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

Inheritance diagram for bpp::MapSequenceContainer:

Collaboration diagram for bpp::MapSequenceContainer:

Public Member Functions
	MapSequenceContainer (const std::map< std::string, Sequence > &ms, const Alphabet alpha)

	MapSequenceContainer (const Alphabet *alpha)

	MapSequenceContainer (const MapSequenceContainer &msc)

MapSequenceContainer &	operator= (const MapSequenceContainer &msc)

virtual	~MapSequenceContainer ()

const Sequence &	getSequenceByKey (const std::string &key) const throw (SequenceNotFoundException)
	Get a sequence. More...

void	setSequenceByKey (const std::string &key, const Sequence &sequence, bool checkNames=true) throw (SequenceNotFoundException)
	Set a sequence. More...

Sequence *	removeSequenceByKey (const std::string &key) throw (SequenceNotFoundException)
	Remove a sequence. More...

void	deleteSequenceByKey (const std::string &key) throw (SequenceNotFoundException)
	Delete a sequence. More...

void	addSequence (const std::string &key, const Sequence &sequence, bool checkNames=true) throw (Exception)
	Add a sequence and key. More...

std::vector< std::string >	getKeys () const

std::string	getKey (size_t pos) const throw (IndexOutOfBoundsException)

std::string	getKey (const std::string &name) const throw (SequenceNotFoundException)

The clonable interface
MapSequenceContainer *	clone () const

The SequenceContainer interface implementation:
const Sequence &	getSequence (const std::string &name) const throw (SequenceNotFoundException)
	Retrieve a sequence object from the container. More...

bool	hasSequence (const std::string &name) const
	Check if a sequence with a given name is present in the container. More...

void	addSequence (const Sequence &sequence, bool checkNames=true) throw (Exception)
	The SequenceContainer method. Calls the addSeqeucne(key, Sequence) method while using the resut of sequence.getName() as a key. More...

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

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

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

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

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

MapSequenceContainer *	createEmptyContainer () const
	Return a copy of this container, but with no sequence inside. More...

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

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

int &	operator() (const std::string &sequenceName, size_t elementIndex)
	Element access operator. More...

const int &	operator() (const std::string &sequenceName, size_t elementIndex) const
	Element access operator. More...

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

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

int &	operator() (size_t sequenceIndex, size_t elementIndex)
	Element access operator. More...

const int &	operator() (size_t sequenceIndex, size_t elementIndex) const
	Element access operator. More...

The OrderedSequenceContainer interface implementation:
const Sequence &	getSequence (size_t sequenceIndex) const throw (IndexOutOfBoundsException)
	Retrieve a sequence object from the container. More...

size_t	getSequencePosition (const std::string &name) const throw (SequenceNotFoundException)
	Get the position of a sequence in sequence container from its name. More...

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

Sequence *	removeSequence (size_t sequenceIndex) throw (IndexOutOfBoundsException)
	Extract (and remove) a sequence from the container. More...

void	deleteSequence (size_t sequenceIndex) throw (IndexOutOfBoundsException)
	Delete a sequence of the container. More...

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

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

void	setSequencesNames (const std::vector< std::string > &names, bool checkNames) throw (Exception)
	Set all sequence names. More...

AbstractSequenceContainer methods.
Sequence &	getSequence_ (size_t i) throw (IndexOutOfBoundsException)

Sequence &	getSequence_ (const std::string &name) throw (SequenceNotFoundException)

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

Private Attributes
std::map< std::string, Sequence * >	sequences_

Detailed Description

MapSequenceContainer class.

Sequences are stored using a key std::string, in a map object. Sequences are ordered according to the key order (defined by the < operator).

Definition at line 63 of file MapSequenceContainer.h.

Constructor & Destructor Documentation

◆ MapSequenceContainer() [1/3]

MapSequenceContainer::MapSequenceContainer	(	const std::map< std::string, Sequence *> &	ms,
		const Alphabet *	alpha
	)

Definition at line 50 of file MapSequenceContainer.cpp.

References addSequence().

Referenced by clone(), and createEmptyContainer().

◆ MapSequenceContainer() [2/3]

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

inline

Definition at line 71 of file MapSequenceContainer.h.

◆ MapSequenceContainer() [3/3]

MapSequenceContainer::MapSequenceContainer ( const MapSequenceContainer & msc )

Definition at line 61 of file MapSequenceContainer.cpp.

References addSequence(), getKey(), getNumberOfSequences(), and getSequence().

