bpp::VectorProbabilisticSiteContainer Member List

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

AbstractProbabilisticSequenceContainer(const Alphabet *alpha)	bpp::AbstractProbabilisticSequenceContainer	inline
AbstractProbabilisticSequenceContainer(const AbstractProbabilisticSequenceContainer &sc)	bpp::AbstractProbabilisticSequenceContainer	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
VectorPositionedContainer< ProbabilisticSite >::addObject(std::shared_ptr< ProbabilisticSite > object, size_t objectIndex, bool checkPosition=false)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::addObject(std::shared_ptr< ProbabilisticSequence > object, size_t objectIndex, const std::string &name, bool check=false)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::bpp::PositionedNamedContainer::addObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0	bpp::PositionedNamedContainer< T >	protectedpure virtual
VectorMappedContainer< ProbabilisticSequence >::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< ProbabilisticSite >::addObject_(std::shared_ptr< ProbabilisticSite > object, size_t objectIndex, bool checkPosition=false) const	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::addObject_(std::shared_ptr< ProbabilisticSequence > object, size_t objectIndex, const std::string &name, bool check=false) const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::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
addSequence(const ProbabilisticSequence &sequence, bool checkName=true)	bpp::VectorProbabilisticSiteContainer	virtual
addSequence(const Sequence &sequence, bool checkName=true)	bpp::VectorProbabilisticSiteContainer	virtual
addSite(std::shared_ptr< ProbabilisticSite > site, bool checkPosition=false)	bpp::VectorProbabilisticSiteContainer	virtual
AlignedValuesContainer()	bpp::AlignedValuesContainer	inline
alphabet_	bpp::AbstractValuesContainer	protected
VectorPositionedContainer< ProbabilisticSite >::appendObject(std::shared_ptr< ProbabilisticSite > object)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::appendObject(std::shared_ptr< ProbabilisticSequence > object, const std::string &name, bool check=true)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
bpp::VectorPositionedContainer::appendObject(std::shared_ptr< T > object)	bpp::VectorPositionedContainer< T >	inlineprotected
changeName(const std::string &okey, const std::string &nkey)	bpp::MappedNamedContainer< T >	inline
clear()	bpp::VectorProbabilisticSiteContainer	virtual
clearComments()	bpp::Commentable	inline
clone() const	bpp::VectorProbabilisticSiteContainer	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::VectorProbabilisticSiteContainer	virtual
deleteGeneralComments()	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
VectorPositionedContainer< ProbabilisticSite >::deleteObject(size_t objectIndex)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::deleteObject(size_t objectIndex)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::deleteObject(const std::string &name)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorPositionedContainer< ProbabilisticSite >::deleteObjects(size_t objectIndex, size_t length)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::deleteObjects(size_t objectIndex, size_t length)	bpp::VectorPositionedContainer< T >	inlineprotected
deleteSites(size_t siteIndex, size_t length)	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getAlphabet() const	bpp::AbstractValuesContainer	inlinevirtual
getComments(const std::string &name) const	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
getComments(size_t sequenceIndex) const	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
bpp::OrderedValuesContainer::getComments(const std::string &name) const=0	bpp::OrderedValuesContainer
bpp::Commentable::getComments() const	bpp::Commentable	inline
getGeneralComments() const	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
getName(size_t sequenceIndex) const	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
getNumberOfObjects() const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
getNumberOfSequences() const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getNumberOfSites() const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
VectorPositionedContainer< ProbabilisticSite >::getObject(size_t objectIndex) const	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotectedvirtual
VectorPositionedContainer< ProbabilisticSite >::getObject(size_t objectIndex)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::getObject(size_t objectIndex) const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::getObject(size_t objectIndex)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::getObject(const std::string &name) const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::getObject(const std::string &name)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorPositionedContainer< ProbabilisticSite >::getObject_(size_t objectIndex) const	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::getObject_(size_t objectIndex) const	bpp::VectorPositionedContainer< T >	inlineprotected
