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

Inheritance diagram for bpp::SiteContainer:

Collaboration diagram for bpp::SiteContainer:

Public Member Functions
	SiteContainer ()

virtual	~SiteContainer ()

SiteContainer *	clone () const =0

virtual const Site &	getSite (size_t siteIndex) const =0
	Get a site from the container. More...

virtual Site &	getSite (size_t siteIndex)=0

virtual const CruxSymbolListSite &	getSymbolListSite (size_t siteIndex) const =0
	Get a CruxSymbolListSite from a given position. More...

virtual CruxSymbolListSite &	getSymbolListSite (size_t siteIndex)=0

virtual void	setSite (size_t siteIndex, const Site &site, bool checkPosition=true)=0
	Set a site in the container. More...

virtual void	addSite (const Site &site, bool checkPosition)=0
	Add a site in the container. More...

virtual void	addSite (const Site &site, int position, bool checkPosition)=0
	Add a site in the container. More...

virtual void	addSite (const Site &site, size_t siteIndex, bool checkPosition)=0
	Add a site in the container. More...

virtual void	addSite (const Site &site, size_t siteIndex, int position, bool checkPosition)=0
	Add a site in the container. More...

virtual std::shared_ptr< Site >	removeSite (size_t siteIndex)=0
	Remove a site from the container. More...

virtual void	deleteSite (size_t siteIndex)=0
	Delete a site from the container. More...

virtual const Sequence &	getSequence (size_t sequenceIndex) const =0
	Retrieve a sequence object from the container. More...

virtual const Sequence &	getSequence (const std::string &name) const =0
	Retrieve a sequence object from the container. More...

virtual void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...

virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...

virtual std::shared_ptr< Sequence >	removeSequence (size_t sequenceIndex)=0
	Extract (and remove) a sequence from the container. More...

virtual std::shared_ptr< Sequence >	removeSequence (const std::string &name)=0
	Extract (and remove) a sequence from the container. More...

virtual double	operator() (size_t siteIndex, const std::string &sequenceName, int state) const =0

virtual double	operator() (size_t siteIndex, size_t sequenceIndex, int state) const =0

virtual std::string	toString (const std::string &name) const =0
	Convert a particular sequence to a string. More...

virtual std::string	toString (size_t sequenceIndex) const =0

virtual const Comments &	getComments (const std::string &name) const =0
	Get comments of a particular sequence. More...

virtual const Comments &	getComments (size_t sequenceIndex) const =0

virtual void	setComments (const std::string &name, const Comments &comments)=0
	Set the comments of a particular sequence. More...

virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0

virtual const Alphabet *	getAlphabet () const =0
	Get container's alphabet. More...

virtual bool	hasSequence (const std::string &name) const =0
	Check if a sequence with a given name is present in the container. More...

virtual size_t	getNumberOfSequences () const =0
	Get the number of sequences in the container. More...

virtual std::vector< std::string >	getSequenceNames () const =0
	Get all the names of the sequences in the container. More...

virtual void	setSequenceNames (const std::vector< std::string > &names, bool checkNames)=0
	Set all sequence names. More...

virtual double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const =0
	get value of a state in a position More...

virtual double	getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const =0

virtual double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const=0
	get value of a state in a position More...

virtual const Comments &	getGeneralComments () const =0
	Get the comments of this container. More...

virtual void	setGeneralComments (const Comments &comments)=0
	Set the comments of this container. More...

virtual void	deleteGeneralComments ()=0
	Delete the comments associated to this container. More...

virtual void	clear ()=0
	Delete all data in the container. More...

virtual SequencedValuesContainer *	createEmptyContainer () const =0
	Return a copy of this container, but with no data inside. More...

virtual const std::string &	getName (size_t sequenceIndex) const =0
	Get the name of a particular row of the alignement (aka sequence). More...

virtual size_t	getSequencePosition (const std::string &name) const =0
	Get the position of a sequence in sequence container from its name. More...

virtual void	deleteSites (size_t siteIndex, size_t length)=0
	Remove a continuous range of sites in the container. More...

virtual size_t	getNumberOfSites () const =0
	Get the number of aligned positions in the container. More...

virtual void	reindexSites ()=0
	Set all positions attributes. More...

virtual Vint	getSitePositions () const =0
	Get all position attributes of sites. More...

virtual void	setSitePositions (Vint vPositions)=0
	Set all position attributes of sites. More...

