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< const Sequence > &vs, const Alphabet alpha) throw (AlphabetMismatchException)
	Build a new container from a std::vector of pointers toward sequence objects. 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...

virtual	~VectorSequenceContainer ()
	Container destructor: delete all sequences in the container. 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.
Clonable *	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 Sequence &	getSequence (const std::string &name) const throw (SequenceNotFoundException)
	Retrieve a sequence object from the container. More...

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

Sequence *	removeSequence (const std::string &name) throw (SequenceNotFoundException)
	Extract (and remove) a sequence from the container. More...

void	deleteSequence (const std::string &name) throw (SequenceNotFoundException)
	Delete a sequence of the container. More...

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

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

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

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

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

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

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

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

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

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

const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
	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.
void	setComments (const std::string &name, const Comments &comments) throw (SequenceNotFoundException)
	Set the comments of a particular sequence. More...

void	setComments (size_t sequenceIndex, const Comments &comments) throw (IndexOutOfBoundsException)
	Set the comments of a particular sequence. More...

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

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

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

Sequence *	removeSequence (size_t sequenceIndex) throw (IndexOutOfBoundsException)
	Extract (and remove) a sequence from the container. More...

void	deleteSequence (size_t sequenceIndex) throw (IndexOutOfBoundsException)
	Delete a sequence of the container. More...

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

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

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

const std::vector< int > &	getContent (const std::string &name) const throw (SequenceNotFoundException)
	Get the content of a sequence. More...

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

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

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

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

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

From the OrderedSequenceContainer interface
virtual const std::vector< int > &	getContent (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get the content of a sequence. More...

virtual std::string	toString (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Convert a particular sequence to a string. More...

virtual const Comments &	getComments (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get comments of a particular sequence. More...

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

Protected Member Functions
AbstractSequenceContainer methods.
Sequence &	getSequence_ (size_t i) throw (IndexOutOfBoundsException)

Sequence &	getSequence_ (const std::string &name) throw (SequenceNotFoundException)

Private Attributes
std::vector< Sequence * >	sequences_
	A std::vector of pointers toward the sequences stored in the container. More...

Detailed Description

The VectorSequenceContainer class.

This is the simplest implementation of the OrderedSequenceContainer interface. Sequences are stored in a std::vector of pointers. The container is responsible for the creation and destruction of the sequence objects it contains.

Definition at line 63 of file VectorSequenceContainer.h.

Constructor & Destructor Documentation

◆ VectorSequenceContainer() [1/5]

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

Build a new container from a std::vector of pointers toward sequence objects.

The addSequence() method is called uppon each Sequence object, hence each sequence is copied into the container.

Parameters

vs	The std::vector of pointers toward sequence objects.
alpha	The alphabet to all sequences.

Exceptions

AlphabetMismatchException if one sequence does not match the specified alphabet.

Class constructors:

Definition at line 49 of file VectorSequenceContainer.cpp.

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 94 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 64 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.

Definition at line 76 of file VectorSequenceContainer.cpp.

References addSequence(), bpp::OrderedSequenceContainer::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.

Definition at line 88 of file VectorSequenceContainer.cpp.

References addSequence(), bpp::SequenceContainer::getGeneralComments(), bpp::SequenceContainer::getSequence(), bpp::SequenceContainer::getSequencesNames(), and bpp::AbstractSequenceContainer::setGeneralComments().

◆ ~VectorSequenceContainer()

virtual bpp::VectorSequenceContainer::~VectorSequenceContainer ( )

inlinevirtual

Container destructor: delete all sequences in the container.

Definition at line 149 of file VectorSequenceContainer.h.

References clear().

Member Function Documentation

◆ addSequence() [1/2]

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

virtual

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.

Exceptions

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

Implements bpp::SequenceContainer.

Reimplemented in bpp::AlignedSequenceContainer.

Definition at line 284 of file VectorSequenceContainer.cpp.

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

◆ addSequence() [2/2]

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

virtual

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 307 of file VectorSequenceContainer.cpp.

◆ clear()

void VectorSequenceContainer::clear ( )

virtual

Delete all sequences in the container.

Implements bpp::SequenceContainer.

Definition at line 371 of file VectorSequenceContainer.cpp.

References sequences_.

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

◆ clone()

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

inline

Definition at line 158 of file VectorSequenceContainer.h.

References VectorSequenceContainer().

◆ createEmptyContainer()

VectorSequenceContainer * VectorSequenceContainer::createEmptyContainer ( ) const

virtual

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

This method creates a new SequenceContainer 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::SequenceContainer.

Definition at line 391 of file VectorSequenceContainer.cpp.

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

◆ deleteGeneralComments()

void bpp::AbstractSequenceContainer::deleteGeneralComments ( )

inlinevirtualinherited

Delete the comments associated to this container.

Implements bpp::SequenceContainer.

Definition at line 150 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::comments_.

◆ deleteSequence() [1/2]

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

inlinevirtual

Delete a sequence of the container.

Parameters

name	The name of the sequence.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 180 of file VectorSequenceContainer.h.

References getSequencePosition().

