bpp::SiteContainer Class Reference

The SiteContainer interface. More...

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

Inheritance diagram for bpp::SiteContainer:

Collaboration diagram for bpp::SiteContainer:

List of all members.

Public Member Functions
	SiteContainer ()
virtual	~SiteContainer ()
SiteContainer *	clone () const =0
virtual const Site &	getSite (size_t siteIndex) const =0 throw (IndexOutOfBoundsException)
	Get a site from the container.
virtual void	setSite (size_t siteIndex, const Site &site, bool checkPosition)=0 throw (Exception)
	Set a site in the container.
virtual void	addSite (const Site &site, bool checkPosition)=0 throw (Exception)
	Add a site in the container.
virtual void	addSite (const Site &site, int position, bool checkPosition)=0 throw (Exception)
	Add a site in the container.
virtual void	addSite (const Site &site, size_t siteIndex, bool checkPosition)=0 throw (Exception)
	Add a site in the container.
virtual void	addSite (const Site &site, size_t siteIndex, int position, bool checkPosition)=0 throw (Exception)
	Add a site in the container.
virtual Site *	removeSite (size_t siteIndex)=0 throw (IndexOutOfBoundsException, Exception)
	Remove a site from the container.
virtual void	deleteSite (size_t siteIndex)=0 throw (IndexOutOfBoundsException, Exception)
	Delete a site in the container.
virtual void	deleteSites (size_t siteIndex, size_t length)=0 throw (IndexOutOfBoundsException, Exception)
	Delete a continuous range of sites in the container.
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the container.
virtual void	reindexSites ()=0
	Set all positions attributes.
virtual Vint	getSitePositions () const =0
	Get all position attributes of sites.
virtual const std::vector< int > &	getContent (size_t sequenceIndex) const =0 throw (IndexOutOfBoundsException)
	Get the content of a sequence.
virtual std::string	toString (size_t sequenceIndex) const =0 throw (IndexOutOfBoundsException)
	Convert a particular sequence to a string.
virtual const Sequence &	getSequence (size_t sequenceIndex) const =0 throw (IndexOutOfBoundsException)
	Retrieve a sequence object from the container.
virtual void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName)=0 throw (Exception)
	Replace a sequence in the container.
virtual Sequence *	removeSequence (size_t sequenceIndex)=0 throw (IndexOutOfBoundsException, Exception)
	Extract (and remove) a sequence from the container.
virtual void	deleteSequence (size_t sequenceIndex)=0 throw (IndexOutOfBoundsException, Exception)
	Delete a sequence of the container.
virtual const std::string &	getName (size_t sequenceIndex) const =0 throw (IndexOutOfBoundsException)
	Get the name of a particular sequence.
virtual const Comments &	getComments (size_t sequenceIndex) const =0 throw (IndexOutOfBoundsException)
	Get comments of a particular sequence.
virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0 throw (IndexOutOfBoundsException)
	Set the comments of a particular sequence.
virtual size_t	getSequencePosition (const std::string &name) const =0 throw (SequenceNotFoundException)
	Get the position of a sequence in sequence container from its name.
virtual const Alphabet *	getAlphabet () const =0
	Get sequence container's alphabet.
virtual bool	hasSequence (const std::string &name) const =0
	Check if a sequence with a given name is present in the container.
virtual void	addSequence (const Sequence &sequence, bool checkName)=0 throw (Exception)
	Add a sequence to the container.
virtual const Comments &	getGeneralComments () const =0
	Get the comments of this container.
virtual void	setGeneralComments (const Comments &comments)=0
	Set the comments of this container.
virtual void	deleteGeneralComments ()=0
	Delete the comments associated to this container.
virtual void	clear ()=0
	Delete all sequences in the container.
virtual SequenceContainer *	createEmptyContainer () const =0
	Return a copy of this container, but with no sequence inside.
SequenceContainer methods.
virtual const std::vector< int > &	getContent (const std::string &name) const =0 throw (SequenceNotFoundException)
	Get the content of a sequence.
virtual std::string	toString (const std::string &name) const =0 throw (SequenceNotFoundException)
	Convert a particular sequence to a string.
virtual const Sequence &	getSequence (const std::string &name) const =0 throw (SequenceNotFoundException)
	Retrieve a sequence object from the container.
virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0 throw (Exception)
	Replace a sequence in the container.
virtual Sequence *	removeSequence (const std::string &name)=0 throw (SequenceNotFoundException, Exception)
	Extract (and remove) a sequence from the container.
virtual void	deleteSequence (const std::string &name)=0 throw (SequenceNotFoundException, Exception)
	Delete a sequence of the container.
virtual const Comments &	getComments (const std::string &name) const =0 throw (SequenceNotFoundException)
	Get comments of a particular sequence.
virtual void	setComments (const std::string &name, const Comments &comments)=0 throw (SequenceNotFoundException)
	Set the comments of a particular sequence.
virtual size_t	getNumberOfSequences () const =0
	Get the number of sequences in the container.
virtual std::vector< std::string >	getSequencesNames () const =0
	Get all the names of the sequences in the container.
virtual void	setSequencesNames (const std::vector< std::string > &names, bool checkNames)=0 throw (Exception)
	Set all sequence names.
Provide direct access to sequences content.
Warning: These operators allow you to modifiy the content of the sequences. No checking is performed for your modifications, so use with care, or consider using the setContent() methods.
virtual int &	valueAt (size_t sequenceIndex, size_t elementIndex)=0 throw (IndexOutOfBoundsException)
	Element access operator.
virtual const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const =0 throw (IndexOutOfBoundsException)
	Element access operator.
virtual int &	operator() (size_t sequenceIndex, size_t elementIndex)=0
	Element access operator.
virtual const int &	operator() (size_t sequenceIndex, size_t elementIndex) const =0
	Element access operator.
Provide direct access to sequences content.
Warning: These operators allow you to modifiy the content of the sequences. No checking is performed for your modifications, so use with care, or consider using the setContent() methods.
virtual int &	valueAt (const std::string &sequenceName, size_t elementIndex)=0 throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function.
virtual const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const =0 throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function.
virtual int &	operator() (const std::string &sequenceName, size_t elementIndex)=0
	Element access operator.
virtual const int &	operator() (const std::string &sequenceName, size_t elementIndex) const =0
	Element access operator.

