The VectorProbabilisticSiteContainer class. More...

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

Inheritance diagram for bpp::VectorProbabilisticSiteContainer:

Collaboration diagram for bpp::VectorProbabilisticSiteContainer:

Public Member Functions
	VectorProbabilisticSiteContainer (const Alphabet *alpha)
	Build a new emtpy container. More...

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

	VectorProbabilisticSiteContainer (const AlignedValuesContainer &avc)
	Build a new container from an AlignedValuesContainer. More...

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

virtual	~VectorProbabilisticSiteContainer ()

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

const std::shared_ptr< ProbabilisticSite >	getSite (size_t i) const
	Get a site from the container. More...

std::shared_ptr< ProbabilisticSite >	getSite (size_t i)

const ProbabilisticSequence &	getSequence (std::size_t i) const
	Get Sequence from a position in the container. More...

const ProbabilisticSequence &	getSequence (const std::string &name) const
	Get Sequence from its name in 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::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	setComments (size_t sequenceIndex, const Comments &comments)

std::string	toString (const std::string &name) const
	Output to string. More...

virtual std::string	toString (const std::string &name) const=0
	Convert a particular sequence to a string. More...

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

virtual const Comments &	getComments (const std::string &name) const=0
	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...

virtual void	setComments (const std::string &name, const Comments &comments)=0
	Set the comments of a particular sequence. More...

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

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

void	clearComments ()

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

CruxSymbolListSite &	getSymbolListSite (size_t siteIndex)

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.
	VectorProbabilisticSiteContainer (const VectorProbabilisticSiteContainer &vpsc)
	Copy contructors. More...

	VectorProbabilisticSiteContainer (const OrderedSequenceContainer &osc)

VectorProbabilisticSiteContainer &	operator= (const VectorProbabilisticSiteContainer &vpsc)

VectorProbabilisticSiteContainer *	clone () const

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

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...

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...

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

Protected Member Functions
const std::shared_ptr< ProbabilisticSite >	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< ProbabilisticSite >	getObject (size_t objectIndex)

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

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

std::shared_ptr< ProbabilisticSite >	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< ProbabilisticSite > object)

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

void	addObject_ (std::shared_ptr< ProbabilisticSite > 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< ProbabilisticSequence >	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< ProbabilisticSequence >	getObject (size_t objectIndex)

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

std::shared_ptr< ProbabilisticSequence >	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< ProbabilisticSequence > 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< ProbabilisticSequence > 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< ProbabilisticSequence > object, const std::string &name, bool check=true)

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

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

std::shared_ptr< ProbabilisticSequence >	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< ProbabilisticSequence > 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< ProbabilisticSite > >	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_

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

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

void	addSite (std::shared_ptr< ProbabilisticSite > site, bool checkPosition=false)
	Add a site at the end of the container. More...

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

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

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

void	setSequence (size_t sequenceIndex, const ProbabilisticSequence &sequence, bool checkName)

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

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

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...

void	realloc (size_t n)

Detailed Description

The VectorProbabilisticSiteContainer class.

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

This is a modified copy of VectorSiteContainer with the minimum changes necessary for it to work with bppML and bppAncestor

See also: ProbabilisticSequence, ProbabilisticSite, VectorSiteContainer

Definition at line 72 of file VectorProbabilisticSiteContainer.h.

Constructor & Destructor Documentation

◆ VectorProbabilisticSiteContainer() [1/6]

VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer ( const Alphabet * alpha )

Build a new emtpy container.

Definition at line 50 of file VectorProbabilisticSiteContainer.cpp.

Referenced by clone(), and createEmptyContainer().

◆ VectorProbabilisticSiteContainer() [2/6]

VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer	(	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. Those sites are cloned in the container.
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 59 of file VectorProbabilisticSiteContainer.cpp.

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

◆ VectorProbabilisticSiteContainer() [3/6]

VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer ( const AlignedValuesContainer & avc )

Build a new container from an AlignedValuesContainer.

Definition at line 101 of file VectorProbabilisticSiteContainer.cpp.

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

◆ VectorProbabilisticSiteContainer() [4/6]

VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer	(	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 88 of file VectorProbabilisticSiteContainer.cpp.

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

◆ VectorProbabilisticSiteContainer() [5/6]

VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer ( const VectorProbabilisticSiteContainer & vpsc )

Copy contructors.

Sites are cloned.

