bpp::VectorProbabilisticSequenceContainer Class Reference

The VectorProbabilisticSequenceContainer class. More...

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

Inheritance diagram for bpp::VectorProbabilisticSequenceContainer:

Collaboration diagram for bpp::VectorProbabilisticSequenceContainer:

Public Member Functions
	VectorProbabilisticSequenceContainer (const std::vector< std::shared_ptr< ProbabilisticSequence >> &vs, const Alphabet *alpha)
	Build a container with shared Sequences. More...
	VectorProbabilisticSequenceContainer (const Alphabet *alpha)
	Build an empty container that will contain sequences of a particular alphabet. More...
VectorProbabilisticSequenceContainer &	operator= (const VectorProbabilisticSequenceContainer &vsc)
	Assign from a VectorProbabilisticSequenceContainer. 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...
std::string	toString (size_t sequenceIndex) const
const Comments &	getComments (const std::string &name) const
	Get comments of a particular sequence. More...
virtual const Comments &	getComments (size_t sequenceIndex) const
void	setComments (const std::string &name, const Comments &comments)
	Set the comments of a particular sequence. More...
const std::string &	getName (size_t sequenceIndex) const
	Get the name of a particular row of the alignement (aka sequence). More...
size_t	getSequencePosition (const std::string &name) const
	Get the position of a sequence in sequence container from its name. More...
const ProbabilisticSequence &	getSequence (size_t sequenceIndex) const
void	setSequence (size_t sequenceIndex, const ProbabilisticSequence &sequence, bool checkName=true)
std::shared_ptr< ProbabilisticSequence >	removeSequence (size_t sequenceIndex)
void	setComments (size_t sequenceIndex, const Comments &comments)
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 const Comments &	getComments (const std::string &name) const=0
	Get comments of a particular sequence. More...
const Comments &	getComments () const
	Get the comments. More...
virtual std::string	toString (const std::string &name) const=0
	Convert a particular sequence to a string. 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 ()
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:
	VectorProbabilisticSequenceContainer (const VectorProbabilisticSequenceContainer &vsc)
	Copy from a VectorProbabilisticSequenceContainer. More...
The Clonable interface.
VectorProbabilisticSequenceContainer *	clone () const
The SequenceContainer interface.
bool	hasSequence (const std::string &name) const
	Check if a sequence with a given name is present in the container. More...
const ProbabilisticSequence &	getSequence (const std::string &name) const
void	setSequence (const std::string &name, const ProbabilisticSequence &sequence, bool checkName=true)
std::shared_ptr< ProbabilisticSequence >	removeSequence (const std::string &name)
size_t	getNumberOfSequences () const
	Get the number of sequences in the container. More...
std::vector< std::string >	getSequenceNames () const
	Get all the names of the sequences in the container. More...
void	setSequenceNames (const std::vector< std::string > &names, bool checkNames=true)
	Set all sequence names. More...
VectorProbabilisticSequenceContainer *	createEmptyContainer () const
	Return a copy of this container, but with no data inside. More...
Add sequence to this container.
virtual void	addSequence (const ProbabilisticSequence &sequence, bool checkName=true)
	Add a sequence at the end of the container. More...
virtual void	addSequence (const std::shared_ptr< ProbabilisticSequence > sequence, bool checkName=true)
	Add a sequence at the end of the container. More...
virtual void	addSequence (const ProbabilisticSequence &sequence, size_t sequenceIndex, bool checkName=true)
	Add a sequence to the container at a particular position. 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< 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
AbstractSequenceContainer methods.
ProbabilisticSequence &	getSequence_ (size_t i)
ProbabilisticSequence &	getSequence_ (const std::string &name)
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
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 VectorProbabilisticSequenceContainer class.

This is the simplest implementation of the OrderedValuesContainer interface for ProbabilisticSequences ProbabilisticSequences are stored in a std::vector of shared pointers.

Definition at line 63 of file VectorProbabilisticSequenceContainer.h.

Constructor & Destructor Documentation

VectorProbabilisticSequenceContainer() [1/3]

VectorProbabilisticSequenceContainer::VectorProbabilisticSequenceContainer	(	const std::vector< std::shared_ptr< ProbabilisticSequence >> &	vs,
		const Alphabet *	alpha
	)

Build a container with shared Sequences.

Class constructors:

Definition at line 51 of file VectorProbabilisticSequenceContainer.cpp.