SequenceContainer methods.
virtual const Sequence &	getSequence (const std::string &name) const=0
	Retrieve a sequence object from the container. More...

virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...

virtual std::shared_ptr< Sequence >	removeSequence (const std::string &name)=0
	Extract (and remove) a sequence from the container. More...

virtual std::string	toString (size_t sequenceIndex) const=0

virtual const Comments &	getComments (size_t sequenceIndex) const=0

virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0

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
	Element access function. More...

virtual const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const =0
	Element access function. More...

virtual int &	valueAt (size_t sequenceIndex, size_t elementIndex)=0
	Element access operator. More...

virtual const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const =0
	Element access operator. More...

virtual int &	operator() (size_t sequenceIndex, size_t elementIndex)=0
	Element access operator. More...

virtual const int &	operator() (size_t sequenceIndex, size_t elementIndex) const =0
	Element access operator. More...

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 &	operator() (const std::string &sequenceName, size_t elementIndex)=0
	Element access operator. More...

virtual const int &	operator() (const std::string &sequenceName, size_t elementIndex) const =0
	Element access operator. More...

virtual void	addSequence (const Sequence &sequence, bool checkName)=0
	Add a sequence to the container. More...

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.

Definition at line 62 of file SiteContainer.h.

Constructor & Destructor Documentation

◆ SiteContainer()

bpp::SiteContainer::SiteContainer ( )

inline

Definition at line 67 of file SiteContainer.h.

◆ ~SiteContainer()

virtual bpp::SiteContainer::~SiteContainer ( )

inlinevirtual

Definition at line 68 of file SiteContainer.h.

Member Function Documentation

◆ addSequence()

virtual void bpp::SequenceContainer::addSequence	(	const Sequence &	sequence,
		bool	checkName
	)

pure virtualinherited

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::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

Referenced by bpp::SequenceContainerTools::append(), bpp::Clustal::appendAlignmentFromStream(), bpp::DCSE::appendAlignmentFromStream(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), bpp::GenBank::appendSequencesFromStream(), bpp::Mase::appendSequencesFromStream(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceApplicationTools::getAlignedContainer(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SequenceContainerTools::merge(), bpp::Phylip::readInterleaved(), and bpp::Phylip::readSequential().

◆ addSite() [1/4]

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		bool	checkPosition
	)

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

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

◆ addSite() [2/4]

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		int	position,
		bool	checkPosition
	)

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

◆ addSite() [3/4]

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		size_t	siteIndex,
		bool	checkPosition
	)

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

◆ addSite() [4/4]

virtual void bpp::SiteContainer::addSite	(	const Site &	site,
		size_t	siteIndex,
		int	position,
		bool	checkPosition
	)

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

◆ clear()

virtual void bpp::SequencedValuesContainer::clear ( )

pure virtualinherited

Delete all data in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

◆ clone()

SiteContainer* bpp::SiteContainer::clone ( ) const

pure virtual

Implements bpp::AlignedValuesContainer.

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

◆ createEmptyContainer()

virtual SequencedValuesContainer* bpp::SequencedValuesContainer::createEmptyContainer ( ) const

pure virtualinherited

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

This method creates a new SequencedValuesContainer 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::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

◆ deleteGeneralComments()

virtual void bpp::SequencedValuesContainer::deleteGeneralComments ( )

pure virtualinherited

Delete the comments associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ deleteSite()

virtual void bpp::SiteContainer::deleteSite ( size_t siteIndex )

pure virtual

Delete a site from the container.

The site is deleted (ie the container is shortened).

Parameters

siteIndex The position of the site in the container.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

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

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

◆ deleteSites()

virtual void bpp::AlignedValuesContainer::deleteSites	(	size_t	siteIndex,
		size_t	length
	)

pure virtualinherited

Remove 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::VectorSiteContainer, bpp::VectorProbabilisticSiteContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

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

◆ getAlphabet()

virtual const Alphabet* bpp::SequencedValuesContainer::getAlphabet ( ) const

pure virtualinherited

Get container's alphabet.

Returns: The alphabet associated to this container.

Implemented in bpp::AbstractValuesContainer.

◆ getComments() [1/3]

virtual const Comments& bpp::SequencedValuesContainer::getComments ( const std::string & name ) const

pure virtualinherited

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.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::SequenceContainerTools::getCodonPosition(), and bpp::Mase::writeSequences().

