The VectorSequenceContainer class. More...

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

Inheritance diagram for bpp::VectorSequenceContainer:

Collaboration diagram for bpp::VectorSequenceContainer:

Public Member Functions
	VectorSequenceContainer (const std::vector< std::shared_ptr< Sequence >> &vs, const Alphabet *alpha)
	Build a container with shared Sequences. More...

	VectorSequenceContainer (const Alphabet *alpha)
	Build an empty container that will contain sequences of a particular alphabet. More...

VectorSequenceContainer &	operator= (const VectorSequenceContainer &vsc)
	Assign from a VectorSequenceContainer. More...

VectorSequenceContainer &	operator= (const OrderedSequenceContainer &osc)
	Copy from an OrderedSequenceContainer. More...

VectorSequenceContainer &	operator= (const SequenceContainer &osc)
	Copy from a SequenceContainer. More...

void	clear ()
	Delete all objects 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
	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...

Copy contructors:
	VectorSequenceContainer (const VectorSequenceContainer &vsc)
	Copy from a VectorSequenceContainer. More...

	VectorSequenceContainer (const OrderedSequenceContainer &osc)
	Copy from an OrderedSequenceContainer. More...

	VectorSequenceContainer (const SequenceContainer &osc)
	Copy from a SequenceContainer. More...

The Clonable interface.
VectorSequenceContainer *	clone () const

The SequenceContainer interface.
bool	hasSequence (const std::string &name) const
	check if there is a Sequence with this name in the map (same as hasSequenceByKey). More...

bool	hasSequenceByName (const std::string &name) const

bool	hasSequenceByKey (const std::string &name) const
	check if there is a Sequence with this key in the map. More...

const Sequence &	getSequence (const std::string &name) const
	get the Sequence with this name in the map (same as getSequenceByKey). More...

const Sequence &	getSequenceByName (const std::string &name) const

const Sequence &	getSequenceByKey (const std::string &name) const
	check if there is a Sequence with this key in the map. More...

void	setSequence (const std::string &name, const Sequence &sequence, bool checkName=true)
	Copy a Sequence to the given key in the map. More...

std::shared_ptr< Sequence >	removeSequence (const std::string &name)
	get the Sequence with this name in the map (same as removeSequenceByKey). More...

std::shared_ptr< Sequence >	removeSequenceByKey (const std::string &name)
	remove & return a Sequence with this key from the map. More...

std::shared_ptr< Sequence >	removeSequenceByName (const std::string &name)
	remove & return a Sequence with this name. More...

void	deleteSequence (const std::string &name)
	delete the Sequence with this name in the map (same as deleteSequenceByKey). More...

void	deleteSequence (size_t pos)

void	deleteSequenceByKey (const std::string &name)
	remove & return a Sequence with this key from the map. More...

void	deleteSequenceByName (const std::string &name)
	remove & return a Sequence with this name. More...

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

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

std::vector< std::string >	getSequenceNames () const
	get Sequences proper names (may be different from the keys used to store them in the map), in the order of the vector. More...

std::vector< std::string >	getSequenceKeys () const
	get Sequences keys (ie the strings used to store them in the map, may be different from their proper names), in the order of the vector. More...

void	setSequenceNames (const std::vector< std::string > &names, bool checkNames=true)
	set the proper names of the Sequences, in the order of the vector. More...

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

int &	valueAt (const std::string &sequenceName, size_t elementIndex)
	Get the value of an element, given sequenceName in the map and the elementIndex position. More...

const int &	valueAt (const std::string &key, size_t elementIndex) const
	Get the value at a Position in a Sequence with given sequenceName in the map (may be not the actual name of the Sequence.. 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...

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

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

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

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

void	setComments (size_t sequenceIndex, const Comments &comments)

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

virtual void	addSequence (const Sequence &sequence, const std::string &key)
	Add a sequence with a given key at the end of the container. More...

virtual void	addSequence (const std::shared_ptr< Sequence > sequence, bool checkName=true)
	Add a sequence at the end of the container. More...

virtual void	addSequence (const Sequence &sequence, size_t sequenceIndex, bool checkName=true)
	Add a sequence to the container at a particular position. More...

virtual void	addSequence (const Sequence &sequence, size_t sequenceIndex, const std::string &key)
	Add a sequence to the container at a particular position with a given key. More...

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

AbstractSequenceContainer methods.
Sequence &	getSequence_ (size_t i)

Sequence &	getSequence_ (const std::string &key)
	getSequence with given key More...

