bpp::BasicSequence Member List

This is the complete list of members for bpp::BasicSequence, 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 CoreSequence &s)	bpp::AbstractCoreSequence	inline
bpp::addElement(const T &c)=0	bpp::CoreSymbolList< T >	pure virtual
bpp::addElement(size_t pos, const T &c)=0	bpp::CoreSymbolList< T >	pure virtual
bpp::BasicIntSymbolList::addElement(const std::string &c)	bpp::BasicIntSymbolList	virtual
bpp::BasicIntSymbolList::addElement(size_t pos, const std::string &c)	bpp::BasicIntSymbolList	virtual
SymbolList< int >::addElement(const int &v)	bpp::SymbolList< int >	inline
SymbolList< int >::addElement(size_t pos, const int &v)	bpp::SymbolList< int >	inline
alphabet_	bpp::SymbolList< int >	private
append(const Sequence &seq)	bpp::BasicSequence	virtual
append(const std::vector< int > &content)	bpp::BasicSequence	virtual
append(const std::vector< std::string > &content)	bpp::BasicSequence	virtual
append(const std::string &content)	bpp::BasicSequence	virtual
BasicIntSymbolList(const Alphabet *alpha)	bpp::BasicIntSymbolList	inline
BasicIntSymbolList(const std::vector< std::string > &list, const Alphabet *alpha)	bpp::BasicIntSymbolList
BasicIntSymbolList(const std::vector< int > &list, const Alphabet *alpha)	bpp::BasicIntSymbolList
BasicIntSymbolList(const BasicIntSymbolList &list)	bpp::BasicIntSymbolList
BasicSequence(const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const std::string &name, const std::string &sequence, const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const std::string &name, const std::string &sequence, const Comments &comments, const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const std::string &name, const std::vector< std::string > &sequence, const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const std::string &name, const std::vector< int > &sequence, const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const std::string &name, const std::vector< int > &sequence, const Comments &comments, const Alphabet *alpha)	bpp::BasicSequence
BasicSequence(const Sequence &s)	bpp::BasicSequence
BasicSequence(const BasicSequence &s)	bpp::BasicSequence
clearComments()	bpp::BasicSequence	inlinevirtual
clone() const	bpp::BasicSequence	inlinevirtual
Commentable()	bpp::Commentable	inline
Commentable(const Comments &comments)	bpp::Commentable	inline
Commentable(const Commentable &com)	bpp::Commentable	inline
comments_	bpp::Commentable	protected
content_	bpp::SymbolList< int >	protected
CoreSequence()	bpp::CoreSequence	inline
bpp::deleteElement(size_t pos)=0	bpp::CruxSymbolList	pure virtual
bpp::BasicIntSymbolList::deleteElement(size_t pos)	bpp::SymbolList< int >	inlinevirtual
bpp::deleteElements(size_t pos, size_t len)=0	bpp::CruxSymbolList	pure virtual
bpp::BasicIntSymbolList::deleteElements(size_t pos, size_t len)	bpp::SymbolList< int >	inlinevirtual
bpp::getAlphabet() const =0	bpp::CruxSymbolList	pure virtual
bpp::BasicIntSymbolList::getAlphabet() const	bpp::SymbolList< int >	inlinevirtual
getChar(size_t pos) const	bpp::BasicSequence	inlinevirtual
bpp::getComments() const =0	bpp::CoreSequence	pure virtual
bpp::AbstractCoreSequence::getComments() const	bpp::AbstractCoreSequence	inlinevirtual
bpp::getContent() const =0	bpp::CoreSymbolList< T >	pure virtual
bpp::BasicIntSymbolList::getContent() const	bpp::SymbolList< int >	inlinevirtual
bpp::getElement(size_t pos) const =0	bpp::CoreSymbolList< T >	pure virtual
bpp::BasicIntSymbolList::getElement(size_t pos) const	bpp::SymbolList< int >	inlinevirtual
bpp::getName() const =0	bpp::CoreSequence	pure virtual
bpp::AbstractCoreSequence::getName() const	bpp::AbstractCoreSequence	inlinevirtual
bpp::getStateValueAt(size_t siteIndex, int state) const	bpp::CruxSymbolList	inlinevirtual
