bpp::AlignedSequenceContainer Member List

This is the complete list of members for bpp::AlignedSequenceContainer, including all inherited members.

AbstractSequenceContainer(const Alphabet *alpha)	bpp::AbstractSequenceContainer	inline
AbstractSequenceContainer(const AbstractSequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
AbstractSequenceContainer(const SequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
AbstractValuesContainer(const Alphabet *alpha)	bpp::AbstractValuesContainer	inline
AbstractValuesContainer(const Comments &comments, const Alphabet *alpha)	bpp::AbstractValuesContainer	inline
AbstractValuesContainer(const AbstractValuesContainer &sc)	bpp::AbstractValuesContainer	inline
bpp::addObject(std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false)	bpp::VectorMappedContainer< Sequence >	inlineprotected
bpp::PositionedNamedContainer::addObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0	bpp::PositionedNamedContainer< T >	protectedpure virtual
bpp::MappedNamedContainer::addObject(std::shared_ptr< T > object, const std::string &name, bool checkName=false)	bpp::MappedNamedContainer< T >	inlineprotected
bpp::VectorPositionedContainer::addObject(std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false)	bpp::VectorPositionedContainer< T >	inlineprotected
VectorPositionedContainer< Site >::addObject(std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false)	bpp::VectorPositionedContainer< Site >	inlineprotected
bpp::addObject_(std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false) const	bpp::VectorMappedContainer< Sequence >	inlineprotected
bpp::MappedNamedContainer::addObject_(std::shared_ptr< T > object, const std::string &name, bool checkName=false) const	bpp::MappedNamedContainer< T >	inlineprotected
bpp::VectorPositionedContainer::addObject_(std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) const	bpp::VectorPositionedContainer< T >	inlineprotected
VectorPositionedContainer< Site >::addObject_(std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false) const	bpp::VectorPositionedContainer< Site >	inlineprotected
addSequence(const Sequence &sequence, bool checkName=true)	bpp::AlignedSequenceContainer	virtual
addSequence(const Sequence &sequence, size_t sequenceIndex, bool checkName=true)	bpp::AlignedSequenceContainer	virtual
bpp::VectorSequenceContainer::addSequence(const Sequence &sequence, const std::string &key)	bpp::VectorSequenceContainer	inlinevirtual
bpp::VectorSequenceContainer::addSequence(const std::shared_ptr< Sequence > sequence, bool checkName=true)	bpp::VectorSequenceContainer	inlinevirtual
bpp::VectorSequenceContainer::addSequence(const Sequence &sequence, size_t sequenceIndex, const std::string &key)	bpp::VectorSequenceContainer	inlinevirtual
addSite(const Site &site, bool checkPosition=true)	bpp::AlignedSequenceContainer	virtual
addSite(const Site &site, int position, bool checkPosition=true)	bpp::AlignedSequenceContainer	virtual
addSite(const Site &site, size_t siteIndex, bool checkPosition=true)	bpp::AlignedSequenceContainer	virtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition=true)	bpp::AlignedSequenceContainer	virtual
AlignedSequenceContainer(std::vector< std::shared_ptr< Sequence >> vseq, const Alphabet *alpha)	bpp::AlignedSequenceContainer
AlignedSequenceContainer(const Alphabet *alpha)	bpp::AlignedSequenceContainer	inline
AlignedSequenceContainer(const AlignedSequenceContainer &asc)	bpp::AlignedSequenceContainer	inline
AlignedSequenceContainer(const SiteContainer &sc)	bpp::AlignedSequenceContainer	inline
AlignedSequenceContainer(const OrderedSequenceContainer &osc)	bpp::AlignedSequenceContainer
AlignedValuesContainer()	bpp::AlignedValuesContainer	inline
alphabet_	bpp::AbstractValuesContainer	protected
bpp::appendObject(std::shared_ptr< Sequence > object, const std::string &name, bool check=true)	bpp::VectorMappedContainer< Sequence >	inlineprotected
