bpp::CompressedVectorSiteContainer Member List

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

AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet)	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inline
AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet, const Comments &comments)	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inline
AbstractTemplateSequenceContainer(const AbstractTemplateSequenceContainer< Sequence, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inline
AbstractTemplateSequenceContainer(const TemplateSequenceContainerInterface< Sequence, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inline
addSequence(const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence) override	bpp::CompressedVectorSiteContainer	inline
AbstractTemplateSequenceContainer< Sequence, std::string >::addSequence(const HashType &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
addSite(std::unique_ptr< Site > &site, bool checkCoordinate=false) override	bpp::CompressedVectorSiteContainer	virtual
addSite(std::unique_ptr< Site > &site, size_t sitePosition, bool checkCoordinate=false) override	bpp::CompressedVectorSiteContainer	virtual
alphabet() const override	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inlinevirtual
alphabet_	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	protected
clear() override	bpp::CompressedVectorSiteContainer	inlinevirtual
bpp::clearComments()=0	bpp::Commentable	pure virtual
bpp::SimpleCommentable::clearComments() override	bpp::SimpleCommentable	inlinevirtual
clone() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
Commentable()	bpp::Commentable	inline
comments_	bpp::SimpleCommentable	protected
CompressedVectorSiteContainer(std::vector< std::unique_ptr< Site >> &vs, std::shared_ptr< const Alphabet > &alphabet)	bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(size_t size, std::shared_ptr< const Alphabet > &alphabet)	bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const std::vector< std::string > &names, std::shared_ptr< const Alphabet > &alphabet)	bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(std::shared_ptr< const Alphabet > &alphabet)	bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const CompressedVectorSiteContainer &vsc)	bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const SiteContainerInterface &sc)	bpp::CompressedVectorSiteContainer
createEmptyContainer() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
deleteSequence(size_t sequencePosition) override	bpp::CompressedVectorSiteContainer	inlinevirtual
deleteSequence(const std::string &sequenceKey) override	bpp::CompressedVectorSiteContainer	inlinevirtual
deleteSite(size_t sitePosition) override	bpp::CompressedVectorSiteContainer	virtual
deleteSites(size_t sitePosition, size_t length) override	bpp::CompressedVectorSiteContainer	virtual
getAlphabet() const override	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inlinevirtual
bpp::getComments() const =0	bpp::Commentable	pure virtual
bpp::SimpleCommentable::getComments() const override	bpp::SimpleCommentable	inlinevirtual
getNumberOfSequences() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getNumberOfSites() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getNumberOfUniqueSites() const	bpp::CompressedVectorSiteContainer	inline
getSequenceComments() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getSequenceKeys() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getSequenceNames() const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getSequencePosition(const std::string &sequenceKey) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getSite_(size_t sitePosition)	bpp::CompressedVectorSiteContainer	inlineprotected
getSiteCoordinates() const override	bpp::CompressedVectorSiteContainer	virtual
getSiteIndex_(const Site &site)	bpp::CompressedVectorSiteContainer	protected
getStateValueAt(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
hasSequence(const std::string &name) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
index_	bpp::CompressedVectorSiteContainer	protected
insertSequence(size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey) override	bpp::CompressedVectorSiteContainer	inline
AbstractTemplateSequenceContainer< Sequence, std::string >::insertSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const HashType &sequenceKey)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
operator()(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
operator()(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
operator=(const CompressedVectorSiteContainer &vsc)	bpp::CompressedVectorSiteContainer
operator=(const SiteContainerInterface &sc)	bpp::CompressedVectorSiteContainer
AbstractTemplateSequenceContainer< Sequence, std::string >::operator=(const AbstractTemplateSequenceContainer< Sequence, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inline
