bpp::MapSequenceContainer Class Reference

MapSequenceContainer class. More...

#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
	Get a sequence. More...
void	setSequenceByKey (const std::string &key, const Sequence &sequence, bool checkNames=true)
	Set a sequence. More...
Sequence *	removeSequenceByKey (const std::string &key)
	Remove a sequence. More...
void	deleteSequenceByKey (const std::string &key)
	Delete a sequence. More...
void	addSequence (const std::string &key, const Sequence &sequence, bool checkNames=true)
	Add a sequence and key. More...
std::vector< std::string >	getKeys () const
std::string	getKey (size_t pos) const
std::string	getKey (const std::string &name) const
std::string	toString (const std::string &name) const
	Convert a particular sequence to a string. More...
const Comments &	getComments (const std::string &name) const
	Get comments of a particular sequence. More...
const Comments &	getComments () const
	Get the comments. More...
void	setComments (const std::string &name, const Comments &comments)
	Set the comments of a particular sequence. More...
void	setComments (const Comments &comments)
	Set the comments. More...
virtual const Alphabet *	getAlphabet () const =0
	Get container's alphabet. 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 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...
void	clearComments ()
The clonable interface
MapSequenceContainer *	clone () const
The SequenceContainer interface implementation:
const Sequence &	getSequence (const std::string &name) const
	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)
	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)
	Replace a sequence in the container. More...
Sequence *	removeSequence (const std::string &name)
	Extract (and remove) a sequence from the container. More...
void	deleteSequence (const std::string &name)
size_t	getNumberOfSequences () const
	Get the number of sequences in the container. More...
void	clear ()
	Delete all data in the container. More...
MapSequenceContainer *	createEmptyContainer () const
	Return a copy of this container, but with no data inside. More...
int &	valueAt (const std::string &sequenceName, size_t elementIndex)
	Element access function. More...
const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const
	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)
	Element access operator. More...
const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const
	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
	Retrieve a sequence object from the container. More...
size_t	getSequencePosition (const std::string &name) const
	Get the position of a sequence in sequence container from its name. More...
void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName=true)
	Replace a sequence in the container. More...
Sequence *	removeSequence (size_t sequenceIndex)
	Extract (and remove) a sequence from the container. More...
void	deleteSequence (size_t sequenceIndex)
void	setComments (size_t sequenceIndex, const Comments &comments)
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)
	Set all sequence names. More...
AbstractSequenceContainer methods.
Sequence &	getSequence_ (size_t i)
Sequence &	getSequence_ (const std::string &name)
SequencedValuesContainer methods.
double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const
	get value of a state in a position More...
double	operator() (size_t siteIndex, const std::string &sequenceName, int state) const
OrderedValuesContainer methods.
double	getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const
double	operator() (size_t siteIndex, size_t sequenceIndex, int state) const
From the OrderedSequenceContainer interface
virtual std::string	toString (size_t sequenceIndex) const
virtual const Comments &	getComments (size_t sequenceIndex) const
virtual const std::string &	getName (size_t sequenceIndex) const
	Get the name of a particular row of the alignement (aka sequence). More...
SequenceContainer methods.
virtual std::string	toString (size_t sequenceIndex) const=0
virtual const Comments &	getComments (size_t sequenceIndex) const=0
virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0
From the SequencedValuesContainer interface
const Alphabet *	getAlphabet () const
	Get container's alphabet. 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...

Protected Attributes
const Alphabet *	alphabet_
	The container's alphabet. More...
Comments	comments_

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 52 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 63 of file MapSequenceContainer.cpp.

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

~MapSequenceContainer()

MapSequenceContainer::~MapSequenceContainer ( )

virtual

Definition at line 91 of file MapSequenceContainer.cpp.

References clear().

Member Function Documentation

addSequence() [1/2]

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

inlinevirtual

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

Implements bpp::SequencedValuesContainer.

Definition at line 160 of file MapSequenceContainer.h.

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

addSequence() [2/2]

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

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 367 of file MapSequenceContainer.cpp.

References bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::Sequence::getName(), and sequences_.

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

clear()

void MapSequenceContainer::clear ( )

virtual

Delete all data in the container.

Implements bpp::SequencedValuesContainer.

Definition at line 488 of file MapSequenceContainer.cpp.

References sequences_.

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

clearComments()

void bpp::Commentable::clearComments ( )

inlineinherited

Definition at line 100 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::BasicSequence::clearComments(), bpp::SequenceWithAnnotation::clearComments(), bpp::SequenceWithQuality::clearComments(), bpp::AbstractProbabilisticSequenceContainer::deleteGeneralComments(), and bpp::AbstractValuesContainer::deleteGeneralComments().

clone()

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

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 143 of file MapSequenceContainer.h.