getObjectName(size_t objectIndex) const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
getObjectNames() const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
getObjectPosition(const std::string &name) const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
getSequence(std::size_t i) const	bpp::VectorProbabilisticSiteContainer	virtual
getSequence(const std::string &name) const	bpp::VectorProbabilisticSiteContainer	virtual
getSequenceNames() const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getSequencePosition(const std::string &name) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getSite(size_t i) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getSite(size_t i)	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getSitePositions() const	bpp::VectorProbabilisticSiteContainer	virtual
VectorPositionedContainer< ProbabilisticSite >::getSize() const	bpp::VectorPositionedContainer< ProbabilisticSite >	inlinevirtual
VectorMappedContainer< ProbabilisticSequence >::getSize() const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlinevirtual
getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
bpp::AbstractProbabilisticSequenceContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0	bpp::OrderedValuesContainer
getSymbolListSite(size_t siteIndex) const	bpp::ProbabilisticSiteContainer	inlinevirtual
getSymbolListSite(size_t siteIndex)	bpp::ProbabilisticSiteContainer	inlinevirtual
hasObject(const std::string &name) const	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
hasSequence(const std::string &name) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
VectorPositionedContainer< ProbabilisticSite >::insertObject(std::shared_ptr< ProbabilisticSite > object, size_t objectIndex)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::insertObject(std::shared_ptr< ProbabilisticSequence > object, size_t objectIndex, const std::string &name)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
VectorMappedContainer< ProbabilisticSequence >::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
isAvailableName(std::string objectName) const	bpp::MappedNamedContainer< T >	inline
VectorPositionedContainer< ProbabilisticSite >::isAvailablePosition(size_t objectIndex) const	bpp::VectorPositionedContainer< ProbabilisticSite >	inline
VectorMappedContainer< ProbabilisticSequence >::isAvailablePosition(size_t objectIndex) const	bpp::VectorPositionedContainer< T >	inline
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< ProbabilisticSequence >	private
mObjects_	bpp::MappedNamedContainer< T >	private
bpp::NamedContainer()	bpp::NamedContainer< T >	inlineprivate
bpp::MappedNamedContainer::NamedContainer()	bpp::NamedContainer< T >	inline
VectorPositionedContainer< ProbabilisticSite >::nullify()	bpp::VectorPositionedContainer< ProbabilisticSite >	inline
VectorMappedContainer< ProbabilisticSequence >::nullify()	bpp::VectorPositionedContainer< T >	inline
operator()(size_t siteIndex, const std::string &sequenceName, int state) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
operator()(size_t siteIndex, size_t sequenceIndex, int state) const	bpp::VectorProbabilisticSiteContainer	inlinevirtual
operator=(const VectorProbabilisticSiteContainer &vpsc)	bpp::VectorProbabilisticSiteContainer
bpp::AbstractProbabilisticSequenceContainer::operator=(const AbstractProbabilisticSequenceContainer &sc)	bpp::AbstractProbabilisticSequenceContainer	inline
bpp::AbstractValuesContainer::operator=(const AbstractValuesContainer &sc)	bpp::AbstractValuesContainer	inline
bpp::Commentable::operator=(const Commentable &com)	bpp::Commentable	inline
VectorPositionedContainer< ProbabilisticSite >::operator=(const VectorPositionedContainer< ProbabilisticSite > &vsc)	bpp::VectorPositionedContainer< ProbabilisticSite >	inline
VectorMappedContainer< ProbabilisticSequence >::operator=(const VectorMappedContainer &vsc)	bpp::VectorMappedContainer< ProbabilisticSequence >	inline
VectorMappedContainer< ProbabilisticSequence >::bpp::MappedNamedContainer::operator=(const MappedNamedContainer &msc)	bpp::MappedNamedContainer< T >	inline
bpp::VectorPositionedContainer::operator=(const VectorPositionedContainer< T > &vsc)	bpp::VectorPositionedContainer< T >	inline
OrderedValuesContainer()	bpp::OrderedValuesContainer	inline
VectorPositionedContainer< ProbabilisticSite >::PositionedContainer()	bpp::PositionedContainer< T >	inline
VectorMappedContainer< ProbabilisticSequence >::bpp::PositionedContainer()	bpp::PositionedContainer< T >	inline
VectorPositionedContainer< ProbabilisticSite >::positions_	bpp::VectorPositionedContainer< ProbabilisticSite >	protected
VectorMappedContainer< ProbabilisticSequence >::positions_	bpp::VectorPositionedContainer< T >	protected
ProbabilisticSequenceContainer()	bpp::ProbabilisticSequenceContainer	inline
ProbabilisticSiteContainer()	bpp::ProbabilisticSiteContainer	inline
realloc(size_t n)	bpp::VectorProbabilisticSiteContainer	protected
reindexSites()	bpp::VectorProbabilisticSiteContainer	virtual
VectorPositionedContainer< ProbabilisticSite >::removeObject(size_t objectIndex)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::removeObject(size_t objectIndex)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