bpp::VectorPositionedContainer::appendObject(std::shared_ptr< T > object)	bpp::VectorPositionedContainer< T >	inlineprotected
VectorPositionedContainer< Site >::appendObject(std::shared_ptr< Site > object)	bpp::VectorPositionedContainer< Site >	inlineprotected
changeName(const std::string &okey, const std::string &nkey)	bpp::MappedNamedContainer< T >	inline
checkSize_(const Sequence &sequence)	bpp::AlignedSequenceContainer	inlineprotected
clear()	bpp::AlignedSequenceContainer	virtual
clearComments()	bpp::Commentable	inline
clone() const	bpp::AlignedSequenceContainer	inlinevirtual
Commentable()	bpp::Commentable	inline
Commentable(const Comments &comments)	bpp::Commentable	inline
Commentable(const Commentable &com)	bpp::Commentable	inline
comments_	bpp::Commentable	protected
createEmptyContainer() const	bpp::AlignedSequenceContainer	virtual
bpp::deleteGeneralComments()=0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::deleteGeneralComments()	bpp::AbstractValuesContainer	inlinevirtual
bpp::deleteObject(size_t objectIndex)	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
bpp::deleteObject(const std::string &name)	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
VectorPositionedContainer< Site >::deleteObject(size_t objectIndex)	bpp::VectorPositionedContainer< Site >	inlineprotectedvirtual
bpp::deleteObjects(size_t objectIndex, size_t length)	bpp::VectorPositionedContainer< T >	inlineprotected
VectorPositionedContainer< Site >::deleteObjects(size_t objectIndex, size_t length)	bpp::VectorPositionedContainer< Site >	inlineprotected
deleteSequence(const std::string &name)	bpp::VectorSequenceContainer	inline
deleteSequence(size_t pos)	bpp::VectorSequenceContainer	inline
deleteSequenceByKey(const std::string &name)	bpp::VectorSequenceContainer	inline
deleteSequenceByName(const std::string &name)	bpp::VectorSequenceContainer
deleteSite(size_t siteIndex)	bpp::AlignedSequenceContainer	virtual
deleteSites(size_t siteIndex, size_t length)	bpp::AlignedSequenceContainer	virtual
bpp::getAlphabet() const =0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::getAlphabet() const	bpp::AbstractValuesContainer	inlinevirtual
getComments(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
getComments(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
bpp::OrderedSequenceContainer::getComments(size_t sequenceIndex) const=0	bpp::OrderedSequenceContainer
bpp::Commentable::getComments() const	bpp::Commentable	inline
bpp::getGeneralComments() const =0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::getGeneralComments() const	bpp::AbstractValuesContainer	inlinevirtual
getKeys() const	bpp::VectorSequenceContainer	inline
getName(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
getNumberOfObjects() const	bpp::VectorMappedContainer< Sequence >	inlineprotected
getNumberOfSequences() const	bpp::VectorSequenceContainer	inlinevirtual
getNumberOfSites() const	bpp::AlignedSequenceContainer	inlinevirtual
bpp::getObject(size_t objectIndex) const	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
bpp::getObject(size_t objectIndex)	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
bpp::getObject(const std::string &name) const	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
bpp::getObject(const std::string &name)	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
VectorPositionedContainer< Site >::getObject(size_t objectIndex) const	bpp::VectorPositionedContainer< Site >	inlineprotectedvirtual
VectorPositionedContainer< Site >::getObject(size_t objectIndex)	bpp::VectorPositionedContainer< Site >	inlineprotectedvirtual
bpp::getObject_(size_t objectIndex) const	bpp::VectorPositionedContainer< T >	inlineprotected
VectorPositionedContainer< Site >::getObject_(size_t objectIndex) const	bpp::VectorPositionedContainer< Site >	inlineprotected
getObjectName(size_t objectIndex) const	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
getObjectNames() const	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
