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

Inheritance diagram for bpp::VectorSiteContainer:

Collaboration diagram for bpp::VectorSiteContainer:

Public Member Functions
	VectorSiteContainer (const std::vector< const CruxSymbolListSite * > &vs, const Alphabet *alpha, bool checkPositions=true)
	Build a new container from a set of sites. More...

	VectorSiteContainer (const std::vector< const Site * > &vs, const Alphabet *alpha, bool checkPositions=true)

	VectorSiteContainer (size_t size, const Alphabet *alpha)
	Build a new empty container with specified size. More...

	VectorSiteContainer (const std::vector< std::string > &names, const Alphabet *alpha)
	Build a new empty container with specified sequence names. More...

	VectorSiteContainer (const Alphabet *alpha)
	Build a new empty container. More...

	VectorSiteContainer (const VectorSiteContainer &vsc)

	VectorSiteContainer (const SiteContainer &sc)

	VectorSiteContainer (const OrderedSequenceContainer &osc)

	VectorSiteContainer (const SequenceContainer &sc)

	VectorSiteContainer (const AlignedValuesContainer &avc)

VectorSiteContainer &	operator= (const VectorSiteContainer &vsc)

VectorSiteContainer &	operator= (const SiteContainer &sc)

VectorSiteContainer &	operator= (const OrderedSequenceContainer &osc)

VectorSiteContainer &	operator= (const SequenceContainer &sc)

virtual	~VectorSiteContainer ()

void	addSequence (const Sequence &sequence, bool checkName=true)
	Add a sequence to the container. More...

void	addSequence (const Sequence &sequence, size_t sequenceIndex, bool checkName=true)

void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)
	Replace a sequence in the container. More...

void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName)
	Replace a sequence in the container. More...

std::string	toString (const std::string &name) const
	Convert a particular sequence to a string. More...

const Comments &	getComments (const std::string &name) const
	Get comments of a particular sequence. More...

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

void	setComments (const std::string &name, const Comments &comments)
	Set the comments of a particular sequence. More...

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

virtual const Alphabet *	getAlphabet () const =0
	Get container's alphabet. More...

virtual double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const=0
	get value of a state in a position More...

virtual const Comments &	getGeneralComments () const =0
	Get the comments of this container. More...

virtual void	setGeneralComments (const Comments &comments)=0
	Set the comments of this container. More...

virtual void	deleteGeneralComments ()=0
	Delete the comments associated to this container. More...

void	clearComments ()

size_t	getSize () const
	the size More...

bool	isAvailablePosition (size_t objectIndex) const

void	setSize (size_t size)

void	nullify ()
	Nullify all elements. More...

size_t	getSize () const
	Get the number of objects in the container. More...

void	setSize (size_t size)

void	changeName (const std::string &okey, const std::string &nkey)
	change the key of an object. More...

bool	isAvailableName (std::string objectName) const
	Return if the name is in the map keys and the mapped object is nullptr or empty. More...

bool	isAvailablePosition (size_t objectIndex) const

void	nullify ()
	Nullify all elements. More...

The Clonable interface.
VectorSiteContainer *	clone () const

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

const CruxSymbolListSite &	getSymbolListSite (size_t siteIndex) const
	Get a CruxSymbolListSite from a given position. More...

Site &	getSite (size_t siteIndex)

CruxSymbolListSite &	getSymbolListSite (size_t siteIndex)

void	setSite (size_t siteIndex, const Site &site, bool checkPosition=true)
	Set a site in the container. More...

std::shared_ptr< Site >	removeSite (size_t siteIndex)
	Remove a site from the container. More...

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

void	addSite (const Site &site, bool checkPosition=true)
	Add a site in the container. More...

void	addSite (const Site &site, int position, bool checkPosition=true)
	Add a site in the container. More...

void	addSite (const Site &site, size_t siteIndex, bool checkPosition=true)
	Add a site in the container. More...

void	addSite (const Site &site, size_t siteIndex, int position, bool checkPosition=true)
	Add a site in the container. More...

From AlignedValuesContainer interface
void	deleteSites (size_t siteIndex, size_t length)
	Remove a continuous range of sites in the container. More...

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

void	reindexSites ()
	Set all positions attributes. More...

Vint	getSitePositions () const
	Get all position attributes of sites. More...

void	setSitePositions (Vint vPositions)
	Set all position attributes of sites. More...

The SequenceContainer interface.
void	setComments (size_t sequenceIndex, const Comments &comments)

const Sequence &	getSequence (size_t sequenceIndex) const
	Retrieve a sequence object from the container. More...

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

bool	hasSequence (const std::string &name) const
	Check if a sequence with a given name is present in the container. More...

size_t	getSequencePosition (const std::string &name) const
	Get the position of a sequence in sequence container from its name. More...

std::shared_ptr< Sequence >	removeSequence (size_t sequenceIndex)
	Extract (and remove) a sequence from the container. More...

std::shared_ptr< Sequence >	removeSequence (const std::string &name)
	Extract (and remove) a sequence from the container. More...

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

std::vector< std::string >	getSequenceNames () const
	Get all the names of the sequences in the container. More...

void	setSequenceNames (const std::vector< std::string > &names, bool checkNames=true)
	Set all sequence names. More...

void	clear ()
	Delete all objects in the container. More...

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

int &	valueAt (const std::string &sequenceName, size_t elementIndex)
	Element access function. More...

const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const
	Element access function. More...

int &	operator() (const std::string &sequenceName, size_t elementIndex)
	Element access operator. More...

const int &	operator() (const std::string &sequenceName, size_t elementIndex) const
	Element access operator. More...

int &	valueAt (size_t sequenceIndex, size_t elementIndex)
	Element access operator. More...

const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const
	Element access operator. More...

int &	operator() (size_t sequenceIndex, size_t elementIndex)
	Element access operator. More...

const int &	operator() (size_t sequenceIndex, size_t elementIndex) const
	Element access operator. More...

virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0

SequencedValuesContainer methods.
double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const
	get value of a state in a position More...

double	operator() (size_t siteIndex, const std::string &sequenceName, int state) const

OrderedValuesContainer methods.
double	getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const

double	operator() (size_t siteIndex, size_t sequenceIndex, int state) const

From the OrderedSequenceContainer interface
virtual std::string	toString (size_t sequenceIndex) const

virtual const Comments &	getComments (size_t sequenceIndex) const

virtual const std::string &	getName (size_t sequenceIndex) const
	Get the name of a particular row of the alignement (aka sequence). More...

SequenceContainer methods.
virtual std::string	toString (size_t sequenceIndex) const=0

virtual const Comments &	getComments (size_t sequenceIndex) const=0

virtual const Sequence &	getSequence (const std::string &name) const=0
	Retrieve a sequence object from the container. More...

virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...

virtual std::shared_ptr< Sequence >	removeSequence (const std::string &name)=0
	Extract (and remove) a sequence from the container. More...

From the SequencedValuesContainer interface
const Alphabet *	getAlphabet () const
	Get container's alphabet. More...

const Comments &	getGeneralComments () const
	Get the comments of this container. More...

void	setGeneralComments (const Comments &comments)
	Set the comments of this container. More...

void	deleteGeneralComments ()
	Delete the comments associated to this container. More...

