bpp-seq3: bpp::AlignedSequenceContainer Class Reference

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

Definition at line 519 of file AlignedSequenceContainer.cpp.

References bpp::VectorPositionedContainer< T >::clear(), bpp::VectorSequenceContainer::clear(), and length_.

◆ clearComments()

void bpp::Commentable::clearComments ( )

inlineinherited

Definition at line 102 of file Commentable.h.

References bpp::Commentable::comments_.

◆ clone()

AlignedSequenceContainer* bpp::AlignedSequenceContainer::clone ( ) const

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 157 of file AlignedSequenceContainer.h.

References AlignedSequenceContainer().

◆ createEmptyContainer()

AlignedSequenceContainer * AlignedSequenceContainer::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.

Definition at line 528 of file AlignedSequenceContainer.cpp.

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

◆ deleteGeneralComments() [1/2]

void bpp::AbstractValuesContainer::deleteGeneralComments ( )

inlinevirtualinherited

Delete the comments associated to this container.

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.

◆ deleteObject() [1/3]

void bpp::VectorMappedContainer< Sequence >::deleteObject ( const std::string & name )

inlineprotectedvirtualinherited

Remove a object.

Parameters

name	The key of the object.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 293 of file VectorMappedContainer.h.

◆ deleteObject() [2/3]

void bpp::VectorMappedContainer< Sequence >::deleteObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Delete an object from the container.

Parameters

objectIndex The index of the object in the container.

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 273 of file VectorMappedContainer.h.

◆ deleteObject() [3/3]

void bpp::VectorPositionedContainer< Site >::deleteObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Delete an object from the container.

Parameters

objectIndex The index of the object in the container.

Definition at line 230 of file VectorPositionedContainer.h.

◆ deleteObjects() [1/2]

void bpp::VectorPositionedContainer< Site >::deleteObjects	(	size_t	objectIndex,
		size_t	length
	)

inlineprotectedinherited

Definition at line 238 of file VectorPositionedContainer.h.

◆ deleteObjects() [2/2]

template<class T >

void bpp::VectorPositionedContainer< T >::deleteObjects	(	size_t	objectIndex,
		size_t	length
	)

inlineprotectedinherited

Definition at line 238 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by deleteSites(), bpp::VectorProbabilisticSiteContainer::deleteSites(), and bpp::VectorSiteContainer::deleteSites().

◆ deleteSequence() [1/2]

void bpp::VectorSequenceContainer::deleteSequence ( const std::string & name )

inlineinherited

delete the Sequence with this name in the map (same as deleteSequenceByKey).

Definition at line 268 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::deleteSequenceByKey().

Referenced by bpp::VectorSequenceContainer::deleteSequenceByKey(), and bpp::VectorSequenceContainer::deleteSequenceByName().

◆ deleteSequence() [2/2]

void bpp::VectorSequenceContainer::deleteSequence ( size_t pos )

inlineinherited

Definition at line 273 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::deleteObject().

◆ deleteSequenceByKey()

void bpp::VectorSequenceContainer::deleteSequenceByKey ( const std::string & name )

inlineinherited

remove & return a Sequence with this key from the map.

Definition at line 283 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::deleteSequence(), and bpp::VectorSequenceContainer::getSequencePosition().

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

◆ deleteSequenceByName()

void VectorSequenceContainer::deleteSequenceByName ( const std::string & name )

inherited

remove & return a Sequence with this name.

Definition at line 190 of file VectorSequenceContainer.cpp.

References bpp::VectorSequenceContainer::deleteSequence(), bpp::CoreSequence::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ deleteSite()

void AlignedSequenceContainer::deleteSite ( size_t siteIndex )

virtual

Delete a site from the container.

The site is deleted (ie the container is shortened).

Parameters

siteIndex The position of the site in the container.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 238 of file AlignedSequenceContainer.cpp.

References bpp::CruxSymbolList::deleteElement(), bpp::VectorPositionedContainer< T >::deleteObject(), bpp::VectorSequenceContainer::getNumberOfSequences(), getNumberOfSites(), bpp::VectorSequenceContainer::getSequence_(), length_, and positions_.

◆ deleteSites()

void AlignedSequenceContainer::deleteSites	(	size_t	siteIndex,
		size_t	length
	)

virtual

Remove a continuous range of sites in the container.

Parameters

siteIndex	The position of the first site in the container.
length	The length of the region to delete, starting at pposition siteIndex.

