bpp::AbstractSequenceContainer Class Reference

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 ()
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...
void	setComments (const std::string &name, const Comments &comments)
	Set the comments of a particular sequence. More...
virtual const Sequence &	getSequence (size_t sequenceIndex) const =0
	Retrieve a sequence object from the container. More...
virtual const Sequence &	getSequence (const std::string &name) const =0
	Retrieve a sequence object from the container. More...
virtual void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...
virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...
virtual std::shared_ptr< Sequence >	removeSequence (size_t sequenceIndex)=0
	Extract (and remove) a sequence from the container. More...
virtual std::shared_ptr< Sequence >	removeSequence (const std::string &name)=0
	Extract (and remove) a sequence from the container. More...
virtual double	operator() (size_t siteIndex, const std::string &sequenceName, int state) const =0
virtual double	operator() (size_t siteIndex, size_t sequenceIndex, int state) const =0
virtual const Alphabet *	getAlphabet () const =0
	Get container's alphabet. More...
virtual bool	hasSequence (const std::string &name) const =0
	Check if a sequence with a given name is present in the container. More...
virtual size_t	getNumberOfSequences () const =0
	Get the number of sequences in the container. More...
virtual std::vector< std::string >	getSequenceNames () const =0
	Get all the names of the sequences in the container. More...
virtual void	setSequenceNames (const std::vector< std::string > &names, bool checkNames)=0
	Set all sequence names. More...
virtual double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const =0
	get value of a state in a position More...
virtual double	getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const =0
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...
virtual void	clear ()=0
	Delete all data in the container. More...
virtual SequencedValuesContainer *	createEmptyContainer () const =0
	Return a copy of this container, but with no data inside. More...
virtual Clonable *	clone () const=0
OrderedValuesContainer *	clone () const =0
virtual size_t	getSequencePosition (const std::string &name) const =0
	Get the position of a sequence in sequence container from its name. More...
void	setComments (const Comments &comments)
	Set the comments. More...
const Comments &	getComments () const
	Get the comments. More...
void	clearComments ()
From the OrderedSequenceContainer interface
virtual const std::string &	getName (size_t sequenceIndex) const
	Get the name of a particular row of the alignement (aka sequence). More...
virtual std::string	toString (size_t sequenceIndex) const
virtual const Comments &	getComments (size_t sequenceIndex) const
virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0
SequenceContainer methods.
virtual const Sequence &	getSequence (const std::string &name) const=0
	Retrieve a sequence object from the container. More...
virtual void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)=0
	Replace a sequence in the container. More...
virtual std::shared_ptr< Sequence >	removeSequence (const std::string &name)=0
	Extract (and remove) a sequence from the container. More...
virtual 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
Provide direct access to sequences content.
Warning These operators allow you to modifiy the content of the sequences. No checking is performed for your modifications, so use with care, or consider using the setContent() methods.
virtual int &	valueAt (const std::string &sequenceName, size_t elementIndex)=0
	Element access function. More...
virtual const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const =0
	Element access function. More...
virtual int &	valueAt (size_t sequenceIndex, size_t elementIndex)=0
	Element access operator. More...
virtual const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const =0
	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...
virtual void	addSequence (const Sequence &sequence, bool checkName)=0
	Add a sequence to the container. More...
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_

Detailed Description

Partial implementation of the OrderedSequenceContainer interface.

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

Definition at line 56 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 68 of file AbstractSequenceContainer.h.

AbstractSequenceContainer() [2/3]

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

inline

Definition at line 71 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 86 of file AbstractSequenceContainer.h.

~AbstractSequenceContainer()

virtual bpp::AbstractSequenceContainer::~AbstractSequenceContainer ( )

inlinevirtual

Definition at line 103 of file AbstractSequenceContainer.h.

Member Function Documentation

addSequence()

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

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

Referenced by bpp::SequenceContainerTools::append(), bpp::Clustal::appendAlignmentFromStream(), bpp::DCSE::appendAlignmentFromStream(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), bpp::GenBank::appendSequencesFromStream(), bpp::Mase::appendSequencesFromStream(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceApplicationTools::getAlignedContainer(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SequenceContainerTools::merge(), bpp::Phylip::readInterleaved(), and bpp::Phylip::readSequential().

clear()

virtual void bpp::SequencedValuesContainer::clear ( )

pure virtualinherited

Delete all data in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

clearComments()

void bpp::Commentable::clearComments ( )

inlineinherited

Definition at line 102 of file Commentable.h.

References bpp::Commentable::comments_.

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

clone()

OrderedValuesContainer* bpp::OrderedValuesContainer::clone ( ) const

pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::SiteContainer, bpp::ProbabilisticSiteContainer, bpp::AlignedValuesContainer, bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

createEmptyContainer()

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

pure virtualinherited

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

This method creates a new SequencedValuesContainer objet. The class of this container depends on the derivative class.

Returns

A new empty container, with the same alphabet as this one.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

deleteGeneralComments() [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.

