bpp::PolymorphismSequenceContainer Member List

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

AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet)	AbstractTemplateSequenceContainer< SequenceType, std::string >
AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet, const Comments &comments)	AbstractTemplateSequenceContainer< SequenceType, std::string >
AbstractTemplateSequenceContainer(const AbstractTemplateSequenceContainer< SequenceType, std::string > &sc)	AbstractTemplateSequenceContainer< SequenceType, std::string >
AbstractTemplateSequenceContainer(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	AbstractTemplateSequenceContainer< SequenceType, std::string >
addSequence(const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence) override	bpp::PolymorphismSequenceContainer	inline
bpp::TemplateVectorSiteContainer::addSequence(const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequence) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
addSequenceWithFrequency(const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence, unsigned int frequency)	bpp::PolymorphismSequenceContainer	inline
addSite(std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
addSite(std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate=true) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
addSite(std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
addSite(std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate=true) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
alphabet() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
alphabet_	bpp::TemplateVectorSiteContainer< class, class >	protected
clear() override	bpp::PolymorphismSequenceContainer	inlinevirtual
clearComments()=0	bpp::TemplateVectorSiteContainer< class, class >	pure virtual
clearComments() override	bpp::TemplateVectorSiteContainer< class, class >	virtual
clone() const override	bpp::PolymorphismSequenceContainer	inlinevirtual
Commentable()	bpp::Commentable
comments_	bpp::TemplateVectorSiteContainer< class, class >	protected
count_	bpp::PolymorphismSequenceContainer	private
createEmptyContainer() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
createEmptyContainer() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
decrementSequenceCount(size_t index)	bpp::PolymorphismSequenceContainer
decrementSequenceCount(const std::string &name)	bpp::PolymorphismSequenceContainer
deleteSequence(size_t sequencePosition) override	bpp::PolymorphismSequenceContainer	virtual
deleteSequence(const std::string &sequenceKey) override	bpp::PolymorphismSequenceContainer	virtual
deleteSite(size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
deleteSite(size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
deleteSites(size_t sitePosition, size_t length) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
deleteSites(size_t sitePosition, size_t length) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getAllGroupsIds() const	bpp::PolymorphismSequenceContainer
getAlphabet() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getComments() const=0	bpp::TemplateVectorSiteContainer< class, class >	pure virtual
getComments() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getGroupId(size_t index) const	bpp::PolymorphismSequenceContainer	inline
getGroupId(const std::string &name) const	bpp::PolymorphismSequenceContainer	inline
getNumberOfGroups() const	bpp::PolymorphismSequenceContainer	inline
getNumberOfSequences() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getNumberOfSequences() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getNumberOfSites() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getNumberOfSites() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequenceComments() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequenceComments() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequenceCount(size_t index) const	bpp::PolymorphismSequenceContainer
getSequenceCount(const std::string &name) const	bpp::PolymorphismSequenceContainer
getSequenceKeys() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequenceKeys() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequenceNames() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequenceNames() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequencePosition(const std::string &sequenceKey) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSequencePosition(const std::string &sequenceKey) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSiteCoordinates() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getSiteCoordinates() const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getStateValueAt(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getStateValueAt(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
group_	bpp::PolymorphismSequenceContainer	private
hasOutgroup() const	bpp::PolymorphismSequenceContainer
hasSequence(const std::string &sequenceKey) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
