The Container of Aligned Values interface. More...

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

Inheritance diagram for bpp::AlignedValuesContainer:

Collaboration diagram for bpp::AlignedValuesContainer:

Public Member Functions
	AlignedValuesContainer ()

virtual	~AlignedValuesContainer ()

AlignedValuesContainer *	clone () const =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	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 Container of Aligned Values interface.

Container implementing the AlignedValuesContainer interface deal with aligned data.

Definition at line 62 of file AlignedValuesContainer.h.

Constructor & Destructor Documentation

◆ AlignedValuesContainer()

bpp::AlignedValuesContainer::AlignedValuesContainer ( )

inline

Definition at line 66 of file AlignedValuesContainer.h.

◆ ~AlignedValuesContainer()

virtual bpp::AlignedValuesContainer::~AlignedValuesContainer ( )

inlinevirtual

Definition at line 67 of file AlignedValuesContainer.h.

Member Function Documentation

◆ 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()

AlignedValuesContainer* bpp::AlignedValuesContainer::clone ( ) const

pure virtual

Implements bpp::OrderedValuesContainer.

Implemented in bpp::SiteContainer, bpp::ProbabilisticSiteContainer, bpp::VectorSiteContainer, bpp::VectorProbabilisticSiteContainer, 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.

◆ deleteSites()

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

pure virtual

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 virtual

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().

◆ getSitePositions()

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

pure virtual

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::AlignedValuesContainer::getSymbolListSite ( size_t siteIndex ) const

pure virtual

Get a CruxSymbolListSite from a given position.

Parameters

siteIndex The position

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

Referenced by bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::getCompleteSites(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), and bpp::VectorSiteContainer::VectorSiteContainer().

◆ getSymbolListSite() [2/2]

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

pure virtual

Implemented in bpp::SiteContainer, bpp::VectorSiteContainer, bpp::ProbabilisticSiteContainer, 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()() [1/2]

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 virtual

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 virtual

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/AlignedValuesContainer.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AlignedValuesContainer()

◆ ~AlignedValuesContainer()

Member Function Documentation

◆ clear()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSites()

◆ getAlphabet()

◆ getComments() [1/3]

◆ getComments() [2/3]

◆ getComments() [3/3]

◆ getGeneralComments()

◆ getName()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getSequenceNames()

◆ getSequencePosition()

◆ 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]