bpp::SiteContainer Member List

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

addSequence(const Sequence &sequence, bool checkName)=0	bpp::SequenceContainer	pure virtual
addSite(const Site &site, bool checkPosition)=0	bpp::SiteContainer	pure virtual
addSite(const Site &site, int position, bool checkPosition)=0	bpp::SiteContainer	pure virtual
addSite(const Site &site, size_t siteIndex, bool checkPosition)=0	bpp::SiteContainer	pure virtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition)=0	bpp::SiteContainer	pure virtual
AlignedValuesContainer()	bpp::AlignedValuesContainer	inline
clear()=0	bpp::SequencedValuesContainer	pure virtual
clone() const =0	bpp::SiteContainer	pure virtual
createEmptyContainer() const =0	bpp::SequencedValuesContainer	pure virtual
deleteGeneralComments()=0	bpp::SequencedValuesContainer	pure virtual
deleteSite(size_t siteIndex)=0	bpp::SiteContainer	pure virtual
deleteSites(size_t siteIndex, size_t length)=0	bpp::AlignedValuesContainer	pure virtual
getAlphabet() const =0	bpp::SequencedValuesContainer	pure virtual
getComments(size_t sequenceIndex) const=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::getComments(const std::string &name) const =0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::getComments(size_t sequenceIndex) const =0	bpp::OrderedValuesContainer	pure virtual
getGeneralComments() const =0	bpp::SequencedValuesContainer	pure virtual
getName(size_t sequenceIndex) const =0	bpp::OrderedValuesContainer	pure virtual
getNumberOfSequences() const =0	bpp::SequencedValuesContainer	pure virtual
getNumberOfSites() const =0	bpp::AlignedValuesContainer	pure virtual
getSequence(size_t sequenceIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
getSequence(const std::string &name) const=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::getSequence(const std::string &name) const =0	bpp::SequenceContainer	pure virtual
getSequenceNames() const =0	bpp::SequencedValuesContainer	pure virtual
getSequencePosition(const std::string &name) const =0	bpp::OrderedValuesContainer	pure virtual
getSite(size_t siteIndex) const =0	bpp::SiteContainer	pure virtual
getSite(size_t siteIndex)=0	bpp::SiteContainer	pure virtual
getSitePositions() const =0	bpp::AlignedValuesContainer	pure virtual
bpp::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const =0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const =0	bpp::OrderedValuesContainer	pure virtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0	bpp::OrderedValuesContainer
getSymbolListSite(size_t siteIndex) const =0	bpp::SiteContainer	pure virtual
getSymbolListSite(size_t siteIndex)=0	bpp::SiteContainer	pure virtual
hasSequence(const std::string &name) const =0	bpp::SequencedValuesContainer	pure virtual
operator()(size_t sequenceIndex, size_t elementIndex)=0	bpp::OrderedSequenceContainer	pure virtual
operator()(size_t sequenceIndex, size_t elementIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
bpp::SequenceContainer::operator()(const std::string &sequenceName, size_t elementIndex)=0	bpp::SequenceContainer	pure virtual
bpp::SequenceContainer::operator()(const std::string &sequenceName, size_t elementIndex) const =0	bpp::SequenceContainer	pure virtual
bpp::SequencedValuesContainer::operator()(size_t siteIndex, const std::string &sequenceName, int state) const =0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::operator()(size_t siteIndex, size_t sequenceIndex, int state) const =0	bpp::OrderedValuesContainer	pure virtual
OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inline
OrderedValuesContainer()	bpp::OrderedValuesContainer	inline
reindexSites()=0	bpp::AlignedValuesContainer	pure virtual
removeSequence(size_t sequenceIndex)=0	bpp::OrderedSequenceContainer	pure virtual
removeSequence(const std::string &name)=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::removeSequence(const std::string &name)=0	bpp::SequenceContainer	pure virtual
removeSite(size_t siteIndex)=0	bpp::SiteContainer	pure virtual
SequenceContainer()	bpp::SequenceContainer	inline
setComments(size_t sequenceIndex, const Comments &comments)=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::setComments(const std::string &name, const Comments &comments)=0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::setComments(size_t sequenceIndex, const Comments &comments)=0	bpp::OrderedValuesContainer	pure virtual
setGeneralComments(const Comments &comments)=0	bpp::SequencedValuesContainer	pure virtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)=0	bpp::OrderedSequenceContainer	pure virtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0	bpp::SequenceContainer	pure virtual
setSequenceNames(const std::vector< std::string > &names, bool checkNames)=0	bpp::SequencedValuesContainer	pure virtual
setSite(size_t siteIndex, const Site &site, bool checkPosition=true)=0	bpp::SiteContainer	pure virtual
setSitePositions(Vint vPositions)=0	bpp::AlignedValuesContainer	pure virtual
SiteContainer()	bpp::SiteContainer	inline
toString(size_t sequenceIndex) const=0	bpp::OrderedSequenceContainer
bpp::SequenceContainer::toString(const std::string &name) const =0	bpp::SequencedValuesContainer	pure virtual
bpp::OrderedValuesContainer::toString(size_t sequenceIndex) const =0	bpp::OrderedValuesContainer	pure virtual
valueAt(const std::string &sequenceName, size_t elementIndex)=0	bpp::OrderedSequenceContainer	pure virtual
valueAt(const std::string &sequenceName, size_t elementIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
valueAt(size_t sequenceIndex, size_t elementIndex)=0	bpp::OrderedSequenceContainer	pure virtual
valueAt(size_t sequenceIndex, size_t elementIndex) const =0	bpp::OrderedSequenceContainer	pure virtual
~AlignedValuesContainer()	bpp::AlignedValuesContainer	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~OrderedSequenceContainer()	bpp::OrderedSequenceContainer	inlinevirtual
~OrderedValuesContainer()	bpp::OrderedValuesContainer	inlinevirtual
~SequenceContainer()	bpp::SequenceContainer	inlinevirtual
~SiteContainer()	bpp::SiteContainer	inlinevirtual