bpp::SequenceContainer Class Reference

The SequenceContainer interface. More...

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

Inheritance diagram for bpp::SequenceContainer:

Collaboration diagram for bpp::SequenceContainer:

List of all members.

Public Member Functions
	SequenceContainer ()
virtual	~SequenceContainer ()
virtual const Alphabet *	getAlphabet () const =0
	Get sequence container's alphabet.
virtual const std::vector< int > &	getContent (const std::string &name) const =0 throw (SequenceNotFoundException)
	Get the content of a sequence.
virtual std::string	toString (const std::string &name) const =0 throw (SequenceNotFoundException)
	Convert a particular sequence to a string.
virtual const Sequence &	getSequence (const std::string &name) const =0 throw (SequenceNotFoundException)
	Retrieve a sequence object from the container.
virtual bool	hasSequence (const std::string &name) const =0
	Check if a sequence with a given name is present in the container.
virtual void	addSequence (const Sequence &sequence, bool checkName)=0 throw (Exception)
	Add a sequence to the container.
virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0 throw (Exception)
	Replace a sequence in the container.
virtual Sequence *	removeSequence (const std::string &name)=0 throw (SequenceNotFoundException, Exception)
	Extract (and remove) a sequence from the container.
virtual void	deleteSequence (const std::string &name)=0 throw (SequenceNotFoundException, Exception)
	Delete a sequence of the container.
virtual size_t	getNumberOfSequences () const =0
	Get the number of sequences in the container.
virtual std::vector< std::string >	getSequencesNames () const =0
	Get all the names of the sequences in the container.
virtual void	setSequencesNames (const std::vector< std::string > &names, bool checkNames)=0 throw (Exception)
	Set all sequence names.
virtual const Comments &	getComments (const std::string &name) const =0 throw (SequenceNotFoundException)
	Get comments of a particular sequence.
virtual void	setComments (const std::string &name, const Comments &comments)=0 throw (SequenceNotFoundException)
	Set the comments of a particular sequence.
virtual const Comments &	getGeneralComments () const =0
	Get the comments of this container.
virtual void	setGeneralComments (const Comments &comments)=0
	Set the comments of this container.
virtual void	deleteGeneralComments ()=0
	Delete the comments associated to this container.
virtual void	clear ()=0
	Delete all sequences in the container.
virtual SequenceContainer *	createEmptyContainer () const =0
	Return a copy of this container, but with no sequence inside.
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 throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function.
virtual const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const =0 throw (SequenceNotFoundException, IndexOutOfBoundsException)
	Element access function.
virtual int &	operator() (const std::string &sequenceName, size_t elementIndex)=0
	Element access operator.
virtual const int &	operator() (const std::string &sequenceName, size_t elementIndex) const =0
	Element access operator.

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Detailed Description

The SequenceContainer interface.

This interface is the most general one in the container hierarchy. 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 : 1. 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); 2. to delete a sequence from a container, one must use the appropriate method (removeSequence() and deleteSequence()). 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 80 of file SequenceContainer.h.

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Constructor & Destructor Documentation

bpp::SequenceContainer::SequenceContainer

(

)

[inline]

Definition at line 84 of file SequenceContainer.h.

virtual bpp::SequenceContainer::~SequenceContainer

(

)

[inline, virtual]

Definition at line 85 of file SequenceContainer.h.

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Member Function Documentation

virtual void bpp::SequenceContainer::addSequence	(	const Sequence &	sequence,
		bool	checkName
	)		throw (Exception) [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::VectorSequenceContainer, bpp::CompressedVectorSiteContainer, bpp::VectorSiteContainer, bpp::AlignedSequenceContainer, and bpp::MapSequenceContainer.

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

virtual void bpp::SequenceContainer::clear

(

)

[pure virtual]

Delete all sequences in the container.

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

virtual SequenceContainer* bpp::SequenceContainer::createEmptyContainer

(

)

const [pure virtual]

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.

virtual void bpp::SequenceContainer::deleteGeneralComments

(

)

[pure virtual]

Delete the comments associated to this container.

Implemented in bpp::AbstractSequenceContainer.

virtual void bpp::SequenceContainer::deleteSequence

(

const std::string &

name

)

throw (SequenceNotFoundException, Exception) [pure virtual]

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.

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

virtual const Alphabet* bpp::SequenceContainer::getAlphabet

(

)

const [pure virtual]

Get sequence container's alphabet.

Returns:

The alphabet associated to this container.

Implemented in bpp::AbstractSequenceContainer.

Referenced by bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getConsensus(), bpp::SequenceContainerTools::getFrequencies(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::AbstractSequenceContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::sampleSites(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

virtual const Comments& bpp::SequenceContainer::getComments

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure virtual]

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::OrderedSequenceContainer, and bpp::AbstractSequenceContainer.

virtual const std::vector<int>& bpp::SequenceContainer::getContent

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure virtual]

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.

Implemented in bpp::OrderedSequenceContainer, and bpp::AbstractSequenceContainer.

Referenced by bpp::SequenceContainerTools::getCounts(), and bpp::SequenceContainerTools::getFrequencies().

virtual const Comments& bpp::SequenceContainer::getGeneralComments

(

)

const [pure virtual]

Get the comments of this container.

Returns:

The comments associated to this container.

Implemented in bpp::AbstractSequenceContainer.

Referenced by bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractSequenceContainer::operator=(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

virtual size_t bpp::SequenceContainer::getNumberOfSequences

(

)

const [pure virtual]

Get the number of sequences in the container.

Returns:

The number of sequences in the container.

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

Referenced by bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

virtual const Sequence& bpp::SequenceContainer::getSequence

(

const std::string &

name

)

const throw (SequenceNotFoundException) [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.

Exceptions:

SequenceNotFoundException

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

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

Referenced by bpp::VectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

virtual std::vector<std::string> bpp::SequenceContainer::getSequencesNames

(

)

const [pure virtual]

Get all the names of the sequences in the container.

Returns:

A vector of strings with all sequence names.

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

Referenced by bpp::SequenceContainerTools::getCounts(), bpp::SequenceContainerTools::getFrequencies(), bpp::VectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

virtual bool bpp::SequenceContainer::hasSequence

(

const std::string &

name

)

const [pure virtual]

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.

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

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

virtual Sequence* bpp::SequenceContainer::removeSequence

(

const std::string &

name

)

throw (SequenceNotFoundException, Exception) [pure virtual]

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.

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

virtual void bpp::SequenceContainer::setComments	(	const std::string &	name,
		const Comments &	comments
	)		throw (SequenceNotFoundException) [pure 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.

Implemented in bpp::VectorSequenceContainer, bpp::OrderedSequenceContainer, and bpp::AbstractSequenceContainer.

virtual void bpp::SequenceContainer::setGeneralComments

(

const Comments &

comments

)

[pure virtual]

Set the comments of this container.

Parameters:

comments

The comments to be associated to this container.

Implemented in bpp::AbstractSequenceContainer.

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

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.

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

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

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

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

virtual std::string bpp::SequenceContainer::toString

(

const std::string &

name

)

const throw (SequenceNotFoundException) [pure virtual]

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::OrderedSequenceContainer, and bpp::AbstractSequenceContainer.

Referenced by bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

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

Exceptions:

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

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

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

Exceptions:

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

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

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

• Bpp/Seq/Container/SequenceContainer.h