getObjectPosition(const std::string &name) const	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
getSequence(const std::string &name) const	bpp::VectorSequenceContainer	inlinevirtual
getSequence(size_t sequenceIndex) const	bpp::VectorSequenceContainer	inlinevirtual
bpp::AbstractSequenceContainer::getSequence(const std::string &name) const=0	bpp::OrderedSequenceContainer
getSequence_(size_t i)	bpp::VectorSequenceContainer	inlineprotected
getSequence_(const std::string &key)	bpp::VectorSequenceContainer	inlineprotected
getSequenceByKey(const std::string &name) const	bpp::VectorSequenceContainer	inline
getSequenceByName(const std::string &name) const	bpp::VectorSequenceContainer
getSequenceKeys() const	bpp::VectorSequenceContainer	inline
getSequenceNames() const	bpp::VectorSequenceContainer	virtual
getSequencePosition(const std::string &name) const	bpp::VectorSequenceContainer	inlinevirtual
getSite(size_t siteIndex) const	bpp::AlignedSequenceContainer	virtual
getSite(size_t siteIndex)	bpp::AlignedSequenceContainer	virtual
getSitePositions() const	bpp::AlignedSequenceContainer	inlinevirtual
bpp::getSize() const	bpp::VectorMappedContainer< Sequence >	inlinevirtual
VectorPositionedContainer< Site >::getSize() const	bpp::VectorPositionedContainer< Site >	inlinevirtual
getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const	bpp::VectorSequenceContainer	inlineprotectedvirtual
getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const	bpp::VectorSequenceContainer	inlineprotectedvirtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0	bpp::OrderedValuesContainer
getSymbolListSite(size_t siteIndex) const	bpp::AlignedSequenceContainer	inlinevirtual
getSymbolListSite(size_t siteIndex)	bpp::AlignedSequenceContainer	inlinevirtual
hasObject(const std::string &name) const	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
hasSequence(const std::string &name) const	bpp::VectorSequenceContainer	inlinevirtual
hasSequenceByKey(const std::string &name) const	bpp::VectorSequenceContainer	inline
hasSequenceByName(const std::string &name) const	bpp::VectorSequenceContainer
bpp::insertObject(std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name)	bpp::VectorMappedContainer< Sequence >	inlineprotected
bpp::PositionedNamedContainer::insertObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name)=0	bpp::PositionedNamedContainer< T >	protectedpure virtual
bpp::VectorPositionedContainer::insertObject(std::shared_ptr< T > object, size_t objectIndex)	bpp::VectorPositionedContainer< T >	inlineprotected
VectorPositionedContainer< Site >::insertObject(std::shared_ptr< Site > object, size_t objectIndex)	bpp::VectorPositionedContainer< Site >	inlineprotected
isAvailableName(std::string objectName) const	bpp::MappedNamedContainer< T >	inline
bpp::isAvailablePosition(size_t objectIndex) const	bpp::VectorPositionedContainer< T >	inline
VectorPositionedContainer< Site >::isAvailablePosition(size_t objectIndex) const	bpp::VectorPositionedContainer< Site >	inline
length_	bpp::AlignedSequenceContainer	private
MappedNamedContainer()	bpp::MappedNamedContainer< T >	inline
MappedNamedContainer(const std::map< std::string, std::shared_ptr< T > > &ms)	bpp::MappedNamedContainer< T >	inline
MappedNamedContainer(const MappedNamedContainer &msc)	bpp::MappedNamedContainer< T >	inline
mNames_	bpp::VectorMappedContainer< Sequence >	private
mObjects_	bpp::MappedNamedContainer< T >	private
bpp::NamedContainer()	bpp::NamedContainer< T >	inlineprivate
bpp::MappedNamedContainer::NamedContainer()	bpp::NamedContainer< T >	inline
bpp::nullify()	bpp::VectorPositionedContainer< T >	inline
VectorPositionedContainer< Site >::nullify()	bpp::VectorPositionedContainer< Site >	inline
operator()(const std::string &sequenceName, size_t elementIndex)	bpp::VectorSequenceContainer	inlinevirtual
