The SequenceContainer interface. More...

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

Inheritance diagram for bpp::SequenceContainer:

Collaboration diagram for bpp::SequenceContainer:

Public Member Functions
	SequenceContainer ()

virtual	~SequenceContainer ()

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

virtual std::string	toString (const std::string &name) const =0
	Convert a particular sequence to a string. 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	operator() (size_t siteIndex, const std::string &sequenceName, int state) const =0

virtual const Comments &	getComments (const std::string &name) const =0
	Get 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 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 Clonable *	clone () const=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 &	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 SequenceContainer interface.

This interface is the most general one in the container hierarchy for sequences. No assumption is made on the sequences in the container (no ordering, no alignment). Sequences may be retrieved using their names, which must be unique.

The container is the only one responsible for the allocation/destruction of sequences it contains. This means that any sequence passed to it will be copied into the container. The container also provides methods that send const pointers towards these sequences (without performing any copy of the underlying objects).

Notes :

methods for adding sequences to the container are not declared here (so they can't be used throught this interface), because these methods take sequence container's type specific parameters (i.e. a key for map sequence containers);
to delete a sequence from a container, one must use the appropriate method (removeSequence()). These methods performs a few check, and properly update pointers. You should never delete a sequence from a container by yourself.

See also: Sequence

Definition at line 82 of file SequenceContainer.h.

Constructor & Destructor Documentation

◆ SequenceContainer()

bpp::SequenceContainer::SequenceContainer ( )

inline

Definition at line 86 of file SequenceContainer.h.

◆ ~SequenceContainer()

virtual bpp::SequenceContainer::~SequenceContainer ( )

inlinevirtual

Definition at line 87 of file SequenceContainer.h.

Member Function Documentation

◆ addSequence()

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

pure virtual

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().

◆ 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.

◆ 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.

◆ 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()

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().

◆ 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().

◆ 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.

◆ getSequence()

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

pure virtual

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().

◆ 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.

◆ getStateValueAt()

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.

◆ 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()() [1/3]

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

pure virtual

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()() [2/3]

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

pure virtual

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()() [3/3]

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.

◆ removeSequence()

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

pure virtual

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().

◆ setComments()

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.

◆ 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()

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

pure virtual

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.

◆ 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().

◆ toString()

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().

◆ valueAt() [1/2]

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

pure virtual

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.

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

◆ valueAt() [2/2]

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

pure virtual

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.

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

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

Bpp/Seq/Container/SequenceContainer.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SequenceContainer()

◆ ~SequenceContainer()

Member Function Documentation

◆ addSequence()

◆ clear()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ getAlphabet()

◆ getComments()

◆ getGeneralComments()

◆ getNumberOfSequences()

◆ getSequence()

◆ getSequenceNames()

◆ getStateValueAt()

◆ hasSequence()

◆ operator()() [1/3]

◆ operator()() [2/3]

◆ operator()() [3/3]

◆ removeSequence()

◆ setComments()

◆ setGeneralComments()

◆ setSequence()

◆ setSequenceNames()

◆ toString()

◆ valueAt() [1/2]

◆ valueAt() [2/2]