SequencedValuesContainer methods.
double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const
	get Value at given state with given key in the Sequence Map 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

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

Comments	comments_

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

Private Member Functions
virtual void	setSize (size_t size)

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 VectorSequenceContainer class.

This is the simplest implementation of the OrderedSequenceContainer interface. std::shared_ptr<Sequence> are stored in a std::vector, as well as in a std::map.

Definition at line 67 of file VectorSequenceContainer.h.

Constructor & Destructor Documentation

◆ VectorSequenceContainer() [1/5]

VectorSequenceContainer::VectorSequenceContainer	(	const std::vector< std::shared_ptr< Sequence >> &	vs,
		const Alphabet *	alpha
	)

Build a container with shared Sequences.

The keys of the map are the names of the Sequences

Class constructors:

Definition at line 51 of file VectorSequenceContainer.cpp.

References addSequence().

Referenced by clone(), and createEmptyContainer().

◆ VectorSequenceContainer() [2/5]

bpp::VectorSequenceContainer::VectorSequenceContainer ( const Alphabet * alpha )

inline

Build an empty container that will contain sequences of a particular alphabet.

Parameters

alpha The alphabet of the container.

Definition at line 88 of file VectorSequenceContainer.h.

◆ VectorSequenceContainer() [3/5]

VectorSequenceContainer::VectorSequenceContainer ( const VectorSequenceContainer & vsc )

Copy from a VectorSequenceContainer.

Parameters

vsc	The VectorSequenceContainer to copy into this container.

Copy constructors:

Definition at line 65 of file VectorSequenceContainer.cpp.

References addSequence(), getNumberOfSequences(), and getSequence().

◆ VectorSequenceContainer() [4/5]

VectorSequenceContainer::VectorSequenceContainer ( const OrderedSequenceContainer & osc )

Copy from an OrderedSequenceContainer.

Parameters

osc	The OrderedSequenceContainer to copy into this container.

The keys of the map are the names of the Sequences

Definition at line 77 of file VectorSequenceContainer.cpp.

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

◆ VectorSequenceContainer() [5/5]

VectorSequenceContainer::VectorSequenceContainer ( const SequenceContainer & osc )

Copy from a SequenceContainer.

Parameters

osc	The SequenceContainer to copy into this container.

The keys of the map are the names of the Sequences

Definition at line 89 of file VectorSequenceContainer.cpp.

References addSequence(), bpp::SequencedValuesContainer::getGeneralComments(), bpp::SequenceContainer::getSequence(), bpp::SequencedValuesContainer::getSequenceNames(), and bpp::AbstractValuesContainer::setGeneralComments().

Member Function Documentation

◆ addObject() [1/4]

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() [2/4]

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() [3/4]

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() [4/4]

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_() [1/3]

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_() [2/3]

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_() [3/3]

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() [1/5]

virtual void bpp::VectorSequenceContainer::addSequence	(	const Sequence &	sequence,
		bool	checkName = `true`
	)

inlinevirtual

Add a sequence at the end of the container.

The sequence is copied into the container. If checkNames is set to true, the method check if the name of the sequence is already used in the container, and sends an exception if it is the case. Otherwise, do not check the name: the method is hence faster, but use it at your own risks!

Parameters

sequence	The sequence to add.
checkName	Tell if the method must check the name of the sequence before adding it.

Implements bpp::SequenceContainer.

Reimplemented in bpp::AlignedSequenceContainer.

Definition at line 442 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::appendObject(), bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), and bpp::CoreSequence::getName().

Referenced by bpp::AlignedSequenceContainer::addSequence(), bpp::SequenceContainerTools::createContainerOfSpecifiedSize(), bpp::SequenceContainerTools::getCodonPosition(), operator=(), and VectorSequenceContainer().

◆ addSequence() [2/5]

virtual void bpp::VectorSequenceContainer::addSequence	(	const Sequence &	sequence,
		const std::string &	key
	)

inlinevirtual

Add a sequence with a given key at the end of the container.

The sequence is copied into the container. If checkNames is set to true, the method check if the name of the sequence is already used in the container, and sends an exception if it is the case. Otherwise, do not check the name: the method is hence faster, but use it at your own risks!

Parameters

sequence	The sequence to add.
key	the key in the map

Definition at line 463 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::appendObject(), bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), and bpp::Alphabet::getAlphabetType().