---

Detailed Description

The SiteContainer interface.

Container implementing the SiteContainer interface deal with aligned sequences. This interface provides methods to retrieve, add or set sites in the alignment. As for SequenceContainers, the maintenance of Sites is up to the container. All site objects are cloned befored being added and retrieved. All sites stored are deleted in the destructor of the container or after having called the deleteSite() method.

Definition at line 63 of file SiteContainer.h.

---

Constructor & Destructor Documentation

bpp::SiteContainer::SiteContainer

(

)

[inline]

Definition at line 67 of file SiteContainer.h.

virtual bpp::SiteContainer::~SiteContainer

(

)

[inline, virtual]

Definition at line 68 of file SiteContainer.h.

---

Member Function Documentation

virtual void bpp::SequenceContainer::addSequence	(	const Sequence &	sequence,
		bool	checkName
	)		throw (Exception) [pure virtual, inherited]

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.

Implemented in bpp::VectorSequenceContainer, bpp::CompressedVectorSiteContainer, bpp::VectorSiteContainer, bpp::AlignedSequenceContainer, and bpp::MapSequenceContainer.

Referenced by bpp::SequenceContainerTools::append(), and bpp::NexusIOSequence::appendAlignmentFromStream().

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		bool	checkPosition
	)		throw (Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

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

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		int	position,
		bool	checkPosition
	)		throw (Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		size_t	siteIndex,
		bool	checkPosition
	)		throw (Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		size_t	siteIndex,
		int	position,
		bool	checkPosition
	)		throw (Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual void bpp::SequenceContainer::clear

(

)

[pure virtual, inherited]

Delete all sequences in the container.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, bpp::MapSequenceContainer, and bpp::AlignedSequenceContainer.

SiteContainer* bpp::SiteContainer::clone

(

)

const [pure virtual]

Implements bpp::Clonable.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual SequenceContainer* bpp::SequenceContainer::createEmptyContainer

(

)

const [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, bpp::MapSequenceContainer, and bpp::AlignedSequenceContainer.

virtual void bpp::SequenceContainer::deleteGeneralComments

(

)

[pure virtual, inherited]

Delete the comments associated to this container.

Implemented in bpp::AbstractSequenceContainer.

virtual void bpp::OrderedSequenceContainer::deleteSequence

(

size_t

sequenceIndex

)

throw (IndexOutOfBoundsException, Exception) [pure virtual, inherited]

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.

Implemented in bpp::VectorSequenceContainer, bpp::MapSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

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

virtual void bpp::OrderedSequenceContainer::deleteSequence

(

const std::string &

name

)

throw (SequenceNotFoundException, Exception) [pure virtual, inherited]

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::SequenceContainer.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual void bpp::SiteContainer::deleteSite

(

size_t

siteIndex

)

throw (IndexOutOfBoundsException, Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

Referenced by bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), and bpp::SiteContainerTools::removeGapSites().

virtual void bpp::SiteContainer::deleteSites	(	size_t	siteIndex,
		size_t	length
	)		throw (IndexOutOfBoundsException, Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

Referenced by bpp::SiteContainerTools::removeGapOnlySites(), and bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites().

virtual const Alphabet* bpp::SequenceContainer::getAlphabet

(

)

const [pure virtual, inherited]

Get sequence container's alphabet.

