bpp::Sequence Member List

This is the complete list of members for bpp::Sequence, 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
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
addElement(const std::string &c) override	bpp::Sequence	inline
addElement(size_t pos, const std::string &c) override	bpp::Sequence	inline
addElement(const T &v) override	bpp::Sequence	inline
addElement(size_t pos, const T &v) override	bpp::Sequence	inline
bpp::SequenceInterface::addElement(const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::SequenceInterface::addElement(size_t pos, const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
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
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
append(const SequenceInterface &seq) override	bpp::Sequence	virtual
append(const std::vector< int > &content) override	bpp::Sequence	virtual
append(const std::vector< std::string > &content) override	bpp::Sequence	virtual
append(const std::string &content) override	bpp::Sequence	virtual
bpp::clearComments()=0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::clearComments() override	bpp::SimpleCommentable	inlinevirtual
clone() const override	bpp::Sequence	inlinevirtual
Commentable()	bpp::Commentable	inline
comments_	bpp::SimpleCommentable	protected
content_	bpp::AbstractTemplateSymbolList< int >	protected
CoreSequenceInterface()	bpp::CoreSequenceInterface	inline
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
ElementType typedef	bpp::SequenceInterface
bpp::getAlphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::getAlphabet() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
getChar(size_t pos) const override	bpp::Sequence	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::IntSymbolList::AbstractTemplateSymbolList< int >::getContent() const override	bpp::AbstractTemplateSymbolList< int >	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
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::Sequence	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
name_	bpp::AbstractCoreSequence	private
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 SequenceInterface &s)	bpp::Sequence	inline
operator=(const Sequence &s)	bpp::Sequence	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::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
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
Sequence(std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const std::string &name, const std::string &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const std::string &name, const std::string &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const std::string &name, const std::vector< std::string > &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const std::string &name, const std::vector< int > &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const std::string &name, const std::vector< int > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::Sequence	inline
Sequence(const SequenceInterface &s)	bpp::Sequence	inline
Sequence(const Sequence &s)	bpp::Sequence	inline
bpp::setComments(const Comments &comments)=0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::setComments(const Comments &comments) override	bpp::SimpleCommentable	inlinevirtual
setContent(const std::string &sequence) override	bpp::Sequence	virtual
setContent(const std::vector< std::string > &list) override	bpp::Sequence	inlinevirtual
setContent(const std::vector< int > &list) override	bpp::Sequence	inlinevirtual
bpp::IntSymbolListInterface::setContent(const std::vector< T > &list)=0	bpp::IntSymbolListInterface
bpp::TemplateCoreSymbolListInterface::setContent(const std::vector< T > &list)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
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::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::Sequence	virtual
setToSizeR(size_t newSize) override	bpp::Sequence	virtual
bpp::shuffle()=0	bpp::CruxSymbolListInterface	pure virtual
bpp::IntSymbolList::AbstractTemplateSymbolList< int >::shuffle() override	bpp::AbstractTemplateSymbolList< int >	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::IntSymbolList::AbstractTemplateSymbolList< int >::size() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
SymbolType typedef	bpp::IntSymbolListInterface
toString() const override	bpp::Sequence	inlinevirtual
~AbstractCoreSequence()	bpp::AbstractCoreSequence	inlinevirtual
~AbstractTemplateSymbolList()	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~CoreSequenceInterface()	bpp::CoreSequenceInterface	inlinevirtual
~CruxSymbolListInterface()	bpp::CruxSymbolListInterface	inlinevirtual
~IntSymbolList()	bpp::IntSymbolList	inlinevirtual
~IntSymbolListInterface()	bpp::IntSymbolListInterface	inlinevirtual
~Sequence()	bpp::Sequence	inlinevirtual
~SequenceInterface()	bpp::SequenceInterface	inlinevirtual
~SimpleCommentable()	bpp::SimpleCommentable	inlinevirtual
~TemplateCoreSymbolListInterface()	bpp::TemplateCoreSymbolListInterface< T >	inlinevirtual