Protected Member Functions
void	realloc (size_t n)

const std::shared_ptr< Site >	getObject (size_t objectIndex) const
	Retrieve an object from the container. Set as protected since they will be public under T specific names. More...

std::shared_ptr< Site >	getObject (size_t objectIndex)

void	addObject (std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false)
	Add an object. More...

void	insertObject (std::shared_ptr< Site > object, size_t objectIndex)
	Insert an object. More...

std::shared_ptr< Site >	removeObject (size_t objectIndex)
	Extract and remove a object from the container. More...

void	deleteObject (size_t objectIndex)
	Delete an object from the container. More...

void	deleteObjects (size_t objectIndex, size_t length)

void	appendObject (std::shared_ptr< Site > object)

std::shared_ptr< Site >	getObject_ (size_t objectIndex) const

void	addObject_ (std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false) const

size_t	getNumberOfObjects () const

size_t	getObjectPosition (const std::string &name) const
	Link between position & name. More...

std::string	getObjectName (size_t objectIndex) const

const std::shared_ptr< Sequence >	getObject (size_t objectIndex) const
	Retrieve an object from the container. Set as protected since they will be public under T specific names. More...

std::shared_ptr< Sequence >	getObject (size_t objectIndex)

const std::shared_ptr< Sequence >	getObject (const std::string &name) const
	Get a object. More...

std::shared_ptr< Sequence >	getObject (const std::string &name)

bool	hasObject (const std::string &name) const
	Check if a object with a given name is present in the container. More...

std::vector< std::string >	getObjectNames () const

void	setObjectNames (const std::vector< std::string > &names)

void	setObjectName (size_t pos, const std::string &name)

void	addObject (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false)

virtual void	addObject (std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0

void	addObject (std::shared_ptr< T > object, const std::string &name, bool checkName=false)
	Set a object. More...

void	addObject (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false)
	Add an object. More...

void	insertObject (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name)

virtual void	insertObject (std::shared_ptr< T > object, size_t objectIndex, const std::string &name)=0

void	insertObject (std::shared_ptr< T > object, size_t objectIndex)
	Insert an object. More...

void	appendObject (std::shared_ptr< Sequence > object, const std::string &name, bool check=true)

void	appendObject (std::shared_ptr< T > object)

std::shared_ptr< Sequence >	removeObject (size_t objectIndex)
	Extract and remove a object from the container. More...

std::shared_ptr< Sequence >	removeObject (const std::string &name)
	Remove and returns a object. More...

void	deleteObject (size_t objectIndex)
	Delete an object from the container. More...

void	deleteObject (const std::string &name)
	Remove a object. More...

void	addObject_ (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false) const

void	addObject_ (std::shared_ptr< T > object, const std::string &name, bool checkName=false) const

void	addObject_ (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) const

void	deleteObjects (size_t objectIndex, size_t length)

std::shared_ptr< T >	getObject_ (size_t objectIndex) const

Protected Attributes
const Alphabet *	alphabet_
	The container's alphabet. More...

Comments	comments_

std::vector< std::shared_ptr< Site > >	positions_

std::vector< std::shared_ptr< T > >	positions_

Private Attributes
std::vector< std::string >	vNames_

std::map< std::string, size_t >	mNames_

std::map< std::string, std::shared_ptr< T > >	mObjects_

Detailed Description

The VectorSiteContainer class.

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

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

See VectorSequenceContainer for an alternative implementation.

See also: Sequence, Site, AlignedSequenceContainer

Definition at line 75 of file VectorSiteContainer.h.

Constructor & Destructor Documentation

◆ VectorSiteContainer() [1/10]

VectorSiteContainer::VectorSiteContainer	(	const std::vector< const CruxSymbolListSite * > &	vs,
		const Alphabet *	alpha,
		bool	checkPositions = `true`
	)

Build a new container from a set of sites.

Parameters

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

Exceptions

Exception If sites differ in size or in alphabet.

Class constructors:

Definition at line 53 of file VectorSiteContainer.cpp.

References addSite(), and bpp::TextTools::toString().

Referenced by clone(), and createEmptyContainer().

◆ VectorSiteContainer() [2/10]

VectorSiteContainer::VectorSiteContainer	(	const std::vector< const Site * > &	vs,
		const Alphabet *	alpha,
		bool	checkPositions = `true`
	)

Definition at line 81 of file VectorSiteContainer.cpp.

References addSite(), and bpp::TextTools::toString().

◆ VectorSiteContainer() [3/10]

VectorSiteContainer::VectorSiteContainer	(	size_t	size,
		const Alphabet *	alpha
	)

Build a new empty container with specified size.

Parameters

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

Definition at line 108 of file VectorSiteContainer.cpp.

References bpp::TextTools::toString().

◆ VectorSiteContainer() [4/10]

VectorSiteContainer::VectorSiteContainer	(	const std::vector< std::string > &	names,
		const Alphabet *	alpha
	)

Build a new empty container with specified sequence names.

Parameters

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

Definition at line 121 of file VectorSiteContainer.cpp.

References bpp::VectorMappedContainer< T >::appendObject().

◆ VectorSiteContainer() [5/10]

VectorSiteContainer::VectorSiteContainer ( const Alphabet * alpha )

Build a new empty container.

Parameters

alpha The alphabet for this container.

Definition at line 134 of file VectorSiteContainer.cpp.

◆ VectorSiteContainer() [6/10]

VectorSiteContainer::VectorSiteContainer ( const VectorSiteContainer & vsc )

Definition at line 142 of file VectorSiteContainer.cpp.

References addSite(), getNumberOfSites(), and getSite().

◆ VectorSiteContainer() [7/10]

VectorSiteContainer::VectorSiteContainer ( const SiteContainer & sc )

Definition at line 155 of file VectorSiteContainer.cpp.

References addSite(), bpp::VectorMappedContainer< T >::appendObject(), bpp::AlignedValuesContainer::getNumberOfSites(), bpp::SequencedValuesContainer::getSequenceNames(), and bpp::SiteContainer::getSite().

◆ VectorSiteContainer() [8/10]

VectorSiteContainer::VectorSiteContainer ( const OrderedSequenceContainer & osc )

Definition at line 170 of file VectorSiteContainer.cpp.

References addSequence(), bpp::SequencedValuesContainer::getNumberOfSequences(), bpp::OrderedSequenceContainer::getSequence(), and reindexSites().

◆ VectorSiteContainer() [9/10]

VectorSiteContainer::VectorSiteContainer ( const SequenceContainer & sc )

Definition at line 183 of file VectorSiteContainer.cpp.

References addSequence(), bpp::SequenceContainer::getSequence(), bpp::SequencedValuesContainer::getSequenceNames(), and reindexSites().

◆ VectorSiteContainer() [10/10]

VectorSiteContainer::VectorSiteContainer ( const AlignedValuesContainer & avc )

Definition at line 196 of file VectorSiteContainer.cpp.

References addSite(), bpp::OrderedValuesContainer::getName(), bpp::SequencedValuesContainer::getNumberOfSequences(), bpp::AlignedValuesContainer::getNumberOfSites(), bpp::AlignedValuesContainer::getSymbolListSite(), and bpp::TextTools::toString().

◆ ~VectorSiteContainer()

virtual bpp::VectorSiteContainer::~VectorSiteContainer ( )

inlinevirtual

Definition at line 131 of file VectorSiteContainer.h.

References clear().

Member Function Documentation

◆ addObject() [1/5]

void bpp::VectorMappedContainer< Sequence >::addObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name,
		bool	check = `false`
	)

inlineprotectedinherited

Definition at line 226 of file VectorMappedContainer.h.

◆ addObject() [2/5]

void bpp::VectorPositionedContainer< Site >::addObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		bool	checkPosition = `false`
	)

inlineprotectedinherited

Add an object.

Parameters

object	The object to add.
objectIndex	The new position of the object
checkPosition	Look if the position is empty.

Definition at line 192 of file VectorPositionedContainer.h.

◆ addObject() [3/5]

template<class T >

void bpp::MappedNamedContainer< T >::addObject	(	std::shared_ptr< T >	object,
		const std::string &	name,
		bool	checkName = `false`
	)

inlineprotectedinherited

Set a object.

Parameters

name	The key of the object.
object	The new object that will be associated to the key.
checkName	Tell is the object name must be checked.