Exceptions

IndexOutOfBoundsException If the specified range is not valid.

Implements bpp::AlignedValuesContainer.

Definition at line 259 of file AlignedSequenceContainer.cpp.

References bpp::CruxSymbolList::deleteElements(), bpp::VectorPositionedContainer< T >::deleteObjects(), bpp::VectorSequenceContainer::getNumberOfSequences(), getNumberOfSites(), bpp::VectorSequenceContainer::getSequence_(), length_, and positions_.

◆ getAlphabet() [1/2]

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

inlinevirtualinherited

Get container's alphabet.

Returns: The alphabet associated to this container.

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

Definition at line 99 of file AbstractValuesContainer.h.

References bpp::AbstractValuesContainer::alphabet_.

◆ 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.

◆ 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_.

◆ 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.

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

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

inlinevirtualinherited

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

◆ getGeneralComments() [1/2]

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

inlinevirtualinherited

Get the comments of this container.

Returns: The comments associated to this container.

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

Definition at line 101 of file AbstractValuesContainer.h.

References bpp::Commentable::getComments().

◆ 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 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().

◆ getKeys()

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

inlineinherited

Returns: The list of key used to index the sequences.

Definition at line 297 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObjectNames().

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

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

◆ getNumberOfObjects()

size_t bpp::VectorMappedContainer< Sequence >::getNumberOfObjects ( ) const

inlineprotectedinherited

Definition at line 144 of file VectorMappedContainer.h.

◆ getNumberOfSequences()

size_t bpp::VectorSequenceContainer::getNumberOfSequences ( ) const

inlinevirtualinherited

Get the number of sequences in the container.

Returns: The number of sequences in the container.

Definition at line 299 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getSize().

Referenced by addSequence(), addSite(), deleteSite(), deleteSites(), getSite(), bpp::VectorSequenceContainer::getStateValueAt(), removeSite(), setSequence(), bpp::VectorSequenceContainer::setSequenceNames(), setSite(), and bpp::VectorSequenceContainer::VectorSequenceContainer().

◆ getNumberOfSites()

size_t bpp::AlignedSequenceContainer::getNumberOfSites ( ) const

inlinevirtual

Get the number of aligned positions in the container.

Returns: The number of sites in the container.

Implements bpp::AlignedValuesContainer.

Definition at line 209 of file AlignedSequenceContainer.h.

References length_.

Referenced by addSite(), deleteSite(), deleteSites(), getSite(), operator=(), removeSite(), setSite(), and setSitePositions().

◆ getObject() [1/6]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( const std::string & name )

inlineprotectedvirtualinherited

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 188 of file VectorMappedContainer.h.

◆ getObject() [2/6]

const std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( const std::string & name ) const

inlineprotectedvirtualinherited

Get a object.

Parameters

name	The key of the object to retrieve.

Returns: The object associated to the given key.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 183 of file VectorMappedContainer.h.

◆ getObject() [3/6]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 172 of file VectorMappedContainer.h.

◆ getObject() [4/6]

std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::getObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Definition at line 177 of file VectorPositionedContainer.h.

◆ getObject() [5/6]

const std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::getObject ( size_t objectIndex ) const

inlineprotectedvirtualinherited

Retrieve an object from the container. Set as protected since they will be public under T specific names.

Parameters

objectIndex The position of the object.

Returns: A reference toward the Object object with corresponding name.

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 167 of file VectorMappedContainer.h.

◆ getObject() [6/6]

const std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::getObject ( size_t objectIndex ) const

inlineprotectedvirtualinherited

Retrieve an object from the container. Set as protected since they will be public under T specific names.

Parameters

objectIndex The position of the object.

Returns: A reference toward the Object object with corresponding name.

Definition at line 170 of file VectorPositionedContainer.h.

◆ getObject_() [1/2]

std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::getObject_ ( size_t objectIndex ) const

inlineprotectedinherited

Definition at line 251 of file VectorPositionedContainer.h.

◆ getObject_() [2/2]

template<class T >

std::shared_ptr<T> bpp::VectorPositionedContainer< T >::getObject_ ( size_t objectIndex ) const

inlineprotectedinherited

Definition at line 251 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

◆ getObjectName()

std::string bpp::VectorMappedContainer< Sequence >::getObjectName ( size_t objectIndex ) const

inlineprotectedvirtualinherited

Implements bpp::PositionedNamedContainer< T >.

Definition at line 158 of file VectorMappedContainer.h.