hasSequence(const std::string &sequenceKey) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
incrementSequenceCount(size_t index)	bpp::PolymorphismSequenceContainer
incrementSequenceCount(const std::string &name)	bpp::PolymorphismSequenceContainer
ingroup_	bpp::PolymorphismSequenceContainer	private
insertSequence(size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey) override	bpp::PolymorphismSequenceContainer	inline
bpp::TemplateVectorSiteContainer::insertSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequence, const std::string &sequenceKey) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
insertSequenceWithFrequency(size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey, unsigned int frequency)	bpp::PolymorphismSequenceContainer	inline
isIngroupMember(size_t index) const	bpp::PolymorphismSequenceContainer	inline
isIngroupMember(const std::string &name) const	bpp::PolymorphismSequenceContainer	inline
operator()(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
operator()(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
operator()(size_t sitePosition, const std::string &sequenceKey, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
operator()(size_t sitePosition, size_t sequencePosition, int state) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
operator=(const PolymorphismSequenceContainer &psc)	bpp::PolymorphismSequenceContainer
bpp::TemplateVectorSiteContainer::operator=(const TemplateVectorSiteContainer< SiteType, SequenceType > &vsc)	bpp::TemplateVectorSiteContainer< class, class >
bpp::TemplateVectorSiteContainer::operator=(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)	bpp::TemplateVectorSiteContainer< class, class >
bpp::TemplateVectorSiteContainer::operator=(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	bpp::TemplateVectorSiteContainer< class, class >
AbstractTemplateSequenceContainer< SequenceType, std::string >::operator=(const AbstractTemplateSequenceContainer< SequenceType, std::string > &sc)	AbstractTemplateSequenceContainer< SequenceType, std::string >
bpp::SimpleCommentable::operator=(const SimpleCommentable &com)	bpp::SimpleCommentable
PolymorphismSequenceContainer(std::shared_ptr< const Alphabet > alpha)	bpp::PolymorphismSequenceContainer	inline
PolymorphismSequenceContainer(size_t size, std::shared_ptr< const Alphabet > alpha)	bpp::PolymorphismSequenceContainer	inline
PolymorphismSequenceContainer(const std::vector< std::string > &names, std::shared_ptr< const Alphabet > alpha)	bpp::PolymorphismSequenceContainer	inline
PolymorphismSequenceContainer(const SequenceContainerInterface &sc)	bpp::PolymorphismSequenceContainer	inline
PolymorphismSequenceContainer(const SequenceContainerInterface &sc, bool count)	bpp::PolymorphismSequenceContainer
PolymorphismSequenceContainer(const PolymorphismSequenceContainer &psc)	bpp::PolymorphismSequenceContainer
realloc_(size_t n)	bpp::TemplateVectorSiteContainer< class, class >	protected
reindexSites() override	bpp::TemplateVectorSiteContainer< class, class >	virtual
reindexSites() override	bpp::TemplateVectorSiteContainer< class, class >	virtual
removeSequence(size_t sequencePosition) override	bpp::PolymorphismSequenceContainer	virtual
removeSequence(const std::string &sequenceKey) override	bpp::PolymorphismSequenceContainer	virtual
removeSite(size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
removeSite(size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequence(const std::string &sequenceKey) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequence(size_t sequencePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequence(const std::string &sequenceKey) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequence(size_t sequencePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequenceComments_	bpp::TemplateVectorSiteContainer< class, class >	protected
sequenceContainer_	bpp::TemplateVectorSiteContainer< class, class >	protected
sequenceKey(size_t sequencePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequenceKey(size_t sequencePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
sequenceNames_	bpp::TemplateVectorSiteContainer< class, class >	protected
setAsIngroupMember(size_t index)	bpp::PolymorphismSequenceContainer
setAsIngroupMember(const std::string &name)	bpp::PolymorphismSequenceContainer
setAsOutgroupMember(size_t index)	bpp::PolymorphismSequenceContainer
setAsOutgroupMember(const std::string &name)	bpp::PolymorphismSequenceContainer
setComments(const Comments &comments)=0	bpp::TemplateVectorSiteContainer< class, class >	pure virtual
setComments(const Comments &comments) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setGroupId(size_t index, size_t group_id)	bpp::PolymorphismSequenceContainer	inline
setGroupId(const std::string &name, size_t group_id)	bpp::PolymorphismSequenceContainer	inline
