Partial implementation of the OrderedSequenceContainer interface. More...

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

Inheritance diagram for bpp::AbstractSequenceContainer:

Collaboration diagram for bpp::AbstractSequenceContainer:

Public Member Functions
	AbstractSequenceContainer (const Alphabet *alpha)
	This constructor initialize the alphabet pointer. More...

	AbstractSequenceContainer (const AbstractSequenceContainer &sc)

AbstractSequenceContainer &	operator= (const AbstractSequenceContainer &sc)

	AbstractSequenceContainer (const SequenceContainer &sc)
	Copy constructor from any SequenceContainer object. More...

AbstractSequenceContainer &	operator= (const SequenceContainer &sc)
	Assignation operator from any SequenceContainer object. More...

virtual	~AbstractSequenceContainer ()

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

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

virtual Sequence *	removeSequence (size_t sequenceIndex)=0 throw (IndexOutOfBoundsException, Exception)
	Extract (and remove) a sequence from the container. More...

virtual void	deleteSequence (size_t sequenceIndex)=0 throw (IndexOutOfBoundsException, Exception)
	Delete a sequence of the container. More...

virtual size_t	getSequencePosition (const std::string &name) const =0 throw (SequenceNotFoundException)
	Get the position of a sequence in sequence container from its name. 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 void	addSequence (const Sequence &sequence, bool checkName)=0 throw (Exception)
	Add a sequence to the container. More...

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

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

From the SequenceContainer interface
const Alphabet *	getAlphabet () const
	Get sequence container's alphabet. More...

const std::vector< int > &	getContent (const std::string &name) const throw (SequenceNotFoundException)
	Get the content of a sequence. More...

std::string	toString (const std::string &name) const throw (SequenceNotFoundException)
	Convert a particular sequence to a string. More...

const Comments &	getComments (const std::string &name) const throw (SequenceNotFoundException)
	Get comments of a particular sequence. More...

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

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

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

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

From the OrderedSequenceContainer interface
virtual const std::string &	getName (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get the name of a particular sequence. More...

virtual const std::vector< int > &	getContent (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get the content of a sequence. More...

virtual std::string	toString (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Convert a particular sequence to a string. More...

virtual const Comments &	getComments (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Get comments of a particular sequence. More...

virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0 throw (IndexOutOfBoundsException)
	Set the comments of a particular sequence. More...

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

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

virtual Sequence *	removeSequence (const std::string &name)=0 throw (SequenceNotFoundException, Exception)
	Extract (and remove) a sequence from the container. More...

virtual void	deleteSequence (const std::string &name)=0 throw (SequenceNotFoundException, Exception)
	Delete a sequence of the container. More...

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

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

virtual void	setSequencesNames (const std::vector< std::string > &names, bool checkNames)=0 throw (Exception)
	Set all sequence names. 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 &	valueAt (const std::string &sequenceName, size_t elementIndex)=0 throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function. More...

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

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

virtual const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const =0 throw (IndexOutOfBoundsException)
	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...

Private Attributes
const Alphabet *	alphabet_
	The container's alphabet. More...

Comments	comments_
	The container's comments. More...

Detailed Description

Partial implementation of the OrderedSequenceContainer interface.

This abstract class provides an alphabet and comments, with associated methods.

Definition at line 57 of file AbstractSequenceContainer.h.

Constructor & Destructor Documentation

◆ AbstractSequenceContainer() [1/3]

bpp::AbstractSequenceContainer::AbstractSequenceContainer ( const Alphabet * alpha )

inline

This constructor initialize the alphabet pointer.

This constructor is to be called by constructors of derived classes.

Parameters

alpha The alphabet to be associated to this container.

Definition at line 81 of file AbstractSequenceContainer.h.

◆ AbstractSequenceContainer() [2/3]

bpp::AbstractSequenceContainer::AbstractSequenceContainer ( const AbstractSequenceContainer & sc )

inline

Definition at line 84 of file AbstractSequenceContainer.h.