bpp::BasicIntSymbolList::getStateValueAt(size_t siteIndex, int state) const	bpp::BasicIntSymbolList	inlinevirtual
bpp::getValue(size_t pos) const =0	bpp::CoreSymbolList< T >	pure virtual
bpp::BasicIntSymbolList::getValue(size_t pos) const	bpp::SymbolList< int >	inlinevirtual
IntSymbolList()	bpp::IntSymbolList	inline
name_	bpp::AbstractCoreSequence	private
bpp::operator()(size_t siteIndex, int state) const	bpp::CruxSymbolList	inlinevirtual
bpp::BasicIntSymbolList::operator()(size_t siteIndex, int state) const	bpp::BasicIntSymbolList	inlinevirtual
operator=(const Sequence &s)	bpp::BasicSequence
operator=(const BasicSequence &s)	bpp::BasicSequence
bpp::AbstractCoreSequence::operator=(const AbstractCoreSequence &s)	bpp::AbstractCoreSequence	inline
bpp::AbstractCoreSequence::operator=(const CoreSequence &s)	bpp::AbstractCoreSequence	inline
bpp::Commentable::operator=(const Commentable &com)	bpp::Commentable	inline
bpp::BasicIntSymbolList::operator=(const IntSymbolList &list)	bpp::BasicIntSymbolList
bpp::BasicIntSymbolList::operator=(const BasicIntSymbolList &list)	bpp::BasicIntSymbolList
bpp::IntSymbolList::operator=(const CoreSymbolList< int > &list)	bpp::SymbolList< int >	inline
bpp::IntSymbolList::operator=(const SymbolList< int > &list)	bpp::SymbolList< int >	inline
bpp::operator[](size_t pos) const =0	bpp::CoreSymbolList< T >	pure virtual
bpp::operator[](size_t pos)=0	bpp::CoreSymbolList< T >	pure virtual
bpp::BasicIntSymbolList::operator[](size_t pos) const	bpp::SymbolList< int >	inlinevirtual
bpp::BasicIntSymbolList::operator[](size_t pos)	bpp::SymbolList< int >	inlinevirtual
bpp::setComments(const Comments &comments)=0	bpp::CoreSequence	pure virtual
bpp::AbstractCoreSequence::setComments(const Comments &comments)	bpp::AbstractCoreSequence	inlinevirtual
setContent(const std::string &sequence)	bpp::BasicSequence	virtual
setContent(const std::vector< std::string > &list)	bpp::BasicSequence	inlinevirtual
setContent(const std::vector< int > &list)	bpp::BasicSequence	inlinevirtual
bpp::CoreSequenceSymbolList::setContent(const std::vector< T > &list)=0	bpp::CoreSymbolList< T >	pure virtual
bpp::setElement(size_t pos, const T &c)=0	bpp::CoreSymbolList< T >	pure virtual
bpp::BasicIntSymbolList::setElement(size_t pos, const std::string &c)	bpp::BasicIntSymbolList	virtual
SymbolList< int >::setElement(size_t pos, const int &v)	bpp::SymbolList< int >	inline
bpp::setName(const std::string &name)=0	bpp::CoreSequence	pure virtual
bpp::AbstractCoreSequence::setName(const std::string &name)	bpp::AbstractCoreSequence	inlinevirtual
setToSizeL(size_t newSize)	bpp::BasicSequence	virtual
setToSizeR(size_t newSize)	bpp::BasicSequence	virtual
bpp::shuffle()=0	bpp::CruxSymbolList	pure virtual
bpp::BasicIntSymbolList::shuffle()	bpp::SymbolList< int >	inlinevirtual
bpp::size() const =0	bpp::CruxSymbolList	pure virtual
bpp::BasicIntSymbolList::size() const	bpp::SymbolList< int >	inlinevirtual
SymbolList(const Alphabet *alpha)	bpp::SymbolList< int >	inline
SymbolList(const std::vector< int > &list, const Alphabet *alpha)	bpp::SymbolList< int >	inline
SymbolList(const SymbolList< int > &list)	bpp::SymbolList< int >	inline
SymbolList(const CoreSymbolList< int > &list)	bpp::SymbolList< int >	inline
toString() const	bpp::BasicSequence	inlinevirtual
~AbstractCoreSequence()	bpp::AbstractCoreSequence	inlinevirtual
~BasicIntSymbolList()	bpp::BasicIntSymbolList	inlinevirtual
~BasicSequence()	bpp::BasicSequence	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~CoreSequence()	bpp::CoreSequence	inlinevirtual
~CoreSequenceSymbolList()	bpp::CoreSequenceSymbolList< T >	inlinevirtual
~CoreSymbolList()	bpp::CoreSymbolList< T >	inlinevirtual
~CruxSymbolList()	bpp::CruxSymbolList	inlinevirtual
~IntSymbolList()	bpp::IntSymbolList	inlinevirtual
~Sequence()	bpp::Sequence	inlinevirtual
~SymbolList()	bpp::SymbolList< int >	inlinevirtual