bpp::CodonSiteTools Member List

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

areSymbolListsIdentical(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2)	bpp::SymbolListTools	static
areSymbolListsIdentical(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2)	bpp::SymbolListTools	static
areSymbolListsIdentical(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2)	bpp::SymbolListTools	inlinestatic
changeGapsToUnknownCharacters(IntSymbolListInterface &l)	bpp::SymbolListTools	static
changeGapsToUnknownCharacters(ProbabilisticSymbolListInterface &l)	bpp::SymbolListTools	static
changeGapsToUnknownCharacters(CruxSymbolListInterface &l)	bpp::SymbolListTools	inlinestatic
changeUnresolvedCharactersToGaps(IntSymbolListInterface &l)	bpp::SymbolListTools	static
changeUnresolvedCharactersToGaps(ProbabilisticSymbolListInterface &l)	bpp::SymbolListTools	static
changeUnresolvedCharactersToGaps(CruxSymbolListInterface &l)	bpp::SymbolListTools	inlinestatic
CodonSiteTools()	bpp::CodonSiteTools	inline
entropy(const CruxSymbolListInterface &list, bool resolveUnknowns)	bpp::SymbolListTools	inlinestatic
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 IntSymbolListInterface &list, std::map< int, count_type > &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const ProbabilisticSymbolListInterface &list, std::map< int, double_t > &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const CruxSymbolListInterface &list, std::map< int, double > &counts, bool resolveUnknowns=false)	bpp::SymbolListTools	inlinestatic
getCounts(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2, std::map< int, std::map< int, count_type >> &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts, bool resolveUnknowns)	bpp::SymbolListTools	inlinestatic
getCountsResolveUnknowns(const IntSymbolListInterface &list, std::map< int, double > &counts)	bpp::SymbolListTools	inlinestatic
getCountsResolveUnknowns(const ProbabilisticSymbolListInterface &list, std::map< int, double > &counts)	bpp::SymbolListTools	inlinestatic
getCountsResolveUnknowns(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts)	bpp::SymbolListTools	static
getCountsResolveUnknowns(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts)	bpp::SymbolListTools	static
getFrequencies(const CruxSymbolListInterface &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)	bpp::SymbolListTools	static
getFrequencies(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, std::map< int, std::map< int, double >> &frequencies, bool resolveUnknowns=false)	bpp::SymbolListTools	static
getGCContent(const IntSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true)	bpp::SymbolListTools	static
getGCContent(const ProbabilisticSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true)	bpp::SymbolListTools	static
getGCContent(const CruxSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true)	bpp::SymbolListTools	inlinestatic
getMajorAllele(const CruxSymbolListInterface &list)	bpp::SymbolListTools	static
getMajorAlleleFrequency(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
getMinorAllele(const CruxSymbolListInterface &list)	bpp::SymbolListTools	static
getMinorAlleleFrequency(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
getNumberOfDistinctCharacters(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
getNumberOfDistinctPositions(const IntSymbolListInterface &l1, const IntSymbolListInterface &l2)	bpp::SymbolListTools	static
getNumberOfDistinctPositions(const ProbabilisticSymbolListInterface &l1, const ProbabilisticSymbolListInterface &l2)	bpp::SymbolListTools	static
getNumberOfDistinctPositions(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2)	bpp::SymbolListTools	inlinestatic
getNumberOfPositionsWithoutGap(const IntSymbolListInterface &l1, const IntSymbolListInterface &l2)	bpp::SymbolListTools	static
getNumberOfPositionsWithoutGap(const ProbabilisticSymbolListInterface &l1, const ProbabilisticSymbolListInterface &l2)	bpp::SymbolListTools	static
getNumberOfPositionsWithoutGap(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2)	bpp::SymbolListTools	inlinestatic
hasGap(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
hasGap(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
hasGap(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
hasGapOrStop(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
hasSingleton(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
hasStop(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
hasUnknown(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
hasUnknown(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
hasUnknown(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
hasUnresolved(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
heterozygosity(const CruxSymbolListInterface &list)	bpp::SymbolListTools	static
isComplete(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
isComplete(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
isComplete(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
isConstant(const IntSymbolListInterface &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true)	bpp::SymbolListTools	static
isConstant(const ProbabilisticSymbolListInterface &site, bool unresolvedRaisesException=true)	bpp::SymbolListTools	static
isConstant(const CruxSymbolListInterface &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true)	bpp::SymbolListTools	inlinestatic
isDoubleton(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
isFourFoldDegenerated(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
isGapOnly(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
isGapOnly(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
isGapOnly(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
isGapOrUnresolvedOnly(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
isGapOrUnresolvedOnly(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
isGapOrUnresolvedOnly(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
isMonoSitePolymorphic(const Site &site)	bpp::CodonSiteTools	static
isParsimonyInformativeSite(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
isSynonymousPolymorphic(const Site &site, const GeneticCode &gCode)	bpp::CodonSiteTools	static
isTriplet(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
jointEntropy(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, bool resolveUnknowns)	bpp::SymbolListTools	static
meanNumberOfSynonymousPositions(const Site &site, const GeneticCode &gCode, double ratio=1)	bpp::CodonSiteTools	static
mutualInformation(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, bool resolveUnknowns)	bpp::SymbolListTools	static
numberOfDifferences(int i, int j, const CodonAlphabet &ca)	bpp::CodonSiteTools	static
numberOfGaps(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
numberOfGaps(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
numberOfGaps(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
numberOfNonSynonymousSubstitutions(const Site &site, const GeneticCode &gCode, double freqmin=0.)	bpp::CodonSiteTools	static
numberOfSubstitutions(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
numberOfUnresolved(const IntSymbolListInterface &site)	bpp::SymbolListTools	static
numberOfUnresolved(const ProbabilisticSymbolListInterface &site)	bpp::SymbolListTools	static
numberOfUnresolved(const CruxSymbolListInterface &site)	bpp::SymbolListTools	inlinestatic
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
variabilityFactorial(const IntSymbolListInterface &list)	bpp::SymbolListTools	static
variabilityShannon(const CruxSymbolListInterface &list, bool resolveUnknowns)	bpp::SymbolListTools	static
~CodonSiteTools()	bpp::CodonSiteTools	inlinevirtual
~SymbolListTools()	bpp::SymbolListTools	inlinevirtual