◆ AbstractSequenceContainer() [3/3]

bpp::AbstractSequenceContainer::AbstractSequenceContainer ( const SequenceContainer & sc )

inline

Copy constructor from any SequenceContainer object.

Parameters

sc	Another sequence container.

Definition at line 99 of file AbstractSequenceContainer.h.

◆ ~AbstractSequenceContainer()

virtual bpp::AbstractSequenceContainer::~AbstractSequenceContainer ( )

inlinevirtual

Definition at line 114 of file AbstractSequenceContainer.h.

Member Function Documentation

◆ addSequence()

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

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

Referenced by bpp::SequenceContainerTools::append(), and bpp::NexusIOSequence::appendAlignmentFromStream().

◆ clear()

virtual void bpp::SequenceContainer::clear ( )

pure virtualinherited

Delete all sequences in the container.

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

◆ createEmptyContainer()

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

pure virtualinherited

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

This method creates a new SequenceContainer 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::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, bpp::MapSequenceContainer, and bpp::AlignedSequenceContainer.

◆ deleteGeneralComments()

void bpp::AbstractSequenceContainer::deleteGeneralComments ( )

inlinevirtual

Delete the comments associated to this container.

Implements bpp::SequenceContainer.

Definition at line 150 of file AbstractSequenceContainer.h.

References comments_.

◆ deleteSequence() [1/2]

virtual void bpp::OrderedSequenceContainer::deleteSequence	(	size_t	sequenceIndex	)
throw	(	IndexOutOfBoundsException,
		Exception
	)

pure virtualinherited

Delete a sequence of the container.

Parameters

sequenceIndex The position of the sequence.

Exceptions

IndexOutOfBoundsException If the position does not match any sequence in the container.

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

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

◆ deleteSequence() [2/2]

virtual void bpp::OrderedSequenceContainer::deleteSequence	(	const std::string &	name	)
throw	(	SequenceNotFoundException,
		Exception
	)

pure virtualinherited

Delete a sequence of the container.

Parameters

name	The name of the sequence.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::SequenceContainer.

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

◆ getAlphabet()

const Alphabet* bpp::AbstractSequenceContainer::getAlphabet ( ) const

inlinevirtual

Get sequence container's alphabet.

Returns: The alphabet associated to this container.

Implements bpp::SequenceContainer.

Definition at line 123 of file AbstractSequenceContainer.h.

References alphabet_.

Referenced by bpp::MapSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), and bpp::VectorSiteContainer::realloc().

◆ getComments() [1/2]

const Comments& bpp::AbstractSequenceContainer::getComments	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 134 of file AbstractSequenceContainer.h.

References bpp::Sequence::getComments(), and bpp::OrderedSequenceContainer::getSequence().

Referenced by bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), and bpp::VectorSiteContainer::VectorSiteContainer().

◆ getComments() [2/2]

virtual const Comments& bpp::AbstractSequenceContainer::getComments	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 177 of file AbstractSequenceContainer.h.

References bpp::Sequence::getComments(), and bpp::OrderedSequenceContainer::getSequence().

◆ getContent() [1/2]

const std::vector<int>& bpp::AbstractSequenceContainer::getContent	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

inlinevirtual

Get the content of a sequence.

Parameters

name	The name of the sequence.

Returns: The content of the sequence as a vector of integers.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::OrderedSequenceContainer.

Definition at line 124 of file AbstractSequenceContainer.h.

References bpp::SymbolList::getContent(), and bpp::OrderedSequenceContainer::getSequence().

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

◆ getContent() [2/2]

virtual const std::vector<int>& bpp::AbstractSequenceContainer::getContent	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtual

Get the content of a sequence.

Parameters

sequenceIndex The position of the sequence.

Returns: The content of the sequence as a vector of integers.

Exceptions

IndexOutOfBoundsException If the position does not match any sequence in the container.

Implements bpp::OrderedSequenceContainer.

Definition at line 167 of file AbstractSequenceContainer.h.

References bpp::SymbolList::getContent(), and bpp::OrderedSequenceContainer::getSequence().

◆ getGeneralComments()

const Comments& bpp::AbstractSequenceContainer::getGeneralComments ( ) const

inlinevirtual

Get the comments of this container.

