bpp::Site Member List

This is the complete list of members for bpp::Site, 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
AbstractTemplateSymbolList(std::shared_ptr< const Alphabet > alpha)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList(const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList(const AbstractTemplateSymbolList< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList(const TemplateCoreSymbolListInterface< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
bpp::addElement(const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::addElement(size_t pos, const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::addElement(const T &c)=0	bpp::IntSymbolListInterface
bpp::addElement(size_t pos, const T &c)=0	bpp::IntSymbolListInterface
bpp::TemplateCoreSymbolListInterface::addElement(const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::TemplateCoreSymbolListInterface::addElement(size_t pos, const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::IntSymbolList::addElement(const std::string &c) override	bpp::IntSymbolList	inlinevirtual
bpp::IntSymbolList::addElement(size_t pos, const std::string &c) override	bpp::IntSymbolList	inlinevirtual
bpp::IntSymbolList::addElement(const T &v) override	bpp::IntSymbolList	inline
AbstractTemplateSymbolList< int >::addElement(const int &v) override	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList< int >::addElement(size_t pos, const int &v) override	bpp::AbstractTemplateSymbolList< int >	inline
bpp::alphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::alphabet() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
alphabet_	bpp::AbstractTemplateSymbolList< int >	private
clone() const	bpp::Site	inlinevirtual
content_	bpp::AbstractTemplateSymbolList< int >	protected
coordinate_	bpp::AbstractCoreSite	private
bpp::deleteElement(size_t pos)=0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::deleteElement(size_t pos) override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::deleteElements(size_t pos, size_t len)=0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::deleteElements(size_t pos, size_t len) override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::getAlphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::getAlphabet() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::getChar(size_t pos) const =0	bpp::IntSymbolListInterface	pure virtual
bpp::IntSymbolList::getChar(size_t pos) const override	bpp::IntSymbolList	virtual
bpp::getContent() const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::getContent() const override	bpp::AbstractTemplateSymbolList< int >	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::IntSymbolList::AbstractTemplateSymbolList< int >::getElement(size_t pos) const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
getStateValueAt(size_t sequencePosition, int state) const	bpp::Site	inlinevirtual
bpp::getValue(size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::getValue(size_t pos) const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
IntSymbolList(std::shared_ptr< const Alphabet > alpha)	bpp::IntSymbolList	inline
IntSymbolList(const std::vector< std::string > &list, std::shared_ptr< const Alphabet > alpha)	bpp::IntSymbolList	inline
IntSymbolList(const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)	bpp::IntSymbolList	inline
IntSymbolList(const IntSymbolList &list)	bpp::IntSymbolList	inline
IntSymbolListInterface()	bpp::IntSymbolListInterface	inline
bpp::operator()(size_t position, int state) const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::operator()(size_t siteIndex, int state) const override	bpp::IntSymbolList	inlinevirtual
operator<(const SiteInterface &site)	bpp::SiteInterface	inlinevirtual
operator=(const Site &s)	bpp::Site	inline
bpp::AbstractCoreSite::operator=(const CoreSiteInterface &site)	bpp::AbstractCoreSite	inline
bpp::AbstractCoreSite::operator=(const AbstractCoreSite &site)	bpp::AbstractCoreSite	inline
bpp::IntSymbolList::operator=(const IntSymbolListInterface &list)	bpp::IntSymbolList
bpp::IntSymbolList::operator=(const IntSymbolList &list)	bpp::IntSymbolList	inline
AbstractTemplateSymbolList< int >::operator=(const TemplateCoreSymbolListInterface< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList< int >::operator=(const AbstractTemplateSymbolList< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
operator==(const SiteInterface &site)	bpp::SiteInterface	inlinevirtual
bpp::operator[](size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::operator[](size_t pos)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::operator[](size_t pos) const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
AbstractTemplateSymbolList< int >::operator[](size_t pos) override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::setContent(const std::vector< std::string > &list)=0	bpp::IntSymbolListInterface	pure virtual
bpp::setContent(const std::vector< T > &list)=0	bpp::IntSymbolListInterface
bpp::TemplateCoreSymbolListInterface::setContent(const std::vector< T > &list)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::IntSymbolList::setContent(const std::vector< int > &list) override	bpp::IntSymbolList	virtual
bpp::IntSymbolList::setContent(const std::vector< std::string > &list) override	bpp::IntSymbolList	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 std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::setElement(size_t pos, const T &c)=0	bpp::IntSymbolListInterface
bpp::TemplateCoreSymbolListInterface::setElement(size_t pos, const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::IntSymbolList::setElement(size_t pos, const std::string &c) override	bpp::IntSymbolList	inlinevirtual
bpp::IntSymbolList::setElement(size_t pos, const T &v) override	bpp::IntSymbolList	inline
AbstractTemplateSymbolList< int >::setElement(size_t pos, const int &v) override	bpp::AbstractTemplateSymbolList< int >	inline
bpp::shuffle()=0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::shuffle() override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
Site(std::shared_ptr< const Alphabet > &alphabet)	bpp::Site	inline
Site(std::shared_ptr< const Alphabet > &alphabet, int coordinate)	bpp::Site	inline
Site(const std::vector< std::string > &site, std::shared_ptr< const Alphabet > &alphabet)	bpp::Site	inline
Site(const std::vector< std::string > &site, std::shared_ptr< const Alphabet > &alphabet, int coordinate)	bpp::Site	inline
Site(const std::vector< int > &site, std::shared_ptr< const Alphabet > &alphabet)	bpp::Site	inline
Site(const std::vector< int > &site, std::shared_ptr< const Alphabet > alphabet, int coordinate)	bpp::Site	inline
Site(const Site &site)	bpp::Site	inline
bpp::size() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::size() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
SymbolType typedef	bpp::IntSymbolListInterface
bpp::toString() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::toString() const override	bpp::IntSymbolList	inlinevirtual
~AbstractCoreSite()	bpp::AbstractCoreSite	inlinevirtual
~AbstractTemplateSymbolList()	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~CoreSiteInterface()	bpp::CoreSiteInterface	inlinevirtual
~CruxSymbolListInterface()	bpp::CruxSymbolListInterface	inlinevirtual
~IntSymbolList()	bpp::IntSymbolList	inlinevirtual
~IntSymbolListInterface()	bpp::IntSymbolListInterface	inlinevirtual
~Site()	bpp::Site	inlinevirtual
~SiteInterface()	bpp::SiteInterface	inlinevirtual
~TemplateCoreSymbolListInterface()	bpp::TemplateCoreSymbolListInterface< T >	inlinevirtual