◆ getObjectNames()

std::vector<std::string> bpp::VectorMappedContainer< Sequence >::getObjectNames ( ) const

inlineprotectedvirtualinherited

Returns: All objects keys.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 198 of file VectorMappedContainer.h.

◆ getObjectPosition()

size_t bpp::VectorMappedContainer< Sequence >::getObjectPosition ( const std::string & name ) const

inlineprotectedvirtualinherited

Link between position & name.

Implements bpp::PositionedNamedContainer< T >.

Definition at line 149 of file VectorMappedContainer.h.

◆ getSequence() [1/3]

const Sequence& bpp::VectorSequenceContainer::getSequence ( const std::string & name ) const

inlinevirtualinherited

get the Sequence with this name in the map (same as getSequenceByKey).

Implements bpp::SequenceContainer.

Definition at line 207 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::getSequenceByKey().

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

◆ 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.

◆ getSequence() [3/3]

const Sequence& bpp::VectorSequenceContainer::getSequence ( size_t sequenceIndex ) const

inlinevirtualinherited

Retrieve a sequence object from the container.

Parameters

sequenceIndex The position of the sequence.

Returns: A reference toward the Sequence object with corresponding name.

Definition at line 397 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObject().

◆ getSequence_() [1/2]

Sequence& bpp::VectorSequenceContainer::getSequence_ ( const std::string & key )

inlineprotectedinherited

getSequence with given key

Definition at line 553 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObject().

◆ getSequence_() [2/2]

Sequence& bpp::VectorSequenceContainer::getSequence_ ( size_t i )

inlineprotectedinherited

Definition at line 542 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObject().

Referenced by addSite(), deleteSite(), deleteSites(), bpp::VectorSequenceContainer::operator()(), removeSite(), bpp::VectorSequenceContainer::setComments(), bpp::VectorSequenceContainer::setSequenceNames(), setSite(), and bpp::VectorSequenceContainer::valueAt().

◆ getSequenceByKey()

const Sequence& bpp::VectorSequenceContainer::getSequenceByKey ( const std::string & name ) const

inlineinherited

check if there is a Sequence with this key in the map.

Definition at line 219 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObject().

Referenced by bpp::VectorSequenceContainer::getSequence(), and bpp::VectorSequenceContainer::valueAt().

◆ getSequenceByName()

const Sequence & VectorSequenceContainer::getSequenceByName ( const std::string & name ) const

inherited

Definition at line 156 of file VectorSequenceContainer.cpp.

References bpp::CoreSequence::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ getSequenceKeys()

std::vector<std::string> bpp::VectorSequenceContainer::getSequenceKeys ( ) const

inlineinherited

get Sequences keys (ie the strings used to store them in the map, may be different from their proper names), in the order of the vector.

Definition at line 316 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObjectNames().

◆ getSequenceNames()

std::vector< std::string > VectorSequenceContainer::getSequenceNames ( ) const

virtualinherited

get Sequences proper names (may be different from the keys used to store them in the map), in the order of the vector.

References bpp::VectorPositionedContainer< T >::addObject(), bpp::AbstractValuesContainer::getAlphabet(), bpp::VectorSequenceContainer::getNumberOfSequences(), getNumberOfSites(), bpp::VectorPositionedContainer< T >::getObject(), bpp::OrderedSequenceContainer::getSequence(), and length_.

Definition at line 168 of file VectorSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ getSequencePosition()

size_t bpp::VectorSequenceContainer::getSequencePosition ( const std::string & name ) const

inlinevirtualinherited

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 392 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::getObjectPosition().

Referenced by bpp::VectorSequenceContainer::deleteSequenceByKey(), bpp::VectorSequenceContainer::removeSequenceByKey(), and bpp::VectorSequenceContainer::setSequence().

◆ getSite() [1/2]

Site & AlignedSequenceContainer::getSite ( size_t siteIndex )

virtual

Implements bpp::SiteContainer.

Definition at line 160 of file AlignedSequenceContainer.cpp.

◆ getSite() [2/2]

const Site & AlignedSequenceContainer::getSite ( size_t siteIndex ) const

virtual

Get a site from the container.

Parameters

siteIndex The position of the site in the container.

Returns: A site objet corresponding to site i in the alignment.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 142 of file AlignedSequenceContainer.cpp.