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::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::VectorProbabilisticSiteContainer::addSite(), bpp::Pasta::appendSequencesFromStream(), bpp::AlignedSequenceContainer::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::VectorProbabilisticSequenceContainer::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::VectorProbabilisticSiteContainer::getStateValueAt(), bpp::VectorSiteContainer::getStateValueAt(), bpp::VectorProbabilisticSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::CompressedVectorSiteContainer::operator()(), bpp::VectorProbabilisticSiteContainer::operator()(), bpp::VectorSiteContainer::operator()(), bpp::VectorProbabilisticSequenceContainer::operator()(), bpp::VectorSequenceContainer::operator()(), bpp::VectorProbabilisticSiteContainer::realloc(), bpp::VectorSiteContainer::realloc(), bpp::CompressedVectorSiteContainer::removeSite(), bpp::CompressedVectorSiteContainer::setComments(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), 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(), 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::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 93 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::AbstractCoreSequence::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

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::SequencedValuesContainer.

Definition at line 111 of file AbstractSequenceContainer.h.

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

getComments() [3/4]

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

inlinevirtual

Implements bpp::AbstractValuesContainer.

Definition at line 137 of file AbstractSequenceContainer.h.

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

getComments() [4/4]

virtual const Comments& bpp::OrderedValuesContainer::getComments

inherited

Referenced by bpp::CompressedVectorSiteContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::VectorSiteContainer::getSequence(), bpp::CompressedVectorSiteContainer::removeSite(), bpp::VectorSiteContainer::setSequence(), bpp::CompressedVectorSiteContainer::setSite(), and bpp::VectorSiteContainer::setSite().

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::VectorProbabilisticSequenceContainer::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(), operator=(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

getName()

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

inlinevirtual

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::CoreSequence::getName(), and bpp::OrderedSequenceContainer::getSequence().

Referenced by bpp::VectorSequenceContainer::getSequenceNames(), and bpp::VectorSequenceContainer::hasSequenceByName().

getNumberOfSequences()

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

pure virtualinherited

Get the number of sequences in the container.

Returns

The number of sequences in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SimpleSequenceContainerIterator::hasMoreSequences(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Clustal::writeAlignment(), bpp::Phylip::writeAlignment(), bpp::Stockholm::writeAlignment(), bpp::Phylip::writeInterleaved(), and bpp::Phylip::writeSequential().

getSequence() [1/3]

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

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.

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

Referenced by bpp::SequenceContainerTools::append(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SequenceContainerTools::getCounts(), bpp::SequenceContainerTools::getFrequencies(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SequenceContainerTools::merge(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Pasta::writeAlignedValues(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequences(), and bpp::Phylip::writeSequential().

getSequence() [2/3]

virtual const Sequence& bpp::SequenceContainer::getSequence

inherited

Retrieve a sequence object from the container.

Parameters

name	The name of the sequence.

Returns

A reference toward the Sequence with corresponding name.

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::VectorSequenceContainer::deleteSequenceByName(), getComments(), getName(), bpp::CompressedVectorSiteContainer::getSequence(), bpp::VectorSiteContainer::getSequence(), bpp::VectorSequenceContainer::getSequenceByName(), bpp::VectorSequenceContainer::getSequenceNames(), bpp::AlignedSequenceContainer::getSite(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::hasSequenceByName(), bpp::VectorSequenceContainer::operator()(), bpp::VectorSiteContainer::removeSequence(), bpp::VectorSequenceContainer::removeSequenceByName(), toString(), and bpp::VectorSequenceContainer::valueAt().

getSequence() [3/3]

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

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.

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

Referenced by bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::SequenceContainerTools::append(), bpp::NexusIOSequence::appendAlignmentFromStream(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SequenceContainerTools::getSelectedSequences(), bpp::SiteContainerTools::getSequencePositions(), bpp::SimpleSequenceContainerIterator::nextSequence(), bpp::VectorSequenceContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SiteContainerTools::translateSequence(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Clustal::writeAlignment(), and bpp::Stockholm::writeAlignment().

getSequenceNames()

virtual std::vector<std::string> bpp::SequencedValuesContainer::getSequenceNames ( ) const

pure virtualinherited

Get all the names of the sequences in the container.

Returns

A vector of strings with all sequence names.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::SequenceContainerTools::append(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::computeSimilarityMatrix(), bpp::SequenceContainerTools::convertAlphabet(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SiteContainerTools::getCompleteSites(), bpp::SequenceContainerTools::getCounts(), bpp::SequenceContainerTools::getFrequencies(), bpp::SiteContainerTools::getSelectedSites(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::SequenceContainerTools::keepOnlySelectedSequences(), bpp::SequenceContainerTools::merge(), bpp::SiteContainerTools::merge(), bpp::VectorSequenceContainer::operator=(), bpp::CompressedVectorSiteContainer::operator=(), bpp::VectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), bpp::SiteContainerTools::removeGapSites(), bpp::SiteContainerTools::removeStopCodonSites(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SequenceApplicationTools::restrictSelectedSequencesByName(), bpp::SiteContainerTools::sampleSites(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(), bpp::VectorSequenceContainer::VectorSequenceContainer(), bpp::VectorSiteContainer::VectorSiteContainer(), bpp::Pasta::writeAlignedValues(), bpp::Stockholm::writeAlignment(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequences(), bpp::Mase::writeSequences(), and bpp::Phylip::writeSequential().