◆ deleteSequence() [2/2]

void VectorSequenceContainer::deleteSequence	(	size_t	sequenceIndex	)
throw	(	IndexOutOfBoundsException
	)

virtual

Delete a sequence of the container.

Parameters

sequenceIndex The position of the sequence.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 272 of file VectorSequenceContainer.cpp.

◆ getAlphabet()

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

inlinevirtualinherited

Get sequence container's alphabet.

Returns: The alphabet associated to this container.

Implements bpp::SequenceContainer.

Definition at line 123 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::alphabet_.

Referenced by bpp::MapSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), and bpp::VectorSiteContainer::realloc().

◆ getComments() [1/2]

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

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::OrderedSequenceContainer.

Definition at line 134 of file AbstractSequenceContainer.h.

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

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

◆ getComments() [2/2]

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

inlinevirtualinherited

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 177 of file AbstractSequenceContainer.h.

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

◆ getContent() [1/2]

const std::vector<int>& bpp::AbstractSequenceContainer::getContent	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

inlinevirtualinherited

Get the content of a sequence.

Parameters

name	The name of the sequence.

Returns: The content of the sequence as a vector of integers.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 124 of file AbstractSequenceContainer.h.

References bpp::SymbolList::getContent(), and bpp::OrderedSequenceContainer::getSequence().

Referenced by bpp::SequenceContainerTools::getCodonPosition().

◆ getContent() [2/2]

virtual const std::vector<int>& bpp::AbstractSequenceContainer::getContent	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtualinherited

Get the content of a sequence.

Parameters

sequenceIndex The position of the sequence.

Returns: The content of the sequence as a vector of integers.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 167 of file AbstractSequenceContainer.h.

References bpp::SymbolList::getContent(), and bpp::OrderedSequenceContainer::getSequence().

◆ getGeneralComments()

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

inlinevirtualinherited

Get the comments of this container.

Returns: The comments associated to this container.

Implements bpp::SequenceContainer.

Definition at line 140 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::comments_.

Referenced by bpp::MapSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), createEmptyContainer(), and bpp::CompressedVectorSiteContainer::createEmptyContainer().

◆ getName()

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

inlinevirtualinherited

Get the name of a particular 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::OrderedSequenceContainer.

Definition at line 162 of file AbstractSequenceContainer.h.

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

Referenced by getSequencesNames(), and hasSequence().

◆ 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::OrderedSequenceContainer.

Definition at line 185 of file VectorSequenceContainer.h.

References sequences_.

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

◆ getSequence() [1/2]

const Sequence & VectorSequenceContainer::getSequence	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

virtual

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns: A reference toward the Sequence with corresponding name.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 181 of file VectorSequenceContainer.cpp.

Referenced by operator()(), operator=(), valueAt(), and VectorSequenceContainer().

◆ getSequence() [2/2]

const Sequence & VectorSequenceContainer::getSequence	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

virtual

Retrieve a sequence object from the container.

Parameters

sequenceIndex The position of the sequence.

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

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 158 of file VectorSequenceContainer.cpp.

◆ getSequence_() [1/2]

Sequence & VectorSequenceContainer::getSequence_	(	size_t	i	)
throw	(	IndexOutOfBoundsException
	)

protected

Definition at line 194 of file VectorSequenceContainer.cpp.

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

◆ getSequence_() [2/2]

Sequence & VectorSequenceContainer::getSequence_	(	const std::string &	name	)
throw	(	SequenceNotFoundException
	)

protected

Definition at line 204 of file VectorSequenceContainer.cpp.

◆ getSequencePosition()

size_t VectorSequenceContainer::getSequencePosition	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

virtual

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::OrderedSequenceContainer.

Definition at line 217 of file VectorSequenceContainer.cpp.

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

◆ getSequencesNames()

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

virtual

Get all the names of the sequences in the container.

Returns: A vector of strings with all sequence names.

Implements bpp::OrderedSequenceContainer.

Definition at line 332 of file VectorSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getName(), and sequences_.

◆ hasSequence()

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

virtual

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::SequenceContainer.

Definition at line 168 of file VectorSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getName(), and sequences_.

◆ operator()() [1/4]

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 202 of file VectorSequenceContainer.h.

References getSequence_().

◆ operator()() [2/4]

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 207 of file VectorSequenceContainer.h.

References getSequence().

◆ operator()() [3/4]

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 222 of file VectorSequenceContainer.h.

References getSequence_().

◆ operator()() [4/4]

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 226 of file VectorSequenceContainer.h.

References getSequence().

◆ operator=() [1/3]

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

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

◆ operator=() [2/3]

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

Copy from an OrderedSequenceContainer.

Parameters

osc	The OrderedSequenceContainer to copy into this container.

Definition at line 121 of file VectorSequenceContainer.cpp.

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

◆ operator=() [3/3]

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

Copy from a SequenceContainer.

Parameters

osc	The SequenceContainer to copy into this container.

Definition at line 139 of file VectorSequenceContainer.cpp.

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

◆ removeSequence() [1/2]

Sequence* bpp::VectorSequenceContainer::removeSequence	(	const std::string &	name	)
throw	(	SequenceNotFoundException
	)

inlinevirtual

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 175 of file VectorSequenceContainer.h.

