bpp::ProbabilisticSequence Member List

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

AbstractCoreSequence(const std::string &name)	bpp::AbstractCoreSequence	inline
AbstractCoreSequence(const std::string &name, const Comments &comments)	bpp::AbstractCoreSequence	inline
AbstractCoreSequence()	bpp::AbstractCoreSequence	inline
AbstractCoreSequence(const AbstractCoreSequence &s)	bpp::AbstractCoreSequence	inline
AbstractCoreSequence(const CoreSequenceInterface &s)	bpp::AbstractCoreSequence	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
bpp::clearComments()=0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::clearComments() override	bpp::SimpleCommentable	inlinevirtual
clone() const override	bpp::ProbabilisticSequence	inlinevirtual
Commentable()	bpp::Commentable	inline
comments_	bpp::SimpleCommentable	protected
content_	bpp::ProbabilisticSymbolList	protected
CoreSequenceInterface()	bpp::CoreSequenceInterface	inline
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
ElementType typedef	bpp::ProbabilisticSequenceInterface
bpp::getAlphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::getAlphabet() const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::getComments() const =0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::getComments() const override	bpp::SimpleCommentable	inlinevirtual
bpp::getContent() const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::getContent() const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::getElement(size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::ProbabilisticSymbolList::getElement(size_t pos) const override	bpp::ProbabilisticSymbolList	inlinevirtual
bpp::getName() const =0	bpp::CoreSequenceInterface	pure virtual
bpp::AbstractCoreSequence::getName() const override	bpp::AbstractCoreSequence	inlinevirtual
getStateValueAt(size_t sitePosition, int state) const override	bpp::ProbabilisticSequence	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
name_	bpp::AbstractCoreSequence	private
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 ProbabilisticSequence &sequence)	bpp::ProbabilisticSequence	inline
bpp::AbstractCoreSequence::operator=(const AbstractCoreSequence &s)	bpp::AbstractCoreSequence	inline
bpp::AbstractCoreSequence::operator=(const CoreSequenceInterface &s)	bpp::AbstractCoreSequence	inline
bpp::SimpleCommentable::operator=(const SimpleCommentable &com)	bpp::SimpleCommentable	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
ProbabilisticSequence(std::shared_ptr< const Alphabet > &alphabet)	bpp::ProbabilisticSequence	inline
ProbabilisticSequence(const std::string &name, const std::vector< ProbabilisticSequence::SymbolType > &sequence, std::shared_ptr< const Alphabet > &alphabet)	bpp::ProbabilisticSequence	inline
ProbabilisticSequence(const std::string &name, const DTable &sequence, std::shared_ptr< const Alphabet > &alphabet)	bpp::ProbabilisticSequence	inline
ProbabilisticSequence(const std::string &name, const std::vector< ProbabilisticSequence::SymbolType > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alphabet)	bpp::ProbabilisticSequence	inline
ProbabilisticSequence(const std::string &name, const DTable &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alphabet)	bpp::ProbabilisticSequence	inline
ProbabilisticSequence(const ProbabilisticSequence &sequence)	bpp::ProbabilisticSequence	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::setComments(const Comments &comments)=0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::setComments(const Comments &comments) override	bpp::SimpleCommentable	inlinevirtual
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::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::setName(const std::string &name)=0	bpp::CoreSequenceInterface	pure virtual
bpp::AbstractCoreSequence::setName(const std::string &name) override	bpp::AbstractCoreSequence	inlinevirtual
setToSizeL(size_t newSize) override	bpp::ProbabilisticSequence	virtual
setToSizeR(size_t newSize) override	bpp::ProbabilisticSequence	virtual
bpp::shuffle()=0	bpp::CruxSymbolListInterface	pure virtual
bpp::ProbabilisticSymbolList::shuffle() override	bpp::ProbabilisticSymbolList	inlinevirtual
SimpleCommentable()	bpp::SimpleCommentable	inline
SimpleCommentable(const Comments &comments)	bpp::SimpleCommentable	inline
SimpleCommentable(const SimpleCommentable &com)	bpp::SimpleCommentable	inline
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
~AbstractCoreSequence()	bpp::AbstractCoreSequence	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~CoreSequenceInterface()	bpp::CoreSequenceInterface	inlinevirtual
~CruxSymbolListInterface()	bpp::CruxSymbolListInterface	inlinevirtual
~ProbabilisticSequence()	bpp::ProbabilisticSequence	inlinevirtual
~ProbabilisticSequenceInterface()	bpp::ProbabilisticSequenceInterface	inlinevirtual
~ProbabilisticSymbolList()	bpp::ProbabilisticSymbolList	inlinevirtual
~ProbabilisticSymbolListInterface()	bpp::ProbabilisticSymbolListInterface	inlinevirtual
~SimpleCommentable()	bpp::SimpleCommentable	inlinevirtual
~TemplateCoreSymbolListInterface()	bpp::TemplateCoreSymbolListInterface< T >	inlinevirtual