#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.
	VectorSiteContainer (size_t size, const Alphabet *alpha)
	Build a new empty container with specified size.
	VectorSiteContainer (const std::vector< std::string > &names, const Alphabet *alpha)
	Build a new empty container with specified sequence names.
	VectorSiteContainer (const Alphabet *alpha)
	Build a new empty container.
	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)
	Assignation operator from any SequenceContainer object.
virtual	~VectorSiteContainer ()
void	addSequence (const Sequence &sequence, bool checkName=true) throw (Exception)
	Add a sequence to the container.
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.
void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName) throw (Exception)
	Replace a sequence in the container.
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.
void	setSite (size_t siteIndex, const Site &site, bool checkPosition=true) throw (Exception)
	Set a site in the container.
Site *	removeSite (size_t siteIndex) throw (IndexOutOfBoundsException)
	Remove a site from the container.
void	deleteSite (size_t siteIndex) throw (IndexOutOfBoundsException)
	Delete a site in the container.
void	deleteSites (size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
	Delete a continuous range of sites in the container.
void	addSite (const Site &site, bool checkPosition=true) throw (Exception)
	Add a site in the container.
void	addSite (const Site &site, int position, bool checkPosition=true) throw (Exception)
	Add a site in the container.
void	addSite (const Site &site, size_t siteIndex, bool checkPosition=true) throw (Exception)
	Add a site in the container.
void	addSite (const Site &site, size_t siteIndex, int position, bool checkPosition=true) throw (Exception)
	Add a site in the container.
size_t	getNumberOfSites () const
	Get the number of sites in the container.
void	reindexSites ()
	Set all positions attributes.
Vint	getSitePositions () const
	Get all position attributes of sites.
The SequenceContainer interface.
void	setComments (size_t sequenceIndex, const Comments &comments) throw (IndexOutOfBoundsException)
	Set the comments of a particular sequence.
const Sequence &	getSequence (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Retrieve a sequence object from the container.
const Sequence &	getSequence (const std::string &name) const throw (SequenceNotFoundException)
	Retrieve a sequence object from the container.
bool	hasSequence (const std::string &name) const
	Check if a sequence with a given name is present in the container.
size_t	getSequencePosition (const std::string &name) const throw (SequenceNotFoundException)
	Get the position of a sequence in sequence container from its name.
Sequence *	removeSequence (size_t sequenceIndex) throw (IndexOutOfBoundsException)
	Extract (and remove) a sequence from the container.
Sequence *	removeSequence (const std::string &name) throw (SequenceNotFoundException)
	Extract (and remove) a sequence from the container.
void	deleteSequence (size_t sequenceIndex) throw (IndexOutOfBoundsException)
	Delete a sequence of the container.
void	deleteSequence (const std::string &name) throw (SequenceNotFoundException)
	Delete a sequence of the container.
size_t	getNumberOfSequences () const
	Get the number of sequences in the container.
std::vector< std::string >	getSequencesNames () const
	Get all the names of the sequences in the container.
void	setSequencesNames (const std::vector< std::string > &names, bool checkNames=true) throw (Exception)
	Set all sequence names.
void	clear ()
	Delete all sequences in the container.
VectorSiteContainer *	createEmptyContainer () const
	Return a copy of this container, but with no sequence inside.
int &	valueAt (const std::string &sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function.
const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function.
int &	operator() (const std::string &sequenceName, size_t elementIndex)
	Element access operator.
const int &	operator() (const std::string &sequenceName, size_t elementIndex) const
	Element access operator.
int &	valueAt (size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
	Element access operator.
const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
	Element access operator.
int &	operator() (size_t sequenceIndex, size_t elementIndex)
	Element access operator.
const int &	operator() (size_t sequenceIndex, size_t elementIndex) const
	Element access operator.
From the SequenceContainer interface
const Alphabet *	getAlphabet () const
	Get sequence container's alphabet.
const std::vector< int > &	getContent (const std::string &name) const throw (SequenceNotFoundException)
	Get the content of a sequence.
std::string	toString (const std::string &name) const throw (SequenceNotFoundException)
	Convert a particular sequence to a string.
const Comments &	getComments (const std::string &name) const throw (SequenceNotFoundException)
	Get comments of a particular sequence.
void	setComments (const std::string &name, const Comments &comments) throw (SequenceNotFoundException)
	Set the comments of a particular sequence.
const Comments &	getGeneralComments () const
	Get the comments of this container.
void	setGeneralComments (const Comments &comments)
	Set the comments of this container.
void	deleteGeneralComments ()
	Delete the comments associated to this container.
From the OrderedSequenceContainer interface
virtual const std::vector< int > &	getContent (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get the content of a sequence.
virtual std::string	toString (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Convert a particular sequence to a string.
virtual const Comments &	getComments (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get comments of a particular sequence.
virtual const std::string &	getName (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get the name of a particular sequence.
Protected Member Functions
void	realloc (size_t n)
Protected Attributes
std::vector< Site * >	sites_
std::vector< std::string >	names_
std::vector< Comments * >	comments_
	The container's 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::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::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_, names_, and bpp::AbstractSequenceContainer::toString().

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::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::VectorSiteContainer ( const VectorSiteContainer & vsc )

Definition at line 129 of file VectorSiteContainer.cpp.