VectorMappedContainer< ProbabilisticSequence >::removeObject(const std::string &name)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotectedvirtual
setComments(size_t sequenceIndex, const Comments &comments)	bpp::VectorProbabilisticSiteContainer	inlinevirtual
bpp::AbstractProbabilisticSequenceContainer::setComments(const std::string &name, const Comments &comments)	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
bpp::OrderedValuesContainer::setComments(const std::string &name, const Comments &comments)=0	bpp::OrderedValuesContainer
bpp::Commentable::setComments(const Comments &comments)	bpp::Commentable	inline
setGeneralComments(const Comments &comments)	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
setObjectName(size_t pos, const std::string &name)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
setObjectNames(const std::vector< std::string > &names)	bpp::VectorMappedContainer< ProbabilisticSequence >	inlineprotected
setSequence(const std::string &name, const ProbabilisticSequence &sequence, bool checkName)	bpp::VectorProbabilisticSiteContainer	virtual
setSequence(size_t sequenceIndex, const ProbabilisticSequence &sequence, bool checkName)	bpp::VectorProbabilisticSiteContainer
setSequenceNames(const std::vector< std::string > &names, bool checkNames=true)	bpp::VectorProbabilisticSiteContainer	inlinevirtual
setSitePositions(Vint vPositions)	bpp::VectorProbabilisticSiteContainer	virtual
VectorPositionedContainer< ProbabilisticSite >::setSize(size_t size)	bpp::VectorPositionedContainer< ProbabilisticSite >	inlinevirtual
VectorMappedContainer< ProbabilisticSequence >::bpp::VectorPositionedContainer::setSize(size_t size)	bpp::VectorPositionedContainer< T >	inlinevirtual
toString(const std::string &name) const	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
toString(size_t sequenceIndex) const	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
bpp::AbstractValuesContainer::toString(const std::string &name) const=0	bpp::OrderedValuesContainer
VectorMappedContainer()	bpp::VectorMappedContainer< ProbabilisticSequence >	inline
VectorMappedContainer(const VectorMappedContainer &vsc)	bpp::VectorMappedContainer< ProbabilisticSequence >	inline
VectorPositionedContainer< ProbabilisticSite >::VectorPositionedContainer(const std::vector< std::shared_ptr< ProbabilisticSite > > &vs)	bpp::VectorPositionedContainer< ProbabilisticSite >	inline
VectorPositionedContainer< ProbabilisticSite >::VectorPositionedContainer(size_t size=0)	bpp::VectorPositionedContainer< ProbabilisticSite >	inline
VectorPositionedContainer< ProbabilisticSite >::VectorPositionedContainer(const VectorPositionedContainer< ProbabilisticSite > &vsc)	bpp::VectorPositionedContainer< ProbabilisticSite >	inline
VectorMappedContainer< ProbabilisticSequence >::VectorPositionedContainer(const std::vector< std::shared_ptr< T > > &vs)	bpp::VectorPositionedContainer< T >	inline
VectorMappedContainer< ProbabilisticSequence >::VectorPositionedContainer(size_t size=0)	bpp::VectorPositionedContainer< T >	inline
VectorMappedContainer< ProbabilisticSequence >::VectorPositionedContainer(const VectorPositionedContainer< T > &vsc)	bpp::VectorPositionedContainer< T >	inline
VectorProbabilisticSiteContainer(const Alphabet *alpha)	bpp::VectorProbabilisticSiteContainer
VectorProbabilisticSiteContainer(const std::vector< const CruxSymbolListSite * > &vs, const Alphabet *alpha, bool checkPositions=true)	bpp::VectorProbabilisticSiteContainer
VectorProbabilisticSiteContainer(const AlignedValuesContainer &avc)	bpp::VectorProbabilisticSiteContainer
VectorProbabilisticSiteContainer(const std::vector< std::string > &names, const Alphabet *alpha)	bpp::VectorProbabilisticSiteContainer
VectorProbabilisticSiteContainer(const VectorProbabilisticSiteContainer &vpsc)	bpp::VectorProbabilisticSiteContainer
VectorProbabilisticSiteContainer(const OrderedSequenceContainer &osc)	bpp::VectorProbabilisticSiteContainer
vNames_	bpp::VectorMappedContainer< ProbabilisticSequence >	private
~AbstractProbabilisticSequenceContainer()	bpp::AbstractProbabilisticSequenceContainer	inlinevirtual
~AbstractValuesContainer()	bpp::AbstractValuesContainer	inlinevirtual
~AlignedValuesContainer()	bpp::AlignedValuesContainer	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~MappedNamedContainer()	bpp::MappedNamedContainer< T >	inlinevirtual
~NamedContainer()	bpp::NamedContainer< T >	inlineprivatevirtual
~OrderedValuesContainer()	bpp::OrderedValuesContainer	inlinevirtual
~PositionedContainer()	bpp::PositionedContainer< T >	inlinevirtual
~PositionedNamedContainer()	bpp::PositionedNamedContainer< T >	inlinevirtual
~ProbabilisticSequenceContainer()	bpp::ProbabilisticSequenceContainer	inlinevirtual
~ProbabilisticSiteContainer()	bpp::ProbabilisticSiteContainer	inlinevirtual
VectorPositionedContainer< ProbabilisticSite >::~VectorPositionedContainer()	bpp::VectorPositionedContainer< ProbabilisticSite >	inlinevirtual
VectorMappedContainer< ProbabilisticSequence >::~VectorPositionedContainer()	bpp::VectorPositionedContainer< T >	inlinevirtual
~VectorProbabilisticSiteContainer()	bpp::VectorProbabilisticSiteContainer	inlinevirtual