector with all site coordinates.

Implements bpp::TemplateAlignmentDataInterface< HashType >.

Definition at line 433 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_.

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

◆ getStateValueAt() [1/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Get the value of a state at a given position.

Parameters

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

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

Definition at line 184 of file VectorSequenceContainer.h.

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

◆ getStateValueAt() [2/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Get value of a state at a given position.

Parameters

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

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

Definition at line 194 of file VectorSequenceContainer.h.

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

◆ hasSequence()

template<class SequenceType >

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

inlineoverridevirtualinherited

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

Parameters

sequenceKey The key to which the sequence is associated.

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

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

Definition at line 249 of file VectorSequenceContainer.h.

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

◆ insertSequence()

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 525 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateVectorSequenceContainer< SequenceType >::insertSequence(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ operator()() [1/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Get the value of a state at a given position.

Same as getValueAt.

Parameters

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

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

Definition at line 189 of file VectorSequenceContainer.h.

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

◆ operator()() [2/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Get the value of a state at a given position.

Same as getValueAt.

Parameters

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

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

Definition at line 199 of file VectorSequenceContainer.h.

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

◆ operator=() [1/3]

template<class SequenceType , class SiteType >

TemplateAlignedSequenceContainer& bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::operator= ( const TemplateAlignedSequenceContainer< SequenceType, SiteType > & asc )

inline

Definition at line 154 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getSiteCoordinates(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ operator=() [2/3]

template<class SequenceType , class SiteType >

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

inline

Definition at line 180 of file AlignedSequenceContainer.h.

References bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::reindexSites(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ operator=() [3/3]

template<class SequenceType , class SiteType >

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

inline

Definition at line 167 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >::getNumberOfSites(), bpp::TemplateAlignmentDataInterface< HashType >::getSiteCoordinates(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ reindexSites()

template<class SequenceType , class SiteType >

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

inlineoverridevirtual

Set all coordinate attributes.

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

Definition at line 447 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_.

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

◆ removeSequence() [1/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Remove a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

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

Definition at line 273 of file VectorSequenceContainer.h.

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

◆ removeSequence() [2/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Remove a sequence from the container.

Parameters

sequencePosition The position of the sequence.

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

Definition at line 319 of file VectorSequenceContainer.h.

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

◆ removeSite()

template<class SequenceType , class SiteType >

std::unique_ptr<SiteType> bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 275 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::removeObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::site(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ sequence() [1/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Retrieve a sequence object from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Returns: A reference toward the Sequence with corresponding name.

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

Definition at line 254 of file VectorSequenceContainer.h.

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

◆ sequence() [2/2]

template<class SequenceType >

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

inlineoverridevirtualinherited

Retrieve a sequence object from the container.

Parameters

sequencePosition The position of the sequence.

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

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

Definition at line 290 of file VectorSequenceContainer.h.

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

◆ sequence_() [1/2]

template<class SequenceType >

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

inlineprotectedvirtualinherited

getSequence with given key

Definition at line 387 of file VectorSequenceContainer.h.

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

◆ sequence_() [2/2]

template<class SequenceType >

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

inlineprotectedvirtualinherited

Definition at line 377 of file VectorSequenceContainer.h.

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

◆ sequenceKey()

template<class SequenceType >

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

inlineoverridevirtualinherited

Get the key associated to a given sequence.

Parameters

sequencePosition The position of the sequence in the container.

Returns: The key to which the sequence is associated.

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

Definition at line 219 of file VectorSequenceContainer.h.

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

◆ setComments() [1/2]

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

inlineoverridevirtualinherited

Set the comments.

Parameters

comments The new comments.

Implements bpp::Commentable.

Definition at line 86 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

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

◆ setComments() [2/2]

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

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SimpleCommentable.

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

◆ setSequence() [1/3]

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 463 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence().

