The Container of Aligned Values interface. More...

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

Inheritance diagram for bpp::TemplateAlignmentDataInterface< HashType >:

Collaboration diagram for bpp::TemplateAlignmentDataInterface< HashType >:

Public Member Functions
	TemplateAlignmentDataInterface ()

virtual	~TemplateAlignmentDataInterface ()

TemplateAlignmentDataInterface *	clone () const override=0

virtual const CoreSiteInterface &	site (size_t siteIndex) const =0
	Get a site from a given position. 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	getSiteCoordinates () const =0
	Get all coordinates of sites. More...

virtual void	setSiteCoordinates (const Vint &vCoordinates)=0
	Set all coordinates of sites. More...

virtual const Alphabet &	alphabet () const=0
	Get the container's alphabet. More...

virtual std::shared_ptr< const Alphabet >	getAlphabet () const=0
	Get a pointer toward the container's alphabet. More...

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

virtual std::vector< std::string >	getSequenceKeys () const=0

virtual void	setSequenceKeys (const std::vector< std::string > &sequenceKeys)=0
	Reset all sequence keys. More...

virtual double	getStateValueAt (size_t sitePosition, const std::string &sequenceKey, int state) const=0
	Get the value of a state at a given position. More...

virtual double	getStateValueAt (size_t sitePosition, size_t sequencePosition, int state) const=0
	Get value of a state at a given position. More...

virtual double	operator() (size_t sitePosition, const std::string &sequenceKey, int state) const=0
	Get the value of a state at a given position. More...

virtual double	operator() (size_t sitePosition, size_t sequencePosition, int state) const=0
	Get the value of a state at a given position. More...

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

virtual TemplateSequenceDataInterface< std::string > *	createEmptyContainer () const=0
	Return a copy of this container, but with no data inside. More...

virtual bool	hasSequence (const std::string &sequenceKey) const=0
	Check if a certain key is associated to a sequence in the container. More...

virtual const Comments &	getComments () const =0
	Get the comments. More...

virtual void	setComments (const Comments &comments)=0
	Set the comments. More...

virtual void	clearComments ()=0

Access by key
virtual const CoreSequenceInterface &	sequence (const std::string &sequenceKey) const=0
	Retrieve a sequence object from the container. More...

virtual void	deleteSequence (const std::string &sequenceKey)=0
	Remove and delete a sequence from the container. More...

Access by position
virtual const CoreSequenceInterface &	sequence (size_t sequencePosition) const=0
	Retrieve a sequence object from the container. More...

virtual void	deleteSequence (size_t sequencePosition)=0
	Remove and delete a sequence from the container. More...

Index management
Position to key and key to position.
virtual const std::string &	sequenceKey (size_t sequencePosition) const=0
	Get the key associated to a given sequence. More...

virtual size_t	getSequencePosition (const std::string &sequenceKey) const=0
	Get the position of a sequence with a given key in the container. More...

Access sequence names
virtual std::vector< std::string >	getSequenceNames () const=0

virtual void	setSequenceNames (const std::vector< std::string > &names, bool updateKeys)=0
	Batch-set all sequence names. More...

virtual std::vector< Comments >	getSequenceComments () const=0

Detailed Description

template<class HashType = std::string>
class bpp::TemplateAlignmentDataInterface< HashType >

The Container of Aligned Values interface.

Container implementing the AlignedValuesContainer interface deal with aligned data.

Definition at line 24 of file AlignmentData.h.

Constructor & Destructor Documentation

◆ TemplateAlignmentDataInterface()

template<class HashType = std::string>

bpp::TemplateAlignmentDataInterface< HashType >::TemplateAlignmentDataInterface ( )

inline

Definition at line 28 of file AlignmentData.h.

◆ ~TemplateAlignmentDataInterface()

template<class HashType = std::string>

virtual bpp::TemplateAlignmentDataInterface< HashType >::~TemplateAlignmentDataInterface ( )

inlinevirtual

Definition at line 29 of file AlignmentData.h.

Member Function Documentation

◆ alphabet()

virtual const Alphabet& bpp::TemplateSequenceDataInterface< std::string >::alphabet ( ) const

pure virtualinherited

Get the container's alphabet.

Returns: The alphabet associated to this container.

Implemented in bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >, and bpp::AbstractTemplateSequenceContainer< Sequence, std::string >.

◆ clear()

virtual void bpp::TemplateSequenceDataInterface< std::string >::clear ( )

pure virtualinherited

Delete all data in the container.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ clearComments()

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

◆ clone()

template<class HashType = std::string>

TemplateAlignmentDataInterface* bpp::TemplateAlignmentDataInterface< HashType >::clone ( ) const

overridepure virtual

Implements bpp::TemplateSequenceDataInterface< std::string >.

