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

Inheritance diagram for bpp::VectorSiteContainer:

Collaboration diagram for bpp::VectorSiteContainer:

Public Member Functions
	VectorSiteContainer (const std::vector< const Site > &vs, const Alphabet alpha, bool checkPositions=true) throw (Exception)
	Build a new container from a set of sites. More...

	VectorSiteContainer (size_t size, const Alphabet *alpha)
	Build a new empty container with specified size. More...

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

	VectorSiteContainer (const Alphabet *alpha)
	Build a new empty container. More...

	VectorSiteContainer (const VectorSiteContainer &vsc)

	VectorSiteContainer (const SiteContainer &sc)

	VectorSiteContainer (const OrderedSequenceContainer &osc)

	VectorSiteContainer (const SequenceContainer &sc)

VectorSiteContainer &	operator= (const VectorSiteContainer &vsc)

VectorSiteContainer &	operator= (const SiteContainer &sc)

VectorSiteContainer &	operator= (const OrderedSequenceContainer &osc)

VectorSiteContainer &	operator= (const SequenceContainer &sc)

virtual	~VectorSiteContainer ()

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

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

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

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

The Clonable interface.
VectorSiteContainer *	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)
	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...

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

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

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

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

const Sequence &	getSequence (const std::string &name) const throw (SequenceNotFoundException)
	Retrieve a sequence object from the container. More...

bool	hasSequence (const std::string &name) const
	Check if a sequence with a given name is present in the container. More...

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

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

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

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

VectorSiteContainer *	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...

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...

void	setComments (const std::string &name, const Comments &comments) throw (SequenceNotFoundException)
	Set the 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
void	realloc (size_t n)

Protected Attributes
std::vector< Site * >	sites_

std::vector< std::string >	names_

std::vector< Comments * >	comments_

std::vector< Sequence * >	sequences_

Detailed Description

The VectorSiteContainer class.

Sites are stored in a std::vector of pointers. Site access is hence in $O(1)$ , and sequence access in $O(l)$ , where $l$ is the number of sites in the container.

See AlignedSequenceContainer for an alternative implementation.

See also: Sequence, Site, AlignedSequenceContainer

Definition at line 68 of file VectorSiteContainer.h.

Constructor & Destructor Documentation

◆ VectorSiteContainer() [1/8]

VectorSiteContainer::VectorSiteContainer	(	const std::vector< const Site *> &	vs,
		const Alphabet *	alpha,
		bool	checkPositions = `true`
	)
throw	(	Exception
	)

Build a new container from a set of sites.

Parameters

vs	A std::vector of sites.
alpha	The common alphabet for all sites.
checkPositions	Check for the redundancy of site position tag. This may turn to be very time consuming!

Exceptions

Exception If sites differ in size or in alphabet.

Class constructors:

Definition at line 52 of file VectorSiteContainer.cpp.

Referenced by clone(), and createEmptyContainer().

◆ VectorSiteContainer() [2/8]

VectorSiteContainer::VectorSiteContainer	(	size_t	size,
		const Alphabet *	alpha
	)

Build a new empty container with specified size.

Parameters

size	Number of sequences in the container.
alpha	The alphabet for this container.

Definition at line 85 of file VectorSiteContainer.cpp.

References comments_, and names_.

◆ VectorSiteContainer() [3/8]

VectorSiteContainer::VectorSiteContainer	(	const std::vector< std::string > &	names,
		const Alphabet *	alpha
	)

Build a new empty container with specified sequence names.

Parameters

names	Sequence names. This will set the number of sequences in the container.
alpha	The alphabet for this container.

Definition at line 102 of file VectorSiteContainer.cpp.

References comments_, and names_.

◆ VectorSiteContainer() [4/8]

VectorSiteContainer::VectorSiteContainer ( const Alphabet * alpha )

Build a new empty container.

Parameters

alpha The alphabet for this container.

Definition at line 119 of file VectorSiteContainer.cpp.

◆ VectorSiteContainer() [5/8]

VectorSiteContainer::VectorSiteContainer ( const VectorSiteContainer & vsc )

Definition at line 129 of file VectorSiteContainer.cpp.