◆ ~MapSequenceContainer()

MapSequenceContainer::~MapSequenceContainer ( )

virtual

Definition at line 87 of file MapSequenceContainer.cpp.

References clear().

Member Function Documentation

◆ addSequence() [1/2]

void MapSequenceContainer::addSequence	(	const std::string &	key,
		const Sequence &	sequence,
		bool	checkNames = `true`
	)
throw	(	Exception
	)

Add a sequence and key.

Parameters

key	The key of the new sequence.
sequence	The new sequence that will be associated to the key.
checkNames	Tell is the sequence name must be checked.

Definition at line 344 of file MapSequenceContainer.cpp.

Referenced by addSequence(), MapSequenceContainer(), and operator=().

◆ addSequence() [2/2]

void bpp::MapSequenceContainer::addSequence	(	const Sequence &	sequence,
		bool	checkNames = `true`
	)
throw	(	Exception
	)

inlinevirtual

The SequenceContainer method. Calls the addSeqeucne(key, Sequence) method while using the resut of sequence.getName() as a key.

Implements bpp::SequenceContainer.

Definition at line 166 of file MapSequenceContainer.h.

References addSequence(), and bpp::Sequence::getName().

◆ clear()

void MapSequenceContainer::clear ( )

virtual

Delete all sequences in the container.

Implements bpp::SequenceContainer.

Definition at line 447 of file MapSequenceContainer.cpp.

References sequences_.

Referenced by operator=(), and ~MapSequenceContainer().

◆ clone()

MapSequenceContainer* bpp::MapSequenceContainer::clone ( ) const

inline

Definition at line 149 of file MapSequenceContainer.h.

References MapSequenceContainer().

◆ createEmptyContainer()

MapSequenceContainer * MapSequenceContainer::createEmptyContainer ( ) const

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.

Implements bpp::SequenceContainer.

Definition at line 458 of file MapSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getAlphabet(), bpp::AbstractSequenceContainer::getGeneralComments(), MapSequenceContainer(), and bpp::AbstractSequenceContainer::setGeneralComments().

◆ deleteGeneralComments()

void bpp::AbstractSequenceContainer::deleteGeneralComments ( )

inlinevirtualinherited

Delete the comments associated to this container.

Implements bpp::SequenceContainer.

Definition at line 150 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::comments_.

◆ deleteSequence() [1/2]

void MapSequenceContainer::deleteSequence	(	const std::string &	name	)
throw	(	SequenceNotFoundException
	)

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 318 of file MapSequenceContainer.cpp.

◆ deleteSequence() [2/2]

void MapSequenceContainer::deleteSequence	(	size_t	sequenceIndex	)
throw	(	IndexOutOfBoundsException
	)

virtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 306 of file MapSequenceContainer.cpp.

◆ deleteSequenceByKey()

void MapSequenceContainer::deleteSequenceByKey	(	const std::string &	key	)
throw	(	SequenceNotFoundException
	)

Delete a sequence.

Parameters

key	The key of the sequence.

Exceptions

SequenceNotFoundException If no sequence is associated to the given key.

Definition at line 333 of file MapSequenceContainer.cpp.

◆ getAlphabet()

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

inlinevirtualinherited

Get sequence container's alphabet.

Returns: The alphabet associated to this container.

Implements bpp::SequenceContainer.

Definition at line 123 of file AbstractSequenceContainer.h.

References bpp::AbstractSequenceContainer::alphabet_.

Referenced by 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
	)

inlinevirtualinherited

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
	)

inlinevirtualinherited

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
	)

inlinevirtualinherited

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
	)

inlinevirtualinherited

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

inlinevirtualinherited

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 bpp::AbstractSequenceContainer::comments_.

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

◆ getKey() [1/2]

string MapSequenceContainer::getKey	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

Returns: The key of a given sequence specified by its position in the container.

Parameters

pos	The index of the sequence.

Exceptions

IndexOutOfBoundsException If pos is not a valid index.

Definition at line 380 of file MapSequenceContainer.cpp.

Referenced by MapSequenceContainer().

◆ getKey() [2/2]

string MapSequenceContainer::getKey	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

Returns: The key of a given sequence specified by its name.

Parameters

name	The name of the sequence.

Exceptions

SequenceNotFoundException If no sequence was found with the given name.

Definition at line 391 of file MapSequenceContainer.cpp.

References bpp::SequenceNotFoundException::getSequenceId().