References MapSequenceContainer().

createEmptyContainer()

MapSequenceContainer * MapSequenceContainer::createEmptyContainer ( ) const

virtual

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.

Implements bpp::SequencedValuesContainer.

Definition at line 501 of file MapSequenceContainer.cpp.

References bpp::AbstractValuesContainer::getAlphabet(), and MapSequenceContainer().

deleteGeneralComments() [1/2]

void bpp::AbstractValuesContainer::deleteGeneralComments ( )

inlinevirtualinherited

Delete the comments associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 115 of file AbstractValuesContainer.h.

References bpp::Commentable::clearComments().

deleteGeneralComments() [2/2]

virtual void bpp::SequencedValuesContainer::deleteGeneralComments ( )

pure virtualinherited

Delete the comments associated to this container.

Implemented in bpp::AbstractValuesContainer, and bpp::AbstractProbabilisticSequenceContainer.

deleteSequence() [1/2]

void MapSequenceContainer::deleteSequence

(

const std::string &

name

)

Definition at line 340 of file MapSequenceContainer.cpp.

References sequences_.

deleteSequence() [2/2]

void MapSequenceContainer::deleteSequence

(

size_t

sequenceIndex

)

Definition at line 325 of file MapSequenceContainer.cpp.

References sequences_.

deleteSequenceByKey()

void MapSequenceContainer::deleteSequenceByKey

(

const std::string &

key

)

Delete a sequence.

Parameters

key	The key of the sequence.

Definition at line 356 of file MapSequenceContainer.cpp.

References sequences_.

getAlphabet() [1/2]

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

inlinevirtualinherited

Get container's alphabet.

Returns

The alphabet associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 99 of file AbstractValuesContainer.h.

References bpp::AbstractValuesContainer::alphabet_.

Referenced by bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::Pasta::appendSequencesFromStream(), bpp::VectorProbabilisticSiteContainer::appendSite(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), createEmptyContainer(), bpp::VectorProbabilisticSiteContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::getSequence(), bpp::VectorSiteContainer::getSequence(), bpp::VectorProbabilisticSiteContainer::getSequence(), bpp::AlignedSequenceContainer::getSite(), bpp::CompressedVectorSiteContainer::getStateValueAt(), bpp::VectorSiteContainer::getStateValueAt(), getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::CompressedVectorSiteContainer::operator()(), bpp::VectorSiteContainer::operator()(), operator()(), bpp::VectorSequenceContainer::operator()(), bpp::CompressedVectorSiteContainer::operator=(), bpp::VectorSiteContainer::realloc(), bpp::VectorSiteContainer::setSequence(), setSequence(), bpp::VectorSequenceContainer::setSequence(), setSequenceByKey(), bpp::AlignedSequenceContainer::setSite(), bpp::CompressedVectorSiteContainer::setSite(), and bpp::VectorSiteContainer::setSite().

getAlphabet() [2/2]

virtual const Alphabet* bpp::SequencedValuesContainer::getAlphabet ( ) const

pure virtualinherited

Get container's alphabet.

Returns

The alphabet associated to this container.

Implemented in bpp::AbstractValuesContainer.

Referenced by bpp::Clustal::appendAlignmentFromStream(), bpp::DCSE::appendAlignmentFromStream(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), bpp::GenBank::appendSequencesFromStream(), bpp::Mase::appendSequencesFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SiteContainerTools::getCompleteSites(), bpp::SiteContainerTools::getConsensus(), bpp::SequenceContainerTools::getFrequencies(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSequences(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::SequenceContainerTools::merge(), bpp::SiteContainerTools::merge(), bpp::AbstractSequenceContainer::operator=(), bpp::Phylip::readInterleaved(), bpp::Phylip::readSequential(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SiteContainerTools::sampleSites(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Pasta::writeAlignedValues(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

getComments() [1/4]

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

inlineinherited

Get the comments.

Returns

The comments.

Definition at line 91 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::AbstractCoreSequence::getComments(), bpp::BasicSequence::getComments(), bpp::SequenceWithAnnotation::getComments(), bpp::SequenceWithQuality::getComments(), bpp::AbstractProbabilisticSequenceContainer::getGeneralComments(), bpp::AbstractValuesContainer::getGeneralComments(), and bpp::VectorProbabilisticSiteContainer::getSequence().

getComments() [2/4]

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

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 111 of file AbstractSequenceContainer.h.

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

getComments() [3/4]

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

inlinevirtualinherited

Implements bpp::AbstractValuesContainer.

Definition at line 137 of file AbstractSequenceContainer.h.

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

getComments() [4/4]

virtual const Comments& bpp::OrderedValuesContainer::getComments

inherited

Referenced by bpp::CompressedVectorSiteContainer::getSequence(), and bpp::VectorSiteContainer::getSequence().

getGeneralComments() [1/2]

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

inlinevirtualinherited

Get the comments of this container.