◆ getComments() [2/3]

virtual const Comments& bpp::OrderedValuesContainer::getComments ( size_t sequenceIndex ) const

pure virtualinherited

Implemented in bpp::AbstractValuesContainer, bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ getComments() [3/3]

virtual const Comments& bpp::OrderedValuesContainer::getComments

inherited

Referenced by bpp::CompressedVectorSiteContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::VectorSiteContainer::getSequence(), bpp::CompressedVectorSiteContainer::removeSite(), bpp::VectorSiteContainer::setSequence(), bpp::CompressedVectorSiteContainer::setSite(), and bpp::VectorSiteContainer::setSite().

◆ getGeneralComments()

virtual const Comments& bpp::SequencedValuesContainer::getGeneralComments ( ) const

pure virtualinherited

Get the comments of this container.

Returns: The comments associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::Mase::appendSequencesFromStream(), bpp::MaseTools::getSelectedSequences(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSelectedSites(), bpp::AbstractSequenceContainer::operator=(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

◆ getName()

virtual const std::string& bpp::OrderedValuesContainer::getName ( size_t sequenceIndex ) const

pure virtualinherited

Get the name of a particular row of the alignement (aka 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::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::VectorSiteContainer::VectorSiteContainer().

◆ getNumberOfSequences()

virtual size_t bpp::SequencedValuesContainer::getNumberOfSequences ( ) const

pure virtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ getNumberOfSites()

virtual size_t bpp::AlignedValuesContainer::getNumberOfSites ( ) const

pure virtualinherited

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

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

◆ getSequence() [1/3]

virtual const Sequence& bpp::SequenceContainer::getSequence ( const std::string & name ) const

pure virtualinherited

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns: A reference toward the Sequence with corresponding name.

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

Referenced by bpp::SequenceContainerTools::append(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SequenceContainerTools::getCounts(), bpp::SequenceContainerTools::getFrequencies(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SequenceContainerTools::merge(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Pasta::writeAlignedValues(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequences(), and bpp::Phylip::writeSequential().

◆ getSequence() [2/3]

virtual const Sequence& bpp::SequenceContainer::getSequence

inherited

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns: A reference toward the Sequence with corresponding name.

◆ getSequence() [3/3]

virtual const Sequence& bpp::OrderedSequenceContainer::getSequence ( size_t sequenceIndex ) const

pure virtualinherited

Retrieve a sequence object from the container.

Parameters

sequenceIndex The position of the sequence.

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

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

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SiteContainerTools::getSequencePositions(), bpp::SimpleSequenceContainerIterator::nextSequence(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SiteContainerTools::translateSequence(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Clustal::writeAlignment(), and bpp::Stockholm::writeAlignment().

◆ getSequenceNames()

virtual std::vector<std::string> bpp::SequencedValuesContainer::getSequenceNames ( ) const

pure virtualinherited

Get all the names of the sequences in the container.

Returns: A vector of strings with all sequence names.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ getSequencePosition()

virtual size_t bpp::OrderedValuesContainer::getSequencePosition ( const std::string & name ) const

pure virtualinherited

Get the position of a sequence in sequence container from its name.

Parameters

name	The name of the sequence.

Returns: The position of the sequence with name 'name', if it exists.

Exceptions

SequenceNotFoundException If no sequence with name 'name' could be found.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::AbstractProbabilisticSequenceContainer::setComments(), bpp::AbstractSequenceContainer::setComments(), and bpp::AbstractValuesContainer::setComments().

◆ getSite() [1/2]

virtual const Site& bpp::SiteContainer::getSite ( size_t siteIndex ) const

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

◆ getSite() [2/2]

virtual Site& bpp::SiteContainer::getSite ( size_t siteIndex )

pure virtual

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

◆ getSitePositions()

virtual Vint bpp::AlignedValuesContainer::getSitePositions ( ) const

pure virtualinherited

Get all position attributes of sites.

Returns: A vector with all site positions.

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

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

◆ getStateValueAt() [1/3]

virtual double bpp::SequencedValuesContainer::getStateValueAt	(	size_t	siteIndex,
		const std::string &	sequenceName,
		int	state
	)		const

pure virtualinherited

get value of a state in a position

Parameters

siteIndex	index of the site
sequenceName	name of the sequence in the container
state	state in the alphabet

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ getStateValueAt() [2/3]

virtual double bpp::SequencedValuesContainer::getStateValueAt

inherited

get value of a state in a position

Parameters

siteIndex	index of the site
sequenceName	name of the sequence in the container
state	state in the alphabet

◆ getStateValueAt() [3/3]

virtual double bpp::OrderedValuesContainer::getStateValueAt	(	size_t	siteIndex,
		size_t	sequenceIndex,
		int	state
	)		const

pure virtualinherited

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ getSymbolListSite() [1/2]

virtual const CruxSymbolListSite& bpp::SiteContainer::getSymbolListSite ( size_t siteIndex ) const

pure virtual

Get a CruxSymbolListSite from a given position.

