bpp::CodonSiteTools Member List

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

changeGapsToUnknownCharacters(SymbolList &l)	bpp::SymbolListTools	static
changeUnresolvedCharactersToGaps(SymbolList &l)	bpp::SymbolListTools	static
CodonSiteTools()	bpp::CodonSiteTools	inline
fixedDifferences(const Site &siteIn, const Site &siteOut, int i, int j, const GeneticCode &gCode)	bpp::CodonSiteTools	static
generateCodonSiteWithoutRareVariant(const Site &site, const GeneticCode &gCode, double freqmin)	bpp::CodonSiteTools	static
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
getNumberOfDistinctPositions(const SymbolList &l1, const SymbolList &l2)	bpp::SymbolListTools	static
getNumberOfPositionsWithoutGap(const SymbolList &l1, const SymbolList &l2)	bpp::SymbolListTools	static
hasGapOrStop(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
hasStop(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
isFourFoldDegenerated(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
isMonoSitePolymorphic(const Site &site)	bpp::CodonSiteTools	static
isSynonymousPolymorphic(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
meanNumberOfSynonymousPositions(const Site &site, const GeneticCode &gCode, double ratio=1)	bpp::CodonSiteTools	static
numberOfDifferences(int i, int j, const CodonAlphabet &ca)	bpp::CodonSiteTools	static
numberOfNonSynonymousSubstitutions(const Site &site, const GeneticCode &gCode, double freqmin=0.)	bpp::CodonSiteTools	static
numberOfSubsitutions(const Site &site, const GeneticCode &gCode, double freqmin=0.)	bpp::CodonSiteTools	static
numberOfSynonymousDifferences(int i, int j, const GeneticCode &gCode, bool minchange=false)	bpp::CodonSiteTools	static
numberOfSynonymousPositions(int i, const GeneticCode &gCode, double ratio=1.0)	bpp::CodonSiteTools	static
piNonSynonymous(const Site &site, const GeneticCode &gCode, bool minchange=false)	bpp::CodonSiteTools	static
piSynonymous(const Site &site, const GeneticCode &gCode, bool minchange=false)	bpp::CodonSiteTools	static
SymbolListTools()	bpp::SymbolListTools	inline
~CodonSiteTools()	bpp::CodonSiteTools	inlinevirtual
~SymbolListTools()	bpp::SymbolListTools	inlinevirtual