Returns

The comments associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 101 of file AbstractValuesContainer.h.

References bpp::Commentable::getComments().

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

getGeneralComments() [2/2]

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().

getKey() [1/2]

string MapSequenceContainer::getKey

(

const std::string &

name

)

const

Returns

The key of a given sequence specified by its name.

Parameters

name	The name of the sequence.

Definition at line 422 of file MapSequenceContainer.cpp.

References getKey(), bpp::SequenceNotFoundException::getSequenceId(), and getSequencePosition().

getKey() [2/2]

string MapSequenceContainer::getKey

(

size_t

pos

)

const

Returns

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

Parameters

pos	The index of the sequence.

Definition at line 408 of file MapSequenceContainer.cpp.

References getNumberOfSequences(), and sequences_.

Referenced by getKey(), MapSequenceContainer(), and setSequence().

getKeys()

vector< string > MapSequenceContainer::getKeys

(

)

const

Returns

All sequences keys.

Definition at line 396 of file MapSequenceContainer.cpp.

References sequences_.

Referenced by operator=().

getName()

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

inlinevirtualinherited

Get the name of a particular row of the alignement (aka 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::OrderedValuesContainer.

Definition at line 127 of file AbstractSequenceContainer.h.

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

Referenced by bpp::CompressedVectorSiteContainer::getSequence().

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 167 of file MapSequenceContainer.h.

References sequences_.

Referenced by getKey(), getStateValueAt(), MapSequenceContainer(), operator=(), setComments(), and setSequencesNames().

getSequence() [1/2]

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

virtual

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns

A reference toward the Sequence with corresponding name.

Implements bpp::OrderedSequenceContainer.

Definition at line 115 of file MapSequenceContainer.cpp.

References sequences_.

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

getSequence() [2/2]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 98 of file MapSequenceContainer.cpp.

References sequences_.

getSequence_() [1/2]

Sequence & MapSequenceContainer::getSequence_

(

const std::string &

name

)

Definition at line 155 of file MapSequenceContainer.cpp.

References sequences_.

getSequence_() [2/2]

Sequence & MapSequenceContainer::getSequence_

(

size_t

i

)

Definition at line 141 of file MapSequenceContainer.cpp.

References sequences_.

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

getSequenceByKey()

const Sequence & MapSequenceContainer::getSequenceByKey

(

const std::string &

key

)

const

Get a sequence.

Parameters

key	The key of the sequence to retrieve.

Returns

The sequence associated to the given key.

Definition at line 168 of file MapSequenceContainer.cpp.

References sequences_.

getSequencePosition()

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

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::OrderedValuesContainer.

Definition at line 178 of file MapSequenceContainer.cpp.

References sequences_.

Referenced by getKey().

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 450 of file MapSequenceContainer.cpp.

References sequences_.

getStateValueAt() [1/3]

double bpp::MapSequenceContainer::getStateValueAt ( size_t  siteIndex, const std::string &  sequenceName, int  state  ) const

inlinevirtual

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

Implements bpp::SequencedValuesContainer.

Definition at line 235 of file MapSequenceContainer.h.

References getSequence(), and bpp::CruxSymbolList::getStateValueAt().

getStateValueAt() [2/3]

virtual double bpp::SequencedValuesContainer::getStateValueAt

inherited

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

getStateValueAt() [3/3]

double bpp::MapSequenceContainer::getStateValueAt ( size_t  siteIndex, size_t  sequenceIndex, int  state  ) const

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 256 of file MapSequenceContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getNumberOfSequences(), getSequence(), bpp::Alphabet::isResolvedIn(), and bpp::CruxSymbolList::size().

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::SequencedValuesContainer.

Definition at line 128 of file MapSequenceContainer.cpp.

References sequences_.

operator()() [1/6]

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 179 of file MapSequenceContainer.h.

References getSequence_().

operator()() [2/6]

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 183 of file MapSequenceContainer.h.

References getSequence().

operator()() [3/6]

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 196 of file MapSequenceContainer.h.

References getSequence_().

operator()() [4/6]

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 200 of file MapSequenceContainer.h.

References getSequence().

operator()() [5/6]

double bpp::MapSequenceContainer::operator() ( size_t  siteIndex, const std::string &  sequenceName, int  state  ) const

inlinevirtual

Implements bpp::SequencedValuesContainer.

Definition at line 240 of file MapSequenceContainer.h.

References getSequence().

operator()() [6/6]

double bpp::MapSequenceContainer::operator() ( size_t  siteIndex, size_t  sequenceIndex, int  state  ) const

inlinevirtual

Implements bpp::OrderedValuesContainer.

Definition at line 267 of file MapSequenceContainer.h.