getSequencePosition()

virtual size_t bpp::OrderedValuesContainer::getSequencePosition ( const std::string &  name ) const

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::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::AbstractProbabilisticSequenceContainer::setComments(), setComments(), and bpp::AbstractValuesContainer::setComments().

getStateValueAt() [1/3]

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

pure virtualinherited

get value of a state in a position

Parameters

siteIndex	index of the site
sequenceName	name of the sequence in the container
state	state in the alphabet

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

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]

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

pure virtualinherited

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

hasSequence()

virtual bool bpp::SequencedValuesContainer::hasSequence ( const std::string &  name ) const

pure virtualinherited

Check if a sequence with a given name is present in the container.

Parameters

name	The name of the sequence.

Returns

True if a sequence with the given name is present in the container.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

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

operator()() [1/6]

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

operator()() [2/6]

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

operator()() [3/6]

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

operator()() [4/6]

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

operator()() [5/6]

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

pure virtualinherited

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

operator()() [6/6]

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

pure virtualinherited

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

operator=() [1/2]

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

inline

Definition at line 75 of file AbstractSequenceContainer.h.

References bpp::AbstractValuesContainer::operator=().

Referenced by bpp::CompressedVectorSiteContainer::operator=(), bpp::VectorSequenceContainer::operator=(), and bpp::VectorSiteContainer::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 95 of file AbstractSequenceContainer.h.

References bpp::AbstractValuesContainer::alphabet_, bpp::SequencedValuesContainer::getAlphabet(), bpp::SequencedValuesContainer::getGeneralComments(), and bpp::AbstractValuesContainer::setGeneralComments().

removeSequence() [1/3]

virtual std::shared_ptr<Sequence> bpp::SequenceContainer::removeSequence

inherited

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

Referenced by bpp::VectorSiteContainer::removeSequence(), bpp::VectorSequenceContainer::removeSequenceByKey(), and bpp::VectorSequenceContainer::removeSequenceByName().

removeSequence() [2/3]

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

pure virtualinherited

Extract (and remove) a sequence from the container.

Parameters

name	The name of the sequence.

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

Referenced by bpp::SequenceApplicationTools::restrictSelectedSequencesByName().

removeSequence() [3/3]

virtual std::shared_ptr<Sequence> bpp::OrderedSequenceContainer::removeSequence ( size_t  sequenceIndex )

pure virtualinherited

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex

The position of the sequence.

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

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

setComments() [1/4]

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

inlineinherited

Set the comments.

Parameters

comments

The new comments.

Definition at line 100 of file Commentable.h.

References bpp::Commentable::comments_.

Referenced by bpp::AbstractCoreSequence::operator=(), bpp::AbstractCoreSequence::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  )

inlinevirtual

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::SequencedValuesContainer.

Definition at line 116 of file AbstractSequenceContainer.h.

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

setComments() [3/4]

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

pure virtual

Implements bpp::AbstractValuesContainer.

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

setComments() [4/4]

virtual void bpp::OrderedValuesContainer::setComments

inherited

Referenced by 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::VectorProbabilisticSequenceContainer::createEmptyContainer(), bpp::VectorSequenceContainer::createEmptyContainer(), bpp::VectorSiteContainer::createEmptyContainer(), bpp::SiteContainerTools::getSelectedSites(), 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() [1/3]

virtual void bpp::SequenceContainer::setSequence

inherited

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.

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

setSequence() [2/3]

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

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.

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

setSequence() [3/3]

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

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.

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

setSequenceNames()

virtual void bpp::SequencedValuesContainer::setSequenceNames ( const std::vector< std::string > &  names, bool  checkNames  )

pure virtualinherited

Set all sequence names.

Parameters

names	A vector of strings with all sequence names. Its size must be strictly equal to the the size of the container (the number of sequences).
checkNames	Tell if the container must check if the name of the sequence is already used in the container before adding it.

Exceptions

Exception

If there are redundant names in the input vector.

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, and bpp::CompressedVectorSiteContainer.

Referenced by bpp::SequenceContainerTools::createContainerWithSequenceNames(), bpp::SiteContainerTools::getCompleteSites(), and bpp::SiteContainerTools::getSitesWithoutGaps().

toString() [1/3]

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

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::SequencedValuesContainer.

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

inlinevirtual

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]

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

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.

Implements bpp::SequenceContainer.

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

valueAt() [2/4]

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

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.

Implements bpp::SequenceContainer.

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

valueAt() [3/4]

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

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.

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

valueAt() [4/4]

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

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.

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

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 operator=().

comments_

Comments bpp::Commentable::comments_

protectedinherited

Definition at line 63 of file Commentable.h.

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

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

• Bpp/Seq/Container/AbstractSequenceContainer.h