The ProbabilisticSiteContainer interface. More...

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

Inheritance diagram for bpp::ProbabilisticSiteContainer:

Collaboration diagram for bpp::ProbabilisticSiteContainer:

Public Member Functions
	ProbabilisticSiteContainer ()

virtual	~ProbabilisticSiteContainer ()

ProbabilisticSiteContainer *	clone () const =0

virtual const std::shared_ptr< ProbabilisticSite >	getSite (size_t siteIndex) const =0
	Get a site from the container. More...

virtual std::shared_ptr< ProbabilisticSite >	getSite (size_t siteIndex)=0

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

CruxSymbolListSite &	getSymbolListSite (size_t siteIndex)

virtual void	addSite (std::shared_ptr< ProbabilisticSite > site, bool checkPosition=false)=0
	Add a site at the end of the container. 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...

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

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

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

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

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

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

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

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

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

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 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...

Detailed Description

The ProbabilisticSiteContainer interface.

Container implementing the ProbabilisticSiteContainer interface deal with aligned probabilistic sequences. This interface provides methods to retrieve, add or set sites in the alignment. All site objects are cloned befored being added and retrieved.

Definition at line 61 of file ProbabilisticSiteContainer.h.

Constructor & Destructor Documentation

◆ ProbabilisticSiteContainer()

bpp::ProbabilisticSiteContainer::ProbabilisticSiteContainer ( )

inline

Definition at line 65 of file ProbabilisticSiteContainer.h.

◆ ~ProbabilisticSiteContainer()

virtual bpp::ProbabilisticSiteContainer::~ProbabilisticSiteContainer ( )

inlinevirtual

Definition at line 66 of file ProbabilisticSiteContainer.h.

Member Function Documentation

◆ addSite()

virtual void bpp::ProbabilisticSiteContainer::addSite	(	std::shared_ptr< ProbabilisticSite >	site,
		bool	checkPosition = `false`
	)

pure virtual

Add a site at the end of the container.

Parameters

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

Implemented in bpp::VectorProbabilisticSiteContainer.

◆ 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()

ProbabilisticSiteContainer* bpp::ProbabilisticSiteContainer::clone ( ) const

pure virtual

Implements bpp::AlignedValuesContainer.

Implemented in bpp::VectorProbabilisticSiteContainer.

◆ 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.

◆ 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::SequencedValuesContainer::getComments

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.

◆ getComments() [3/3]

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

pure virtualinherited

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

◆ 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.

◆ 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 std::shared_ptr<ProbabilisticSite> bpp::ProbabilisticSiteContainer::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::VectorProbabilisticSiteContainer.

Referenced by bpp::SiteContainerTools::changeGapsToUnknownCharacters(), and getSymbolListSite().

◆ getSite() [2/2]

virtual std::shared_ptr<ProbabilisticSite> bpp::ProbabilisticSiteContainer::getSite ( size_t siteIndex )

pure virtual

Implemented in bpp::VectorProbabilisticSiteContainer.

◆ 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]

CruxSymbolListSite& bpp::ProbabilisticSiteContainer::getSymbolListSite ( size_t siteIndex )

inlinevirtual

Implements bpp::AlignedValuesContainer.

Definition at line 87 of file ProbabilisticSiteContainer.h.

References getSite().

◆ getSymbolListSite() [2/2]

const CruxSymbolListSite& bpp::ProbabilisticSiteContainer::getSymbolListSite ( size_t siteIndex ) const

inlinevirtual

Get a CruxSymbolListSite from a given position.

Parameters

siteIndex The position

Implements bpp::AlignedValuesContainer.

Definition at line 82 of file ProbabilisticSiteContainer.h.

References getSite().

◆ 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()() [1/2]

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()() [2/2]

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().

◆ setComments() [1/3]

virtual void bpp::SequencedValuesContainer::setComments

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.

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

◆ setComments() [2/3]

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() [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().

◆ 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().

◆ 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::SequencedValuesContainer::toString

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.

◆ toString() [3/3]

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

pure virtualinherited

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

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

Bpp/Seq/Container/ProbabilisticSiteContainer.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ProbabilisticSiteContainer()

◆ ~ProbabilisticSiteContainer()

Member Function Documentation

◆ addSite()

◆ clear()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSites()

◆ getAlphabet()

◆ getComments() [1/3]

◆ getComments() [2/3]

◆ getComments() [3/3]

◆ getGeneralComments()

◆ getName()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ 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()() [1/2]

◆ operator()() [2/2]

◆ reindexSites()

◆ setComments() [1/3]

◆ setComments() [2/3]

◆ setComments() [3/3]

◆ setGeneralComments()

◆ setSequenceNames()

◆ setSitePositions()

◆ toString() [1/3]

◆ toString() [2/3]

◆ toString() [3/3]