Definition at line 126 of file VectorProbabilisticSiteContainer.cpp.

◆ VectorProbabilisticSiteContainer() [6/6]

VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer ( const OrderedSequenceContainer & osc )

Definition at line 135 of file VectorProbabilisticSiteContainer.cpp.

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

◆ ~VectorProbabilisticSiteContainer()

virtual bpp::VectorProbabilisticSiteContainer::~VectorProbabilisticSiteContainer ( )

inlinevirtual

Definition at line 143 of file VectorProbabilisticSiteContainer.h.

Member Function Documentation

◆ addObject() [1/5]

void bpp::VectorMappedContainer< ProbabilisticSequence >::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< ProbabilisticSite >::addObject	(	std::shared_ptr< ProbabilisticSite >	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 bpp::VectorSiteContainer::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< ProbabilisticSequence >::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< ProbabilisticSite >::addObject_	(	std::shared_ptr< ProbabilisticSite >	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 VectorProbabilisticSiteContainer::addSequence	(	const ProbabilisticSequence &	sequence,
		bool	checkName = `true`
	)

virtual

Add a probabilistic 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::AbstractProbabilisticSequenceContainer.

Definition at line 204 of file VectorProbabilisticSiteContainer.cpp.

References addSite(), bpp::VectorMappedContainer< T >::appendObject(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::CoreSequence::getComments(), bpp::ProbabilisticSequence::getContent(), bpp::CoreSequence::getName(), getNumberOfSequences(), getNumberOfSites(), getSite(), bpp::VectorMappedContainer< ProbabilisticSequence >::hasObject(), bpp::AbstractProbabilisticSequenceContainer::setGeneralComments(), bpp::VectorPositionedContainer< T >::setSize(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

Referenced by bpp::Pasta::appendSequencesFromStream(), and VectorProbabilisticSiteContainer().

◆ addSequence() [2/2]

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

virtual

Add a basic sequence to the container, through conversion to a probabilistic sequence.

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::AbstractProbabilisticSequenceContainer.

Definition at line 245 of file VectorProbabilisticSiteContainer.cpp.

References addSite(), bpp::VectorMappedContainer< T >::appendObject(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::CoreSequence::getComments(), bpp::CoreSequence::getName(), getNumberOfSequences(), getNumberOfSites(), getSite(), bpp::Alphabet::getSize(), bpp::CruxSymbolList::getStateValueAt(), bpp::VectorMappedContainer< ProbabilisticSequence >::hasObject(), bpp::AbstractProbabilisticSequenceContainer::setGeneralComments(), bpp::VectorPositionedContainer< T >::setSize(), bpp::CruxSymbolList::size(), and bpp::TextTools::toString().

◆ addSite()

void VectorProbabilisticSiteContainer::addSite	(	std::shared_ptr< ProbabilisticSite >	site,
		bool	checkPosition = `false`
	)

virtual

Add a site at the end of the container.

Parameters

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

Implements bpp::ProbabilisticSiteContainer.

Definition at line 168 of file VectorProbabilisticSiteContainer.cpp.

References bpp::VectorPositionedContainer< T >::appendObject(), bpp::VectorMappedContainer< T >::appendObject(), bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSequences(), getNumberOfSites(), getSite(), bpp::VectorPositionedContainer< T >::nullify(), and bpp::TextTools::toString().

Referenced by addSequence(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), operator=(), realloc(), bpp::SiteContainerTools::sampleSites(), and VectorProbabilisticSiteContainer().

◆ appendObject() [1/3]

void bpp::VectorMappedContainer< ProbabilisticSequence >::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< ProbabilisticSite >::appendObject ( std::shared_ptr< ProbabilisticSite > 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(), bpp::VectorSiteContainer::addSite(), 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(), setSequence(), and bpp::VectorSiteContainer::setSequence().

◆ clear()

void VectorProbabilisticSiteContainer::clear ( )

virtual

Delete all objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 293 of file VectorProbabilisticSiteContainer.cpp.

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

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

◆ 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()

VectorProbabilisticSiteContainer* bpp::VectorProbabilisticSiteContainer::clone ( ) const

inlinevirtual

Implements bpp::ProbabilisticSiteContainer.

Definition at line 136 of file VectorProbabilisticSiteContainer.h.

References VectorProbabilisticSiteContainer().

Referenced by VectorProbabilisticSiteContainer().