References bpp::VectorPositionedContainer< T >::addObject_(), bpp::AbstractValuesContainer::getAlphabet(), bpp::VectorSequenceContainer::getNumberOfSequences(), getNumberOfSites(), bpp::VectorPositionedContainer< T >::getObject(), bpp::OrderedSequenceContainer::getSequence(), and length_.

Referenced by getSymbolListSite(), and removeSite().

◆ getSitePositions()

Vint bpp::AlignedSequenceContainer::getSitePositions ( ) const

inlinevirtual

Get all position attributes of sites.

Returns: A vector with all site positions.

Implements bpp::AlignedValuesContainer.

Definition at line 210 of file AlignedSequenceContainer.h.

References positions_.

Referenced by operator=().

◆ getSize() [1/2]

size_t bpp::VectorMappedContainer< Sequence >::getSize ( ) const

inlinevirtualinherited

Get the number of objects in the container.

Returns: The number of objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 133 of file VectorMappedContainer.h.

◆ getSize() [2/2]

size_t bpp::VectorPositionedContainer< Site >::getSize ( ) const

inlinevirtualinherited

the size

Definition at line 129 of file VectorPositionedContainer.h.

◆ getStateValueAt() [1/3]

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

inlineprotectedvirtualinherited

get Value at given state with given key in the Sequence Map

Definition at line 571 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::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::VectorSequenceContainer::getStateValueAt	(	size_t	siteIndex,
		size_t	sequenceIndex,
		int	state
	)		const

inlineprotectedvirtualinherited

Implements bpp::OrderedValuesContainer.

Definition at line 592 of file VectorSequenceContainer.h.

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

◆ getSymbolListSite() [1/2]

CruxSymbolListSite& bpp::AlignedSequenceContainer::getSymbolListSite ( size_t siteIndex )

inlinevirtual

Implements bpp::SiteContainer.

Definition at line 182 of file AlignedSequenceContainer.h.

References getSite().

◆ getSymbolListSite() [2/2]

const CruxSymbolListSite& bpp::AlignedSequenceContainer::getSymbolListSite ( size_t siteIndex ) const

inlinevirtual

Get a CruxSymbolListSite from a given position.

Parameters

siteIndex The position

Implements bpp::SiteContainer.

Definition at line 177 of file AlignedSequenceContainer.h.

References getSite().

◆ hasObject()

bool bpp::VectorMappedContainer< Sequence >::hasObject ( const std::string & name ) const

inlineprotectedvirtualinherited

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

Parameters

name	The name of the object.

Returns: True if a object with the given name is present in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 193 of file VectorMappedContainer.h.

◆ hasSequence()

bool bpp::VectorSequenceContainer::hasSequence ( const std::string & name ) const

inlinevirtualinherited

check if there is a Sequence with this name in the map (same as hasSequenceByKey).

Definition at line 184 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::hasSequenceByKey().

◆ hasSequenceByKey()

bool bpp::VectorSequenceContainer::hasSequenceByKey ( const std::string & name ) const

inlineinherited

check if there is a Sequence with this key in the map.

Definition at line 196 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::hasObject().

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

◆ hasSequenceByName()

bool VectorSequenceContainer::hasSequenceByName ( const std::string & name ) const

inherited

Definition at line 147 of file VectorSequenceContainer.cpp.

References bpp::AbstractSequenceContainer::getName(), bpp::OrderedSequenceContainer::getSequence(), and bpp::VectorMappedContainer< Sequence >::getSize().

◆ insertObject() [1/4]

void bpp::VectorMappedContainer< Sequence >::insertObject	(	std::shared_ptr< Sequence >	object,
		size_t	objectIndex,
		const std::string &	name
	)

inlineprotectedinherited

Definition at line 235 of file VectorMappedContainer.h.

◆ insertObject() [2/4]

void bpp::VectorPositionedContainer< Site >::insertObject	(	std::shared_ptr< Site >	object,
		size_t	objectIndex
	)

inlineprotectedinherited

Insert an object.

Parameters

object	The object to add.
objectIndex	The new position of the object

Definition at line 209 of file VectorPositionedContainer.h.

◆ insertObject() [3/4]

template<class T >

void bpp::VectorPositionedContainer< T >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex
	)

inlineprotectedinherited

Insert an object.

Parameters

object	The object to add.
objectIndex	The new position of the object

Definition at line 209 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by addSite(), bpp::VectorSiteContainer::addSite(), and bpp::VectorMappedContainer< T >::insertObject().