Definition at line 140 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), and bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::VectorMappedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::appendObject(), and bpp::VectorMappedContainer< T >::insertObject().

◆ addObject() [4/5]

template<class T >

void bpp::VectorPositionedContainer< T >::addObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		bool	checkPosition = `false`
	)

inlineprotectedinherited

Add an object.

Parameters

object	The object to add.
objectIndex	The new position of the object
checkPosition	Look if the position is empty.

Definition at line 192 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::addObject(), bpp::AlignedSequenceContainer::getSite(), bpp::CompressedVectorSiteContainer::setSite(), and setSite().

◆ addObject() [5/5]

template<class T >

virtual void bpp::PositionedNamedContainer< T >::addObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name,
		bool	check = `false`
	)

protectedpure virtualinherited

Implemented in bpp::VectorMappedContainer< T >.

◆ addObject_() [1/4]

void bpp::VectorMappedContainer< Sequence >::addObject_	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name,
		bool	check = `false`
	)		const

inlineprotectedinherited

Definition at line 298 of file VectorMappedContainer.h.

◆ addObject_() [2/4]

void bpp::VectorPositionedContainer< Site >::addObject_	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		bool	checkPosition = `false`
	)		const

inlineprotectedinherited

Definition at line 258 of file VectorPositionedContainer.h.

◆ addObject_() [3/4]

template<class T >

void bpp::MappedNamedContainer< T >::addObject_	(	std::shared_ptr< T >	object,
		const std::string &	name,
		bool	checkName = `false`
	)		const

inlineprotectedinherited

Definition at line 234 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), and bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::VectorMappedContainer< T >::addObject_().

◆ addObject_() [4/4]

template<class T >

void bpp::VectorPositionedContainer< T >::addObject_	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		bool	checkPosition = `false`
	)		const

inlineprotectedinherited

Definition at line 258 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::addObject_(), and bpp::AlignedSequenceContainer::getSite().

◆ addSequence() [1/2]

void VectorSiteContainer::addSequence	(	const Sequence &	sequence,
		bool	checkName = `true`
	)

virtual

Add a sequence to the container.

Parameters

sequence	The sequence to add.
checkName	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Exceptions

Exception Any other kind of exception, if the name of the sequence is already used, are whatever else depending on the implementation.

Implements bpp::SequenceContainer.

Definition at line 633 of file VectorSiteContainer.cpp.

References bpp::Site::addElement(), bpp::VectorMappedContainer< T >::appendObject(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::CoreSequence::getComments(), bpp::CoreSequence::getName(), getNumberOfSequences(), getNumberOfSites(), getSite(), bpp::CoreSymbolList< T >::getValue(), realloc(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

Referenced by bpp::SequenceApplicationTools::getSiteContainer(), operator=(), and VectorSiteContainer().

◆ addSequence() [2/2]

void VectorSiteContainer::addSequence	(	const Sequence &	sequence,
		size_t	sequenceIndex,
		bool	checkName = `true`
	)

Definition at line 661 of file VectorSiteContainer.cpp.

References bpp::Site::addElement(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::CoreSequence::getComments(), bpp::CoreSequence::getName(), getNumberOfSequences(), getNumberOfSites(), getSite(), bpp::CoreSymbolList< T >::getValue(), bpp::VectorMappedContainer< T >::insertObject(), and bpp::CruxSymbolList::size().

◆ addSite() [1/4]

void VectorSiteContainer::addSite	(	const Site &	site,
		bool	checkPosition = `true`
	)

virtual

Add a site in the container.

Parameters

site	The site to add.
checkPosition	Look if the position of the new site match a position attribute in the container.

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 320 of file VectorSiteContainer.cpp.

References bpp::VectorPositionedContainer< T >::appendObject(), bpp::Site::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::OrderedSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), bpp::AbstractCoreSite::getPosition(), getSite(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

Referenced by bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), operator=(), realloc(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SiteContainerTools::sampleSites(), and VectorSiteContainer().

◆ addSite() [2/4]

void VectorSiteContainer::addSite	(	const Site &	site,
		int	position,
		bool	checkPosition = `true`
	)

virtual

Add a site in the container.

Parameters

site	The site to add.
position	The new position of the site, to superseed the one in 'site'.
checkPosition	Look if the position of the new site match a position attribute in the container.

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 361 of file VectorSiteContainer.cpp.

References bpp::VectorPositionedContainer< T >::appendObject(), bpp::Site::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), getNumberOfSequences(), getNumberOfSites(), bpp::AbstractCoreSite::getPosition(), getSite(), bpp::VectorPositionedContainer< T >::nullify(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

◆ addSite() [3/4]

void VectorSiteContainer::addSite	(	const Site &	site,
		size_t	siteIndex,
		bool	checkPosition = `true`
	)

virtual

Add a site in the container.

Parameters

site	The site to add.
siteIndex	The position where to insert the site.
checkPosition	Look if the position of the new site match a position attribute in the container.

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 395 of file VectorSiteContainer.cpp.

References bpp::Site::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::OrderedSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), bpp::AbstractCoreSite::getPosition(), getSite(), bpp::VectorPositionedContainer< T >::insertObject(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

◆ addSite() [4/4]

void VectorSiteContainer::addSite	(	const Site &	site,
		size_t	siteIndex,
		int	position,
		bool	checkPosition = `true`
	)

virtual

Add a site in the container.

Parameters

site	The site to add.
siteIndex	The position where to insert the site.
position	The new position of the site, to superseed the one in 'site'.
checkPosition	Look if the position of the new site match a position attribute in the container.

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 437 of file VectorSiteContainer.cpp.

References bpp::Site::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::OrderedSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), bpp::AbstractCoreSite::getPosition(), getSite(), bpp::VectorPositionedContainer< T >::insertObject(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

◆ appendObject() [1/3]

void bpp::VectorMappedContainer< Sequence >::appendObject	(	std::shared_ptr< T >	object,
		const std::string &	name,
		bool	check = `true`
	)

inlineprotectedinherited

Definition at line 250 of file VectorMappedContainer.h.

◆ appendObject() [2/3]

void bpp::VectorPositionedContainer< Site >::appendObject ( std::shared_ptr< T > object )

inlineprotectedinherited

Definition at line 246 of file VectorPositionedContainer.h.

◆ appendObject() [3/3]

template<class T >

void bpp::VectorPositionedContainer< T >::appendObject ( std::shared_ptr< T > object )

inlineprotectedinherited

Definition at line 246 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), addSite(), bpp::VectorProbabilisticSiteContainer::addSite(), bpp::VectorMappedContainer< T >::appendObject(), and bpp::CompressedVectorSiteContainer::setSite().

◆ changeName()

template<class T >

void bpp::MappedNamedContainer< T >::changeName	(	const std::string &	okey,
		const std::string &	nkey
	)

inlineinherited

change the key of an object.

Parameters

okey	The present key of the object.
nkey	The next key of the object.

Definition at line 199 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), and bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::VectorMappedContainer< T >::setObjectName(), bpp::VectorMappedContainer< T >::setObjectNames(), bpp::VectorProbabilisticSiteContainer::setSequence(), and setSequence().

◆ clear()

void VectorSiteContainer::clear ( )

virtual

Delete all objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 688 of file VectorSiteContainer.cpp.

References bpp::VectorMappedContainer< T >::clear(), and bpp::VectorPositionedContainer< T >::clear().

Referenced by operator=(), realloc(), and ~VectorSiteContainer().

◆ clearComments()

void bpp::Commentable::clearComments ( )

inlineinherited

Definition at line 102 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::BasicProbabilisticSequence::clearComments(), bpp::BasicSequence::clearComments(), bpp::SequenceWithAnnotation::clearComments(), bpp::SequenceWithQuality::clearComments(), bpp::AbstractProbabilisticSequenceContainer::deleteGeneralComments(), and bpp::AbstractValuesContainer::deleteGeneralComments().