◆ createEmptyContainer()

VectorProbabilisticSiteContainer * VectorProbabilisticSiteContainer::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 348 of file VectorProbabilisticSiteContainer.cpp.

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

◆ deleteGeneralComments()

void bpp::AbstractProbabilisticSequenceContainer::deleteGeneralComments ( )

inlinevirtualinherited

Delete the comments associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 157 of file AbstractProbabilisticSequenceContainer.h.

References bpp::Commentable::clearComments().

◆ deleteObject() [1/3]

void bpp::VectorMappedContainer< ProbabilisticSequence >::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< ProbabilisticSequence >::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< ProbabilisticSite >::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]

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(), deleteSites(), and bpp::VectorSiteContainer::deleteSites().

◆ deleteObjects() [2/2]

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

inlineprotectedinherited

Definition at line 238 of file VectorPositionedContainer.h.

◆ deleteSites()

void bpp::VectorProbabilisticSiteContainer::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 305 of file VectorProbabilisticSiteContainer.h.

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

◆ getAlphabet()

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_.

◆ 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 getSequence().

◆ getComments() [2/4]

const Comments& bpp::AbstractProbabilisticSequenceContainer::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 121 of file AbstractProbabilisticSequenceContainer.h.

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

◆ getComments() [3/4]

virtual const Comments& bpp::SequencedValuesContainer::getComments

inherited

Get comments of a particular sequence.

Parameters

sequenceIndex The position of the sequence.

Returns: The comments associated to sequence at position 'sequenceIndex'.

Exceptions

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

◆ getComments() [4/4]

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

inlinevirtualinherited

Implements bpp::AbstractValuesContainer.

Definition at line 162 of file AbstractProbabilisticSequenceContainer.h.

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

◆ getGeneralComments()

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

inlinevirtualinherited

Get the comments of this container.

Returns: The comments associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 147 of file AbstractProbabilisticSequenceContainer.h.

References bpp::Commentable::getComments().

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

◆ getName()

virtual const std::string& bpp::AbstractProbabilisticSequenceContainer::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 137 of file AbstractProbabilisticSequenceContainer.h.

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

◆ getNumberOfObjects()

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

inlineprotectedinherited

Definition at line 144 of file VectorMappedContainer.h.

◆ getNumberOfSequences()

size_t bpp::VectorProbabilisticSiteContainer::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 146 of file VectorProbabilisticSiteContainer.h.

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

Referenced by addSequence(), addSite(), getSequence(), getStateValueAt(), and setSequence().

◆ getNumberOfSites()

size_t bpp::VectorProbabilisticSiteContainer::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 310 of file VectorProbabilisticSiteContainer.h.

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

Referenced by addSequence(), addSite(), getSequence(), getSite(), getSitePositions(), getStateValueAt(), operator=(), reindexSites(), setSequence(), and setSitePositions().

◆ getObject() [1/6]

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

inlineprotectedvirtualinherited

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 172 of file VectorMappedContainer.h.

◆ getObject() [4/6]

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

inlineprotectedvirtualinherited

Implements bpp::PositionedContainer< T >.

Definition at line 177 of file VectorPositionedContainer.h.

◆ getObject() [5/6]

const std::shared_ptr<ProbabilisticSequence > bpp::VectorMappedContainer< ProbabilisticSequence >::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<ProbabilisticSite > bpp::VectorPositionedContainer< ProbabilisticSite >::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]

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_.

◆ getObject_() [2/2]

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

inlineprotectedinherited

Definition at line 251 of file VectorPositionedContainer.h.

◆ getObjectName()

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

inlineprotectedvirtualinherited

Link between position & name.

Implements bpp::PositionedNamedContainer< T >.

Definition at line 149 of file VectorMappedContainer.h.

◆ getSequence() [1/2]

const ProbabilisticSequence & VectorProbabilisticSiteContainer::getSequence ( const std::string & name ) const

virtual

Get Sequence from its name in the container.

Parameters

name	Name of the sequence

Returns: A read-only reference to the selected sequence.

Implements bpp::AbstractProbabilisticSequenceContainer.

Definition at line 388 of file VectorProbabilisticSiteContainer.cpp.

References getSequence(), and getSequencePosition().

◆ getSequence() [2/2]

const ProbabilisticSequence & VectorProbabilisticSiteContainer::getSequence ( std::size_t i ) const

virtual

Get Sequence from a position in the container.

