bpp::ProbabilisticSite Member List

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

AbstractCoreSite()	bpp::AbstractCoreSite	inline
AbstractCoreSite(int coordinate)	bpp::AbstractCoreSite	inline
AbstractCoreSite(const CoreSiteInterface &site)	bpp::AbstractCoreSite	inline
AbstractCoreSite(const AbstractCoreSite &site)	bpp::AbstractCoreSite	inline
bpp::addElement(const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::addElement(size_t pos, const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::addElement(const std::vector< double > &element) override	bpp::ProbabilisticSymbolList
bpp::ProbabilisticSymbolList::addElement(size_t pos, const std::vector< double > &element) override	bpp::ProbabilisticSymbolList
bpp::alphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::alphabet() const override	bpp::ProbabilisticSymbolList	inlinevirtual
alphabet_	bpp::ProbabilisticSymbolList	private
clone() const	bpp::ProbabilisticSite	inlinevirtual
content_	bpp::ProbabilisticSymbolList	protected
coordinate_	bpp::AbstractCoreSite	private
bpp::deleteElement(size_t pos)=0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::deleteElement(size_t pos) override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::deleteElements(size_t pos, size_t len)=0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::deleteElements(size_t pos, size_t len) override	bpp::ProbabilisticSymbolList	inlinevirtual
DTable typedef	bpp::ProbabilisticSymbolListInterface
bpp::getAlphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::getAlphabet() const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::getContent() const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::getContent() const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::getCoordinate() const =0	bpp::CoreSiteInterface	pure virtual
bpp::AbstractCoreSite::getCoordinate() const override	bpp::AbstractCoreSite	inlinevirtual
bpp::getElement(size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::getElement(size_t pos) const override	bpp::ProbabilisticSymbolList	inlinevirtual
getStateValueAt(size_t sequencePosition, int state) const	bpp::ProbabilisticSite	inlinevirtual
bpp::getTable() const =0	bpp::ProbabilisticSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::getTable() const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::getValue(size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::getValue(size_t pos) const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::operator()(size_t position, int state) const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::operator()(size_t siteIndex, int state) const override	bpp::ProbabilisticSymbolList	inlinevirtual
operator=(const ProbabilisticSite &site)	bpp::ProbabilisticSite	inline
operator=(const ProbabilisticSiteInterface &site)	bpp::ProbabilisticSite	inline
bpp::AbstractCoreSite::operator=(const CoreSiteInterface &site)	bpp::AbstractCoreSite	inline
bpp::AbstractCoreSite::operator=(const AbstractCoreSite &site)	bpp::AbstractCoreSite	inline
bpp::ProbabilisticSymbolList::operator=(const ProbabilisticSymbolListInterface &list)	bpp::ProbabilisticSymbolList
bpp::ProbabilisticSymbolList::operator=(const ProbabilisticSymbolList &list)	bpp::ProbabilisticSymbolList
bpp::operator[](size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::operator[](size_t pos)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::operator[](size_t pos) const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::ProbabilisticSymbolList::operator[](size_t pos) override	bpp::ProbabilisticSymbolList	inlinevirtual
ProbabilisticSite(std::shared_ptr< const Alphabet > &alpha)	bpp::ProbabilisticSite	inline
ProbabilisticSite(std::shared_ptr< const Alphabet > &alpha, int position)	bpp::ProbabilisticSite	inline
ProbabilisticSite(const Table< double > &site, std::shared_ptr< const Alphabet > &alpha)	bpp::ProbabilisticSite	inline
ProbabilisticSite(const Table< double > &site, std::shared_ptr< const Alphabet > &alpha, int position)	bpp::ProbabilisticSite	inline
ProbabilisticSite(const ProbabilisticSite &site)	bpp::ProbabilisticSite	inline
ProbabilisticSite(const ProbabilisticSiteInterface &site)	bpp::ProbabilisticSite	inline
ProbabilisticSymbolList(std::shared_ptr< const Alphabet > &alpha)	bpp::ProbabilisticSymbolList
ProbabilisticSymbolList(const DTable &list, std::shared_ptr< const Alphabet > &alpha)	bpp::ProbabilisticSymbolList
ProbabilisticSymbolList(const std::vector< std::vector< double >> &list, std::shared_ptr< const Alphabet > &alpha)	bpp::ProbabilisticSymbolList
ProbabilisticSymbolList(const ProbabilisticSymbolListInterface &list)	bpp::ProbabilisticSymbolList
ProbabilisticSymbolList(const CruxSymbolListInterface &list)	bpp::ProbabilisticSymbolList
ProbabilisticSymbolList(const ProbabilisticSymbolList &list)	bpp::ProbabilisticSymbolList
ProbabilisticSymbolListInterface()	bpp::ProbabilisticSymbolListInterface	inline
bpp::setContent(const DTable &list)=0	bpp::ProbabilisticSymbolListInterface	pure virtual
bpp::setContent(const std::vector< T > &list)=0	bpp::ProbabilisticSymbolListInterface
bpp::TemplateCoreSymbolListInterface::setContent(const std::vector< T > &list)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::setContent(const std::vector< std::vector< double >> &list) override	bpp::ProbabilisticSymbolList
bpp::ProbabilisticSymbolList::setContent(const DTable &list) override	bpp::ProbabilisticSymbolList	virtual
bpp::setCoordinate(int coordinate)=0	bpp::CoreSiteInterface	pure virtual
bpp::AbstractCoreSite::setCoordinate(int coordinate) override	bpp::AbstractCoreSite	inlinevirtual
bpp::setElement(size_t pos, const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::setElement(size_t pos, const std::vector< double > &element) override	bpp::ProbabilisticSymbolList
bpp::shuffle()=0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::shuffle() override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::size() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::size() const override	bpp::ProbabilisticSymbolList	inlinevirtual
SymbolType typedef	bpp::ProbabilisticSymbolListInterface
bpp::toString() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::toString() const override	bpp::ProbabilisticSymbolList	virtual
~AbstractCoreSite()	bpp::AbstractCoreSite	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~CoreSiteInterface()	bpp::CoreSiteInterface	inlinevirtual
~CruxSymbolListInterface()	bpp::CruxSymbolListInterface	inlinevirtual
~ProbabilisticSite()	bpp::ProbabilisticSite	inlinevirtual
~ProbabilisticSiteInterface()	bpp::ProbabilisticSiteInterface	inlinevirtual
~ProbabilisticSymbolList()	bpp::ProbabilisticSymbolList	inlinevirtual
~ProbabilisticSymbolListInterface()	bpp::ProbabilisticSymbolListInterface	inlinevirtual
~TemplateCoreSymbolListInterface()	bpp::TemplateCoreSymbolListInterface< T >	inlinevirtual