◆ addSequence() [3/5]

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

inlinevirtual

Add a sequence to the container at a particular position.

The sequence is copied into the container. If checkName is set to true, the method check if the name of the sequence is already used in the container, and sends an exception if it is the case. Otherwise, do not check the name: the method is hence faster, but use it at your own risks!

Parameters

sequence	The sequence to add.
sequenceIndex	The position where to insert the new sequence. All the following sequences will be pushed.
checkName	Tell if the method must check the name of the sequence before adding it.

Exceptions

Exception If the sequence couldn't be added to the container.

Reimplemented in bpp::AlignedSequenceContainer.

Definition at line 510 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::addObject(), bpp::Sequence::clone(), and bpp::CoreSequence::getName().

◆ addSequence() [4/5]

virtual void bpp::VectorSequenceContainer::addSequence	(	const Sequence &	sequence,
		size_t	sequenceIndex,
		const std::string &	key
	)

inlinevirtual

Add a sequence to the container at a particular position with a given key.

The sequence is copied into the container. If checkName is set to true, the method check if the name of the sequence is already used in the container, and sends an exception if it is the case. Otherwise, do not check the name: the method is hence faster, but use it at your own risks!

Parameters

sequence	The sequence to add.
key	the key in the map
sequenceIndex	The position where to insert the new sequence. All the following sequences will be pushed.

Exceptions

Exception If the sequence couldn't be added to the container.

Definition at line 531 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::addObject(), and bpp::Sequence::clone().

◆ addSequence() [5/5]

virtual void bpp::VectorSequenceContainer::addSequence	(	const std::shared_ptr< Sequence >	sequence,
		bool	checkName = `true`
	)

inlinevirtual

Add a sequence at the end of the container.

The sequence is shared with the container. If checkNames is set to true, the method check if the name of the sequence is already used in the container, and sends an exception if it is the case. Otherwise, do not check the name: the method is hence faster, but use it at your own risks!

Parameters

sequence	The sequence to add.
checkName	Tell if the method must check the name of the sequence before adding it.

Exceptions

Exception If the sequence couldn't be added to the container.

Definition at line 486 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::appendObject(), and bpp::AbstractValuesContainer::getAlphabet().

◆ appendObject() [1/2]

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() [2/2]

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(), 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 bpp::VectorSiteContainer::setSequence().

◆ clear()

void bpp::VectorSequenceContainer::clear ( )

inlinevirtual

Delete all objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 158 of file VectorSequenceContainer.h.

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

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

◆ 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()

VectorSequenceContainer* bpp::VectorSequenceContainer::clone ( ) const

inlinevirtual

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 169 of file VectorSequenceContainer.h.

References VectorSequenceContainer().

◆ createEmptyContainer()

VectorSequenceContainer * VectorSequenceContainer::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 233 of file VectorSequenceContainer.cpp.

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

◆ 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() [1/2]

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() [2/2]

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.

◆ deleteObjects()

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 bpp::VectorSiteContainer::deleteSites().

◆ deleteSequence() [1/2]

void bpp::VectorSequenceContainer::deleteSequence ( const std::string & name )

inline

delete the Sequence with this name in the map (same as deleteSequenceByKey).

Definition at line 268 of file VectorSequenceContainer.h.

References deleteSequenceByKey().

Referenced by deleteSequenceByKey(), and deleteSequenceByName().

◆ deleteSequence() [2/2]

void bpp::VectorSequenceContainer::deleteSequence ( size_t pos )

inline

Definition at line 273 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::deleteObject().

◆ deleteSequenceByKey()

void bpp::VectorSequenceContainer::deleteSequenceByKey ( const std::string & name )

inline

remove & return a Sequence with this key from the map.

Definition at line 283 of file VectorSequenceContainer.h.

References deleteSequence(), and getSequencePosition().

Referenced by deleteSequence().

◆ deleteSequenceByName()

void VectorSequenceContainer::deleteSequenceByName ( const std::string & name )

remove & return a Sequence with this name.

Definition at line 190 of file VectorSequenceContainer.cpp.

References deleteSequence(), bpp::CoreSequence::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ 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(), bpp::VectorSiteContainer::addSite(), bpp::VectorSiteContainer::getSequence(), bpp::CompressedVectorSiteContainer::removeSite(), bpp::VectorSiteContainer::setSequence(), bpp::CompressedVectorSiteContainer::setSite(), and bpp::VectorSiteContainer::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(), createEmptyContainer(), and bpp::VectorSiteContainer::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=(), VectorSequenceContainer(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

◆ getKeys()

std::vector<std::string> bpp::VectorSequenceContainer::getKeys ( ) const

inline

Returns: The list of key used to index the sequences.