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

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::VectorSiteContainer ( const OrderedSequenceContainer & osc )

Definition at line 171 of file VectorSiteContainer.cpp.

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

VectorSiteContainer::VectorSiteContainer ( const SequenceContainer & sc )

Definition at line 187 of file VectorSiteContainer.cpp.

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

virtual bpp::VectorSiteContainer::~VectorSiteContainer ( ) [inline, virtual]

Definition at line 122 of file VectorSiteContainer.h.

References clear().

Member Function Documentation

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.

References bpp::TextTools::toString().

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

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

Definition at line 730 of file VectorSiteContainer.cpp.

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().

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().

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.

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().

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().

VectorSiteContainer* bpp::VectorSiteContainer::clone ( ) const [inline, virtual]

Implements bpp::SiteContainer.

Definition at line 130 of file VectorSiteContainer.h.

References VectorSiteContainer().

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().

void bpp::AbstractSequenceContainer::deleteGeneralComments ( ) [inline, virtual, inherited]

Delete the comments associated to this container.

Implements bpp::SequenceContainer.

Definition at line 150 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::comments_.

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.

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.

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.

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.

const Alphabet* bpp::AbstractSequenceContainer::getAlphabet ( ) const [inline, virtual, inherited]

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().

const Comments& bpp::AbstractSequenceContainer::getComments ( const std::string & name ) const throw (SequenceNotFoundException) [inline, virtual, inherited]

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().

virtual const Comments& bpp::AbstractSequenceContainer::getComments ( size_t sequenceIndex ) const throw (IndexOutOfBoundsException) [inline, virtual, inherited]

Get comments of a particular sequence.

Parameters:

sequenceIndex The position of the sequence.

Returns:: The comments associated to sequence at position 'sequenceIndex'.

Exceptions:

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

Implements bpp::OrderedSequenceContainer.

Definition at line 177 of file AbstractSequenceContainer.h.

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

const std::vector<int>& bpp::AbstractSequenceContainer::getContent ( const std::string & name ) const throw (SequenceNotFoundException) [inline, virtual, inherited]

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().

virtual const std::vector<int>& bpp::AbstractSequenceContainer::getContent ( size_t sequenceIndex ) const throw (IndexOutOfBoundsException) [inline, virtual, inherited]

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().

const Comments& bpp::AbstractSequenceContainer::getGeneralComments ( ) const [inline, virtual, inherited]

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().

virtual const std::string& bpp::AbstractSequenceContainer::getName ( size_t sequenceIndex ) const throw (IndexOutOfBoundsException) [inline, virtual, inherited]

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().

size_t bpp::VectorSiteContainer::getNumberOfSequences ( ) const [inline, virtual]

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().

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().

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().

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.

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().

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=().

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().

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_.

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_.

int& bpp::VectorSiteContainer::operator()	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		`[inline, virtual]`

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_.

const int& bpp::VectorSiteContainer::operator()	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const `[inline, virtual]`

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_.

int& bpp::VectorSiteContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		`[inline, virtual]`

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_.

const int& bpp::VectorSiteContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const `[inline, virtual]`

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_.

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_, sequences_, and setSequencesNames().

Referenced by operator=().

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_, operator=(), sequences_, and setSequencesNames().

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

Definition at line 256 of file VectorSiteContainer.cpp.

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

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

Assignation operator from any SequenceContainer object.

Parameters:

sc	Another sequence container.

Reimplemented from bpp::AbstractSequenceContainer.

Definition at line 273 of file VectorSiteContainer.cpp.

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

void VectorSiteContainer::realloc ( size_t n ) [protected]

Definition at line 800 of file VectorSiteContainer.cpp.

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

void VectorSiteContainer::reindexSites ( ) [virtual]

Set all positions attributes.

Implements bpp::SiteContainer.

Definition at line 494 of file VectorSiteContainer.cpp.

References sites_.

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

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().

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.

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.

void AbstractSequenceContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)		throw (SequenceNotFoundException) `[virtual, inherited]`

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.

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.

void bpp::AbstractSequenceContainer::setGeneralComments ( const Comments & comments ) [inline, virtual, inherited]

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().

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.

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.

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().

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.

std::string bpp::AbstractSequenceContainer::toString ( const std::string & name ) const throw (SequenceNotFoundException) [inline, virtual, inherited]

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().

Referenced by VectorSiteContainer().

virtual std::string bpp::AbstractSequenceContainer::toString ( size_t sequenceIndex ) const throw (IndexOutOfBoundsException) [inline, virtual, inherited]

Convert a particular sequence to a string.

Parameters:

sequenceIndex The position of the sequence.

Returns:: A string describing the content of the sequence.

Exceptions:

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

Implements bpp::OrderedSequenceContainer.

Definition at line 172 of file AbstractSequenceContainer.h.

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

int& bpp::VectorSiteContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		throw (SequenceNotFoundException, IndexOutOfBoundsException) `[inline, virtual]`

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::SequenceContainer.

Definition at line 186 of file VectorSiteContainer.h.

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

const int& bpp::VectorSiteContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const throw (SequenceNotFoundException, IndexOutOfBoundsException) `[inline, virtual]`