References addSequence().

Referenced by clone(), and createEmptyContainer().

VectorProbabilisticSequenceContainer() [2/3]

bpp::VectorProbabilisticSequenceContainer::VectorProbabilisticSequenceContainer ( 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 82 of file VectorProbabilisticSequenceContainer.h.

VectorProbabilisticSequenceContainer() [3/3]

VectorProbabilisticSequenceContainer::VectorProbabilisticSequenceContainer

(

const VectorProbabilisticSequenceContainer &

vsc

)

Copy from a VectorProbabilisticSequenceContainer.

Parameters

vsc	The VectorProbabilisticSequenceContainer to copy into this container.

Copy constructors:

Definition at line 63 of file VectorProbabilisticSequenceContainer.cpp.

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

Member Function Documentation

addObject() [1/4]

void bpp::VectorMappedContainer< ProbabilisticSequence >::addObject ( std::shared_ptr< ProbabilisticSequence >  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< ProbabilisticSequence >::addObject_ ( std::shared_ptr< ProbabilisticSequence >  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() [1/3]

virtual void bpp::VectorProbabilisticSequenceContainer::addSequence ( const ProbabilisticSequence &  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.

Definition at line 244 of file VectorProbabilisticSequenceContainer.h.

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

Referenced by VectorProbabilisticSequenceContainer().

addSequence() [2/3]

virtual void bpp::VectorProbabilisticSequenceContainer::addSequence ( const ProbabilisticSequence &  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.

Definition at line 291 of file VectorProbabilisticSequenceContainer.h.

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

addSequence() [3/3]

virtual void bpp::VectorProbabilisticSequenceContainer::addSequence ( const std::shared_ptr< ProbabilisticSequence >  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 267 of file VectorProbabilisticSequenceContainer.h.

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

appendObject() [1/2]

void bpp::VectorMappedContainer< ProbabilisticSequence >::appendObject ( std::shared_ptr< ProbabilisticSequence >  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::VectorProbabilisticSequenceContainer::clear ( )

inlinevirtual

Delete all objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 107 of file VectorProbabilisticSequenceContainer.h.

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

Referenced by 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()

VectorProbabilisticSequenceContainer* bpp::VectorProbabilisticSequenceContainer::clone ( ) const

inlinevirtual

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 155 of file VectorProbabilisticSequenceContainer.h.

References VectorProbabilisticSequenceContainer().

createEmptyContainer()

VectorProbabilisticSequenceContainer * VectorProbabilisticSequenceContainer::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 116 of file VectorProbabilisticSequenceContainer.cpp.

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

deleteGeneralComments()

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().

deleteObject() [1/2]

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() [2/2]

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.

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().

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_.

Referenced by addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::VectorProbabilisticSiteContainer::addSite(), bpp::Pasta::appendSequencesFromStream(), bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), createEmptyContainer(), bpp::VectorProbabilisticSiteContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::getSequence(), bpp::VectorSiteContainer::getSequence(), bpp::VectorProbabilisticSiteContainer::getSequence(), bpp::AlignedSequenceContainer::getSite(), bpp::CompressedVectorSiteContainer::getStateValueAt(), bpp::VectorProbabilisticSiteContainer::getStateValueAt(), bpp::VectorSiteContainer::getStateValueAt(), getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::CompressedVectorSiteContainer::operator()(), bpp::VectorProbabilisticSiteContainer::operator()(), bpp::VectorSiteContainer::operator()(), operator()(), bpp::VectorSequenceContainer::operator()(), bpp::VectorProbabilisticSiteContainer::realloc(), bpp::VectorSiteContainer::realloc(), bpp::CompressedVectorSiteContainer::removeSite(), bpp::CompressedVectorSiteContainer::setComments(), bpp::VectorProbabilisticSiteContainer::setSequence(), setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::AlignedSequenceContainer::setSite(), bpp::CompressedVectorSiteContainer::setSite(), and bpp::VectorSiteContainer::setSite().

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::VectorProbabilisticSequenceContainer::getComments ( const std::string &  name ) const

inlinevirtual

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 124 of file VectorProbabilisticSequenceContainer.h.

References bpp::CoreSequence::getComments(), and 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::VectorProbabilisticSequenceContainer::getComments ( size_t  sequenceIndex ) const

inlinevirtual

Implements bpp::AbstractValuesContainer.