Returns:

The alphabet associated to this container.

Implemented in bpp::AbstractSequenceContainer.

Referenced by bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getConsensus(), bpp::SequenceContainerTools::getFrequencies(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::AbstractSequenceContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::sampleSites(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

virtual const Comments& bpp::OrderedSequenceContainer::getComments

(

size_t

sequenceIndex

)

const throw (IndexOutOfBoundsException) [pure 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.

Implemented in bpp::AbstractSequenceContainer.

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

virtual const Comments& bpp::OrderedSequenceContainer::getComments

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure 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::SequenceContainer.

Implemented in bpp::AbstractSequenceContainer.

virtual const std::vector<int>& bpp::OrderedSequenceContainer::getContent

(

size_t

sequenceIndex

)

const throw (IndexOutOfBoundsException) [pure 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.

Implemented in bpp::AbstractSequenceContainer.

virtual const std::vector<int>& bpp::OrderedSequenceContainer::getContent

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure 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::SequenceContainer.

Implemented in bpp::AbstractSequenceContainer.

virtual const Comments& bpp::SequenceContainer::getGeneralComments

(

)

const [pure virtual, inherited]

Get the comments of this container.

Returns:

The comments associated to this container.

Implemented in bpp::AbstractSequenceContainer.

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

virtual const std::string& bpp::OrderedSequenceContainer::getName

(

size_t

sequenceIndex

)

const throw (IndexOutOfBoundsException) [pure 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.

Implemented in bpp::AbstractSequenceContainer.

virtual size_t bpp::OrderedSequenceContainer::getNumberOfSequences

(

)

const [pure virtual, inherited]

Get the number of sequences in the container.

Returns:

The number of sequences in the container.

Implements bpp::SequenceContainer.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

Referenced by bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SimpleSequenceContainerIterator::hasMoreSequences(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSequenceContainer::VectorSequenceContainer(), and bpp::VectorSiteContainer::VectorSiteContainer().

virtual size_t bpp::SiteContainer::getNumberOfSites

(

)

const [pure virtual]

Get the number of sites in the container.

Returns:

The number of sites in the container.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

Referenced by bpp::SiteContainerTools::bootstrapSites(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SimpleSiteContainerIterator::hasMoreSites(), bpp::NoGapSiteContainerIterator::hasMoreSites(), bpp::CompleteSiteContainerIterator::hasMoreSites(), bpp::SiteContainerTools::merge(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::AlignedSequenceContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::sampleSites(), bpp::SiteContainerTools::translateSequence(), and bpp::VectorSiteContainer::VectorSiteContainer().

virtual const Sequence& bpp::OrderedSequenceContainer::getSequence

(

size_t

sequenceIndex

)

const throw (IndexOutOfBoundsException) [pure virtual, inherited]

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.

Implemented in bpp::VectorSequenceContainer, bpp::MapSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

Referenced by bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::AbstractSequenceContainer::getComments(), bpp::AbstractSequenceContainer::getContent(), bpp::AbstractSequenceContainer::getName(), bpp::SiteContainerTools::getSequencePositions(), bpp::SimpleSequenceContainerIterator::nextSequence(), bpp::VectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), bpp::AbstractSequenceContainer::toString(), bpp::SiteContainerTools::translateSequence(), bpp::VectorSequenceContainer::VectorSequenceContainer(), and bpp::VectorSiteContainer::VectorSiteContainer().

virtual const Sequence& bpp::OrderedSequenceContainer::getSequence

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure virtual, inherited]

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::SequenceContainer.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual size_t bpp::OrderedSequenceContainer::getSequencePosition

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure virtual, inherited]

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.

Implemented in bpp::VectorSequenceContainer, bpp::MapSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual std::vector<std::string> bpp::OrderedSequenceContainer::getSequencesNames

(

)

const [pure virtual, inherited]

Get all the names of the sequences in the container.

Returns:

A vector of strings with all sequence names.

Implements bpp::SequenceContainer.

Implemented in bpp::MapSequenceContainer, bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, and bpp::VectorSiteContainer.