◆ setSequence() [2/3]

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 491 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ setSequence() [3/3]

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 508 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ setSequenceKeys()

template<class SequenceType >

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

inlineoverridevirtualinherited

Reset all sequence keys.

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

Definition at line 214 of file VectorSequenceContainer.h.

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

◆ setSequenceNames()

template<class SequenceType >

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

inlineoverridevirtualinherited

Batch-set all sequence names.

Parameters

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

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

Definition at line 338 of file VectorSequenceContainer.h.

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

◆ setSite()

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 238 of file AlignedSequenceContainer.h.

References bpp::VectorPositionedContainer< T >::addObject(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::site(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ setSiteCoordinates()

template<class SequenceType , class SiteType >

void bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 435 of file AlignedSequenceContainer.h.

References bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites().

◆ site()

template<class SequenceType , class SiteType >

const SiteType& bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 212 of file AlignedSequenceContainer.h.

References bpp::VectorPositionedContainer< T >::addObject_(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >::getAlphabet(), bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::getNumberOfSites(), bpp::VectorPositionedContainer< T >::getObject(), bpp::VectorPositionedContainer< T >::hasObjectWithPosition(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_, bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::addSite(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::removeSite(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::setSite().

◆ valueAt() [1/4]

template<class SequenceType , class SiteType >

SequenceType::ElementType& bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::valueAt	(	const 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 559 of file AlignedSequenceContainer.h.

References bpp::VectorPositionedContainer< T >::addObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ valueAt() [2/4]

template<class SequenceType >

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

inlineoverridevirtualinherited

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

Parameters

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

Returns: The element at the given position.

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

Definition at line 229 of file VectorSequenceContainer.h.

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

◆ valueAt() [3/4]

template<class SequenceType , class SiteType >

SequenceType::ElementType& bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::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 552 of file AlignedSequenceContainer.h.

References bpp::VectorPositionedContainer< T >::addObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_.

◆ valueAt() [4/4]

template<class SequenceType >

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

inlineoverridevirtualinherited

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

Parameters

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

Returns: The element at the given position.

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

Definition at line 239 of file VectorSequenceContainer.h.

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

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().

◆ coordinates_

template<class SequenceType , class SiteType >

std::vector<int> bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::coordinates_

private

Definition at line 47 of file AlignedSequenceContainer.h.

◆ length_

template<class SequenceType , class SiteType >

size_t bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::length_

private

Definition at line 49 of file AlignedSequenceContainer.h.

◆ sequenceVectorMap_

template<class SequenceType >

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

protectedinherited

Definition at line 34 of file VectorSequenceContainer.h.

◆ siteVector_

template<class SequenceType , class SiteType >

VectorPositionedContainer<SiteType> bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::siteVector_

private

Definition at line 44 of file AlignedSequenceContainer.h.

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

Bpp/Seq/Container/AlignedSequenceContainer.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

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

Constructor & Destructor Documentation

◆ TemplateAlignedSequenceContainer() [1/5]

◆ TemplateAlignedSequenceContainer() [2/5]

◆ TemplateAlignedSequenceContainer() [3/5]

◆ TemplateAlignedSequenceContainer() [4/5]

◆ TemplateAlignedSequenceContainer() [5/5]

◆ ~TemplateAlignedSequenceContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ addSite() [1/2]

◆ addSite() [2/2]

◆ alphabet()

◆ checkSize_()

◆ 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]

◆ reindexSites()

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ removeSite()

◆ sequence() [1/2]

◆ sequence() [2/2]

◆ sequence_() [1/2]

◆ sequence_() [2/2]

◆ sequenceKey()

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setSequence() [1/3]

◆ setSequence() [2/3]

◆ setSequence() [3/3]

◆ setSequenceKeys()

◆ setSequenceNames()

◆ setSite()

◆ setSiteCoordinates()

◆ site()

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ alphabet_

◆ comments_

◆ coordinates_

◆ length_

◆ sequenceVectorMap_

◆ siteVector_

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