bpp::CompressedVectorSiteContainer Member List

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