Implemented in bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >, bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ createEmptyContainer()

virtual TemplateSequenceDataInterface<std::string >* bpp::TemplateSequenceDataInterface< std::string >::createEmptyContainer ( ) const

pure virtualinherited

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

This method creates a new SequencedContainer object. The class of this container depends on the class implementing this interface.

Returns: A new empty container, with the same alphabet as this one.

Implemented in bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateSequenceContainerInterface< SequenceType, HashType >, bpp::TemplateSequenceContainerInterface< SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ deleteSequence() [1/2]

virtual void bpp::TemplateSequenceDataInterface< std::string >::deleteSequence ( const HashType & sequenceKey )

pure virtualinherited

Remove and delete a sequence from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ deleteSequence() [2/2]

virtual void bpp::TemplateSequenceDataInterface< std::string >::deleteSequence ( size_t sequencePosition )

pure virtualinherited

Remove and delete a sequence from the container.

Parameters

sequencePosition The position of the sequence.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ deleteSites()

template<class HashType = std::string>

virtual void bpp::TemplateAlignmentDataInterface< HashType >::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::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >, bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::TemplateSequenceDataInterface< std::string >::getAlphabet ( ) const

pure virtualinherited

Get a pointer toward the container's alphabet.

Returns: A pointer toward the alphabet associated to this container.

Implemented in bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >, bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >, and bpp::AbstractTemplateSequenceContainer< Sequence, std::string >.

◆ getComments()

virtual const Comments& bpp::Commentable::getComments ( ) const

pure virtualinherited

Get the comments.

Returns: The comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Mase::appendSequencesFromStream(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractCoreSequence::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

◆ getNumberOfSequences()

virtual size_t bpp::TemplateSequenceDataInterface< std::string >::getNumberOfSequences ( ) const

pure virtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getNumberOfSites()

template<class HashType = std::string>

virtual size_t bpp::TemplateAlignmentDataInterface< HashType >::getNumberOfSites ( ) const

pure virtual

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

Implemented in bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >, bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ getSequenceComments()

virtual std::vector<Comments> bpp::TemplateSequenceDataInterface< std::string >::getSequenceComments ( ) const

pure virtualinherited

Returns: a vector with all sequence comments.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequenceKeys()

virtual std::vector<std::string > bpp::TemplateSequenceDataInterface< std::string >::getSequenceKeys ( ) const

pure virtualinherited

Returns: a vector with all sequence keys.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequenceNames()

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

pure virtualinherited

Returns: a vector with all sequence names.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSequencePosition()

virtual size_t bpp::TemplateSequenceDataInterface< std::string >::getSequencePosition ( const HashType & sequenceKey ) const

pure virtualinherited

Get the position of a sequence with a given key in the container.

Parameters

sequenceKey The key to which the sequence is associated.

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

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getSiteCoordinates()

template<class HashType = std::string>

virtual Vint bpp::TemplateAlignmentDataInterface< HashType >::getSiteCoordinates ( ) const

pure virtual

Get all coordinates of sites.

Returns: A vector with all site coordinates.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::operator=().

◆ getStateValueAt() [1/2]

virtual double bpp::TemplateSequenceDataInterface< std::string >::getStateValueAt	(	size_t	sitePosition,
		const HashType &	sequenceKey,
		int	state
	)		const

pure virtualinherited

Get the value of a state at a given position.

Parameters

sitePosition	index of the site
sequenceKey	key of the sequence in the container
state	state in the alphabet

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ getStateValueAt() [2/2]

virtual double bpp::TemplateSequenceDataInterface< std::string >::getStateValueAt	(	size_t	sitePosition,
		size_t	sequencePosition,
		int	state
	)		const

pure virtualinherited

Get value of a state at a given position.

Parameters

sitePosition	index of the site
sequencePosition	index of the sequence in the container
state	state in the alphabet

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ hasSequence()

virtual bool bpp::TemplateSequenceDataInterface< std::string >::hasSequence ( const HashType & sequenceKey ) const

pure virtualinherited

Check if a certain key is associated to a sequence in the container.

Parameters

sequenceKey The key to which the sequence is associated.

Returns: True if the key was found in the contained.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ operator()() [1/2]

virtual double bpp::TemplateSequenceDataInterface< std::string >::operator()	(	size_t	sitePosition,
		const HashType &	sequenceKey,
		int	state
	)		const

pure virtualinherited

Get the value of a state at a given position.

Same as getValueAt.

