Aligned sequences container. More...

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

Inheritance diagram for bpp::AlignedSequenceContainer:

Collaboration diagram for bpp::AlignedSequenceContainer:

Public Member Functions
	AlignedSequenceContainer (const Alphabet *alpha)
	Build a new empty container with the specified alphabet. More...

	AlignedSequenceContainer (const AlignedSequenceContainer &asc)
	Copy constructor. More...

	AlignedSequenceContainer (const SiteContainer &sc)
	Convert any SiteContainer object into a AlignedSequenceContainer object. More...

	AlignedSequenceContainer (const OrderedSequenceContainer &osc) throw (SequenceNotAlignedException)
	Try to coerce an OrderedSequenceContainer object into an AlignedSequenceContainer object. More...

AlignedSequenceContainer &	operator= (const AlignedSequenceContainer &asc)

AlignedSequenceContainer &	operator= (const SiteContainer &sc)

AlignedSequenceContainer &	operator= (const OrderedSequenceContainer &osc) throw (SequenceNotAlignedException)

virtual	~AlignedSequenceContainer ()

The Clonable interface.
AlignedSequenceContainer *	clone () const

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

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

Site *	removeSite (size_t siteIndex) throw (IndexOutOfBoundsException)
	Remove a site from the container. More...

void	deleteSite (size_t siteIndex) throw (IndexOutOfBoundsException)
	Delete a site in the container. More...

void	deleteSites (size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception)
	Delete a continuous range of sites in the container. More...

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

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

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

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

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

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

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

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

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

Redefinition of VectorSequenceContainer methods, to check for sequence lengths.
void	setSequence (const std::string &name, const Sequence &sequence, bool checkName=true) throw (Exception)
	Replace a sequence in the container. More...

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

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

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

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...

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...

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

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...

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
bool	checkSize_ (const Sequence &sequence)
	Check sequence's size before insertion in sequence container. More...

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

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

Private Attributes
std::vector< int >	positions_

size_t	length_

std::vector< Site * >	sites_

Detailed Description

Aligned sequences container.

This class inherits from the VectorSequenceContainer and add site access. Sequence addition methods are re-defined to check for sequence lengths. Sequence access is in $O(1)$ , and site access in $O(n)$ , where $n$ is the number of sequences in the container.

See VectorSiteContainer for an alternative implementation.

See also: VectorSequenceContainer, Sequence, Site, VectorSiteContainer

Definition at line 68 of file AlignedSequenceContainer.h.

Constructor & Destructor Documentation

◆ AlignedSequenceContainer() [1/4]

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

inline

Build a new empty container with the specified alphabet.

Parameters

alpha The alphabet to use.

Definition at line 95 of file AlignedSequenceContainer.h.

References reindexSites().

Referenced by clone().

◆ AlignedSequenceContainer() [2/4]

bpp::AlignedSequenceContainer::AlignedSequenceContainer ( const AlignedSequenceContainer & asc )

inline

Copy constructor.

Parameters

asc	The container to copy.

Definition at line 109 of file AlignedSequenceContainer.h.

◆ AlignedSequenceContainer() [3/4]

bpp::AlignedSequenceContainer::AlignedSequenceContainer ( const SiteContainer & sc )

inline

Convert any SiteContainer object into a AlignedSequenceContainer object.

Parameters

sc	The container to copy.

Definition at line 121 of file AlignedSequenceContainer.h.

◆ AlignedSequenceContainer() [4/4]

AlignedSequenceContainer::AlignedSequenceContainer	(	const OrderedSequenceContainer &	osc	)
throw	(	SequenceNotAlignedException
	)

Try to coerce an OrderedSequenceContainer object into an AlignedSequenceContainer object.

Sequences in osc will be considered alligned, and have the same number of sites.

Parameters

osc	The ordered container to coerce.

Exceptions

SequenceNotAlignedException If sequences in osc do not have the same length.

Definition at line 54 of file AlignedSequenceContainer.cpp.

◆ ~AlignedSequenceContainer()

AlignedSequenceContainer::~AlignedSequenceContainer ( )

virtual

Class destructor:

Definition at line 121 of file AlignedSequenceContainer.cpp.

Member Function Documentation

◆ addSequence() [1/2]

void AlignedSequenceContainer::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.

Reimplemented from bpp::VectorSequenceContainer.

Definition at line 474 of file AlignedSequenceContainer.cpp.

References bpp::VectorSequenceContainer::addSequence().

Referenced by bpp::SiteContainerTools::alignNW().

◆ addSequence() [2/2]

void AlignedSequenceContainer::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 from bpp::VectorSequenceContainer.

Definition at line 491 of file AlignedSequenceContainer.cpp.

References bpp::VectorSequenceContainer::addSequence().

◆ addSite() [1/4]

void AlignedSequenceContainer::addSite	(	const Site &	site,
		bool	checkPosition = `true`
	)
throw	(	Exception
	)

virtual

Add a site in the container.