Parameters

siteIndex The position

Implements bpp::AlignedValuesContainer.

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

◆ getSymbolListSite() [2/2]

virtual CruxSymbolListSite& bpp::SiteContainer::getSymbolListSite ( size_t siteIndex )

pure virtual

Implements bpp::AlignedValuesContainer.

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

◆ hasSequence()

virtual bool bpp::SequencedValuesContainer::hasSequence ( const std::string & name ) const

pure virtualinherited

Check if a sequence with a given name is present in the container.

Parameters

name	The name of the sequence.

Returns: True if a sequence with the given name is present in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

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

◆ operator()() [1/6]

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

pure virtualinherited

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::VectorSiteContainer, bpp::VectorSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ operator()() [2/6]

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

pure virtualinherited

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::VectorSiteContainer, bpp::VectorSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ operator()() [3/6]

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

pure virtualinherited

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::VectorSiteContainer, bpp::VectorSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ operator()() [4/6]

virtual int& bpp::OrderedSequenceContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)

pure virtualinherited

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::VectorSiteContainer, bpp::VectorSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ operator()() [5/6]

virtual double bpp::SequencedValuesContainer::operator()	(	size_t	siteIndex,
		const std::string &	sequenceName,
		int	state
	)		const

pure virtualinherited

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ operator()() [6/6]

virtual double bpp::OrderedValuesContainer::operator()	(	size_t	siteIndex,
		size_t	sequenceIndex,
		int	state
	)		const

pure virtualinherited

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ reindexSites()

virtual void bpp::AlignedValuesContainer::reindexSites ( )

pure virtualinherited

Set all positions attributes.

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

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

◆ removeSequence() [1/3]

virtual std::shared_ptr<Sequence> bpp::SequenceContainer::removeSequence

inherited

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Referenced by bpp::VectorSiteContainer::removeSequence(), bpp::VectorSequenceContainer::removeSequenceByKey(), and bpp::VectorSequenceContainer::removeSequenceByName().

◆ removeSequence() [2/3]

virtual std::shared_ptr<Sequence> bpp::SequenceContainer::removeSequence ( const std::string & name )

pure virtualinherited

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

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

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

◆ removeSequence() [3/3]

virtual std::shared_ptr<Sequence> bpp::OrderedSequenceContainer::removeSequence ( size_t sequenceIndex )

pure virtualinherited

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex The position of the sequence.

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

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

◆ removeSite()

virtual std::shared_ptr<Site> bpp::SiteContainer::removeSite ( size_t siteIndex )

pure virtual

Remove a site from the container.

The site is deleted (ie the container is shortened) and a pointer toward it is returned.

Parameters

siteIndex The position of the site in the container.

Returns: A pointer toward the given site in the alignment.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

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

◆ setComments() [1/3]

virtual void bpp::SequencedValuesContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)

pure 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.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractValuesContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ setComments() [2/3]

virtual void bpp::OrderedValuesContainer::setComments

inherited

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

◆ setComments() [3/3]

virtual void bpp::OrderedValuesContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)

pure virtualinherited

Implemented in bpp::AbstractValuesContainer, bpp::AbstractSequenceContainer, bpp::AbstractProbabilisticSequenceContainer, bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

◆ setGeneralComments()

virtual void bpp::SequencedValuesContainer::setGeneralComments ( const Comments & comments )

pure virtualinherited

Set the comments of this container.

Parameters

comments The comments to be associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::Clustal::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), and bpp::Mase::appendSequencesFromStream().

◆ setSequence() [1/3]

virtual void bpp::SequenceContainer::setSequence

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.

Referenced by bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), and bpp::AlignedSequenceContainer::setSequence().

◆ setSequence() [2/3]

virtual void bpp::SequenceContainer::setSequence	(	const std::string &	name,
		const Sequence &	sequence,
		bool	checkName
	)

pure virtualinherited

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.

