bpp::SiteTools Member List

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

areSitesIdentical(const Site &site1, const Site &site2)	bpp::SiteTools	static
changeGapsToUnknownCharacters(SymbolList &l)	bpp::SymbolListTools	static
changeUnresolvedCharactersToGaps(SymbolList &l)	bpp::SymbolListTools	static
entropy(const Site &site, bool resolveUnknowns)	bpp::SiteTools	inlinestatic
getCounts(const SymbolList &list, std::map< int, size_t > &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, size_t > > &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const SymbolList &list, std::map< int, double > &counts, bool resolveUnknowns)	bpp::SymbolListTools	static
getCounts(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, double > > &counts, bool resolveUnknowns)	bpp::SymbolListTools	static
getFrequencies(const SymbolList &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)	bpp::SymbolListTools	static
getFrequencies(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, double > > &frequencies, bool resolveUnknowns=false)	bpp::SymbolListTools	static
getGCContent(const SymbolList &list, bool ignoreUnresolved=true, bool ignoreGap=true)	bpp::SymbolListTools	static
getNumberOfDistinctCharacters(const Site &site)	bpp::SiteTools	static
getNumberOfDistinctPositions(const SymbolList &l1, const SymbolList &l2)	bpp::SymbolListTools	static
getNumberOfPositionsWithoutGap(const SymbolList &l1, const SymbolList &l2)	bpp::SymbolListTools	static
hasGap(const Site &site)	bpp::SiteTools	static
hasSingleton(const Site &site)	bpp::SiteTools	static
hasUnknown(const Site &site)	bpp::SiteTools	static
heterozygosity(const Site &site)	bpp::SiteTools	static
isComplete(const Site &site)	bpp::SiteTools	static
isConstant(const Site &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true)	bpp::SiteTools	static
isGapOnly(const Site &site)	bpp::SiteTools	static
isGapOrUnresolvedOnly(const Site &site)	bpp::SiteTools	static
isParsimonyInformativeSite(const Site &site)	bpp::SiteTools	static
isTriplet(const Site &site)	bpp::SiteTools	static
jointEntropy(const Site &site1, const Site &site2, bool resolveUnknowns)	bpp::SiteTools	static
mutualInformation(const Site &site1, const Site &site2, bool resolveUnknowns)	bpp::SiteTools	static
SiteTools()	bpp::SiteTools	inline
SymbolListTools()	bpp::SymbolListTools	inline
variabilityFactorial(const Site &site)	bpp::SiteTools	static
variabilityShannon(const Site &site, bool resolveUnknowns)	bpp::SiteTools	static
~SiteTools()	bpp::SiteTools	inlinevirtual
~SymbolListTools()	bpp::SymbolListTools	inlinevirtual