◆ insertObject() [4/4]

template<class T >

virtual void bpp::PositionedNamedContainer< T >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name
	)

protectedpure virtualinherited

Implemented in bpp::VectorMappedContainer< T >.

◆ isAvailableName()

template<class T >

bool bpp::MappedNamedContainer< T >::isAvailableName ( std::string objectName ) const

inlineinherited

Return if the name is in the map keys and the mapped object is nullptr or empty.

Definition at line 228 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::getObject(), and bpp::MappedNamedContainer< T >::hasObject().

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

◆ isAvailablePosition() [1/2]

bool bpp::VectorPositionedContainer< Site >::isAvailablePosition ( size_t objectIndex ) const

inlineinherited

Definition at line 134 of file VectorPositionedContainer.h.

◆ isAvailablePosition() [2/2]

template<class T >

bool bpp::VectorPositionedContainer< T >::isAvailablePosition ( size_t objectIndex ) const

inlineinherited

Definition at line 134 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

◆ nullify() [1/2]

void bpp::VectorPositionedContainer< Site >::nullify ( )

inlineinherited

Nullify all elements.

Definition at line 163 of file VectorPositionedContainer.h.

◆ nullify() [2/2]

template<class T >

void bpp::VectorPositionedContainer< T >::nullify ( )

inlineinherited

Nullify all elements.

Definition at line 163 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by addSequence(), bpp::VectorSiteContainer::addSite(), bpp::VectorProbabilisticSiteContainer::addSite(), and setSequence().

◆ operator()() [1/6]

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

inlinevirtualinherited

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 354 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::getSequence_().

◆ operator()() [2/6]

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

inlinevirtualinherited

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 359 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

◆ operator()() [3/6]

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

inlinevirtualinherited

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.

Definition at line 374 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::getSequence_().

◆ operator()() [4/6]

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

inlinevirtualinherited

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.

Definition at line 378 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

◆ operator()() [5/6]

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

inlineprotectedvirtualinherited

Definition at line 576 of file VectorSequenceContainer.h.

References bpp::OrderedSequenceContainer::getSequence().

◆ operator()() [6/6]

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

inlineprotectedvirtualinherited

Implements bpp::OrderedValuesContainer.

Definition at line 603 of file VectorSequenceContainer.h.

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

◆ operator=() [1/3]

AlignedSequenceContainer & AlignedSequenceContainer::operator= ( const AlignedSequenceContainer & asc )

Definition at line 100 of file AlignedSequenceContainer.cpp.

References getNumberOfSites(), getSitePositions(), length_, bpp::VectorPositionedContainer< T >::operator=(), bpp::VectorSequenceContainer::operator=(), and positions_.

◆ operator=() [2/3]

AlignedSequenceContainer & AlignedSequenceContainer::operator= ( const OrderedSequenceContainer & osc )

Definition at line 128 of file AlignedSequenceContainer.cpp.

References length_, bpp::VectorSequenceContainer::operator=(), reindexSites(), and bpp::VectorPositionedContainer< T >::setSize().

◆ operator=() [3/3]

AlignedSequenceContainer & AlignedSequenceContainer::operator= ( const SiteContainer & sc )

Definition at line 114 of file AlignedSequenceContainer.cpp.

References bpp::AlignedValuesContainer::getNumberOfSites(), bpp::AlignedValuesContainer::getSitePositions(), length_, bpp::VectorSequenceContainer::operator=(), positions_, and bpp::VectorPositionedContainer< T >::setSize().

◆ reindexSites()

void AlignedSequenceContainer::reindexSites ( )

virtual

Set all positions attributes.

Implements bpp::AlignedValuesContainer.

Definition at line 427 of file AlignedSequenceContainer.cpp.

References length_, and positions_.

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

◆ removeObject() [1/3]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::removeObject ( const std::string & name )

inlineprotectedvirtualinherited

Remove and returns a object.

Parameters

name	The key of the object.

Returns: The object previously associated to the given key.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 288 of file VectorMappedContainer.h.

◆ removeObject() [2/3]

std::shared_ptr<Sequence > bpp::VectorMappedContainer< Sequence >::removeObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Extract and remove a object from the container.

Parameters

objectIndex The position of the object.

Returns: A smart pointer toward the removed object.

Reimplemented from bpp::VectorPositionedContainer< T >.

Definition at line 259 of file VectorMappedContainer.h.