Parameters

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

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 271 of file AlignedSequenceContainer.cpp.

◆ addSite() [2/4]

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

virtual

Add a site in the container.

Parameters

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

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 312 of file AlignedSequenceContainer.cpp.

◆ addSite() [3/4]

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

virtual

Add a site in the container.

Parameters

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

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 352 of file AlignedSequenceContainer.cpp.

◆ addSite() [4/4]

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

virtual

Add a site in the container.

Parameters

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

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 394 of file AlignedSequenceContainer.cpp.

◆ checkSize_()

bool bpp::AlignedSequenceContainer::checkSize_ ( const Sequence & sequence )

inlineprotected

Check sequence's size before insertion in sequence container.

Parameters

sequence The sequence to check.

Returns: True if sequence length = number of sites in container.

Definition at line 195 of file AlignedSequenceContainer.h.

References length_.

◆ clear()

void AlignedSequenceContainer::clear ( )

virtual

Delete all sequences in the container.

Implements bpp::SequenceContainer.

Definition at line 506 of file AlignedSequenceContainer.cpp.

References bpp::VectorSequenceContainer::clear().

◆ clone()

AlignedSequenceContainer* bpp::AlignedSequenceContainer::clone ( ) const

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 151 of file AlignedSequenceContainer.h.

References AlignedSequenceContainer().

◆ createEmptyContainer()

AlignedSequenceContainer * AlignedSequenceContainer::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 514 of file AlignedSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::setGeneralComments().

◆ 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
	)

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequencePosition().

◆ deleteSequence() [2/2]

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

virtualinherited

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.

◆ deleteSite()

void AlignedSequenceContainer::deleteSite	(	size_t	siteIndex	)
throw	(	IndexOutOfBoundsException
	)

virtual

Delete a site in the container.

Parameters

siteIndex The position of the site in the container.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 220 of file AlignedSequenceContainer.cpp.

◆ deleteSites()

void AlignedSequenceContainer::deleteSites	(	size_t	siteIndex,
		size_t	length
	)
throw	(	IndexOutOfBoundsException,
		Exception
	)

virtual

Delete a continuous range of sites in the container.

Parameters

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

Exceptions

IndexOutOfBoundsException If the specified range is not valid.

Implements bpp::SiteContainer.

Definition at line 243 of file AlignedSequenceContainer.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(), bpp::VectorSequenceContainer::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(), bpp::VectorSequenceContainer::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 bpp::VectorSequenceContainer::getSequencesNames(), and bpp::VectorSequenceContainer::hasSequence().

◆ getNumberOfSequences()

size_t bpp::VectorSequenceContainer::getNumberOfSequences ( ) const

inlinevirtualinherited

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 bpp::VectorSequenceContainer::sequences_.

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

◆ getNumberOfSites()

size_t bpp::AlignedSequenceContainer::getNumberOfSites ( ) const

inlinevirtual

Get the number of sites in the container.

Returns: The number of sites in the container.

Implements bpp::SiteContainer.

Definition at line 168 of file AlignedSequenceContainer.h.

References length_.

Referenced by operator=().

◆ getSequence() [1/2]

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

virtualinherited

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 bpp::VectorSequenceContainer::operator()(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSequenceContainer::valueAt(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

◆ getSequence() [2/2]

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

virtualinherited

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
	)

protectedinherited

Definition at line 194 of file VectorSequenceContainer.cpp.

Referenced by bpp::VectorSequenceContainer::operator()(), and bpp::VectorSequenceContainer::valueAt().

◆ getSequence_() [2/2]

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

protectedinherited

Definition at line 204 of file VectorSequenceContainer.cpp.

◆ getSequencePosition()

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

virtualinherited

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 bpp::VectorSequenceContainer::deleteSequence(), bpp::VectorSequenceContainer::removeSequence(), and bpp::VectorSequenceContainer::setSequence().

◆ getSequencesNames()

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

virtualinherited

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 bpp::VectorSequenceContainer::sequences_.

◆ getSite()

const Site & AlignedSequenceContainer::getSite	(	size_t	siteIndex	)	const
throw	(	IndexOutOfBoundsException
	)

virtual

Get a site from the container.

Parameters

siteIndex The position of the site in the container.

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

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 133 of file AlignedSequenceContainer.cpp.

◆ getSitePositions()

Vint bpp::AlignedSequenceContainer::getSitePositions ( ) const

inlinevirtual

Get all position attributes of sites.

Returns: A vector with all site positions.

Implements bpp::SiteContainer.

Definition at line 169 of file AlignedSequenceContainer.h.

References positions_.

Referenced by operator=().

◆ hasSequence()

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

virtualinherited

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 bpp::VectorSequenceContainer::sequences_.

◆ operator()() [1/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence_().

◆ operator()() [2/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence().

◆ operator()() [3/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence_().

◆ operator()() [4/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence().