◆ clone()

VectorSiteContainer* bpp::VectorSiteContainer::clone ( ) const

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 139 of file VectorSiteContainer.h.

References VectorSiteContainer().

◆ createEmptyContainer()

VectorSiteContainer * VectorSiteContainer::createEmptyContainer ( ) const

virtual

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

This method creates a new SequencedValuesContainer objet. The class of this container depends on the derivative class.

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

Implements bpp::SequencedValuesContainer.

Definition at line 716 of file VectorSiteContainer.cpp.

References bpp::AbstractValuesContainer::getAlphabet(), bpp::AbstractValuesContainer::getGeneralComments(), bpp::AbstractValuesContainer::setGeneralComments(), and VectorSiteContainer().

◆ deleteGeneralComments() [1/2]

void bpp::AbstractValuesContainer::deleteGeneralComments ( )

inlinevirtualinherited

Delete the comments associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 115 of file AbstractValuesContainer.h.

References bpp::Commentable::clearComments().

◆ deleteGeneralComments() [2/2]

virtual void bpp::SequencedValuesContainer::deleteGeneralComments ( )

pure virtualinherited

Delete the comments associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ deleteObject() [1/3]

void bpp::VectorMappedContainer< Sequence >::deleteObject ( const std::string & name )

inlineprotectedvirtualinherited

Remove a object.

Parameters

name	The key of the object.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 293 of file VectorMappedContainer.h.

◆ deleteObject() [2/3]

void bpp::VectorMappedContainer< Sequence >::deleteObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Delete an object from the container.

Parameters

objectIndex The index of the object in the container.

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 273 of file VectorMappedContainer.h.

◆ deleteObject() [3/3]

void bpp::VectorPositionedContainer< Site >::deleteObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Delete an object from the container.

Parameters

objectIndex The index of the object in the container.

Implements bpp::PositionedContainer< T >.

Definition at line 230 of file VectorPositionedContainer.h.

◆ deleteObjects() [1/2]

void bpp::VectorPositionedContainer< Site >::deleteObjects	(	size_t	objectIndex,
		size_t	length
	)

inlineprotectedinherited

Definition at line 238 of file VectorPositionedContainer.h.

◆ deleteObjects() [2/2]

template<class T >

void bpp::VectorPositionedContainer< T >::deleteObjects	(	size_t	objectIndex,
		size_t	length
	)

inlineprotectedinherited

Definition at line 238 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::AlignedSequenceContainer::deleteSites(), bpp::VectorProbabilisticSiteContainer::deleteSites(), and deleteSites().

◆ deleteSite()

void bpp::VectorSiteContainer::deleteSite ( size_t siteIndex )

inlinevirtual

Delete a site from the container.

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

Parameters

siteIndex The position of the site in the container.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 174 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::deleteObject().

◆ deleteSites()

void bpp::VectorSiteContainer::deleteSites	(	size_t	siteIndex,
		size_t	length
	)

inlinevirtual

Remove a continuous range of sites in the container.

Parameters

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

Exceptions

IndexOutOfBoundsException If the specified range is not valid.

Implements bpp::AlignedValuesContainer.

Definition at line 191 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::deleteObjects().

◆ getAlphabet() [1/2]

const Alphabet* bpp::AbstractValuesContainer::getAlphabet ( ) const

inlinevirtualinherited

Get container's alphabet.

Returns: The alphabet associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 99 of file AbstractValuesContainer.h.

References bpp::AbstractValuesContainer::alphabet_.

◆ getAlphabet() [2/2]

virtual const Alphabet* bpp::SequencedValuesContainer::getAlphabet ( ) const

pure virtualinherited

Get container's alphabet.

Returns: The alphabet associated to this container.

Implemented in bpp::AbstractValuesContainer.

◆ getComments() [1/4]

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

inlineinherited

Get the comments.

Returns: The comments.

Definition at line 93 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::AbstractCoreSequence::getComments(), bpp::SequenceWithAnnotation::getComments(), bpp::SequenceWithQuality::getComments(), bpp::AbstractProbabilisticSequenceContainer::getGeneralComments(), bpp::AbstractValuesContainer::getGeneralComments(), and bpp::VectorProbabilisticSiteContainer::getSequence().

◆ getComments() [2/4]

const Comments& bpp::AbstractSequenceContainer::getComments ( const std::string & name ) const

inlinevirtualinherited

Get comments of a particular sequence.

Parameters

name	The name of the sequence.

Returns: The comments associated to sequence with name 'name'.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::SequencedValuesContainer.

Definition at line 111 of file AbstractSequenceContainer.h.

References bpp::CoreSequence::getComments(), and bpp::OrderedSequenceContainer::getSequence().

◆ getComments() [3/4]

virtual const Comments& bpp::AbstractSequenceContainer::getComments ( size_t sequenceIndex ) const

inlinevirtualinherited

Implements bpp::AbstractValuesContainer.

Definition at line 137 of file AbstractSequenceContainer.h.

References bpp::CoreSequence::getComments(), and bpp::OrderedSequenceContainer::getSequence().

◆ getComments() [4/4]

virtual const Comments& bpp::OrderedValuesContainer::getComments

inherited

Referenced by bpp::CompressedVectorSiteContainer::addSite(), addSite(), getSequence(), bpp::CompressedVectorSiteContainer::removeSite(), setSequence(), bpp::CompressedVectorSiteContainer::setSite(), and setSite().

◆ getGeneralComments() [1/2]

const Comments& bpp::AbstractValuesContainer::getGeneralComments ( ) const

inlinevirtualinherited

Get the comments of this container.

Returns: The comments associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 101 of file AbstractValuesContainer.h.

References bpp::Commentable::getComments().

Referenced by bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::VectorProbabilisticSequenceContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), and createEmptyContainer().

◆ getGeneralComments() [2/2]

virtual const Comments& bpp::SequencedValuesContainer::getGeneralComments ( ) const

pure virtualinherited

Get the comments of this container.

Returns: The comments associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::Mase::appendSequencesFromStream(), bpp::MaseTools::getSelectedSequences(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSelectedSites(), bpp::AbstractSequenceContainer::operator=(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

◆ getName()

virtual const std::string& bpp::AbstractSequenceContainer::getName ( size_t sequenceIndex ) const

inlinevirtualinherited

Get the name of a particular row of the alignement (aka sequence).

Parameters

sequenceIndex The position of the sequence.

Returns: The name of the sequence at position 'sequenceIndex'.

Exceptions

IndexOutOfBoundsException If the position does not match any sequence in the container.

Implements bpp::OrderedValuesContainer.

Definition at line 127 of file AbstractSequenceContainer.h.

References bpp::CoreSequence::getName(), and bpp::OrderedSequenceContainer::getSequence().

Referenced by bpp::VectorSequenceContainer::getSequenceNames(), and bpp::VectorSequenceContainer::hasSequenceByName().

◆ getNumberOfObjects()

size_t bpp::VectorMappedContainer< Sequence >::getNumberOfObjects ( ) const

inlineprotectedinherited

Definition at line 144 of file VectorMappedContainer.h.

◆ getNumberOfSequences()

size_t bpp::VectorSiteContainer::getNumberOfSequences ( ) const

inlinevirtual

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implements bpp::SequencedValuesContainer.

Definition at line 255 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getNumberOfObjects().

Referenced by addSequence(), addSite(), getSequence(), bpp::SequenceApplicationTools::getSiteContainer(), getStateValueAt(), setSequence(), setSite(), and valueAt().

◆ getNumberOfSites()

size_t bpp::VectorSiteContainer::getNumberOfSites ( ) const

inlinevirtual

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

Implements bpp::AlignedValuesContainer.