◆ removeObject() [3/3]

std::shared_ptr<Site > bpp::VectorPositionedContainer< Site >::removeObject ( size_t objectIndex )

inlineprotectedvirtualinherited

Extract and remove a object from the container.

Parameters

objectIndex The position of the object.

Returns: A smart pointer toward the removed object.

Definition at line 218 of file VectorPositionedContainer.h.

◆ removeSequence() [1/3]

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

inlinevirtualinherited

get the Sequence with this name in the map (same as removeSequenceByKey).

Implements bpp::SequenceContainer.

Definition at line 240 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::removeSequenceByKey().

◆ removeSequence() [2/3]

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() [3/3]

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

inlinevirtualinherited

Extract (and remove) a sequence from the container.

Parameters

sequenceIndex The position of the sequence.

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

Definition at line 410 of file VectorSequenceContainer.h.

References bpp::VectorMappedContainer< Sequence >::removeObject().

◆ removeSequenceByKey()

std::shared_ptr<Sequence> bpp::VectorSequenceContainer::removeSequenceByKey ( const std::string & name )

inlineinherited

remove & return a Sequence with this key from the map.

Definition at line 250 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::getSequencePosition(), and bpp::OrderedSequenceContainer::removeSequence().

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

◆ removeSequenceByName()

std::shared_ptr< Sequence > VectorSequenceContainer::removeSequenceByName ( const std::string & name )

inherited

remove & return a Sequence with this name.

Definition at line 178 of file VectorSequenceContainer.cpp.

References bpp::CoreSequence::getName(), bpp::OrderedSequenceContainer::getSequence(), bpp::VectorMappedContainer< Sequence >::getSize(), and bpp::OrderedSequenceContainer::removeSequence().

◆ removeSite()

std::shared_ptr< Site > AlignedSequenceContainer::removeSite ( size_t siteIndex )

virtual

Remove a site from the container.

The site is deleted (ie the container is shortened) and a pointer toward it is returned.

Parameters

siteIndex The position of the site in the container.

Returns: A pointer toward the given site in the alignment.

Exceptions

IndexOutOfBoundsException If the specified site does not exists.

Implements bpp::SiteContainer.

Definition at line 214 of file AlignedSequenceContainer.cpp.

References bpp::CruxSymbolList::deleteElement(), bpp::VectorSequenceContainer::getNumberOfSequences(), getNumberOfSites(), bpp::VectorSequenceContainer::getSequence_(), getSite(), length_, positions_, and bpp::VectorPositionedContainer< T >::removeObject().

◆ 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_.

◆ 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.

Definition at line 116 of file AbstractSequenceContainer.h.

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

◆ setComments() [3/4]

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

inlinevirtualinherited

Implements bpp::AbstractSequenceContainer.

Definition at line 415 of file VectorSequenceContainer.h.

References bpp::VectorSequenceContainer::getSequence_(), and bpp::CoreSequence::setComments().

◆ 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.

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

Definition at line 106 of file AbstractValuesContainer.h.

References bpp::Commentable::setComments().

◆ 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().

◆ setObjectName()

void bpp::VectorMappedContainer< Sequence >::setObjectName	(	size_t	pos,
		const std::string &	name
	)

inlineprotectedinherited

Definition at line 219 of file VectorMappedContainer.h.

◆ setObjectNames()

void bpp::VectorMappedContainer< Sequence >::setObjectNames ( const std::vector< std::string > & names )

inlineprotectedinherited

Definition at line 203 of file VectorMappedContainer.h.

◆ 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 setSequence().

◆ setSequence() [2/3]

void AlignedSequenceContainer::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::SequenceContainer.

Definition at line 468 of file AlignedSequenceContainer.cpp.

References checkSize_(), bpp::VectorSequenceContainer::getNumberOfSequences(), length_, bpp::OrderedSequenceContainer::setSequence(), and bpp::CruxSymbolList::size().

◆ setSequence() [3/3]

void AlignedSequenceContainer::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.

Definition at line 450 of file AlignedSequenceContainer.cpp.

References checkSize_(), bpp::VectorSequenceContainer::getNumberOfSequences(), length_, bpp::VectorPositionedContainer< T >::nullify(), bpp::OrderedSequenceContainer::setSequence(), and bpp::CruxSymbolList::size().

◆ setSequenceNames()

void VectorSequenceContainer::setSequenceNames	(	const std::vector< std::string > &	names,
		bool	checkNames = `true`
	)

virtualinherited

set the proper names of the Sequences, in the order of the vector.