References addSite(), comments_, bpp::AbstractSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), and getSite().

◆ VectorSiteContainer() [6/8]

VectorSiteContainer::VectorSiteContainer ( const SiteContainer & sc )

Definition at line 150 of file VectorSiteContainer.cpp.

References addSite(), comments_, bpp::OrderedSequenceContainer::getComments(), bpp::OrderedSequenceContainer::getNumberOfSequences(), bpp::SiteContainer::getNumberOfSites(), and bpp::SiteContainer::getSite().

◆ VectorSiteContainer() [7/8]

VectorSiteContainer::VectorSiteContainer ( const OrderedSequenceContainer & osc )

Definition at line 171 of file VectorSiteContainer.cpp.

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

◆ VectorSiteContainer() [8/8]

VectorSiteContainer::VectorSiteContainer ( const SequenceContainer & sc )

Definition at line 187 of file VectorSiteContainer.cpp.

References addSequence(), bpp::SequenceContainer::getSequence(), bpp::SequenceContainer::getSequencesNames(), and reindexSites().

◆ ~VectorSiteContainer()

virtual bpp::VectorSiteContainer::~VectorSiteContainer ( )

inlinevirtual

Definition at line 122 of file VectorSiteContainer.h.

References clear().

Member Function Documentation

◆ addSequence() [1/2]

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

virtual

Add a sequence to the container.

Parameters

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

Exceptions

Exception Any other kind of exception, if the name of the sequence is already used, are whatever else depending on the implementation.

Implements bpp::SequenceContainer.

Definition at line 690 of file VectorSiteContainer.cpp.

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

◆ addSequence() [2/2]

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

Definition at line 730 of file VectorSiteContainer.cpp.

◆ addSite() [1/4]

void VectorSiteContainer::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 363 of file VectorSiteContainer.cpp.

Referenced by bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SiteContainerTools::sampleSites(), and VectorSiteContainer().

◆ addSite() [2/4]

void VectorSiteContainer::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 392 of file VectorSiteContainer.cpp.

References bpp::Site::setPosition().

◆ addSite() [3/4]

void VectorSiteContainer::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 421 of file VectorSiteContainer.cpp.

◆ addSite() [4/4]

void VectorSiteContainer::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 454 of file VectorSiteContainer.cpp.

References bpp::Site::setPosition().

◆ clear()

void VectorSiteContainer::clear ( )

virtual

Delete all sequences in the container.

Implements bpp::SequenceContainer.

Definition at line 769 of file VectorSiteContainer.cpp.

References comments_, names_, sequences_, and sites_.

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

◆ clone()

VectorSiteContainer* bpp::VectorSiteContainer::clone ( ) const

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 130 of file VectorSiteContainer.h.

References VectorSiteContainer().

◆ createEmptyContainer()

VectorSiteContainer * VectorSiteContainer::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 854 of file VectorSiteContainer.cpp.

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

◆ 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 VectorSiteContainer::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 660 of file VectorSiteContainer.cpp.

◆ deleteSequence() [2/2]

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

virtual

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 681 of file VectorSiteContainer.cpp.

◆ deleteSite()

void VectorSiteContainer::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 340 of file VectorSiteContainer.cpp.

◆ deleteSites()

void VectorSiteContainer::deleteSites	(	size_t	siteIndex,
		size_t	length
	)
throw	(	IndexOutOfBoundsException
	)

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 350 of file VectorSiteContainer.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(), createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), and 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(), operator=(), bpp::CompressedVectorSiteContainer::operator=(), and 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(), 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::VectorSiteContainer::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 176 of file VectorSiteContainer.h.

References names_.

Referenced by bpp::SequenceApplicationTools::getSiteContainer(), operator=(), valueAt(), and VectorSiteContainer().

◆ getNumberOfSites()

size_t VectorSiteContainer::getNumberOfSites ( ) const

virtual

Get the number of sites in the container.

Returns: The number of sites in the container.

Implements bpp::SiteContainer.