Definition at line 196 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::getSize().

Referenced by addSequence(), addSite(), bpp::SequenceApplicationTools::getAlignedContainer(), getSequence(), bpp::SequenceApplicationTools::getSiteContainer(), getSitePositions(), getStateValueAt(), operator=(), reindexSites(), removeSequence(), setSequence(), setSite(), setSitePositions(), valueAt(), and VectorSiteContainer().

◆ getObject() [1/6]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( const std::string & name )

inlineprotectedvirtualinherited

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 188 of file VectorMappedContainer.h.

◆ getObject() [2/6]

const std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( const std::string & name ) const

inlineprotectedvirtualinherited

Get a object.

Parameters

name	The key of the object to retrieve.

Returns: The object associated to the given key.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 183 of file VectorMappedContainer.h.

◆ getObject() [3/6]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 172 of file VectorMappedContainer.h.

◆ getObject() [4/6]

std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::getObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Implements bpp::PositionedContainer< T >.

Definition at line 177 of file VectorPositionedContainer.h.

◆ getObject() [5/6]

const std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( size_t objectIndex ) const

inlineprotectedvirtualinherited

Retrieve an object from the container. Set as protected since they will be public under T specific names.

Parameters

objectIndex The position of the object.

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

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 167 of file VectorMappedContainer.h.

◆ getObject() [6/6]

const std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::getObject ( size_t objectIndex ) const

inlineprotectedvirtualinherited

Retrieve an object from the container. Set as protected since they will be public under T specific names.

Parameters

objectIndex The position of the object.

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

Implements bpp::PositionedContainer< T >.

Definition at line 170 of file VectorPositionedContainer.h.

◆ getObject_() [1/2]

std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::getObject_ ( size_t objectIndex ) const

inlineprotectedinherited

Definition at line 251 of file VectorPositionedContainer.h.

◆ getObject_() [2/2]

template<class T >

std::shared_ptr<T> bpp::VectorPositionedContainer< T >::getObject_ ( size_t objectIndex ) const

inlineprotectedinherited

Definition at line 251 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

◆ getObjectName()

std::string bpp::VectorMappedContainer< Sequence >::getObjectName ( size_t objectIndex ) const

inlineprotectedvirtualinherited

Implements bpp::PositionedNamedContainer< T >.

Definition at line 158 of file VectorMappedContainer.h.

◆ getObjectNames()

std::vector<std::string> bpp::VectorMappedContainer< Sequence >::getObjectNames ( ) const

inlineprotectedvirtualinherited

Returns: All objects keys.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 198 of file VectorMappedContainer.h.

◆ getObjectPosition()

size_t bpp::VectorMappedContainer< Sequence >::getObjectPosition ( const std::string & name ) const

inlineprotectedvirtualinherited

Link between position & name.

Implements bpp::PositionedNamedContainer< T >.

Definition at line 149 of file VectorMappedContainer.h.

◆ getSequence() [1/3]

const Sequence & VectorSiteContainer::getSequence ( const std::string & name ) const

virtual

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns: A reference toward the Sequence with corresponding name.

Implements bpp::SequenceContainer.

Definition at line 547 of file VectorSiteContainer.cpp.

References bpp::OrderedSequenceContainer::getSequence(), and getSequencePosition().

◆ getSequence() [2/3]

virtual const Sequence& bpp::SequenceContainer::getSequence

inherited

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns: A reference toward the Sequence with corresponding name.

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::VectorSequenceContainer::deleteSequenceByName(), bpp::AbstractSequenceContainer::getComments(), bpp::AbstractSequenceContainer::getName(), bpp::CompressedVectorSiteContainer::getSequence(), getSequence(), bpp::VectorSequenceContainer::getSequenceByName(), bpp::VectorSequenceContainer::getSequenceNames(), bpp::AlignedSequenceContainer::getSite(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::hasSequenceByName(), bpp::VectorSequenceContainer::operator()(), removeSequence(), bpp::VectorSequenceContainer::removeSequenceByName(), bpp::AbstractSequenceContainer::toString(), and bpp::VectorSequenceContainer::valueAt().

◆ getSequence() [3/3]

const Sequence & VectorSiteContainer::getSequence ( size_t sequenceIndex ) const

virtual

Retrieve a sequence object from the container.

Parameters

sequenceIndex The position of the sequence.

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

Implements bpp::OrderedSequenceContainer.

Definition at line 518 of file VectorSiteContainer.cpp.

References bpp::VectorMappedContainer< T >::addObject_(), bpp::AbstractValuesContainer::getAlphabet(), bpp::OrderedSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), bpp::VectorMappedContainer< T >::getObject(), bpp::VectorMappedContainer< T >::getObjectName(), getSite(), and bpp::MappedNamedContainer< T >::isAvailableName().

Referenced by bpp::SequenceApplicationTools::getAlignedContainer(), and bpp::SequenceApplicationTools::getSiteContainer().

◆ getSequenceNames()

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

inlinevirtual

Get all the names of the sequences in the container.

Returns: A vector of strings with all sequence names.

Implements bpp::SequencedValuesContainer.

Definition at line 260 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getObjectNames().

Referenced by bpp::SequenceApplicationTools::getAlignedContainer().

◆ getSequencePosition()

size_t bpp::VectorSiteContainer::getSequencePosition ( const std::string & name ) const

inlinevirtual

Get the position of a sequence in sequence container from its name.

Parameters

name	The name of the sequence.

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

Exceptions

SequenceNotFoundException If no sequence with name 'name' could be found.

Implements bpp::OrderedValuesContainer.

Definition at line 245 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::getObjectPosition().

Referenced by getSequence(), operator()(), removeSequence(), setSequence(), and valueAt().

◆ getSite() [1/2]

Site& bpp::VectorSiteContainer::getSite ( size_t siteIndex )

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 157 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::getObject().

◆ getSite() [2/2]

const Site& bpp::VectorSiteContainer::getSite ( size_t siteIndex ) const

inlinevirtual

Get a site from the container.

Parameters

siteIndex The position of the site in the container.

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

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 147 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::getObject().

Referenced by addSequence(), addSite(), bpp::SiteContainerTools::getCompleteSites(), getSequence(), getSitePositions(), bpp::SiteContainerTools::getSitesWithoutGaps(), getSymbolListSite(), operator=(), reindexSites(), removeSequence(), bpp::SiteContainerTools::sampleSites(), setSequence(), setSite(), setSitePositions(), and VectorSiteContainer().

◆ getSitePositions()

Vint VectorSiteContainer::getSitePositions ( ) const

virtual

Get all position attributes of sites.

Returns: A vector with all site positions.

Implements bpp::AlignedValuesContainer.

Definition at line 493 of file VectorSiteContainer.cpp.

References getNumberOfSites(), bpp::AbstractCoreSite::getPosition(), and getSite().

◆ getSize() [1/2]

size_t bpp::VectorMappedContainer< Sequence >::getSize ( ) const

inlinevirtualinherited

Get the number of objects in the container.

Returns: The number of objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 133 of file VectorMappedContainer.h.

◆ getSize() [2/2]

size_t bpp::VectorPositionedContainer< Site >::getSize ( ) const

inlinevirtualinherited

the size

Implements bpp::PositionedContainer< T >.

Definition at line 129 of file VectorPositionedContainer.h.

◆ getStateValueAt() [1/3]

double bpp::VectorSiteContainer::getStateValueAt	(	size_t	siteIndex,
		const std::string &	sequenceName,
		int	state
	)		const

inlinevirtual

get value of a state in a position

Parameters

siteIndex	index of the site
sequenceName	name of the sequence in the container
state	state in the alphabet

Implements bpp::SequencedValuesContainer.

Definition at line 324 of file VectorSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSites(), bpp::Alphabet::isResolvedIn(), and valueAt().