Referenced by bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::SequenceContainerTools::keepOnlySelectedSequences(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), and bpp::SiteContainerTools::sampleSites().

virtual const Site& bpp::SiteContainer::getSite

(

size_t

siteIndex

)

const throw (IndexOutOfBoundsException) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

Referenced by bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::getSelectedSites(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::merge(), bpp::CompleteSiteContainerIterator::nextCompleteSitePosition(), bpp::SimpleSiteContainerIterator::nextSite(), bpp::NoGapSiteContainerIterator::nextSite(), bpp::CompleteSiteContainerIterator::nextSite(), bpp::NoGapSiteContainerIterator::nextSiteWithoutGapPosition(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::CompleteSiteContainerIterator::previousCompleteSitePosition(), bpp::NoGapSiteContainerIterator::previousSiteWithoutGapPosition(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::sampleSites(), and bpp::VectorSiteContainer::VectorSiteContainer().

virtual Vint bpp::SiteContainer::getSitePositions

(

)

const [pure virtual]

Get all position attributes of sites.

Returns:

A vector with all site positions.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

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

virtual bool bpp::SequenceContainer::hasSequence

(

const std::string &

name

)

const [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual int& bpp::OrderedSequenceContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		[pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual const int& bpp::OrderedSequenceContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual int& bpp::SequenceContainer::operator()	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		[pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual const int& bpp::SequenceContainer::operator()	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual void bpp::SiteContainer::reindexSites

(

)

[pure virtual]

Set all positions attributes.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual Sequence* bpp::OrderedSequenceContainer::removeSequence

(

size_t

sequenceIndex

)

throw (IndexOutOfBoundsException, Exception) [pure virtual, inherited]

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.

Implemented in bpp::VectorSequenceContainer, bpp::MapSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual Sequence* bpp::OrderedSequenceContainer::removeSequence

(

const std::string &

name

)

throw (SequenceNotFoundException, Exception) [pure virtual, inherited]

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::SequenceContainer.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::MapSequenceContainer, and bpp::VectorSiteContainer.

virtual Site* bpp::SiteContainer::removeSite

(

size_t

siteIndex

)

throw (IndexOutOfBoundsException, Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual void bpp::OrderedSequenceContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)		throw (IndexOutOfBoundsException) [pure virtual, inherited]

Set the comments of a particular sequence.

Parameters:

sequenceIndex	The position of the sequence.
comments	The comments to set to sequence with position 'i'.

Exceptions:

IndexOutOfBoundsException

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

Implemented in bpp::VectorSequenceContainer, bpp::MapSequenceContainer, bpp::AbstractSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual void bpp::OrderedSequenceContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)		throw (SequenceNotFoundException) [pure 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::SequenceContainer.

Implemented in bpp::VectorSequenceContainer, and bpp::AbstractSequenceContainer.

virtual void bpp::SequenceContainer::setGeneralComments

(

const Comments &

comments

)

[pure virtual, inherited]

Set the comments of this container.

Parameters:

comments

The comments to be associated to this container.

Implemented in bpp::AbstractSequenceContainer.

virtual void bpp::OrderedSequenceContainer::setSequence	(	size_t	sequenceIndex,
		const Sequence &	sequence,
		bool	checkName
	)		throw (Exception) [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, bpp::MapSequenceContainer, and bpp::AlignedSequenceContainer.

virtual void bpp::OrderedSequenceContainer::setSequence	(	const std::string &	name,
		const Sequence &	sequence,
		bool	checkName
	)		throw (Exception) [pure virtual, inherited]

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::SequenceContainer.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSiteContainer, bpp::AlignedSequenceContainer, bpp::VectorSequenceContainer, and bpp::MapSequenceContainer.

virtual void bpp::OrderedSequenceContainer::setSequencesNames	(	const std::vector< std::string > &	names,
		bool	checkNames
	)		throw (Exception) [pure virtual, inherited]

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::SequenceContainer.

Implemented in bpp::MapSequenceContainer, bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, and bpp::VectorSiteContainer.

virtual void bpp::SiteContainer::setSite	(	size_t	siteIndex,
		const Site &	site,
		bool	checkPosition
	)		throw (Exception) [pure 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.

Implemented in bpp::AlignedSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::VectorSiteContainer.

virtual std::string bpp::OrderedSequenceContainer::toString

(

size_t

sequenceIndex

)

const throw (IndexOutOfBoundsException) [pure 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.

Implemented in bpp::AbstractSequenceContainer.

virtual std::string bpp::OrderedSequenceContainer::toString

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure 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::SequenceContainer.

Implemented in bpp::AbstractSequenceContainer.

virtual int& bpp::OrderedSequenceContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		throw (IndexOutOfBoundsException) [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual const int& bpp::OrderedSequenceContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const throw (IndexOutOfBoundsException) [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual int& bpp::SequenceContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		throw (SequenceNotFoundException, IndexOutOfBoundsException) [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

virtual const int& bpp::SequenceContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const throw (SequenceNotFoundException, IndexOutOfBoundsException) [pure virtual, inherited]

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.

Implemented in bpp::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

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

• Bpp/Seq/Container/SiteContainer.h