◆ operator=() [1/3]

AlignedSequenceContainer & AlignedSequenceContainer::operator= ( const AlignedSequenceContainer & asc )

Definition at line 79 of file AlignedSequenceContainer.cpp.

References getNumberOfSites(), getSitePositions(), and bpp::VectorSequenceContainer::operator=().

◆ operator=() [2/3]

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

Definition at line 93 of file AlignedSequenceContainer.cpp.

References bpp::SiteContainer::getNumberOfSites(), bpp::SiteContainer::getSitePositions(), and bpp::VectorSequenceContainer::operator=().

◆ operator=() [3/3]

AlignedSequenceContainer & AlignedSequenceContainer::operator=	(	const OrderedSequenceContainer &	osc	)
throw	(	SequenceNotAlignedException
	)

Definition at line 107 of file AlignedSequenceContainer.cpp.

References bpp::VectorSequenceContainer::operator=().

◆ reindexSites()

void AlignedSequenceContainer::reindexSites ( )

virtual

Set all positions attributes.

Implements bpp::SiteContainer.

Definition at line 435 of file AlignedSequenceContainer.cpp.

Referenced by AlignedSequenceContainer().

◆ removeSequence() [1/2]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequencePosition().

◆ removeSequence() [2/2]

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

virtualinherited

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.

◆ removeSite()

Site * AlignedSequenceContainer::removeSite	(	size_t	siteIndex	)
throw	(	IndexOutOfBoundsException
	)

virtual

Remove a site from the container.

The site is not deleted, a pointer toward it is returned.

Parameters

siteIndex The position of the site in the container.

Returns: A pointer toward site i in the alignment.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 190 of file AlignedSequenceContainer.cpp.

References bpp::BasicSymbolList::deleteElement().

◆ setComments() [1/2]

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

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.

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
	)

virtualinherited

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

◆ setSequence() [1/2]

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

virtual

Replace a sequence in the container.

Parameters

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

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 461 of file AlignedSequenceContainer.cpp.

References bpp::VectorSequenceContainer::setSequence().

◆ setSequence() [2/2]

void AlignedSequenceContainer::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 446 of file AlignedSequenceContainer.cpp.

References bpp::VectorSequenceContainer::setSequence().

◆ setSequencesNames()

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

virtualinherited

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.

◆ setSite()

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

virtual

Set a site in the container.

Parameters

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

Exceptions

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

Implements bpp::SiteContainer.

Definition at line 154 of file AlignedSequenceContainer.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
	)

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence_().

◆ valueAt() [2/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence().

◆ valueAt() [3/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence_().

◆ valueAt() [4/4]

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

inlinevirtualinherited

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 bpp::VectorSequenceContainer::getSequence().

Member Data Documentation

◆ length_

size_t bpp::AlignedSequenceContainer::length_

private

Definition at line 76 of file AlignedSequenceContainer.h.

Referenced by checkSize_(), and getNumberOfSites().

◆ positions_

std::vector<int> bpp::AlignedSequenceContainer::positions_

private

Definition at line 74 of file AlignedSequenceContainer.h.

Referenced by getSitePositions().

◆ sites_

std::vector<Site*> bpp::AlignedSequenceContainer::sites_

mutableprivate

This is used in order to implement the SiteContainer interface. A SiteContainer is expected to work on Site objects, but this class – since it is a VectorSequenceContainer – has its data sored as Sequence object. When the SiteContainer method getSite() is invoked it creates a new Site object and send the address of it. To avoid memory leaks, this object is put into a std::vector so that it can be destroyed when the container is destroyed.

Definition at line 87 of file AlignedSequenceContainer.h.

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

Bpp/Seq/Container/AlignedSequenceContainer.h
Bpp/Seq/Container/AlignedSequenceContainer.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AlignedSequenceContainer() [1/4]

◆ AlignedSequenceContainer() [2/4]

◆ AlignedSequenceContainer() [3/4]

◆ AlignedSequenceContainer() [4/4]

◆ ~AlignedSequenceContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ addSite() [1/4]

◆ addSite() [2/4]

◆ addSite() [3/4]

◆ addSite() [4/4]

◆ checkSize_()

◆ clear()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ deleteSite()

◆ deleteSites()

◆ getAlphabet()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getGeneralComments()

◆ getName()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getSequence() [1/2]

◆ getSequence() [2/2]

◆ getSequence_() [1/2]

◆ getSequence_() [2/2]

◆ getSequencePosition()

◆ getSequencesNames()

◆ getSite()

◆ getSitePositions()

◆ hasSequence()

◆ operator()() [1/4]

◆ operator()() [2/4]

◆ operator()() [3/4]

◆ operator()() [4/4]

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ reindexSites()

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ removeSite()

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setGeneralComments()

◆ setSequence() [1/2]

◆ setSequence() [2/2]

◆ setSequencesNames()

◆ setSite()

◆ toString() [1/2]

◆ toString() [2/2]

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ length_

◆ positions_

◆ sites_