bpp::AbstractSequenceContainer Member List

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

AbstractSequenceContainer(const Alphabet *alpha)	bpp::AbstractSequenceContainer	inline
AbstractSequenceContainer(const AbstractSequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
AbstractSequenceContainer(const SequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
AbstractValuesContainer(const Alphabet *alpha)	bpp::AbstractValuesContainer	inline
AbstractValuesContainer(const Comments &comments, const Alphabet *alpha)	bpp::AbstractValuesContainer	inline
AbstractValuesContainer(const AbstractValuesContainer &sc)	bpp::AbstractValuesContainer	inline
addSequence(const Sequence &sequence, bool checkName)=0	bpp::SequenceContainer	pure virtual
alphabet_	bpp::AbstractValuesContainer	protected
clear()=0	bpp::SequencedValuesContainer	pure virtual
clearComments()	bpp::Commentable	inline
bpp::clone() const=0	bpp::Clonable	pure virtual
bpp::OrderedValuesContainer::clone() const =0	bpp::OrderedValuesContainer	pure virtual
Commentable()	bpp::Commentable	inline
Commentable(const Comments &comments)	bpp::Commentable	inline
Commentable(const Commentable &com)	bpp::Commentable	inline
comments_	bpp::Commentable	protected
createEmptyContainer() const =0	bpp::SequencedValuesContainer	pure virtual
bpp::deleteGeneralComments()=0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::deleteGeneralComments()	bpp::AbstractValuesContainer	inlinevirtual
bpp::getAlphabet() const =0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::getAlphabet() const	bpp::AbstractValuesContainer	inlinevirtual
getComments(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
getComments(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
bpp::OrderedSequenceContainer::getComments(size_t sequenceIndex) const=0	bpp::OrderedSequenceContainer
bpp::Commentable::getComments() const	bpp::Commentable	inline
bpp::getGeneralComments() const =0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::getGeneralComments() const	bpp::AbstractValuesContainer	inlinevirtual
getName(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
getNumberOfSequences() const =0	bpp::SequencedValuesContainer	pure virtual
getSequence(size_t sequenceIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
getSequence(const std::string &name) const=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::getSequence(const std::string &name) const =0	bpp::SequenceContainer	pure virtual
getSequenceNames() const =0	bpp::SequencedValuesContainer	pure virtual
getSequencePosition(const std::string &name) const =0	bpp::OrderedValuesContainer	pure virtual
bpp::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const =0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const =0	bpp::OrderedValuesContainer	pure virtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0	bpp::OrderedValuesContainer
hasSequence(const std::string &name) const =0	bpp::SequencedValuesContainer	pure virtual
operator()(size_t sequenceIndex, size_t elementIndex)=0	bpp::OrderedSequenceContainer	pure virtual
operator()(size_t sequenceIndex, size_t elementIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
bpp::SequenceContainer::operator()(const std::string &sequenceName, size_t elementIndex)=0	bpp::SequenceContainer	pure virtual
bpp::SequenceContainer::operator()(const std::string &sequenceName, size_t elementIndex) const =0	bpp::SequenceContainer	pure virtual
bpp::SequencedValuesContainer::operator()(size_t siteIndex, const std::string &sequenceName, int state) const =0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::operator()(size_t siteIndex, size_t sequenceIndex, int state) const =0	bpp::OrderedValuesContainer	pure virtual
operator=(const AbstractSequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
operator=(const SequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
bpp::AbstractValuesContainer::operator=(const AbstractValuesContainer &sc)	bpp::AbstractValuesContainer	inline
bpp::Commentable::operator=(const Commentable &com)	bpp::Commentable	inline
OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inline
OrderedValuesContainer()	bpp::OrderedValuesContainer	inline
removeSequence(size_t sequenceIndex)=0	bpp::OrderedSequenceContainer	pure virtual
removeSequence(const std::string &name)=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::removeSequence(const std::string &name)=0	bpp::SequenceContainer	pure virtual
SequenceContainer()	bpp::SequenceContainer	inline
setComments(const std::string &name, const Comments &comments)	bpp::AbstractSequenceContainer	inlinevirtual
setComments(size_t sequenceIndex, const Comments &comments)=0	bpp::AbstractSequenceContainer	pure virtual
bpp::OrderedSequenceContainer::setComments(size_t sequenceIndex, const Comments &comments)=0	bpp::OrderedSequenceContainer
bpp::Commentable::setComments(const Comments &comments)	bpp::Commentable	inline
bpp::setGeneralComments(const Comments &comments)=0	bpp::SequencedValuesContainer	pure virtual
bpp::AbstractValuesContainer::setGeneralComments(const Comments &comments)	bpp::AbstractValuesContainer	inlinevirtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)=0	bpp::OrderedSequenceContainer	pure virtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0	bpp::SequenceContainer	pure virtual
setSequenceNames(const std::vector< std::string > &names, bool checkNames)=0	bpp::SequencedValuesContainer	pure virtual
toString(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
toString(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
bpp::OrderedSequenceContainer::toString(size_t sequenceIndex) const=0	bpp::OrderedSequenceContainer
valueAt(const std::string &sequenceName, size_t elementIndex)=0	bpp::OrderedSequenceContainer	pure virtual
valueAt(const std::string &sequenceName, size_t elementIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
valueAt(size_t sequenceIndex, size_t elementIndex)=0	bpp::OrderedSequenceContainer	pure virtual
valueAt(size_t sequenceIndex, size_t elementIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
~AbstractSequenceContainer()	bpp::AbstractSequenceContainer	inlinevirtual
~AbstractValuesContainer()	bpp::AbstractValuesContainer	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inlinevirtual
~OrderedValuesContainer()	bpp::OrderedValuesContainer	inlinevirtual
~SequenceContainer()	bpp::SequenceContainer	inlinevirtual