◆ getStateValueAt() [2/3]

virtual double bpp::SequencedValuesContainer::getStateValueAt

inherited

get value of a state in a position

Parameters

siteIndex	index of the site
sequenceName	name of the sequence in the container
state	state in the alphabet

◆ getStateValueAt() [3/3]

double bpp::VectorSiteContainer::getStateValueAt	(	size_t	siteIndex,
		size_t	sequenceIndex,
		int	state
	)		const

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 354 of file VectorSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSequences(), getNumberOfSites(), bpp::Alphabet::isResolvedIn(), and valueAt().

◆ getSymbolListSite() [1/2]

CruxSymbolListSite& bpp::VectorSiteContainer::getSymbolListSite ( size_t siteIndex )

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 162 of file VectorSiteContainer.h.

References getSite().

◆ getSymbolListSite() [2/2]

const CruxSymbolListSite& bpp::VectorSiteContainer::getSymbolListSite ( size_t siteIndex ) const

inlinevirtual

Get a CruxSymbolListSite from a given position.

Parameters

siteIndex The position

Implements bpp::SiteContainer.

Definition at line 152 of file VectorSiteContainer.h.

References getSite().

◆ hasObject()

bool bpp::VectorMappedContainer< Sequence >::hasObject ( const std::string & name ) const

inlineprotectedvirtualinherited

Check if a object with a given name is present in the container.

Parameters

name	The name of the object.

Returns: True if a object with the given name is present in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 193 of file VectorMappedContainer.h.

◆ hasSequence()

bool bpp::VectorSiteContainer::hasSequence ( const std::string & name ) const

inlinevirtual

Check if a sequence with a given name is present in the container.

Parameters

name	The name of the sequence.

Returns: True if a sequence with the given name is present in the container.

Implements bpp::SequencedValuesContainer.

Definition at line 235 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::hasObject().

◆ insertObject() [1/4]

void bpp::VectorMappedContainer< Sequence >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name
	)

inlineprotectedinherited

Definition at line 235 of file VectorMappedContainer.h.

◆ insertObject() [2/4]

void bpp::VectorPositionedContainer< Site >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex
	)

inlineprotectedinherited

Insert an object.

Parameters

object	The object to add.
objectIndex	The new position of the object

Definition at line 209 of file VectorPositionedContainer.h.

◆ insertObject() [3/4]

template<class T >

void bpp::VectorPositionedContainer< T >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex
	)

inlineprotectedinherited

Insert an object.

Parameters

object	The object to add.
objectIndex	The new position of the object

Definition at line 209 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::AlignedSequenceContainer::addSite(), addSite(), and bpp::VectorMappedContainer< T >::insertObject().

◆ insertObject() [4/4]

template<class T >

virtual void bpp::PositionedNamedContainer< T >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name
	)

protectedpure virtualinherited

Implemented in bpp::VectorMappedContainer< T >.

◆ isAvailableName()

template<class T >

bool bpp::MappedNamedContainer< T >::isAvailableName ( std::string objectName ) const

inlineinherited

Return if the name is in the map keys and the mapped object is nullptr or empty.

Definition at line 228 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::getObject(), and bpp::MappedNamedContainer< T >::hasObject().

Referenced by bpp::CompressedVectorSiteContainer::getSequence(), getSequence(), and bpp::VectorProbabilisticSiteContainer::getSequence().

◆ isAvailablePosition() [1/2]

bool bpp::VectorPositionedContainer< Site >::isAvailablePosition ( size_t objectIndex ) const

inlineinherited

Definition at line 134 of file VectorPositionedContainer.h.

◆ isAvailablePosition() [2/2]

template<class T >

bool bpp::VectorPositionedContainer< T >::isAvailablePosition ( size_t objectIndex ) const

inlineinherited

Definition at line 134 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

◆ nullify() [1/2]

void bpp::VectorPositionedContainer< Site >::nullify ( )

inlineinherited

Nullify all elements.

Definition at line 163 of file VectorPositionedContainer.h.

◆ nullify() [2/2]

template<class T >

void bpp::VectorPositionedContainer< T >::nullify ( )

inlineinherited

Nullify all elements.

Definition at line 163 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::AlignedSequenceContainer::addSequence(), addSite(), bpp::VectorProbabilisticSiteContainer::addSite(), and bpp::AlignedSequenceContainer::setSequence().

◆ operator()() [1/6]

int& bpp::VectorSiteContainer::operator()	(	const std::string &	sequenceName,
		size_t	elementIndex
	)

inlinevirtual

Element access operator.

Allows direct access to the data stored in the container. This method is faster then the valueAt function, but input parameters are not checked!

Parameters

sequenceName	The sequence name.
elementIndex	The element position within the sequence.

Implements bpp::SequenceContainer.

Definition at line 286 of file VectorSiteContainer.h.

References getSequencePosition().

◆ operator()() [2/6]

const int& bpp::VectorSiteContainer::operator()	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const

inlinevirtual

Element access operator.

Allows direct access to the data stored in the container. This method is faster then the valueAt function, but input parameters are not checked!

Parameters

sequenceName	The sequence name.
elementIndex	The element position within the sequence.

Implements bpp::SequenceContainer.

Definition at line 291 of file VectorSiteContainer.h.

References getSequencePosition().

◆ operator()() [3/6]

int& bpp::VectorSiteContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)

inlinevirtual

Element access operator.

Allows direct access to the data stored in the container. This method is faster then the valueAt function, but input parameters are not checked!

Parameters

sequenceIndex	The sequence position.
elementIndex	The element position within the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 310 of file VectorSiteContainer.h.

◆ operator()() [4/6]

const int& bpp::VectorSiteContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const

inlinevirtual

Element access operator.

Allows direct access to the data stored in the container. This method is faster then the valueAt function, but input parameters are not checked!

Parameters

sequenceIndex	The sequence position.
elementIndex	The element position within the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 314 of file VectorSiteContainer.h.

◆ operator()() [5/6]

double bpp::VectorSiteContainer::operator()	(	size_t	siteIndex,
		const std::string &	sequenceName,
		int	state
	)		const

inlinevirtual

Implements bpp::SequencedValuesContainer.

Definition at line 331 of file VectorSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), bpp::Alphabet::isResolvedIn(), and valueAt().

◆ operator()() [6/6]

double bpp::VectorSiteContainer::operator()	(	size_t	siteIndex,
		size_t	sequenceIndex,
		int	state
	)		const

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 362 of file VectorSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), bpp::Alphabet::isResolvedIn(), and valueAt().

◆ operator=() [1/4]

VectorSiteContainer & VectorSiteContainer::operator= ( const OrderedSequenceContainer & osc )

Definition at line 252 of file VectorSiteContainer.cpp.

References addSequence(), clear(), bpp::SequencedValuesContainer::getNumberOfSequences(), bpp::OrderedSequenceContainer::getSequence(), bpp::AbstractSequenceContainer::operator=(), and reindexSites().

◆ operator=() [2/4]

VectorSiteContainer & VectorSiteContainer::operator= ( const SequenceContainer & sc )

Definition at line 268 of file VectorSiteContainer.cpp.

References addSequence(), clear(), bpp::SequenceContainer::getSequence(), bpp::SequencedValuesContainer::getSequenceNames(), bpp::AbstractSequenceContainer::operator=(), and reindexSites().

◆ operator=() [3/4]

VectorSiteContainer & VectorSiteContainer::operator= ( const SiteContainer & sc )

Definition at line 236 of file VectorSiteContainer.cpp.

References addSite(), bpp::VectorMappedContainer< T >::appendObject(), clear(), bpp::AlignedValuesContainer::getNumberOfSites(), bpp::SequencedValuesContainer::getSequenceNames(), bpp::SiteContainer::getSite(), and bpp::AbstractSequenceContainer::operator=().