Definition at line 487 of file VectorSiteContainer.cpp.

References sites_.

Referenced by bpp::SequenceApplicationTools::getSiteContainer(), operator=(), valueAt(), and VectorSiteContainer().

◆ getSequence() [1/2]

const Sequence & VectorSiteContainer::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 517 of file VectorSiteContainer.cpp.

Referenced by bpp::SequenceApplicationTools::getSiteContainer().

◆ getSequence() [2/2]

const Sequence & VectorSiteContainer::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 537 of file VectorSiteContainer.cpp.

◆ getSequencePosition()

size_t VectorSiteContainer::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 559 of file VectorSiteContainer.cpp.

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

◆ getSequencesNames()

vector< string > VectorSiteContainer::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 813 of file VectorSiteContainer.cpp.

References names_.

Referenced by operator=().

◆ getSite()

const Site & VectorSiteContainer::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 290 of file VectorSiteContainer.cpp.

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

◆ getSitePositions()

Vint VectorSiteContainer::getSitePositions ( ) const

virtual

Get all position attributes of sites.

Returns: A vector with all site positions.

Implements bpp::SiteContainer.

Definition at line 505 of file VectorSiteContainer.cpp.

References sites_.

◆ hasSequence()

bool VectorSiteContainer::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 546 of file VectorSiteContainer.cpp.

References names_.

◆ operator()() [1/4]

int& bpp::VectorSiteContainer::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 196 of file VectorSiteContainer.h.

References getSequencePosition(), and sites_.

◆ operator()() [2/4]

const int& bpp::VectorSiteContainer::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 200 of file VectorSiteContainer.h.

References getSequencePosition(), and sites_.

◆ operator()() [3/4]

int& bpp::VectorSiteContainer::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 217 of file VectorSiteContainer.h.

References sites_.

◆ operator()() [4/4]

const int& bpp::VectorSiteContainer::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 221 of file VectorSiteContainer.h.

References sites_.

◆ operator=() [1/4]

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

Definition at line 204 of file VectorSiteContainer.cpp.

References addSite(), clear(), comments_, bpp::AbstractSequenceContainer::getComments(), getNumberOfSequences(), getNumberOfSites(), getSequencesNames(), getSite(), names_, bpp::AbstractSequenceContainer::operator=(), sequences_, and setSequencesNames().

◆ operator=() [2/4]

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

Definition at line 230 of file VectorSiteContainer.cpp.

References addSite(), clear(), comments_, bpp::OrderedSequenceContainer::getComments(), bpp::OrderedSequenceContainer::getNumberOfSequences(), bpp::SiteContainer::getNumberOfSites(), bpp::OrderedSequenceContainer::getSequencesNames(), bpp::SiteContainer::getSite(), names_, bpp::AbstractSequenceContainer::operator=(), sequences_, and setSequencesNames().

◆ operator=() [3/4]

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

Definition at line 256 of file VectorSiteContainer.cpp.

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

◆ operator=() [4/4]

VectorSiteContainer & VectorSiteContainer::operator= ( const SequenceContainer & sc )

Definition at line 273 of file VectorSiteContainer.cpp.

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

◆ realloc()

void VectorSiteContainer::realloc ( size_t n )

protected

Definition at line 800 of file VectorSiteContainer.cpp.

References clear(), bpp::AbstractSequenceContainer::getAlphabet(), reindexSites(), and sites_.

◆ reindexSites()

void VectorSiteContainer::reindexSites ( )

virtual

Set all positions attributes.

Implements bpp::SiteContainer.

Definition at line 494 of file VectorSiteContainer.cpp.

References sites_.

Referenced by bpp::SequenceApplicationTools::getSiteContainer(), operator=(), realloc(), and VectorSiteContainer().

◆ removeSequence() [1/2]

Sequence * VectorSiteContainer::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 625 of file VectorSiteContainer.cpp.

References bpp::SymbolList::deleteElement().

◆ removeSequence() [2/2]

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

virtual

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 651 of file VectorSiteContainer.cpp.

◆ removeSite()

Site * VectorSiteContainer::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 329 of file VectorSiteContainer.cpp.