Definition at line 297 of file VectorSequenceContainer.h.

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

◆ 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 getSequenceNames(), and hasSequenceByName().

◆ getNumberOfObjects()

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

inlineprotectedinherited

Definition at line 144 of file VectorMappedContainer.h.

◆ getNumberOfSequences()

size_t bpp::VectorSequenceContainer::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 299 of file VectorSequenceContainer.h.

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

Referenced by bpp::AlignedSequenceContainer::addSequence(), bpp::AlignedSequenceContainer::addSite(), bpp::AlignedSequenceContainer::deleteSite(), bpp::AlignedSequenceContainer::deleteSites(), bpp::AlignedSequenceContainer::getSite(), getStateValueAt(), bpp::AlignedSequenceContainer::removeSite(), bpp::AlignedSequenceContainer::setSequence(), setSequenceNames(), bpp::AlignedSequenceContainer::setSite(), and VectorSequenceContainer().

◆ getObject() [1/4]

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() [2/4]

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() [3/4]

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() [4/4]

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_()

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& bpp::VectorSequenceContainer::getSequence ( const std::string & name ) const

inlinevirtual

get the Sequence with this name in the map (same as getSequenceByKey).

Implements bpp::SequenceContainer.

Definition at line 207 of file VectorSequenceContainer.h.

References getSequenceByKey().

Referenced by VectorSequenceContainer().

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

◆ getSequence() [3/3]

const Sequence& bpp::VectorSequenceContainer::getSequence ( size_t sequenceIndex ) const

inlinevirtual

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 397 of file VectorSequenceContainer.h.

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

◆ getSequence_() [1/2]

Sequence& bpp::VectorSequenceContainer::getSequence_ ( const std::string & key )

inlineprotected

getSequence with given key

Definition at line 553 of file VectorSequenceContainer.h.

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

◆ getSequence_() [2/2]

Sequence& bpp::VectorSequenceContainer::getSequence_ ( size_t i )

inlineprotected

Definition at line 542 of file VectorSequenceContainer.h.

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

Referenced by bpp::AlignedSequenceContainer::addSite(), bpp::AlignedSequenceContainer::deleteSite(), bpp::AlignedSequenceContainer::deleteSites(), operator()(), bpp::AlignedSequenceContainer::removeSite(), setComments(), setSequenceNames(), bpp::AlignedSequenceContainer::setSite(), and valueAt().

◆ getSequenceByKey()

const Sequence& bpp::VectorSequenceContainer::getSequenceByKey ( const std::string & name ) const

inline

check if there is a Sequence with this key in the map.

Definition at line 219 of file VectorSequenceContainer.h.

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

Referenced by getSequence(), and valueAt().

◆ getSequenceByName()

const Sequence & VectorSequenceContainer::getSequenceByName ( const std::string & name ) const

Definition at line 156 of file VectorSequenceContainer.cpp.

References bpp::CoreSequence::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ getSequenceKeys()

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

inline

get Sequences keys (ie the strings used to store them in the map, may be different from their proper names), in the order of the vector.

Definition at line 316 of file VectorSequenceContainer.h.

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

◆ getSequenceNames()

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

virtual

get Sequences proper names (may be different from the keys used to store them in the map), in the order of the vector.

Implements bpp::SequencedValuesContainer.

Definition at line 168 of file VectorSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ getSequencePosition()

size_t bpp::VectorSequenceContainer::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 392 of file VectorSequenceContainer.h.

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

Referenced by deleteSequenceByKey(), removeSequenceByKey(), and setSequence().

◆ getSize()

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.

◆ getStateValueAt() [1/3]

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

inlineprotectedvirtual

get Value at given state with given key in the Sequence Map

Implements bpp::SequencedValuesContainer.

Definition at line 571 of file VectorSequenceContainer.h.

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

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

inlineprotectedvirtual

Implements bpp::OrderedValuesContainer.

Definition at line 592 of file VectorSequenceContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSequences(), bpp::OrderedSequenceContainer::getSequence(), bpp::Alphabet::isResolvedIn(), and bpp::CruxSymbolList::size().