◆ operator=() [4/4]

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

Definition at line 221 of file VectorSiteContainer.cpp.

References addSite(), clear(), getNumberOfSites(), getSite(), bpp::AbstractSequenceContainer::operator=(), and bpp::VectorMappedContainer< T >::operator=().

◆ realloc()

void VectorSiteContainer::realloc ( size_t n )

protected

Definition at line 696 of file VectorSiteContainer.cpp.

References addSite(), clear(), bpp::AbstractValuesContainer::getAlphabet(), and reindexSites().

Referenced by addSequence(), and setSequence().

◆ reindexSites()

void VectorSiteContainer::reindexSites ( )

virtual

Set all positions attributes.

Implements bpp::AlignedValuesContainer.

Definition at line 483 of file VectorSiteContainer.cpp.

References getNumberOfSites(), getSite(), and bpp::AbstractCoreSite::setPosition().

Referenced by bpp::SequenceApplicationTools::getSiteContainer(), operator=(), realloc(), and VectorSiteContainer().

◆ removeObject() [1/3]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::removeObject ( const std::string & name )

inlineprotectedvirtualinherited

Remove and returns a object.

Parameters

name	The key of the object.

Returns: The object previously associated to the given key.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 288 of file VectorMappedContainer.h.

◆ removeObject() [2/3]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::removeObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Extract and remove a object from the container.

Parameters

objectIndex The position of the object.

Returns: A smart pointer toward the removed object.

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 259 of file VectorMappedContainer.h.

◆ removeObject() [3/3]

std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::removeObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Extract and remove a object from the container.

Parameters

objectIndex The position of the object.

Returns: A smart pointer toward the removed object.

Implements bpp::PositionedContainer< T >.

Definition at line 218 of file VectorPositionedContainer.h.

◆ removeSequence() [1/3]

std::shared_ptr< Sequence > VectorSiteContainer::removeSequence ( const std::string & name )

virtual

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Implements bpp::SequenceContainer.

Definition at line 624 of file VectorSiteContainer.cpp.

References getSequencePosition(), and bpp::OrderedSequenceContainer::removeSequence().

◆ removeSequence() [2/3]

virtual std::shared_ptr<Sequence> bpp::SequenceContainer::removeSequence

inherited

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Referenced by removeSequence(), bpp::VectorSequenceContainer::removeSequenceByKey(), and bpp::VectorSequenceContainer::removeSequenceByName().

◆ removeSequence() [3/3]

std::shared_ptr< Sequence > VectorSiteContainer::removeSequence ( size_t sequenceIndex )

virtual

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex The position of the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 612 of file VectorSiteContainer.cpp.

References bpp::CruxSymbolList::deleteElement(), getNumberOfSites(), bpp::OrderedSequenceContainer::getSequence(), getSite(), and bpp::VectorMappedContainer< T >::removeObject().

◆ removeSite()

std::shared_ptr<Site> bpp::VectorSiteContainer::removeSite ( size_t siteIndex )

inlinevirtual

Remove a site from the container.

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

Parameters

siteIndex 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::SiteContainer.

Definition at line 169 of file VectorSiteContainer.h.

References bpp::VectorPositionedContainer< T >::removeObject().

◆ setComments() [1/4]

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

inlineinherited

Set the comments.

Parameters

comments The new comments.

Definition at line 100 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::AbstractCoreSequence::operator=(), bpp::AbstractCoreSequence::setComments(), bpp::SequenceWithAnnotation::setComments(), bpp::SequenceWithQuality::setComments(), bpp::AbstractProbabilisticSequenceContainer::setGeneralComments(), and bpp::AbstractValuesContainer::setGeneralComments().

◆ setComments() [2/4]

void bpp::AbstractSequenceContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)

inlinevirtualinherited

Set the comments of a particular sequence.

Parameters

name	The name of the sequence.
comments	The comments to set to sequence with name 'name'.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::SequencedValuesContainer.

Definition at line 116 of file AbstractSequenceContainer.h.

References bpp::OrderedValuesContainer::getSequencePosition(), and bpp::OrderedSequenceContainer::setComments().

◆ setComments() [3/4]

void VectorSiteContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)

virtual

Implements bpp::AbstractSequenceContainer.

Definition at line 709 of file VectorSiteContainer.cpp.

References bpp::VectorMappedContainer< T >::getObject().

◆ setComments() [4/4]

virtual void bpp::OrderedValuesContainer::setComments

◆ setGeneralComments() [1/2]

void bpp::AbstractValuesContainer::setGeneralComments ( const Comments & comments )

inlinevirtualinherited

Set the comments of this container.

Parameters

comments The comments to be associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 106 of file AbstractValuesContainer.h.

References bpp::Commentable::setComments().

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::VectorProbabilisticSequenceContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractSequenceContainer::operator=(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

◆ setGeneralComments() [2/2]

virtual void bpp::SequencedValuesContainer::setGeneralComments ( const Comments & comments )

pure virtualinherited

Set the comments of this container.

Parameters

comments The comments to be associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

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

◆ setObjectName()

void bpp::VectorMappedContainer< Sequence >::setObjectName	(	size_t	pos,
		const std::string &	name
	)

inlineprotectedinherited

Definition at line 219 of file VectorMappedContainer.h.

◆ setObjectNames()

void bpp::VectorMappedContainer< Sequence >::setObjectNames ( const std::vector< std::string > & names )

inlineprotectedinherited

Definition at line 203 of file VectorMappedContainer.h.

◆ setSequence() [1/3]

void VectorSiteContainer::setSequence	(	const std::string &	name,
		const Sequence &	sequence,
		bool	checkName
	)

virtual

Replace a sequence in the container.

Parameters

name	The name of the sequence.
sequence	The sequence to add.
checkName	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Implements bpp::SequenceContainer.

Definition at line 556 of file VectorSiteContainer.cpp.

References getSequencePosition(), and bpp::OrderedSequenceContainer::setSequence().

◆ setSequence() [2/3]

virtual void bpp::SequenceContainer::setSequence

inherited

Replace a sequence in the container.

Parameters

name	The name of the sequence.
sequence	The sequence to add.
checkName	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Referenced by setSequence(), bpp::VectorSequenceContainer::setSequence(), and bpp::AlignedSequenceContainer::setSequence().

◆ setSequence() [3/3]

void VectorSiteContainer::setSequence	(	size_t	sequenceIndex,
		const Sequence &	sequence,
		bool	checkName
	)

virtual

Replace a sequence in the container.

Parameters

sequenceIndex	The position of the sequence.
sequence	The sequence to add.
checkName	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Implements bpp::OrderedSequenceContainer.

Definition at line 565 of file VectorSiteContainer.cpp.

References bpp::MappedNamedContainer< T >::changeName(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::OrderedSequenceContainer::getComments(), bpp::CoreSequence::getName(), getNumberOfSequences(), getNumberOfSites(), bpp::VectorMappedContainer< T >::getObject(), bpp::VectorMappedContainer< Sequence >::getObjectName(), getSite(), bpp::CoreSymbolList< T >::getValue(), realloc(), bpp::BasicIntSymbolList::setElement(), and bpp::CruxSymbolList::size().

◆ setSequenceNames()

void bpp::VectorSiteContainer::setSequenceNames	(	const std::vector< std::string > &	names,
		bool	checkNames = `true`
	)

inlinevirtual

Set all sequence names.

Parameters

names	A vector of strings with all sequence names. Its size must be strictly equal to the the size of the container (the number of sequences).
checkNames	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Exceptions

Exception If there are redundant names in the input vector.

Implements bpp::SequencedValuesContainer.

Definition at line 265 of file VectorSiteContainer.h.