Definition at line 129 of file VectorProbabilisticSequenceContainer.h.

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

getGeneralComments()

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(), createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), and bpp::VectorSiteContainer::createEmptyContainer().

getName()

const std::string& bpp::VectorProbabilisticSequenceContainer::getName ( size_t  sequenceIndex ) const

inlinevirtual

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 140 of file VectorProbabilisticSequenceContainer.h.

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

getNumberOfObjects()

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

inlineprotectedinherited

Definition at line 144 of file VectorMappedContainer.h.

getNumberOfSequences()

size_t bpp::VectorProbabilisticSequenceContainer::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 187 of file VectorProbabilisticSequenceContainer.h.

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

Referenced by getStateValueAt(), setSequenceNames(), and VectorProbabilisticSequenceContainer().

getObject() [1/4]

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() [2/4]

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() [3/4]

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() [4/4]

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_()

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< 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& bpp::VectorProbabilisticSequenceContainer::getSequence ( const std::string &  name ) const

inline

Definition at line 172 of file VectorProbabilisticSequenceContainer.h.

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

Referenced by getComments(), getName(), getStateValueAt(), operator()(), toString(), and VectorProbabilisticSequenceContainer().

getSequence() [2/2]

const ProbabilisticSequence& bpp::VectorProbabilisticSequenceContainer::getSequence ( size_t  sequenceIndex ) const

inline

Definition at line 201 of file VectorProbabilisticSequenceContainer.h.

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

getSequence_() [1/2]

ProbabilisticSequence& bpp::VectorProbabilisticSequenceContainer::getSequence_ ( const std::string &  name )

inlineprotected

Definition at line 308 of file VectorProbabilisticSequenceContainer.h.

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

getSequence_() [2/2]

ProbabilisticSequence& bpp::VectorProbabilisticSequenceContainer::getSequence_ ( size_t  i )

inlineprotected

Definition at line 302 of file VectorProbabilisticSequenceContainer.h.

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

Referenced by setComments(), and setSequenceNames().

getSequenceNames()

std::vector<std::string> bpp::VectorProbabilisticSequenceContainer::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 189 of file VectorProbabilisticSequenceContainer.h.

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

getSequencePosition()

size_t bpp::VectorProbabilisticSequenceContainer::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 145 of file VectorProbabilisticSequenceContainer.h.

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

Referenced by removeSequence(), setComments(), and setSequence().

getSize()

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.

getStateValueAt() [1/3]

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

inlineprotectedvirtual

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 313 of file VectorProbabilisticSequenceContainer.h.

References 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::VectorProbabilisticSequenceContainer::getStateValueAt ( size_t  siteIndex, size_t  sequenceIndex, int  state  ) const

inlineprotectedvirtual

Implements bpp::OrderedValuesContainer.

Definition at line 323 of file VectorProbabilisticSequenceContainer.h.

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

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::VectorProbabilisticSequenceContainer::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 167 of file VectorProbabilisticSequenceContainer.h.

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

insertObject() [1/3]

void bpp::VectorMappedContainer< ProbabilisticSequence >::insertObject ( std::shared_ptr< ProbabilisticSequence >  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()() [1/2]

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

inlineprotectedvirtual

Implements bpp::SequencedValuesContainer.

Definition at line 318 of file VectorProbabilisticSequenceContainer.h.

References getSequence().

operator()() [2/2]

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

inlineprotectedvirtual

Implements bpp::OrderedValuesContainer.

Definition at line 334 of file VectorProbabilisticSequenceContainer.h.

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

operator=()

VectorProbabilisticSequenceContainer & VectorProbabilisticSequenceContainer::operator=

(

const VectorProbabilisticSequenceContainer &

vsc

)

Assign from a VectorProbabilisticSequenceContainer.

Parameters

vsc	The VectorProbabilisticSequenceContainer to copy into this container.

Assignation operator:

Definition at line 76 of file VectorProbabilisticSequenceContainer.cpp.

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

removeObject() [1/2]

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() [2/2]

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.

removeSequence() [1/2]

std::shared_ptr<ProbabilisticSequence> bpp::VectorProbabilisticSequenceContainer::removeSequence ( const std::string &  name )

inline

Definition at line 182 of file VectorProbabilisticSequenceContainer.h.