References getSequencePosition().

◆ removeSequence() [2/2]

Sequence * VectorSequenceContainer::removeSequence	(	size_t	sequenceIndex	)
throw	(	IndexOutOfBoundsException
	)

virtual

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex The position of the sequence.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Definition at line 258 of file VectorSequenceContainer.cpp.

◆ setComments() [1/2]

void bpp::VectorSequenceContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)
throw	(	SequenceNotFoundException
	)

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::AbstractSequenceContainer.

Definition at line 238 of file VectorSequenceContainer.h.

References bpp::AbstractSequenceContainer::setComments().

◆ setComments() [2/2]

void VectorSequenceContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)
throw	(	IndexOutOfBoundsException
	)

virtual

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.

Implements bpp::AbstractSequenceContainer.

Definition at line 384 of file VectorSequenceContainer.cpp.

◆ setGeneralComments()

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

inlinevirtualinherited

Set the comments of this container.

Parameters

comments The comments to be associated to this container.

Implements bpp::SequenceContainer.

Definition at line 145 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::comments_.

Referenced by bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::MapSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), and VectorSequenceContainer().

◆ setSequence() [1/2]

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

inlinevirtual

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.

Exceptions

SequenceNotFoundException	If the name does not match any sequence in the container.
Exception	Any other kind of exception, if the name of the sequence is already used, are whatever else depending on the implementation.

Implements bpp::OrderedSequenceContainer.

Definition at line 170 of file VectorSequenceContainer.h.

References getSequencePosition().

Referenced by bpp::AlignedSequenceContainer::setSequence().

◆ setSequence() [2/2]

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

virtual

Replace a sequence in the container.

Parameters

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

Exceptions

IndexOutOfBoundsException	If the position does not match any sequence in the container.
Exception	Any other kind of exception.

Implements bpp::OrderedSequenceContainer.

Definition at line 230 of file VectorSequenceContainer.cpp.

◆ setSequencesNames()

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

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::OrderedSequenceContainer.

Definition at line 344 of file VectorSequenceContainer.cpp.

◆ toString() [1/2]

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

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::OrderedSequenceContainer.

Definition at line 129 of file AbstractSequenceContainer.h.

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

◆ toString() [2/2]

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

inlinevirtualinherited

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 172 of file AbstractSequenceContainer.h.

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

◆ valueAt() [1/4]

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

inlinevirtual

Element access function.

Allows direct access to the data stored in the container.

Parameters

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

Exceptions

SequenceNotFoundException	If no corresponding sequence is found in the container.
IndexOutOfBoundsException	If the element position is not valid.

Implements bpp::OrderedSequenceContainer.

Definition at line 192 of file VectorSequenceContainer.h.

References getSequence_().

◆ valueAt() [2/4]

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

inlinevirtual

Element access function.

Allows direct access to the data stored in the container.

Parameters

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

Exceptions

SequenceNotFoundException	If no corresponding sequence is found in the container.
IndexOutOfBoundsException	If the element position is not valid.

Implements bpp::OrderedSequenceContainer.

Definition at line 197 of file VectorSequenceContainer.h.

References getSequence().

◆ valueAt() [3/4]

int& bpp::VectorSequenceContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)
throw	(	IndexOutOfBoundsException
	)

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.

Exceptions

IndexOutOfBoundsException If a position is not valid.

Implements bpp::OrderedSequenceContainer.

Definition at line 212 of file VectorSequenceContainer.h.

References getSequence_().

◆ valueAt() [4/4]

const int& bpp::VectorSequenceContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const
throw	(	IndexOutOfBoundsException
	)

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.

Exceptions

IndexOutOfBoundsException If a position is not valid.

Implements bpp::OrderedSequenceContainer.

Definition at line 217 of file VectorSequenceContainer.h.

References getSequence().

Member Data Documentation

◆ sequences_

std::vector<Sequence*> bpp::VectorSequenceContainer::sequences_

mutableprivate

A std::vector of pointers toward the sequences stored in the container.

Definition at line 71 of file VectorSequenceContainer.h.

Referenced by clear(), getNumberOfSequences(), getSequencesNames(), and hasSequence().

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

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VectorSequenceContainer() [1/5]

◆ VectorSequenceContainer() [2/5]

◆ VectorSequenceContainer() [3/5]

◆ VectorSequenceContainer() [4/5]

◆ VectorSequenceContainer() [5/5]

◆ ~VectorSequenceContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ clear()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ getAlphabet()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getGeneralComments()

◆ getName()

◆ getNumberOfSequences()

◆ getSequence() [1/2]

◆ getSequence() [2/2]

◆ getSequence_() [1/2]

◆ getSequence_() [2/2]

◆ getSequencePosition()

◆ getSequencesNames()

◆ hasSequence()

◆ operator()() [1/4]

◆ operator()() [2/4]

◆ operator()() [3/4]

◆ operator()() [4/4]

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setGeneralComments()

◆ setSequence() [1/2]

◆ setSequence() [2/2]

◆ setSequencesNames()

◆ toString() [1/2]

◆ toString() [2/2]

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ sequences_