setSequence(const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequence) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequence) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequence, const std::string &sequenceKey) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequence(const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequence) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequence) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequence, const std::string &sequenceKey) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequenceCount(size_t index, unsigned int count)	bpp::PolymorphismSequenceContainer
setSequenceCount(const std::string &name, unsigned int count)	bpp::PolymorphismSequenceContainer
setSequenceKeys(const std::vector< std::string > &sequenceKeys) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequenceKeys(const std::vector< std::string > &sequenceKeys) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequenceNames(const std::vector< std::string > &names, bool updateKeys) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSequenceNames(const std::vector< std::string > &names, bool updateKeys) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSite(size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSite(size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSiteCoordinates(const Vint &vCoordinates) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
setSiteCoordinates(const Vint &vCoordinates) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
SimpleCommentable()	bpp::SimpleCommentable
SimpleCommentable(const Comments &comments)	bpp::SimpleCommentable
SimpleCommentable(const SimpleCommentable &com)	bpp::SimpleCommentable
site(size_t sitePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
site(size_t sitePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
site_(size_t sitePosition)	bpp::TemplateVectorSiteContainer< class, class >	protected
siteContainer_	bpp::TemplateVectorSiteContainer< class, class >	protected
TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< class >
TemplateSequenceContainerInterface()	TemplateSequenceContainerInterface< SequenceType, std::string >
TemplateSequenceDataInterface()	TemplateSequenceDataInterface< std::string >
TemplateSiteContainerInterface()	TemplateSiteContainerInterface< SiteType, SequenceType, std::string >
TemplateVectorSiteContainer(std::vector< std::unique_ptr< SiteType >> &vs, std::shared_ptr< const Alphabet > alphabet, bool checkPositions=true)	bpp::TemplateVectorSiteContainer< class, class >
TemplateVectorSiteContainer(size_t size, std::shared_ptr< const Alphabet > alphabet)	bpp::TemplateVectorSiteContainer< class, class >
TemplateVectorSiteContainer(const std::vector< std::string > &sequenceKeys, std::shared_ptr< const Alphabet > alphabet, bool useKeysAsNames=true)	bpp::TemplateVectorSiteContainer< class, class >
TemplateVectorSiteContainer(std::shared_ptr< const Alphabet > alphabet)	bpp::TemplateVectorSiteContainer< class, class >
TemplateVectorSiteContainer(const TemplateVectorSiteContainer< SiteType, SequenceType > &vsc)	bpp::TemplateVectorSiteContainer< class, class >
TemplateVectorSiteContainer(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sc)	bpp::TemplateVectorSiteContainer< class, class >
TemplateVectorSiteContainer(const TemplateSequenceContainerInterface< SequenceType, std::string > &sc)	bpp::TemplateVectorSiteContainer< class, class >
toSiteContainer() const	bpp::PolymorphismSequenceContainer
valueAt(const std::string &sequenceKey, size_t sitePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(const std::string &sequenceKey, size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(size_t sequencePosition, size_t sitePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(size_t sequencePosition, size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(const std::string &sequenceKey, size_t sitePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(const std::string &sequenceKey, size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(size_t sequencePosition, size_t sitePosition) const override	bpp::TemplateVectorSiteContainer< class, class >	virtual
valueAt(size_t sequencePosition, size_t sitePosition) override	bpp::TemplateVectorSiteContainer< class, class >	virtual
~AbstractTemplateSequenceContainer()	AbstractTemplateSequenceContainer< SequenceType, std::string >	virtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	virtual
~PolymorphismSequenceContainer()	bpp::PolymorphismSequenceContainer	virtual
~SimpleCommentable()	bpp::SimpleCommentable	virtual
~TemplateAlignmentDataInterface()	bpp::TemplateAlignmentDataInterface< class >	virtual
~TemplateSequenceContainerInterface()	TemplateSequenceContainerInterface< SequenceType, std::string >	virtual
~TemplateSequenceDataInterface()	TemplateSequenceDataInterface< std::string >	virtual
~TemplateSiteContainerInterface()	TemplateSiteContainerInterface< SiteType, SequenceType, std::string >	virtual
~TemplateVectorSiteContainer()	bpp::TemplateVectorSiteContainer< class, class >	virtual