bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > Member List

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

addSequence(const HashType &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
addSite(std::unique_ptr< SiteType > &site, bool checkCoordinate)=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
addSite(std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate)=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
alphabet() const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
clear()=0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
clearComments()=0	bpp::Commentable	pure virtual
clone() const override=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
Commentable()	bpp::Commentable	inline
createEmptyContainer() const override=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
deleteSequence(const HashType &sequenceKey)=0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
deleteSequence(size_t sequencePosition)=0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
deleteSite(size_t sitePosition)=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
deleteSites(size_t sitePosition, size_t length) override=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
getAlphabet() const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getComments() const =0	bpp::Commentable	pure virtual
getNumberOfSequences() const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getNumberOfSites() const override=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
getSequenceComments() const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getSequenceKeys() const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getSequenceNames() const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getSequencePosition(const HashType &sequenceKey) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getSiteCoordinates() const=0	bpp::TemplateAlignmentDataInterface< HashType >	pure virtual
getStateValueAt(size_t sitePosition, const HashType &sequenceKey, int state) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
hasSequence(const HashType &sequenceKey) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
insertSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const HashType &sequenceKey)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
operator()(size_t sitePosition, const HashType &sequenceKey, int state) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
operator()(size_t sitePosition, size_t sequencePosition, int state) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
reindexSites() override=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
removeSequence(const HashType &sequenceKey)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
removeSequence(size_t sequencePosition)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
removeSite(size_t sitePosition)=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
TemplateAlignmentDataInterface< HashType >::sequence(const HashType &sequenceKey) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
TemplateAlignmentDataInterface< HashType >::sequence(size_t sequencePosition) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(const HashType &sequenceKey) const override=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(size_t sequencePosition) const override=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
sequenceKey(size_t sequencePosition) const =0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
setComments(const Comments &comments)=0	bpp::Commentable	pure virtual
setSequence(const HashType &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const HashType &sequenceKey)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
setSequenceKeys(const std::vector< HashType > &sequenceKeys)=0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
setSequenceNames(const std::vector< std::string > &names, bool updateKeys)=0	bpp::TemplateSequenceDataInterface< HashType >	pure virtual
setSite(size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true)=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
setSiteCoordinates(const Vint &vCoordinates)=0	bpp::TemplateAlignmentDataInterface< HashType >	pure virtual
site(size_t sitePosition) const override=0	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	pure virtual
TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< HashType >	inline
TemplateSequenceContainerInterface()	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	inline
TemplateSequenceDataInterface()	bpp::TemplateSequenceDataInterface< HashType >	inline
TemplateSiteContainerInterface()	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	inline
valueAt(const HashType &sequenceKey, size_t sitePosition) const=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
valueAt(const HashType &sequenceKey, size_t sitePosition)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
valueAt(size_t sequencePosition, size_t sitePosition) const=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
valueAt(size_t sequencePosition, size_t sitePosition)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< HashType >	inlinevirtual
~TemplateSequenceContainerInterface()	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	inlinevirtual
~TemplateSequenceDataInterface()	bpp::TemplateSequenceDataInterface< HashType >	inlinevirtual
~TemplateSiteContainerInterface()	bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType >	inlinevirtual