◆ getKeys()

vector< string > MapSequenceContainer::getKeys ( ) const

Returns: All sequences keys.

Definition at line 370 of file MapSequenceContainer.cpp.

References sequences_.

Referenced by operator=().

◆ getName()

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

inlinevirtualinherited

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()

size_t bpp::MapSequenceContainer::getNumberOfSequences ( ) const

inlinevirtual

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Implements bpp::OrderedSequenceContainer.

Definition at line 173 of file MapSequenceContainer.h.

References sequences_.

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

◆ getSequence() [1/2]

const Sequence & MapSequenceContainer::getSequence	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 108 of file MapSequenceContainer.cpp.

Referenced by MapSequenceContainer(), operator()(), operator=(), and valueAt().

◆ getSequence() [2/2]

const Sequence & MapSequenceContainer::getSequence	(	size_t	sequenceIndex	)	const
throw	(	IndexOutOfBoundsException
	)

virtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 94 of file MapSequenceContainer.cpp.

◆ getSequence_() [1/2]

Sequence & MapSequenceContainer::getSequence_	(	size_t	i	)
throw	(	IndexOutOfBoundsException
	)

Definition at line 130 of file MapSequenceContainer.cpp.

Referenced by operator()(), and valueAt().

◆ getSequence_() [2/2]

Sequence & MapSequenceContainer::getSequence_	(	const std::string &	name	)
throw	(	SequenceNotFoundException
	)

Definition at line 141 of file MapSequenceContainer.cpp.

◆ getSequenceByKey()

const Sequence & MapSequenceContainer::getSequenceByKey	(	const std::string &	key	)	const
throw	(	SequenceNotFoundException
	)

Get a sequence.

Parameters

key	The key of the sequence to retrieve.

Returns: The sequence associated to the given key.

Exceptions

SequenceNotFoundException If no sequence is associated to the given key.

Definition at line 152 of file MapSequenceContainer.cpp.

◆ getSequencePosition()

size_t MapSequenceContainer::getSequencePosition	(	const std::string &	name	)	const
throw	(	SequenceNotFoundException
	)

virtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 163 of file MapSequenceContainer.cpp.

◆ getSequencesNames()

vector< string > MapSequenceContainer::getSequencesNames ( ) const

virtual

Get all the names of the sequences in the container.

Returns: A vector of strings with all sequence names.

Implements bpp::OrderedSequenceContainer.

Definition at line 416 of file MapSequenceContainer.cpp.

References sequences_.

◆ hasSequence()

bool MapSequenceContainer::hasSequence ( const std::string & name ) const

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.

Implements bpp::SequenceContainer.

Definition at line 119 of file MapSequenceContainer.cpp.

References sequences_.

◆ operator()() [1/4]

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

inlinevirtual

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.

Implements bpp::SequenceContainer.

Definition at line 185 of file MapSequenceContainer.h.

References getSequence_().

◆ operator()() [2/4]

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

inlinevirtual

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.

Implements bpp::SequenceContainer.

Definition at line 189 of file MapSequenceContainer.h.

References getSequence().

◆ operator()() [3/4]

int& bpp::MapSequenceContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 202 of file MapSequenceContainer.h.

References getSequence_().

◆ operator()() [4/4]

const int& bpp::MapSequenceContainer::operator()	(	size_t	sequenceIndex,
		size_t	elementIndex
	)		const

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 206 of file MapSequenceContainer.h.

References getSequence().

◆ operator=()

MapSequenceContainer & MapSequenceContainer::operator= ( const MapSequenceContainer & msc )

Definition at line 70 of file MapSequenceContainer.cpp.

References addSequence(), clear(), getKeys(), getNumberOfSequences(), getSequence(), and bpp::AbstractSequenceContainer::operator=().

◆ removeSequence() [1/2]

Sequence * MapSequenceContainer::removeSequence	(	const std::string &	name	)
throw	(	SequenceNotFoundException
	)

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 278 of file MapSequenceContainer.cpp.

◆ removeSequence() [2/2]

Sequence * MapSequenceContainer::removeSequence	(	size_t	sequenceIndex	)
throw	(	IndexOutOfBoundsException
	)

virtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 265 of file MapSequenceContainer.cpp.

◆ removeSequenceByKey()

Sequence * MapSequenceContainer::removeSequenceByKey	(	const std::string &	key	)
throw	(	SequenceNotFoundException
	)

Remove a sequence.

Parameters

key	The key of the sequence.