◆ setComments() [1/2]

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

virtualinherited

Set the comments of a particular sequence.

Parameters

name	The name of the sequence.
comments	The comments to set to sequence with name 'name'.

Exceptions

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

Implements bpp::OrderedSequenceContainer.

Reimplemented in bpp::VectorSequenceContainer.

Definition at line 48 of file AbstractSequenceContainer.cpp.

Referenced by bpp::VectorSequenceContainer::setComments().

◆ setComments() [2/2]

void VectorSiteContainer::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 847 of file VectorSiteContainer.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(), createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

◆ setSequence() [1/2]

void VectorSiteContainer::setSequence	(	const std::string &	name,
		const Sequence &	sequence,
		bool	checkName
	)
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 572 of file VectorSiteContainer.cpp.

◆ setSequence() [2/2]

void VectorSiteContainer::setSequence	(	size_t	sequenceIndex,
		const Sequence &	sequence,
		bool	checkName
	)
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 581 of file VectorSiteContainer.cpp.

◆ setSequencesNames()

void VectorSiteContainer::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 820 of file VectorSiteContainer.cpp.

Referenced by bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), and bpp::SiteContainerTools::resolveDottedAlignment().

◆ setSite()

void VectorSiteContainer::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 299 of file VectorSiteContainer.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::VectorSiteContainer::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 186 of file VectorSiteContainer.h.

References getNumberOfSites(), getSequencePosition(), and sites_.

◆ valueAt() [2/4]

const int& bpp::VectorSiteContainer::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 191 of file VectorSiteContainer.h.

References getNumberOfSites(), getSequencePosition(), and sites_.

◆ valueAt() [3/4]

int& bpp::VectorSiteContainer::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 205 of file VectorSiteContainer.h.

References getNumberOfSequences(), getNumberOfSites(), and sites_.

◆ valueAt() [4/4]

const int& bpp::VectorSiteContainer::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 211 of file VectorSiteContainer.h.

References getNumberOfSequences(), getNumberOfSites(), and sites_.

Member Data Documentation

◆ comments_

std::vector<Comments*> bpp::VectorSiteContainer::comments_

protected

Definition at line 77 of file VectorSiteContainer.h.

Referenced by clear(), operator=(), and VectorSiteContainer().

◆ names_

std::vector<std::string> bpp::VectorSiteContainer::names_

protected

Definition at line 76 of file VectorSiteContainer.h.

Referenced by clear(), getNumberOfSequences(), getSequencesNames(), hasSequence(), operator=(), and VectorSiteContainer().

◆ sequences_

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

mutableprotected

Definition at line 78 of file VectorSiteContainer.h.

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

◆ sites_

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

protected

Definition at line 75 of file VectorSiteContainer.h.

Referenced by clear(), getNumberOfSites(), getSitePositions(), operator()(), realloc(), reindexSites(), and valueAt().

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

Bpp/Seq/Container/VectorSiteContainer.h
Bpp/Seq/Container/VectorSiteContainer.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VectorSiteContainer() [1/8]

◆ VectorSiteContainer() [2/8]

◆ VectorSiteContainer() [3/8]

◆ VectorSiteContainer() [4/8]

◆ VectorSiteContainer() [5/8]

◆ VectorSiteContainer() [6/8]

◆ VectorSiteContainer() [7/8]

◆ VectorSiteContainer() [8/8]

◆ ~VectorSiteContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ addSite() [1/4]

◆ addSite() [2/4]

◆ addSite() [3/4]

◆ addSite() [4/4]

◆ 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]

◆ getSequencePosition()

◆ getSequencesNames()

◆ getSite()

◆ getSitePositions()

◆ hasSequence()

◆ operator()() [1/4]

◆ operator()() [2/4]

◆ operator()() [3/4]

◆ operator()() [4/4]

◆ operator=() [1/4]

◆ operator=() [2/4]

◆ operator=() [3/4]

◆ operator=() [4/4]

◆ realloc()

◆ 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

◆ comments_

◆ names_

◆ sequences_

◆ sites_