Parameters

sitePosition	index of the site
sequenceKey	key of the sequence in the container
state	state in the alphabet

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ operator()() [2/2]

virtual double bpp::TemplateSequenceDataInterface< std::string >::operator()	(	size_t	sitePosition,
		size_t	sequencePosition,
		int	state
	)		const

pure virtualinherited

Get the value of a state at a given position.

Same as getValueAt.

Parameters

sitePosition	index of the site
sequencePosition	index of the sequence in the container
state	state in the alphabet

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ reindexSites()

template<class HashType = std::string>

virtual void bpp::TemplateAlignmentDataInterface< HashType >::reindexSites ( )

pure virtual

Set all positions attributes.

Implemented in bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >, bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

◆ sequence() [1/2]

virtual const CoreSequenceInterface& bpp::TemplateSequenceDataInterface< std::string >::sequence ( const std::string & sequenceKey ) const

pure virtualinherited

Retrieve a sequence object from the container.

Parameters

sequenceKey The key to which the sequence is associated.

Returns: A reference toward the Sequence with corresponding name.

Implemented in bpp::TemplateSequenceContainerInterface< SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ sequence() [2/2]

virtual const CoreSequenceInterface& bpp::TemplateSequenceDataInterface< std::string >::sequence ( size_t sequencePosition ) const

pure virtualinherited

Retrieve a sequence object from the container.

Parameters

sequencePosition The position of the sequence.

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

Implemented in bpp::TemplateSequenceContainerInterface< SequenceType, HashType >, bpp::TemplateSequenceContainerInterface< SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ sequenceKey()

virtual const std::string & bpp::TemplateSequenceDataInterface< std::string >::sequenceKey ( size_t sequencePosition ) const

pure virtualinherited

Get the key associated to a given sequence.

Parameters

sequencePosition The position of the sequence in the container.

Returns: The key to which the sequence is associated.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ setComments()

virtual void bpp::Commentable::setComments ( const Comments & comments )

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SimpleCommentable.

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

◆ setSequenceKeys()

virtual void bpp::TemplateSequenceDataInterface< std::string >::setSequenceKeys ( const std::vector< HashType > & sequenceKeys )

pure virtualinherited

Reset all sequence keys.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ setSequenceNames()

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

pure virtualinherited

Batch-set all sequence names.

Parameters

names	A vector of sequence names. Must be the same size as the number of sequences in the container, otherwise a DimensionException is thrown.
updateKeys	Tell whether the keys of the sequences should be updated with the new sequence names.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateVectorSequenceContainer< SequenceType >, and bpp::CompressedVectorSiteContainer.

◆ setSiteCoordinates()

template<class HashType = std::string>

virtual void bpp::TemplateAlignmentDataInterface< HashType >::setSiteCoordinates ( const Vint & vCoordinates )

pure virtual

Set all coordinates of sites.

Parameters

vCoordinates A vector with all site coordinates.

Implemented in bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, and bpp::CompressedVectorSiteContainer.

◆ site()

template<class HashType = std::string>

virtual const CoreSiteInterface& bpp::TemplateAlignmentDataInterface< HashType >::site ( size_t siteIndex ) const

pure virtual

Get a site from a given position.

Parameters

siteIndex The position

Implemented in bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >, bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >, bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >, bpp::TemplateVectorSiteContainer< SiteType, SequenceType >, bpp::CompressedVectorSiteContainer, and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >.

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

Bpp/Seq/Container/AlignmentData.h

Public Member Functions

Detailed Description

template<class HashType = std::string> class bpp::TemplateAlignmentDataInterface< HashType >

Constructor & Destructor Documentation

◆ TemplateAlignmentDataInterface()

◆ ~TemplateAlignmentDataInterface()

Member Function Documentation

◆ alphabet()

◆ clear()

◆ clearComments()

◆ clone()

◆ createEmptyContainer()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ deleteSites()

◆ getAlphabet()

◆ getComments()

◆ getNumberOfSequences()

◆ getNumberOfSites()

◆ getSequenceComments()

◆ getSequenceKeys()

◆ getSequenceNames()

◆ getSequencePosition()

◆ getSiteCoordinates()

◆ getStateValueAt() [1/2]

◆ getStateValueAt() [2/2]

◆ hasSequence()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ reindexSites()

◆ sequence() [1/2]

◆ sequence() [2/2]

◆ sequenceKey()

◆ setComments()

◆ setSequenceKeys()

◆ setSequenceNames()

◆ setSiteCoordinates()

◆ site()

template<class HashType = std::string>
class bpp::TemplateAlignmentDataInterface< HashType >