AbstractTemplateSequenceContainer< Sequence, std::string >::operator=(const TemplateSequenceContainerInterface< Sequence, std::string > &sc)	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inline
bpp::SimpleCommentable::operator=(const SimpleCommentable &com)	bpp::SimpleCommentable	inline
reindexSites() override	bpp::CompressedVectorSiteContainer	virtual
removeSequence(size_t sequencePosition) override	bpp::CompressedVectorSiteContainer	inlinevirtual
removeSequence(const std::string &sequenceKey) override	bpp::CompressedVectorSiteContainer	inline
AbstractTemplateSequenceContainer< Sequence, std::string >::removeSequence(const HashType &sequenceKey)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
removeSite(size_t sitePosition) override	bpp::CompressedVectorSiteContainer	virtual
sequence(size_t sequenceIndex) const override	bpp::CompressedVectorSiteContainer	virtual
sequence(const std::string &sequenceKey) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
AbstractTemplateSequenceContainer< Sequence, std::string >::sequence(const HashType &sequenceKey) const override=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
sequenceComments_	bpp::CompressedVectorSiteContainer	protected
sequenceContainer_	bpp::CompressedVectorSiteContainer	protected
sequenceKey(size_t sequencePosition) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
sequenceNames_	bpp::CompressedVectorSiteContainer	protected
bpp::setComments(const Comments &comments)=0	bpp::Commentable	pure virtual
bpp::SimpleCommentable::setComments(const Comments &comments) override	bpp::SimpleCommentable	inlinevirtual
setSequence(size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey) override	bpp::CompressedVectorSiteContainer	inline
setSequence(size_t sequencePosition, std::unique_ptr< Sequence > &sequence) override	bpp::CompressedVectorSiteContainer	inline
setSequence(const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence) override	bpp::CompressedVectorSiteContainer	inline
AbstractTemplateSequenceContainer< Sequence, std::string >::setSequence(const HashType &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
AbstractTemplateSequenceContainer< Sequence, std::string >::setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
AbstractTemplateSequenceContainer< Sequence, std::string >::setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const HashType &sequenceKey)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
setSequenceKeys(const std::vector< std::string > &sequenceKeys) override	bpp::CompressedVectorSiteContainer	inlinevirtual
setSequenceNames(const std::vector< std::string > &names, bool updateKeys) override	bpp::CompressedVectorSiteContainer	inlinevirtual
setSite(size_t sitePosition, std::unique_ptr< Site > &site, bool checkCoordinate=true) override	bpp::CompressedVectorSiteContainer	virtual
setSiteCoordinates(const Vint &coordinates) override	bpp::CompressedVectorSiteContainer	virtual
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::CompressedVectorSiteContainer	inlinevirtual
siteContainer_	bpp::CompressedVectorSiteContainer	protected
TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< HashType >	inline
TemplateSequenceContainerInterface()	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	inline
TemplateSequenceDataInterface()	bpp::TemplateSequenceDataInterface< std::string >	inline
TemplateSiteContainerInterface()	bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >	inline
valueAt(const std::string &sequenceKey, size_t sitePosition) const override	bpp::CompressedVectorSiteContainer	inline
valueAt(const std::string &sequenceKey, size_t sitePosition) override	bpp::CompressedVectorSiteContainer	inline
valueAt(size_t sequencePosition, size_t sitePosition) const override	bpp::CompressedVectorSiteContainer	inlinevirtual
valueAt(size_t sequencePosition, size_t sitePosition) override	bpp::CompressedVectorSiteContainer	inlinevirtual
AbstractTemplateSequenceContainer< Sequence, std::string >::valueAt(const HashType &sequenceKey, size_t sitePosition) const =0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
AbstractTemplateSequenceContainer< Sequence, std::string >::valueAt(const HashType &sequenceKey, size_t sitePosition)=0	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	pure virtual
~AbstractTemplateSequenceContainer()	bpp::AbstractTemplateSequenceContainer< Sequence, std::string >	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~CompressedVectorSiteContainer()	bpp::CompressedVectorSiteContainer	inlinevirtual
~SimpleCommentable()	bpp::SimpleCommentable	inlinevirtual
~TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< HashType >	inlinevirtual
~TemplateSequenceContainerInterface()	bpp::TemplateSequenceContainerInterface< SequenceType, HashType >	inlinevirtual
~TemplateSequenceDataInterface()	bpp::TemplateSequenceDataInterface< std::string >	inlinevirtual
~TemplateSiteContainerInterface()	bpp::TemplateSiteContainerInterface< Site, Sequence, std::string >	inlinevirtual