◆ 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::VectorSequenceContainer::hasSequence ( const std::string & name ) const

inlinevirtual

check if there is a Sequence with this name in the map (same as hasSequenceByKey).

Implements bpp::SequencedValuesContainer.

Definition at line 184 of file VectorSequenceContainer.h.

References hasSequenceByKey().

◆ hasSequenceByKey()

bool bpp::VectorSequenceContainer::hasSequenceByKey ( const std::string & name ) const

inline

check if there is a Sequence with this key in the map.

Definition at line 196 of file VectorSequenceContainer.h.

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

Referenced by hasSequence().

◆ hasSequenceByName()

bool VectorSequenceContainer::hasSequenceByName ( const std::string & name ) const

Definition at line 147 of file VectorSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ insertObject() [1/3]

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() [2/3]

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() [3/3]

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 bpp::VectorProbabilisticSiteContainer::getSequence().

◆ isAvailablePosition()

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()

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

◆ operator()() [1/6]

int& bpp::VectorSequenceContainer::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 354 of file VectorSequenceContainer.h.

References getSequence_().

◆ operator()() [2/6]

const int& bpp::VectorSequenceContainer::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 359 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

◆ operator()() [3/6]

int& bpp::VectorSequenceContainer::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 374 of file VectorSequenceContainer.h.

References getSequence_().

◆ operator()() [4/6]

const int& bpp::VectorSequenceContainer::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 378 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

◆ operator()() [5/6]

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

inlineprotectedvirtual

Implements bpp::SequencedValuesContainer.

Definition at line 576 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

◆ operator()() [6/6]

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

inlineprotectedvirtual

Implements bpp::OrderedValuesContainer.

Definition at line 603 of file VectorSequenceContainer.h.

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

◆ operator=() [1/3]

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

Copy from an OrderedSequenceContainer.

Parameters

osc	The OrderedSequenceContainer to copy into this container.

The keys of the map are the names of the Sequences

Definition at line 115 of file VectorSequenceContainer.cpp.

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

◆ operator=() [2/3]

VectorSequenceContainer & VectorSequenceContainer::operator= ( const SequenceContainer & osc )

Copy from a SequenceContainer.

Parameters

osc	The SequenceContainer to copy into this container.

The keys of the map are the names of the Sequences

Definition at line 133 of file VectorSequenceContainer.cpp.

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

◆ operator=() [3/3]

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

Assign from a VectorSequenceContainer.

Parameters

vsc	The VectorSequenceContainer to copy into this container.

Assignation operator:

Definition at line 105 of file VectorSequenceContainer.cpp.

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

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

◆ removeObject() [1/2]

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() [2/2]

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.

◆ removeSequence() [1/3]

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

inlinevirtual

get the Sequence with this name in the map (same as removeSequenceByKey).

Implements bpp::SequenceContainer.

Definition at line 240 of file VectorSequenceContainer.h.

References removeSequenceByKey().

◆ 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 bpp::VectorSiteContainer::removeSequence(), removeSequenceByKey(), and removeSequenceByName().

◆ removeSequence() [3/3]

std::shared_ptr<Sequence> bpp::VectorSequenceContainer::removeSequence ( size_t sequenceIndex )

inlinevirtual

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex The position of the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 410 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::removeObject().

◆ removeSequenceByKey()

std::shared_ptr<Sequence> bpp::VectorSequenceContainer::removeSequenceByKey ( const std::string & name )

inline

remove & return a Sequence with this key from the map.

Definition at line 250 of file VectorSequenceContainer.h.

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

Referenced by removeSequence().

◆ removeSequenceByName()

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

remove & return a Sequence with this name.

Definition at line 178 of file VectorSequenceContainer.cpp.

References bpp::CoreSequence::getName(), bpp::OrderedSequenceContainer::getSequence(), bpp::VectorMappedContainer< Sequence >::getSize(), and bpp::OrderedSequenceContainer::removeSequence().

◆ 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 bpp::VectorSequenceContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)

inlinevirtual

Implements bpp::AbstractSequenceContainer.

Definition at line 415 of file VectorSequenceContainer.h.

References getSequence_(), and bpp::CoreSequence::setComments().

◆ setComments() [4/4]

virtual void bpp::OrderedValuesContainer::setComments

inherited

Referenced by bpp::AbstractSequenceContainer::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(), createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractSequenceContainer::operator=(), and 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]

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

◆ setSequence() [2/3]

void bpp::VectorSequenceContainer::setSequence	(	const std::string &	name,
		const Sequence &	sequence,
		bool	checkName = `true`
	)

inlinevirtual

Copy a Sequence to the given key in the map.