Parameters

i	index of the sequence

Returns: A read-only reference to the selected sequence.

Implements bpp::AbstractProbabilisticSequenceContainer.

Definition at line 357 of file VectorProbabilisticSiteContainer.cpp.

References bpp::Table< class >::addColumn(), bpp::VectorMappedContainer< T >::addObject_(), bpp::AbstractValuesContainer::getAlphabet(), bpp::Commentable::getComments(), getNumberOfSequences(), getNumberOfSites(), bpp::VectorMappedContainer< T >::getObject(), bpp::VectorMappedContainer< T >::getObjectName(), getSite(), bpp::VectorMappedContainer< ProbabilisticSequence >::getSize(), and bpp::MappedNamedContainer< T >::isAvailableName().

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

◆ getSequenceNames()

std::vector<std::string> bpp::VectorProbabilisticSiteContainer::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 196 of file VectorProbabilisticSiteContainer.h.

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

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

◆ getSequencePosition()

size_t bpp::VectorProbabilisticSiteContainer::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 190 of file VectorProbabilisticSiteContainer.h.

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

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

◆ getSite() [1/2]

std::shared_ptr<ProbabilisticSite> bpp::VectorProbabilisticSiteContainer::getSite ( size_t i )

inlinevirtual

Implements bpp::ProbabilisticSiteContainer.

Definition at line 161 of file VectorProbabilisticSiteContainer.h.

References getNumberOfSites(), and bpp::VectorPositionedContainer< T >::getObject().

◆ getSite() [2/2]

const std::shared_ptr<ProbabilisticSite> bpp::VectorProbabilisticSiteContainer::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::ProbabilisticSiteContainer.

Definition at line 153 of file VectorProbabilisticSiteContainer.h.

References getNumberOfSites(), and bpp::VectorPositionedContainer< T >::getObject().

Referenced by addSequence(), addSite(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), getSequence(), getSitePositions(), bpp::SiteContainerTools::getSitesWithoutGaps(), getStateValueAt(), operator()(), operator=(), reindexSites(), bpp::SiteContainerTools::sampleSites(), setSequence(), and setSitePositions().

◆ getSitePositions()

Vint VectorProbabilisticSiteContainer::getSitePositions ( ) const

virtual

Get all position attributes of sites.

Returns: A vector with all site positions.

Implements bpp::AlignedValuesContainer.

Definition at line 322 of file VectorProbabilisticSiteContainer.cpp.

References getNumberOfSites(), and getSite().

◆ getSize() [1/2]

size_t bpp::VectorMappedContainer< ProbabilisticSequence >::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< ProbabilisticSite >::getSize ( ) const

inlinevirtualinherited

the size

Implements bpp::PositionedContainer< T >.

Definition at line 129 of file VectorPositionedContainer.h.

◆ getStateValueAt() [1/3]

double bpp::VectorProbabilisticSiteContainer::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 231 of file VectorProbabilisticSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSites(), getSequencePosition(), getSite(), and bpp::Alphabet::getStateIndex().

◆ 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::VectorProbabilisticSiteContainer::getStateValueAt	(	size_t	siteIndex,
		size_t	sequenceIndex,
		int	state
	)		const

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 259 of file VectorProbabilisticSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSequences(), getNumberOfSites(), getSite(), and bpp::Alphabet::getStateIndex().

◆ getSymbolListSite() [1/2]

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

inlinevirtualinherited

Implements bpp::AlignedValuesContainer.

Definition at line 87 of file ProbabilisticSiteContainer.h.

References bpp::ProbabilisticSiteContainer::getSite().

◆ getSymbolListSite() [2/2]

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

inlinevirtualinherited

Get a CruxSymbolListSite from a given position.

Parameters

siteIndex The position

Implements bpp::AlignedValuesContainer.

Definition at line 82 of file ProbabilisticSiteContainer.h.

References bpp::ProbabilisticSiteContainer::getSite().

◆ hasObject()

bool bpp::VectorMappedContainer< ProbabilisticSequence >::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::VectorProbabilisticSiteContainer::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 184 of file VectorProbabilisticSiteContainer.h.

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

◆ insertObject() [1/4]

void bpp::VectorMappedContainer< ProbabilisticSequence >::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< ProbabilisticSite >::insertObject	(	std::shared_ptr< ProbabilisticSite >	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(), bpp::VectorSiteContainer::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(), bpp::VectorSiteContainer::getSequence(), and getSequence().

