bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > Member List

This is the complete list of members for bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >, including all inherited members.

AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet)	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inline
AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet, const Comments &comments)	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inline
AbstractTemplateSequenceContainer(const AbstractTemplateSequenceContainer< SequenceType, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inline
AbstractTemplateSequenceContainer(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inline
addSequence(const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
bpp::TemplateVectorSequenceContainer::addSequence(std::unique_ptr< SequenceType > &sequencePtr)	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
addSite(std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
addSite(std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate=true) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
alphabet() const override	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inlinevirtual
alphabet_	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	protected
checkSize_(const Sequence &sequenceRef)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlineprotected
clear() override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
TemplateSequenceContainerInterface< SequenceType, std::clearComments()=0	bpp::Commentable	pure virtual
bpp::SimpleCommentable::clearComments() override	bpp::SimpleCommentable	inlinevirtual
clone() const override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
Commentable()	bpp::Commentable	inline
comments_	bpp::SimpleCommentable	protected
coordinates_	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	private
createEmptyContainer() const override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
deleteSequence(const std::string &sequenceKey) override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
deleteSequence(size_t sequencePosition) override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
deleteSite(size_t sitePosition) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
deleteSites(size_t sitePosition, size_t length) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
getAlphabet() const override	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inlinevirtual
TemplateSequenceContainerInterface< SequenceType, std::getComments() const =0	bpp::Commentable	pure virtual
bpp::SimpleCommentable::getComments() const override	bpp::SimpleCommentable	inlinevirtual
getNumberOfSequences() const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
getNumberOfSites() const override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
getSequenceComments() const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
getSequenceKeys() const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
getSequenceNames() const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
getSequencePosition(const std::string &sequenceKey) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
getSiteCoordinates() const override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
getStateValueAt(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
hasSequence(const std::string &sequenceKey) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
insertSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const std::string &sequenceKey) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
length_	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	private
operator()(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
operator()(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
operator=(const TemplateAlignedSequenceContainer< SequenceType, SiteType > &asc)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
operator=(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
operator=(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
bpp::TemplateVectorSequenceContainer::operator=(const TemplateVectorSequenceContainer &vsc)	bpp::TemplateVectorSequenceContainer< SequenceType >	inline
AbstractTemplateSequenceContainer< SequenceType, std::string >::operator=(const AbstractTemplateSequenceContainer< SequenceType, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inline
bpp::SimpleCommentable::operator=(const SimpleCommentable &com)	bpp::SimpleCommentable	inline
reindexSites() override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
removeSequence(const std::string &sequenceKey) override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
removeSequence(size_t sequencePosition) override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
removeSite(size_t sitePosition) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
sequence(const std::string &sequenceKey) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
sequence(size_t sequencePosition) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
sequence_(size_t sequencePosition)	bpp::TemplateVectorSequenceContainer< SequenceType >	inlineprotectedvirtual
sequence_(const std::string &sequenceKey)	bpp::TemplateVectorSequenceContainer< SequenceType >	inlineprotectedvirtual
sequenceKey(size_t sequencePosition) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
sequenceVectorMap_	bpp::TemplateVectorSequenceContainer< SequenceType >	protected
TemplateSequenceContainerInterface< SequenceType, std::setComments(const Comments &comments)=0	bpp::Commentable	pure virtual
bpp::SimpleCommentable::setComments(const Comments &comments) override	bpp::SimpleCommentable	inlinevirtual
setSequence(const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const std::string &sequenceKey) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
setSequenceKeys(const std::vector< std::string > &sequenceKeys) override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
setSequenceNames(const std::vector< std::string > &names, bool updateKeys) override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
setSite(size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
setSiteCoordinates(const Vint &vCoordinates) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
SimpleCommentable()	bpp::SimpleCommentable	inline
SimpleCommentable(const Comments &comments)	bpp::SimpleCommentable	inline
SimpleCommentable(const SimpleCommentable &com)	bpp::SimpleCommentable	inline
site(size_t sitePosition) const override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
siteVector_	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	private
TemplateAlignedSequenceContainer(std::shared_ptr< const Alphabet > alphabet, std::vector< std::unique_ptr< Sequence >> vs)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
TemplateAlignedSequenceContainer(std::shared_ptr< const Alphabet > alphabet)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
TemplateAlignedSequenceContainer(const TemplateAlignedSequenceContainer< SequenceType, SiteType > &asc)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
TemplateAlignedSequenceContainer(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
TemplateAlignedSequenceContainer(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inline
TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< HashType >	inline
TemplateSequenceContainerInterface()	bpp::TemplateSequenceContainerInterface< SequenceType, std::string >	inline
TemplateSequenceDataInterface()	bpp::TemplateSequenceDataInterface< std::string >	inline
TemplateSiteContainerInterface()	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >	inline
TemplateVectorSequenceContainer(std::shared_ptr< const Alphabet > alphabet, std::vector< std::unique_ptr< SequenceType >> &vs)	bpp::TemplateVectorSequenceContainer< SequenceType >	inline
TemplateVectorSequenceContainer(std::shared_ptr< const Alphabet > alphabet)	bpp::TemplateVectorSequenceContainer< SequenceType >	inline
TemplateVectorSequenceContainer(const TemplateVectorSequenceContainer< SequenceType > &vsc)	bpp::TemplateVectorSequenceContainer< SequenceType >	inline
TemplateVectorSequenceContainer(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	bpp::TemplateVectorSequenceContainer< SequenceType >	inline
valueAt(const std::string &sequenceKey, size_t sitePosition) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
valueAt(const size_t sequencePosition, size_t sitePosition) override	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
bpp::TemplateVectorSequenceContainer::valueAt(const std::string &sequenceKey, size_t elementPosition) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
bpp::TemplateVectorSequenceContainer::valueAt(size_t sequencePosition, size_t elementPosition) const override	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual
~AbstractTemplateSequenceContainer()	bpp::AbstractTemplateSequenceContainer< SequenceType, std::string >	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~SimpleCommentable()	bpp::SimpleCommentable	inlinevirtual
~TemplateAlignedSequenceContainer()	bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >	inlinevirtual
~TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< HashType >	inlinevirtual
~TemplateSequenceContainerInterface()	bpp::TemplateSequenceContainerInterface< SequenceType, std::string >	inlinevirtual
~TemplateSequenceDataInterface()	bpp::TemplateSequenceDataInterface< std::string >	inlinevirtual
~TemplateSiteContainerInterface()	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, std::string >	inlinevirtual
~TemplateVectorSequenceContainer()	bpp::TemplateVectorSequenceContainer< SequenceType >	inlinevirtual