Returns: The comments associated to this container.

Implements bpp::SequenceContainer.

Definition at line 140 of file AbstractSequenceContainer.h.

References comments_.

Referenced by bpp::MapSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), and bpp::CompressedVectorSiteContainer::createEmptyContainer().

◆ getName()

virtual const std::string& bpp::AbstractSequenceContainer::getName	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtual

Get the name of a particular 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.

Implements bpp::OrderedSequenceContainer.

Definition at line 162 of file AbstractSequenceContainer.h.

References bpp::Sequence::getName(), and bpp::OrderedSequenceContainer::getSequence().

Referenced by bpp::VectorSequenceContainer::getSequencesNames(), and bpp::VectorSequenceContainer::hasSequence().

◆ getNumberOfSequences()

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

pure virtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implements bpp::SequenceContainer.

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

Referenced by bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SimpleSequenceContainerIterator::hasMoreSequences(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSequenceContainer::VectorSequenceContainer(), and bpp::VectorSiteContainer::VectorSiteContainer().

◆ getSequence() [1/2]

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

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.

Exceptions

IndexOutOfBoundsException If the position does not match any sequence in the container.

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

Referenced by bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::computeSimilarityMatrix(), getComments(), getContent(), getName(), bpp::SiteContainerTools::getSequencePositions(), bpp::SimpleSequenceContainerIterator::nextSequence(), bpp::VectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), toString(), bpp::SiteContainerTools::translateSequence(), bpp::VectorSequenceContainer::VectorSequenceContainer(), and bpp::VectorSiteContainer::VectorSiteContainer().

◆ getSequence() [2/2]

virtual const Sequence& bpp::OrderedSequenceContainer::getSequence	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

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.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::SequenceContainer.

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

◆ getSequencePosition()

virtual size_t bpp::OrderedSequenceContainer::getSequencePosition	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

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

◆ getSequencesNames()

virtual std::vector<std::string> bpp::OrderedSequenceContainer::getSequencesNames ( ) const

pure virtualinherited

Get all the names of the sequences in the container.

Returns: A vector of strings with all sequence names.

Implements bpp::SequenceContainer.

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

◆ hasSequence()

virtual bool bpp::SequenceContainer::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::CompressedVectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorSiteContainer, and bpp::MapSequenceContainer.

◆ operator()() [1/4]

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

◆ operator()() [2/4]

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

◆ operator()() [3/4]

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

◆ operator()() [4/4]

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

◆ operator=() [1/2]

AbstractSequenceContainer& bpp::AbstractSequenceContainer::operator= ( const AbstractSequenceContainer & sc )

inline

Definition at line 87 of file AbstractSequenceContainer.h.

References alphabet_, and comments_.

Referenced by bpp::MapSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), and bpp::VectorSequenceContainer::operator=().

◆ operator=() [2/2]

AbstractSequenceContainer& bpp::AbstractSequenceContainer::operator= ( const SequenceContainer & sc )

inline

Assignation operator from any SequenceContainer object.

Parameters

sc	Another sequence container.

Definition at line 107 of file AbstractSequenceContainer.h.

References alphabet_, comments_, bpp::SequenceContainer::getAlphabet(), and bpp::SequenceContainer::getGeneralComments().

◆ removeSequence() [1/2]

virtual Sequence* bpp::OrderedSequenceContainer::removeSequence	(	size_t	sequenceIndex	)
throw	(	IndexOutOfBoundsException,
		Exception
	)

pure virtualinherited

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex The position of the sequence.

Exceptions

IndexOutOfBoundsException If the name does not match any sequence in the container.

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

◆ removeSequence() [2/2]

virtual Sequence* bpp::OrderedSequenceContainer::removeSequence	(	const std::string &	name	)
throw	(	SequenceNotFoundException,
		Exception
	)

pure virtualinherited

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Exceptions

SequenceNotFoundException If the name does not match any sequence in the container.

Implements bpp::SequenceContainer.