References bpp::VectorMappedContainer< T >::setObjectNames().

Referenced by bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), and bpp::SiteContainerTools::resolveDottedAlignment().

◆ setSite()

void VectorSiteContainer::setSite	(	size_t	siteIndex,
		const Site &	site,
		bool	checkPosition = `true`
	)

virtual

Set a site in the container.

Parameters

siteIndex	The position of the site in the container.
site	The site to set.
checkPosition	Look if the position of the new site match a position attribute in the container.

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 283 of file VectorSiteContainer.cpp.

References bpp::VectorPositionedContainer< T >::addObject(), bpp::Site::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::OrderedSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), bpp::AbstractCoreSite::getPosition(), getSite(), and bpp::CruxSymbolList::size().

◆ setSitePositions()

void VectorSiteContainer::setSitePositions ( Vint vPositions )

virtual

Set all position attributes of sites.

Parameters

vPositions A vector with all site positions.

Implements bpp::AlignedValuesContainer.

Definition at line 505 of file VectorSiteContainer.cpp.

References getNumberOfSites(), getSite(), and bpp::AbstractCoreSite::setPosition().

◆ setSize() [1/2]

void bpp::VectorPositionedContainer< Site >::setSize ( size_t size )

inlinevirtualinherited

Reimplemented from bpp::PositionedContainer< T >.

Definition at line 139 of file VectorPositionedContainer.h.

◆ setSize() [2/2]

template<class T >

void bpp::VectorPositionedContainer< T >::setSize ( size_t size )

inlinevirtualinherited

Reimplemented from bpp::PositionedContainer< T >.

Definition at line 139 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::AlignedSequenceContainer::addSequence(), bpp::AlignedSequenceContainer::AlignedSequenceContainer(), and bpp::AlignedSequenceContainer::operator=().

◆ toString() [1/3]

std::string bpp::AbstractSequenceContainer::toString ( const std::string & name ) const

inlinevirtualinherited

Convert a particular sequence to a string.

Parameters

name	The name of the sequence.

Returns: A string describing the content of the sequence.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::SequencedValuesContainer.

Definition at line 106 of file AbstractSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence(), and bpp::CruxSymbolList::toString().

◆ toString() [2/3]

virtual std::string bpp::AbstractSequenceContainer::toString ( size_t sequenceIndex ) const

inlinevirtualinherited

Implements bpp::OrderedValuesContainer.

Definition at line 132 of file AbstractSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence(), and bpp::CruxSymbolList::toString().

◆ toString() [3/3]

virtual std::string bpp::OrderedValuesContainer::toString

inherited

◆ valueAt() [1/4]

int& bpp::VectorSiteContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)

inlinevirtual

Element access function.

Allows direct access to the data stored in the container.

Parameters

sequenceName	The sequence name.
elementIndex	The element position within the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 274 of file VectorSiteContainer.h.

References getNumberOfSites(), and getSequencePosition().

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

◆ valueAt() [2/4]

const int& bpp::VectorSiteContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const

inlinevirtual

Element access function.

Allows direct access to the data stored in the container.

Parameters

sequenceName	The sequence name.
elementIndex	The element position within the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 280 of file VectorSiteContainer.h.

References getNumberOfSites(), and getSequencePosition().

◆ valueAt() [3/4]

int& bpp::VectorSiteContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)

inlinevirtual

Element access operator.

Allows direct access to the data stored in the container.

Parameters

sequenceIndex	The sequence position.
elementIndex	The element position within the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 296 of file VectorSiteContainer.h.

References getNumberOfSequences(), and getNumberOfSites().

◆ valueAt() [4/4]

const int& bpp::VectorSiteContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const

inlinevirtual

Element access operator.

Allows direct access to the data stored in the container.

Parameters

sequenceIndex	The sequence position.
elementIndex	The element position within the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 303 of file VectorSiteContainer.h.

References getNumberOfSequences(), and getNumberOfSites().

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::AbstractValuesContainer::alphabet_

protectedinherited

The container's alphabet.

Definition at line 64 of file AbstractValuesContainer.h.

Referenced by bpp::AbstractValuesContainer::getAlphabet(), bpp::AbstractValuesContainer::operator=(), and bpp::AbstractSequenceContainer::operator=().

◆ comments_

Comments bpp::Commentable::comments_

protectedinherited

Definition at line 63 of file Commentable.h.

Referenced by bpp::Commentable::clearComments(), bpp::Commentable::getComments(), bpp::Commentable::operator=(), and bpp::Commentable::setComments().

◆ mNames_

std::map<std::string, size_t> bpp::VectorMappedContainer< Sequence >::mNames_

privateinherited

Definition at line 86 of file VectorMappedContainer.h.

◆ mObjects_

template<class T >

std::map<std::string, std::shared_ptr<T> > bpp::MappedNamedContainer< T >::mObjects_

privateinherited

Definition at line 69 of file MappedNamedContainer.h.

◆ positions_ [1/2]

std::vector< std::shared_ptr<Site > > bpp::VectorPositionedContainer< Site >::positions_

protectedinherited

Definition at line 73 of file VectorPositionedContainer.h.

◆ positions_ [2/2]

template<class T >

std::vector< std::shared_ptr<T> > bpp::VectorPositionedContainer< T >::positions_

protectedinherited

Definition at line 73 of file VectorPositionedContainer.h.

◆ vNames_

std::vector<std::string> bpp::VectorMappedContainer< Sequence >::vNames_

privateinherited

Definition at line 79 of file VectorMappedContainer.h.

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

Bpp/Seq/Container/VectorSiteContainer.h
Bpp/Seq/Container/VectorSiteContainer.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VectorSiteContainer() [1/10]

◆ VectorSiteContainer() [2/10]

◆ VectorSiteContainer() [3/10]

◆ VectorSiteContainer() [4/10]

◆ VectorSiteContainer() [5/10]

◆ VectorSiteContainer() [6/10]

◆ VectorSiteContainer() [7/10]

◆ VectorSiteContainer() [8/10]

◆ VectorSiteContainer() [9/10]

◆ VectorSiteContainer() [10/10]

◆ ~VectorSiteContainer()

Member Function Documentation

◆ addObject() [1/5]

◆ addObject() [2/5]

◆ addObject() [3/5]

◆ addObject() [4/5]

◆ addObject() [5/5]

◆ addObject_() [1/4]

◆ addObject_() [2/4]

◆ addObject_() [3/4]

◆ addObject_() [4/4]

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ addSite() [1/4]

◆ addSite() [2/4]

◆ addSite() [3/4]

◆ addSite() [4/4]

◆ appendObject() [1/3]

◆ appendObject() [2/3]

◆ appendObject() [3/3]

◆ changeName()

◆ clear()

◆ clearComments()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments() [1/2]

◆ deleteGeneralComments() [2/2]

◆ deleteObject() [1/3]

◆ deleteObject() [2/3]

◆ deleteObject() [3/3]

◆ deleteObjects() [1/2]

◆ deleteObjects() [2/2]

◆ deleteSite()

◆ deleteSites()

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getComments() [1/4]

◆ getComments() [2/4]

◆ getComments() [3/4]

◆ getComments() [4/4]

◆ getGeneralComments() [1/2]

◆ getGeneralComments() [2/2]

◆ getName()

◆ getNumberOfObjects()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getObject() [1/6]

◆ getObject() [2/6]

◆ getObject() [3/6]

◆ getObject() [4/6]

◆ getObject() [5/6]

◆ getObject() [6/6]

◆ getObject_() [1/2]

◆ getObject_() [2/2]

◆ getObjectName()

◆ getObjectNames()

◆ getObjectPosition()

◆ getSequence() [1/3]

◆ getSequence() [2/3]

◆ getSequence() [3/3]

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSite() [1/2]

◆ getSite() [2/2]