operator()(const std::string &sequenceName, size_t elementIndex) const	bpp::VectorSequenceContainer	inlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex)	bpp::VectorSequenceContainer	inlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex) const	bpp::VectorSequenceContainer	inlinevirtual
operator()(size_t siteIndex, const std::string &sequenceName, int state) const	bpp::VectorSequenceContainer	inlineprotectedvirtual
operator()(size_t siteIndex, size_t sequenceIndex, int state) const	bpp::VectorSequenceContainer	inlineprotectedvirtual
operator=(const AlignedSequenceContainer &asc)	bpp::AlignedSequenceContainer
operator=(const SiteContainer &sc)	bpp::AlignedSequenceContainer
operator=(const OrderedSequenceContainer &osc)	bpp::AlignedSequenceContainer
bpp::VectorSequenceContainer::operator=(const VectorSequenceContainer &vsc)	bpp::VectorSequenceContainer
bpp::VectorSequenceContainer::operator=(const SequenceContainer &osc)	bpp::VectorSequenceContainer
bpp::AbstractSequenceContainer::operator=(const AbstractSequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
bpp::AbstractValuesContainer::operator=(const AbstractValuesContainer &sc)	bpp::AbstractValuesContainer	inline
bpp::Commentable::operator=(const Commentable &com)	bpp::Commentable	inline
bpp::VectorMappedContainer< Sequence >::operator=(const VectorMappedContainer &vsc)	bpp::VectorMappedContainer< Sequence >	inline
bpp::MappedNamedContainer::operator=(const MappedNamedContainer &msc)	bpp::MappedNamedContainer< T >	inline
bpp::VectorPositionedContainer::operator=(const VectorPositionedContainer< T > &vsc)	bpp::VectorPositionedContainer< T >	inline
VectorPositionedContainer< Site >::operator=(const VectorPositionedContainer< Site > &vsc)	bpp::VectorPositionedContainer< Site >	inline
OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inline
OrderedValuesContainer()	bpp::OrderedValuesContainer	inline
bpp::PositionedContainer()	bpp::PositionedContainer< T >	inlineprivate
bpp::VectorPositionedContainer::PositionedContainer()	bpp::PositionedContainer< T >	inline
positions_	bpp::AlignedSequenceContainer	private
reindexSites()	bpp::AlignedSequenceContainer	virtual
bpp::removeObject(size_t objectIndex)	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
bpp::removeObject(const std::string &name)	bpp::VectorMappedContainer< Sequence >	inlineprotectedvirtual
VectorPositionedContainer< Site >::removeObject(size_t objectIndex)	bpp::VectorPositionedContainer< Site >	inlineprotectedvirtual
removeSequence(const std::string &name)	bpp::VectorSequenceContainer	inlinevirtual
removeSequence(size_t sequenceIndex)	bpp::VectorSequenceContainer	inlinevirtual
bpp::AbstractSequenceContainer::removeSequence(const std::string &name)=0	bpp::OrderedSequenceContainer
removeSequenceByKey(const std::string &name)	bpp::VectorSequenceContainer	inline
removeSequenceByName(const std::string &name)	bpp::VectorSequenceContainer
removeSite(size_t siteIndex)	bpp::AlignedSequenceContainer	virtual
SequenceContainer()	bpp::SequenceContainer	inline
setComments(size_t sequenceIndex, const Comments &comments)	bpp::VectorSequenceContainer	inlinevirtual
bpp::AbstractSequenceContainer::setComments(const std::string &name, const Comments &comments)	bpp::AbstractSequenceContainer	inlinevirtual
bpp::OrderedSequenceContainer::setComments(size_t sequenceIndex, const Comments &comments)=0	bpp::OrderedSequenceContainer
bpp::Commentable::setComments(const Comments &comments)	bpp::Commentable	inline
bpp::setGeneralComments(const Comments &comments)=0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::setGeneralComments(const Comments &comments)	bpp::AbstractValuesContainer	inlinevirtual
setObjectName(size_t pos, const std::string &name)	bpp::VectorMappedContainer< Sequence >	inlineprotected
setObjectNames(const std::vector< std::string > &names)	bpp::VectorMappedContainer< Sequence >	inlineprotected
setSequence(const std::string &name, const Sequence &sequence, bool checkName=true)	bpp::AlignedSequenceContainer	virtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName=true)	bpp::AlignedSequenceContainer	virtual