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

◆ setComments() [1/2]

void AbstractSequenceContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)
throw	(	SequenceNotFoundException
	)

virtual

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.

Implements bpp::OrderedSequenceContainer.

Reimplemented in bpp::VectorSequenceContainer.

Definition at line 48 of file AbstractSequenceContainer.cpp.

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

◆ setComments() [2/2]

virtual void bpp::AbstractSequenceContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)
throw	(	IndexOutOfBoundsException
	)

pure virtual

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.

Implements bpp::OrderedSequenceContainer.

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

◆ setGeneralComments()

void bpp::AbstractSequenceContainer::setGeneralComments ( const Comments & comments )

inlinevirtual

Set the comments of this container.

Parameters

comments The comments to be associated to this container.

Implements bpp::SequenceContainer.

Definition at line 145 of file AbstractSequenceContainer.h.

References comments_.

Referenced by bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::MapSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

◆ setSequence() [1/2]

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

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.

Exceptions

IndexOutOfBoundsException	If the position does not match any sequence in the container.
Exception	Any other kind of exception.

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

◆ setSequence() [2/2]

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

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.

Exceptions

SequenceNotFoundException	If the name does not match any sequence in the container.
Exception	Any other kind of exception, if the name of the sequence is already used, are whatever else depending on the implementation.

Implements bpp::SequenceContainer.

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

◆ setSequencesNames()

virtual void bpp::OrderedSequenceContainer::setSequencesNames	(	const std::vector< std::string > &	names,
		bool	checkNames
	)
throw	(	Exception
	)

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.

Implements bpp::SequenceContainer.

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

◆ toString() [1/2]

std::string bpp::AbstractSequenceContainer::toString	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 129 of file AbstractSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence(), and bpp::SymbolList::toString().

◆ toString() [2/2]

virtual std::string bpp::AbstractSequenceContainer::toString	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 172 of file AbstractSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence(), and bpp::SymbolList::toString().

◆ valueAt() [1/4]

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

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.

Exceptions

SequenceNotFoundException	If no corresponding sequence is found in the container.
IndexOutOfBoundsException	If the element position is not valid.

Implements bpp::SequenceContainer.

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

◆ valueAt() [2/4]

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

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.

Exceptions

SequenceNotFoundException	If no corresponding sequence is found in the container.
IndexOutOfBoundsException	If the element position is not valid.

Implements bpp::SequenceContainer.

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

◆ valueAt() [3/4]

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

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.

Exceptions

IndexOutOfBoundsException If a position is not valid.

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

◆ valueAt() [4/4]

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

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.

Exceptions

IndexOutOfBoundsException If a position is not valid.

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

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::AbstractSequenceContainer::alphabet_

private

The container's alphabet.

Definition at line 65 of file AbstractSequenceContainer.h.

Referenced by getAlphabet(), and operator=().

◆ comments_

Comments bpp::AbstractSequenceContainer::comments_

private

The container's comments.

Definition at line 70 of file AbstractSequenceContainer.h.

Referenced by deleteGeneralComments(), getGeneralComments(), operator=(), and setGeneralComments().

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

Bpp/Seq/Container/AbstractSequenceContainer.h
Bpp/Seq/Container/AbstractSequenceContainer.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractSequenceContainer() [1/3]

◆ AbstractSequenceContainer() [2/3]

◆ AbstractSequenceContainer() [3/3]

◆ ~AbstractSequenceContainer()

Member Function Documentation

◆ addSequence()

◆ clear()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ getAlphabet()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getGeneralComments()

◆ getName()

◆ getNumberOfSequences()

◆ getSequence() [1/2]

◆ getSequence() [2/2]

◆ getSequencePosition()

◆ getSequencesNames()

◆ hasSequence()

◆ operator()() [1/4]

◆ operator()() [2/4]

◆ operator()() [3/4]

◆ operator()() [4/4]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setGeneralComments()

◆ setSequence() [1/2]

◆ setSequence() [2/2]

◆ setSequencesNames()

◆ toString() [1/2]

◆ toString() [2/2]

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ alphabet_

◆ comments_