References bpp::AbstractValuesContainer::getAlphabet(), getSequence(), and bpp::Alphabet::isResolvedIn().

operator=()

MapSequenceContainer & MapSequenceContainer::operator=

(

const MapSequenceContainer &

msc

)

Definition at line 74 of file MapSequenceContainer.cpp.

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

removeSequence() [1/2]

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

virtual

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 296 of file MapSequenceContainer.cpp.

References sequences_.

removeSequence() [2/2]

Sequence * MapSequenceContainer::removeSequence ( size_t  sequenceIndex )

virtual

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex

The position of the sequence.

Implements bpp::OrderedSequenceContainer.

Definition at line 280 of file MapSequenceContainer.cpp.

References sequences_.

removeSequenceByKey()

Sequence * MapSequenceContainer::removeSequenceByKey

(

const std::string &

key

)

Remove a sequence.

Parameters

key	The key of the sequence.

Returns

The sequence previously associated to the given key.

Definition at line 312 of file MapSequenceContainer.cpp.

References sequences_.

setComments() [1/4]

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

inlineinherited

Set the comments.

Parameters

comments

The new comments.

Definition at line 98 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::AbstractCoreSequence::operator=(), bpp::AbstractCoreSequence::setComments(), bpp::BasicSequence::setComments(), bpp::SequenceWithAnnotation::setComments(), bpp::SequenceWithQuality::setComments(), bpp::AbstractProbabilisticSequenceContainer::setGeneralComments(), and bpp::AbstractValuesContainer::setGeneralComments().

setComments() [2/4]

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

inlinevirtualinherited

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.

Definition at line 116 of file AbstractSequenceContainer.h.

References bpp::OrderedValuesContainer::getSequencePosition(), and bpp::OrderedSequenceContainer::setComments().

setComments() [3/4]

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

virtual

Implements bpp::AbstractSequenceContainer.

Definition at line 436 of file MapSequenceContainer.cpp.

References getNumberOfSequences(), and sequences_.

setComments() [4/4]

virtual void bpp::OrderedValuesContainer::setComments

inherited

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

setGeneralComments() [1/2]

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

inlinevirtualinherited

Set the comments of this container.

Parameters

comments

The comments to be associated to this container.

Implements bpp::SequencedValuesContainer.

Definition at line 106 of file AbstractValuesContainer.h.

References bpp::Commentable::setComments().

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

setGeneralComments() [2/2]

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() [1/2]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 224 of file MapSequenceContainer.cpp.

References bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), and sequences_.

setSequence() [2/2]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 194 of file MapSequenceContainer.cpp.

References bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), getKey(), bpp::Sequence::getName(), and sequences_.

setSequenceByKey()

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

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.

Definition at line 252 of file MapSequenceContainer.cpp.

References bpp::Sequence::clone(), bpp::AbstractValuesContainer::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::Sequence::getName(), and sequences_.

setSequencesNames()

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

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 462 of file MapSequenceContainer.cpp.

References getNumberOfSequences(), and sequences_.

toString() [1/3]

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

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 106 of file AbstractSequenceContainer.h.

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

toString() [2/3]

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

inlinevirtualinherited

Implements bpp::OrderedValuesContainer.

Definition at line 132 of file AbstractSequenceContainer.h.

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

toString() [3/3]

virtual std::string bpp::OrderedValuesContainer::toString

inherited

valueAt() [1/4]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 171 of file MapSequenceContainer.h.

References getSequence_().

valueAt() [2/4]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 175 of file MapSequenceContainer.h.

References getSequence().

valueAt() [3/4]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 188 of file MapSequenceContainer.h.

References getSequence_().

valueAt() [4/4]

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

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.

Implements bpp::OrderedSequenceContainer.

Definition at line 192 of file MapSequenceContainer.h.

References getSequence().

Member Data Documentation

alphabet_

const Alphabet* bpp::AbstractValuesContainer::alphabet_

protectedinherited

The container's alphabet.

Definition at line 64 of file AbstractValuesContainer.h.

Referenced by bpp::AbstractValuesContainer::getAlphabet(), bpp::AbstractValuesContainer::operator=(), and bpp::AbstractSequenceContainer::operator=().

comments_

Comments bpp::Commentable::comments_

protectedinherited

Definition at line 62 of file Commentable.h.

Referenced by bpp::Commentable::clearComments(), bpp::Commentable::getComments(), bpp::Commentable::operator=(), and bpp::Commentable::setComments().

sequences_

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

private

Definition at line 67 of file MapSequenceContainer.h.

Referenced by addSequence(), clear(), deleteSequence(), deleteSequenceByKey(), getKey(), getKeys(), getNumberOfSequences(), getSequence(), getSequence_(), getSequenceByKey(), getSequencePosition(), getSequencesNames(), hasSequence(), removeSequence(), removeSequenceByKey(), setComments(), setSequence(), setSequenceByKey(), and setSequencesNames().

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

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