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

◆ setSequence() [3/3]

virtual void bpp::OrderedSequenceContainer::setSequence	(	size_t	sequenceIndex,
		const Sequence &	sequence,
		bool	checkName
	)

pure virtualinherited

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.

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

◆ setSequenceNames()

virtual void bpp::SequencedValuesContainer::setSequenceNames	(	const std::vector< std::string > &	names,
		bool	checkNames
	)

pure virtualinherited

Set all sequence names.

Parameters

names	A vector of strings with all sequence names. Its size must be strictly equal to the the size of the container (the number of sequences).
checkNames	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Exceptions

Exception If there are redundant names in the input vector.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::SequenceContainerTools::createContainerWithSequenceNames(), bpp::SiteContainerTools::getCompleteSites(), and bpp::SiteContainerTools::getSitesWithoutGaps().

◆ setSite()

virtual void bpp::SiteContainer::setSite	(	size_t	siteIndex,
		const Site &	site,
		bool	checkPosition = `true`
	)

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

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

◆ setSitePositions()

virtual void bpp::AlignedValuesContainer::setSitePositions ( Vint vPositions )

pure virtualinherited

Set all position attributes of sites.

Parameters

vPositions A vector with all site positions.

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

◆ toString() [1/3]

virtual std::string bpp::SequencedValuesContainer::toString ( const std::string & name ) const

pure virtualinherited

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.

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

Referenced by bpp::SequenceContainerTools::convertAlphabet(), bpp::Phylip::writeInterleaved(), bpp::Mase::writeSequences(), and bpp::Phylip::writeSequential().

◆ toString() [2/3]

virtual std::string bpp::OrderedValuesContainer::toString ( size_t sequenceIndex ) const

pure virtualinherited

Implemented in bpp::VectorProbabilisticSequenceContainer, bpp::AbstractSequenceContainer, and bpp::AbstractProbabilisticSequenceContainer.

◆ toString() [3/3]

virtual std::string bpp::OrderedValuesContainer::toString

inherited

◆ valueAt() [1/4]

virtual const int& bpp::OrderedSequenceContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)		const

pure virtualinherited

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.

Implements bpp::SequenceContainer.

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

◆ valueAt() [2/4]

virtual int& bpp::OrderedSequenceContainer::valueAt	(	const std::string &	sequenceName,
		size_t	elementIndex
	)

pure virtualinherited

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.

Implements bpp::SequenceContainer.

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

◆ valueAt() [3/4]

virtual const int& bpp::OrderedSequenceContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const

pure virtualinherited

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.

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

◆ valueAt() [4/4]

virtual int& bpp::OrderedSequenceContainer::valueAt	(	size_t	sequenceIndex,
		size_t	elementIndex
	)

pure virtualinherited

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.

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

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

Bpp/Seq/Container/SiteContainer.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SiteContainer()

◆ ~SiteContainer()

Member Function Documentation

◆ addSequence()

◆ addSite() [1/4]

◆ addSite() [2/4]

◆ addSite() [3/4]

◆ addSite() [4/4]

◆ clear()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSite()

◆ deleteSites()

◆ getAlphabet()

◆ getComments() [1/3]

◆ getComments() [2/3]

◆ getComments() [3/3]

◆ getGeneralComments()

◆ getName()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getSequence() [1/3]

◆ getSequence() [2/3]

◆ getSequence() [3/3]

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSite() [1/2]

◆ getSite() [2/2]

◆ getSitePositions()

◆ getStateValueAt() [1/3]

◆ getStateValueAt() [2/3]

◆ getStateValueAt() [3/3]

◆ getSymbolListSite() [1/2]

◆ getSymbolListSite() [2/2]

◆ hasSequence()

◆ operator()() [1/6]

◆ operator()() [2/6]

◆ operator()() [3/6]

◆ operator()() [4/6]

◆ operator()() [5/6]

◆ operator()() [6/6]

◆ reindexSites()

◆ removeSequence() [1/3]

◆ removeSequence() [2/3]

◆ removeSequence() [3/3]

◆ removeSite()

◆ setComments() [1/3]

◆ setComments() [2/3]

◆ setComments() [3/3]

◆ setGeneralComments()

◆ setSequence() [1/3]

◆ setSequence() [2/3]

◆ setSequence() [3/3]

◆ setSequenceNames()

◆ setSite()

◆ setSitePositions()

◆ toString() [1/3]

◆ toString() [2/3]

◆ toString() [3/3]

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]