Returns: The sequence previously associated to the given key.

Exceptions

SequenceNotFoundException If no sequence is associated to the given key.

Definition at line 293 of file MapSequenceContainer.cpp.

◆ setComments() [1/2]

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

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.

Implements bpp::OrderedSequenceContainer.

Reimplemented in bpp::VectorSequenceContainer.

Definition at line 48 of file AbstractSequenceContainer.cpp.

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

◆ setComments() [2/2]

void MapSequenceContainer::setComments	(	size_t	sequenceIndex,
		const Comments &	comments
	)
throw	(	IndexOutOfBoundsException
	)

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::AbstractSequenceContainer.

Definition at line 405 of file MapSequenceContainer.cpp.

◆ setGeneralComments()

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

inlinevirtualinherited

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 bpp::AbstractSequenceContainer::comments_.

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

◆ setSequence() [1/2]

void MapSequenceContainer::setSequence	(	const std::string &	name,
		const Sequence &	sequence,
		bool	checkName = `true`
	)
throw	(	SequenceNotFoundException
	)

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 209 of file MapSequenceContainer.cpp.

◆ setSequence() [2/2]

void MapSequenceContainer::setSequence	(	size_t	sequenceIndex,
		const Sequence &	sequence,
		bool	checkName = `true`
	)
throw	(	IndexOutOfBoundsException
	)

virtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 179 of file MapSequenceContainer.cpp.

◆ setSequenceByKey()

void MapSequenceContainer::setSequenceByKey	(	const std::string &	key,
		const Sequence &	sequence,
		bool	checkNames = `true`
	)
throw	(	SequenceNotFoundException
	)

Set a sequence.

Parameters

key	The key of the sequence.
sequence	The new sequence that will be associated to the key.
checkNames	Tell is the sequence name must be checked.

Exceptions

SequenceNotFoundException If no sequence is associated to the given key.

Definition at line 237 of file MapSequenceContainer.cpp.

◆ setSequencesNames()

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 426 of file MapSequenceContainer.cpp.

◆ toString() [1/2]

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

inlinevirtualinherited

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
	)

inlinevirtualinherited

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]

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

inlinevirtual

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::OrderedSequenceContainer.

Definition at line 177 of file MapSequenceContainer.h.

References getSequence_().

◆ valueAt() [2/4]

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

inlinevirtual

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::OrderedSequenceContainer.

Definition at line 181 of file MapSequenceContainer.h.

References getSequence().

◆ valueAt() [3/4]

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

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 194 of file MapSequenceContainer.h.

References getSequence_().

◆ valueAt() [4/4]

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

inlinevirtual

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 198 of file MapSequenceContainer.h.

References getSequence().

Member Data Documentation

◆ sequences_

std::map<std::string, Sequence*> bpp::MapSequenceContainer::sequences_

private

Definition at line 67 of file MapSequenceContainer.h.

Referenced by clear(), getKeys(), getNumberOfSequences(), getSequencesNames(), and hasSequence().

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

Bpp/Seq/Container/MapSequenceContainer.h
Bpp/Seq/Container/MapSequenceContainer.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MapSequenceContainer() [1/3]

◆ MapSequenceContainer() [2/3]

◆ MapSequenceContainer() [3/3]

◆ ~MapSequenceContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ clear()

◆ clone()

◆ createEmptyContainer()

◆ deleteGeneralComments()

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ deleteSequenceByKey()

◆ getAlphabet()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getGeneralComments()

◆ getKey() [1/2]

◆ getKey() [2/2]

◆ getKeys()

◆ getName()

◆ getNumberOfSequences()

◆ getSequence() [1/2]

◆ getSequence() [2/2]

◆ getSequence_() [1/2]

◆ getSequence_() [2/2]

◆ getSequenceByKey()

◆ getSequencePosition()

◆ getSequencesNames()

◆ hasSequence()

◆ operator()() [1/4]

◆ operator()() [2/4]

◆ operator()() [3/4]

◆ operator()() [4/4]

◆ operator=()

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ removeSequenceByKey()

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setGeneralComments()

◆ setSequence() [1/2]

◆ setSequence() [2/2]

◆ setSequenceByKey()

◆ setSequencesNames()

◆ toString() [1/2]

◆ toString() [2/2]

◆ valueAt() [1/4]

◆ valueAt() [2/4]

◆ valueAt() [3/4]

◆ valueAt() [4/4]

Member Data Documentation

◆ sequences_