Implements bpp::SequenceContainer.

Definition at line 229 of file VectorSequenceContainer.h.

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

◆ setSequence() [3/3]

void bpp::VectorSequenceContainer::setSequence	(	size_t	sequenceIndex,
		const Sequence &	sequence,
		bool	checkName = `true`
	)

inlinevirtual

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 402 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::addObject(), bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), and bpp::CoreSequence::getName().

◆ setSequenceNames()

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

virtual

set the proper names of the Sequences, in the order of the vector.

Implements bpp::SequencedValuesContainer.

Definition at line 205 of file VectorSequenceContainer.cpp.

References getNumberOfSequences(), getSequence_(), bpp::CoreSequence::setName(), and bpp::VectorMappedContainer< Sequence >::setObjectNames().

◆ setSize() [1/2]

template<class T >

virtual void bpp::PositionedContainer< T >::setSize ( size_t size )

inlinevirtualinherited

Reimplemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, and bpp::VectorPositionedContainer< Site >.

Definition at line 76 of file PositionedContainer.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]

const int& bpp::VectorSequenceContainer::valueAt	(	const std::string &	key,
		size_t	elementIndex
	)		const

inlinevirtual

Get the value at a Position in a Sequence with given sequenceName in the map (may be not the actual name of the Sequence..

Implements bpp::OrderedSequenceContainer.

Definition at line 349 of file VectorSequenceContainer.h.

References getSequenceByKey().

◆ valueAt() [2/4]

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

inlinevirtual

Get the value of an element, given sequenceName in the map and the elementIndex position.

Implements bpp::OrderedSequenceContainer.

Definition at line 337 of file VectorSequenceContainer.h.

References getSequence_().

◆ valueAt() [3/4]

int& bpp::VectorSequenceContainer::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 364 of file VectorSequenceContainer.h.

References getSequence_().

◆ valueAt() [4/4]

const int& bpp::VectorSequenceContainer::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 369 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

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_

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/VectorSequenceContainer.h
Bpp/Seq/Container/VectorSequenceContainer.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VectorSequenceContainer() [1/5]

◆ VectorSequenceContainer() [2/5]

◆ VectorSequenceContainer() [3/5]

◆ VectorSequenceContainer() [4/5]

◆ VectorSequenceContainer() [5/5]

Member Function Documentation

◆ addObject() [1/4]

◆ addObject() [2/4]

◆ addObject() [3/4]

◆ addObject() [4/4]

◆ addObject_() [1/3]

◆ addObject_() [2/3]

◆ addObject_() [3/3]

◆ addSequence() [1/5]

◆ addSequence() [2/5]

◆ addSequence() [3/5]

◆ addSequence() [4/5]

◆ addSequence() [5/5]

◆ appendObject() [1/2]

◆ appendObject() [2/2]

◆ changeName()

◆ clear()

◆ clearComments()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments() [1/2]

◆ deleteGeneralComments() [2/2]

◆ deleteObject() [1/2]

◆ deleteObject() [2/2]

◆ deleteObjects()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ deleteSequenceByKey()

◆ deleteSequenceByName()

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getComments() [1/4]

◆ getComments() [2/4]

◆ getComments() [3/4]

◆ getComments() [4/4]

◆ getGeneralComments() [1/2]

◆ getGeneralComments() [2/2]

◆ getKeys()

◆ getName()

◆ getNumberOfObjects()

◆ getNumberOfSequences()

◆ getObject() [1/4]

◆ getObject() [2/4]

◆ getObject() [3/4]

◆ getObject() [4/4]

◆ getObject_()

◆ getObjectName()

◆ getObjectNames()

◆ getObjectPosition()

◆ getSequence() [1/3]

◆ getSequence() [2/3]

◆ getSequence() [3/3]

◆ getSequence_() [1/2]

◆ getSequence_() [2/2]

◆ getSequenceByKey()

◆ getSequenceByName()

◆ getSequenceKeys()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSize()

◆ getStateValueAt() [1/3]

◆ getStateValueAt() [2/3]

◆ getStateValueAt() [3/3]

◆ hasObject()

◆ hasSequence()

◆ hasSequenceByKey()

◆ hasSequenceByName()

◆ insertObject() [1/3]