◆ isAvailablePosition() [1/2]

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_.

◆ isAvailablePosition() [2/2]

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

inlineinherited

Definition at line 134 of file VectorPositionedContainer.h.

◆ nullify() [1/2]

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(), bpp::VectorSiteContainer::addSite(), addSite(), and bpp::AlignedSequenceContainer::setSequence().

◆ nullify() [2/2]

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

inlineinherited

Nullify all elements.

Definition at line 163 of file VectorPositionedContainer.h.

◆ operator()() [1/2]

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

inlinevirtual

Implements bpp::SequencedValuesContainer.

Definition at line 237 of file VectorProbabilisticSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getSequencePosition(), getSite(), and bpp::Alphabet::getStateIndex().

◆ operator()() [2/2]

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

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 266 of file VectorProbabilisticSiteContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getSite(), and bpp::Alphabet::getStateIndex().

◆ operator=()

VectorProbabilisticSiteContainer & VectorProbabilisticSiteContainer::operator= ( const VectorProbabilisticSiteContainer & vpsc )

Definition at line 150 of file VectorProbabilisticSiteContainer.cpp.

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

◆ realloc()

void VectorProbabilisticSiteContainer::realloc ( size_t n )

protected

Definition at line 299 of file VectorProbabilisticSiteContainer.cpp.

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

Referenced by setSequence().

◆ reindexSites()

void VectorProbabilisticSiteContainer::reindexSites ( )

virtual

Set all positions attributes.

Implements bpp::AlignedValuesContainer.

Definition at line 312 of file VectorProbabilisticSiteContainer.cpp.

References getNumberOfSites(), and getSite().

Referenced by realloc().

◆ removeObject() [1/3]

std::shared_ptr<ProbabilisticSequence > bpp::VectorMappedContainer< ProbabilisticSequence >::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<ProbabilisticSequence > bpp::VectorMappedContainer< ProbabilisticSequence >::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<ProbabilisticSite > bpp::VectorPositionedContainer< ProbabilisticSite >::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.

◆ 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::AbstractProbabilisticSequenceContainer::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 126 of file AbstractProbabilisticSequenceContainer.h.

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

◆ setComments() [3/4]

virtual void bpp::SequencedValuesContainer::setComments

inherited

Set the comments of a particular sequence.

Parameters

sequenceIndex	The position of the sequence.
comments	The comments to set to sequence with position 'i'.

Exceptions

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

Referenced by bpp::AbstractProbabilisticSequenceContainer::setComments(), bpp::AbstractValuesContainer::setComments(), and bpp::VectorProbabilisticSequenceContainer::setComments().

◆ setComments() [4/4]

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

inlinevirtual

Implements bpp::AbstractProbabilisticSequenceContainer.

Definition at line 207 of file VectorProbabilisticSiteContainer.h.

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

◆ setGeneralComments()

void bpp::AbstractProbabilisticSequenceContainer::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 152 of file AbstractProbabilisticSequenceContainer.h.

References bpp::Commentable::setComments().

Referenced by addSequence(), bpp::Pasta::appendSequencesFromStream(), and createEmptyContainer().

◆ setObjectName()

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

inlineprotectedinherited

Definition at line 219 of file VectorMappedContainer.h.

◆ setObjectNames()

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

inlineprotectedinherited

Definition at line 203 of file VectorMappedContainer.h.

◆ setSequence() [1/2]

void VectorProbabilisticSiteContainer::setSequence	(	const std::string &	name,
		const ProbabilisticSequence &	sequence,
		bool	checkName
	)

virtual

Replace a probabilistic sequence in the container.

Parameters

name	The name of the sequence in the map.
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::ProbabilisticSequenceContainer.

Definition at line 398 of file VectorProbabilisticSiteContainer.cpp.

References getSequencePosition().

◆ setSequence() [2/2]

void VectorProbabilisticSiteContainer::setSequence	(	size_t	sequenceIndex,
		const ProbabilisticSequence &	sequence,
		bool	checkName
	)

Definition at line 407 of file VectorProbabilisticSiteContainer.cpp.

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

◆ setSequenceNames()

void bpp::VectorProbabilisticSiteContainer::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 201 of file VectorProbabilisticSiteContainer.h.

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

Referenced by VectorProbabilisticSiteContainer().