bpp::AbstractSequenceContainer::setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0	bpp::OrderedSequenceContainer
setSequenceNames(const std::vector< std::string > &names, bool checkNames=true)	bpp::VectorSequenceContainer	virtual
setSite(size_t siteIndex, const Site &site, bool checkPosition=true)	bpp::AlignedSequenceContainer	virtual
setSitePositions(Vint vPositions)	bpp::AlignedSequenceContainer	virtual
bpp::setSize(size_t size)	bpp::PositionedContainer< T >	inlineprivatevirtual
bpp::VectorPositionedContainer::setSize(size_t size)	bpp::VectorPositionedContainer< T >	inlinevirtual
VectorPositionedContainer< Site >::setSize(size_t size)	bpp::VectorPositionedContainer< Site >	inlinevirtual
SiteContainer()	bpp::SiteContainer	inline
toString(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
toString(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
bpp::OrderedSequenceContainer::toString(size_t sequenceIndex) const=0	bpp::OrderedSequenceContainer
valueAt(const std::string &sequenceName, size_t elementIndex)	bpp::VectorSequenceContainer	inlinevirtual
valueAt(const std::string &key, size_t elementIndex) const	bpp::VectorSequenceContainer	inlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex)	bpp::VectorSequenceContainer	inlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex) const	bpp::VectorSequenceContainer	inlinevirtual
VectorMappedContainer()	bpp::VectorMappedContainer< Sequence >	inline
VectorMappedContainer(const VectorMappedContainer &vsc)	bpp::VectorMappedContainer< Sequence >	inline
bpp::VectorPositionedContainer(const std::vector< std::shared_ptr< T > > &vs)	bpp::VectorPositionedContainer< T >	inline
bpp::VectorPositionedContainer(size_t size=0)	bpp::VectorPositionedContainer< T >	inline
bpp::VectorPositionedContainer(const VectorPositionedContainer< T > &vsc)	bpp::VectorPositionedContainer< T >	inline
VectorPositionedContainer< Site >::VectorPositionedContainer(const std::vector< std::shared_ptr< Site > > &vs)	bpp::VectorPositionedContainer< Site >	inline
VectorPositionedContainer< Site >::VectorPositionedContainer(size_t size=0)	bpp::VectorPositionedContainer< Site >	inline
VectorPositionedContainer< Site >::VectorPositionedContainer(const VectorPositionedContainer< Site > &vsc)	bpp::VectorPositionedContainer< Site >	inline
VectorSequenceContainer(const std::vector< std::shared_ptr< Sequence >> &vs, const Alphabet *alpha)	bpp::VectorSequenceContainer
VectorSequenceContainer(const Alphabet *alpha)	bpp::VectorSequenceContainer	inline
VectorSequenceContainer(const VectorSequenceContainer &vsc)	bpp::VectorSequenceContainer
VectorSequenceContainer(const OrderedSequenceContainer &osc)	bpp::VectorSequenceContainer
VectorSequenceContainer(const SequenceContainer &osc)	bpp::VectorSequenceContainer
vNames_	bpp::VectorMappedContainer< Sequence >	private
~AbstractSequenceContainer()	bpp::AbstractSequenceContainer	inlinevirtual
~AbstractValuesContainer()	bpp::AbstractValuesContainer	inlinevirtual
~AlignedSequenceContainer()	bpp::AlignedSequenceContainer	inlinevirtual
~AlignedValuesContainer()	bpp::AlignedValuesContainer	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~MappedNamedContainer()	bpp::MappedNamedContainer< T >	inlinevirtual
~NamedContainer()	bpp::NamedContainer< T >	inlineprivatevirtual
~OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inlinevirtual
~OrderedValuesContainer()	bpp::OrderedValuesContainer	inlinevirtual
~PositionedContainer()	bpp::PositionedContainer< T >	inlineprivatevirtual
~PositionedNamedContainer()	bpp::PositionedNamedContainer< T >	inlinevirtual
~SequenceContainer()	bpp::SequenceContainer	inlinevirtual
~SiteContainer()	bpp::SiteContainer	inlinevirtual
bpp::~VectorPositionedContainer()	bpp::VectorPositionedContainer< T >	inlinevirtual
VectorPositionedContainer< Site >::~VectorPositionedContainer()	bpp::VectorPositionedContainer< Site >	inlinevirtual