References getSequencePosition().

removeSequence() [2/2]

std::shared_ptr<ProbabilisticSequence> bpp::VectorProbabilisticSequenceContainer::removeSequence ( size_t  sequenceIndex )

inline

Definition at line 214 of file VectorProbabilisticSequenceContainer.h.

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

setComments() [1/4]

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

inlineinherited

Set the comments.

Parameters

comments

The new comments.

Definition at line 100 of file Commentable.h.

References bpp::Commentable::comments_.

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

setComments() [2/4]

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

inlinevirtual

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.

Reimplemented from bpp::AbstractValuesContainer.

Definition at line 134 of file VectorProbabilisticSequenceContainer.h.

References 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 setComments().

setComments() [4/4]

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

inlinevirtual

Implements bpp::AbstractValuesContainer.

Definition at line 219 of file VectorProbabilisticSequenceContainer.h.

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

setGeneralComments()

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(), createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractSequenceContainer::operator=(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

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 bpp::VectorProbabilisticSequenceContainer::setSequence ( const std::string &  name, const ProbabilisticSequence &  sequence, bool  checkName = true  )

inline

Definition at line 177 of file VectorProbabilisticSequenceContainer.h.

References getSequencePosition().

setSequence() [2/2]

void bpp::VectorProbabilisticSequenceContainer::setSequence ( size_t  sequenceIndex, const ProbabilisticSequence &  sequence, bool  checkName = true  )

inline

Definition at line 206 of file VectorProbabilisticSequenceContainer.h.

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

setSequenceNames()

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

virtual

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 88 of file VectorProbabilisticSequenceContainer.cpp.

References getNumberOfSequences(), getSequence_(), bpp::CoreSequence::setName(), and bpp::VectorMappedContainer< ProbabilisticSequence >::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::VectorProbabilisticSequenceContainer::toString ( const std::string &  name ) const

inlinevirtual

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 114 of file VectorProbabilisticSequenceContainer.h.

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

toString() [2/3]

virtual std::string bpp::SequencedValuesContainer::toString

inherited

Convert a particular sequence to a string.

Parameters

sequenceIndex

The position of the sequence.

Returns

A string describing the content of the sequence.

Exceptions

IndexOutOfBoundsException

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

toString() [3/3]

std::string bpp::VectorProbabilisticSequenceContainer::toString ( size_t  sequenceIndex ) const

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 119 of file VectorProbabilisticSequenceContainer.h.

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

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< ProbabilisticSequence >::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.

Referenced by bpp::MappedNamedContainer< T >::addObject(), bpp::MappedNamedContainer< T >::addObject_(), bpp::MappedNamedContainer< T >::changeName(), bpp::MappedNamedContainer< T >::clear(), bpp::MappedNamedContainer< T >::deleteObject(), bpp::MappedNamedContainer< T >::getObject(), bpp::MappedNamedContainer< T >::getObjectNames(), bpp::MappedNamedContainer< T >::getSize(), bpp::MappedNamedContainer< T >::hasObject(), bpp::MappedNamedContainer< T >::operator=(), and bpp::MappedNamedContainer< T >::removeObject().

positions_

template<class T >

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

protectedinherited

Definition at line 73 of file VectorPositionedContainer.h.

Referenced by bpp::VectorPositionedContainer< T >::addObject(), bpp::VectorPositionedContainer< T >::addObject_(), bpp::VectorPositionedContainer< T >::appendObject(), bpp::VectorPositionedContainer< T >::clear(), bpp::VectorPositionedContainer< T >::deleteObject(), bpp::VectorPositionedContainer< T >::deleteObjects(), bpp::VectorPositionedContainer< T >::getObject(), bpp::VectorPositionedContainer< T >::getObject_(), bpp::VectorPositionedContainer< T >::getSize(), bpp::VectorPositionedContainer< T >::insertObject(), bpp::VectorPositionedContainer< T >::isAvailablePosition(), bpp::VectorPositionedContainer< T >::nullify(), bpp::VectorPositionedContainer< T >::operator=(), bpp::VectorPositionedContainer< T >::removeObject(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::VectorPositionedContainer< T >::~VectorPositionedContainer().

vNames_

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

privateinherited

Definition at line 79 of file VectorMappedContainer.h.

---

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

• Bpp/Seq/Container/VectorProbabilisticSequenceContainer.h
• Bpp/Seq/Container/VectorProbabilisticSequenceContainer.cpp