bpp::VectorSiteContainer Member List

This is the complete list of members for bpp::VectorSiteContainer, 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
addSequence(const Sequence &sequence, bool checkName=true)	bpp::VectorSiteContainer	virtual
addSequence(const Sequence &sequence, size_t sequenceIndex, bool checkName=true)	bpp::VectorSiteContainer
addSite(const Site &site, bool checkPosition=true)	bpp::VectorSiteContainer	virtual
addSite(const Site &site, int position, bool checkPosition=true)	bpp::VectorSiteContainer	virtual
addSite(const Site &site, size_t siteIndex, bool checkPosition=true)	bpp::VectorSiteContainer	virtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition=true)	bpp::VectorSiteContainer	virtual
clear()	bpp::VectorSiteContainer	virtual
clone() const	bpp::VectorSiteContainer	inlinevirtual
comments_	bpp::VectorSiteContainer	protected
createEmptyContainer() const	bpp::VectorSiteContainer	virtual
deleteGeneralComments()	bpp::AbstractSequenceContainer	inlinevirtual
deleteSequence(size_t sequenceIndex)	bpp::VectorSiteContainer	virtual
deleteSequence(const std::string &name)	bpp::VectorSiteContainer	virtual
deleteSite(size_t siteIndex)	bpp::VectorSiteContainer	virtual
deleteSites(size_t siteIndex, size_t length)	bpp::VectorSiteContainer	virtual
getAlphabet() const	bpp::AbstractSequenceContainer	inlinevirtual
getComments(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
getComments(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
getContent(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
getContent(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
getGeneralComments() const	bpp::AbstractSequenceContainer	inlinevirtual
getName(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
getNumberOfSequences() const	bpp::VectorSiteContainer	inlinevirtual
getNumberOfSites() const	bpp::VectorSiteContainer	virtual
getSequence(size_t sequenceIndex) const	bpp::VectorSiteContainer	virtual
getSequence(const std::string &name) const	bpp::VectorSiteContainer	virtual
getSequencePosition(const std::string &name) const	bpp::VectorSiteContainer	virtual
getSequencesNames() const	bpp::VectorSiteContainer	virtual
getSite(size_t siteIndex) const	bpp::VectorSiteContainer	virtual
getSitePositions() const	bpp::VectorSiteContainer	virtual
hasSequence(const std::string &name) const	bpp::VectorSiteContainer	virtual
names_	bpp::VectorSiteContainer	protected
operator()(const std::string &sequenceName, size_t elementIndex)	bpp::VectorSiteContainer	inlinevirtual
operator()(const std::string &sequenceName, size_t elementIndex) const	bpp::VectorSiteContainer	inlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex)	bpp::VectorSiteContainer	inlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex) const	bpp::VectorSiteContainer	inlinevirtual
operator=(const VectorSiteContainer &vsc)	bpp::VectorSiteContainer
operator=(const SiteContainer &sc)	bpp::VectorSiteContainer
operator=(const OrderedSequenceContainer &osc)	bpp::VectorSiteContainer
operator=(const SequenceContainer &sc)	bpp::VectorSiteContainer
bpp::AbstractSequenceContainer::operator=(const AbstractSequenceContainer &sc)	bpp::AbstractSequenceContainer	inline
OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inline
realloc(size_t n)	bpp::VectorSiteContainer	protected
reindexSites()	bpp::VectorSiteContainer	virtual
removeSequence(size_t sequenceIndex)	bpp::VectorSiteContainer	virtual
removeSequence(const std::string &name)	bpp::VectorSiteContainer	virtual
removeSite(size_t siteIndex)	bpp::VectorSiteContainer	virtual
SequenceContainer()	bpp::SequenceContainer	inline
sequences_	bpp::VectorSiteContainer	mutableprotected
setComments(size_t sequenceIndex, const Comments &comments)	bpp::VectorSiteContainer	virtual
bpp::AbstractSequenceContainer::setComments(const std::string &name, const Comments &comments)	bpp::AbstractSequenceContainer	virtual
setGeneralComments(const Comments &comments)	bpp::AbstractSequenceContainer	inlinevirtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName)	bpp::VectorSiteContainer	virtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)	bpp::VectorSiteContainer	virtual
setSequencesNames(const std::vector< std::string > &names, bool checkNames=true)	bpp::VectorSiteContainer	virtual
setSite(size_t siteIndex, const Site &site, bool checkPosition=true)	bpp::VectorSiteContainer	virtual
SiteContainer()	bpp::SiteContainer	inline
sites_	bpp::VectorSiteContainer	protected
toString(const std::string &name) const	bpp::AbstractSequenceContainer	inlinevirtual
toString(size_t sequenceIndex) const	bpp::AbstractSequenceContainer	inlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex)	bpp::VectorSiteContainer	inlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex) const	bpp::VectorSiteContainer	inlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex)	bpp::VectorSiteContainer	inlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex) const	bpp::VectorSiteContainer	inlinevirtual
VectorSiteContainer(const std::vector< const Site *> &vs, const Alphabet *alpha, bool checkPositions=true)	bpp::VectorSiteContainer
VectorSiteContainer(size_t size, const Alphabet *alpha)	bpp::VectorSiteContainer
VectorSiteContainer(const std::vector< std::string > &names, const Alphabet *alpha)	bpp::VectorSiteContainer
VectorSiteContainer(const Alphabet *alpha)	bpp::VectorSiteContainer
VectorSiteContainer(const VectorSiteContainer &vsc)	bpp::VectorSiteContainer
VectorSiteContainer(const SiteContainer &sc)	bpp::VectorSiteContainer
VectorSiteContainer(const OrderedSequenceContainer &osc)	bpp::VectorSiteContainer
VectorSiteContainer(const SequenceContainer &sc)	bpp::VectorSiteContainer
~AbstractSequenceContainer()	bpp::AbstractSequenceContainer	inlinevirtual
~OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inlinevirtual
~SequenceContainer()	bpp::SequenceContainer	inlinevirtual
~SiteContainer()	bpp::SiteContainer	inlinevirtual
~VectorSiteContainer()	bpp::VectorSiteContainer	inlinevirtual