bpp-seq3  3.0.0
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::SymbolListToolsstatic
areSymbolListsIdentical(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2)bpp::SymbolListToolsstatic
areSymbolListsIdentical(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2)bpp::SymbolListToolsinlinestatic
changeGapsToUnknownCharacters(IntSymbolListInterface &l)bpp::SymbolListToolsstatic
changeGapsToUnknownCharacters(ProbabilisticSymbolListInterface &l)bpp::SymbolListToolsstatic
changeGapsToUnknownCharacters(CruxSymbolListInterface &l)bpp::SymbolListToolsinlinestatic
changeUnresolvedCharactersToGaps(IntSymbolListInterface &l)bpp::SymbolListToolsstatic
changeUnresolvedCharactersToGaps(ProbabilisticSymbolListInterface &l)bpp::SymbolListToolsstatic
changeUnresolvedCharactersToGaps(CruxSymbolListInterface &l)bpp::SymbolListToolsinlinestatic
CodonSiteTools()bpp::CodonSiteToolsinline
entropy(const CruxSymbolListInterface &list, bool resolveUnknowns)bpp::SymbolListToolsinlinestatic
fixedDifferences(const Site &siteIn, const Site &siteOut, int i, int j, const GeneticCode &gCode)bpp::CodonSiteToolsstatic
generateCodonSiteWithoutRareVariant(const Site &site, const GeneticCode &gCode, double freqmin)bpp::CodonSiteToolsstatic
getCounts(const IntSymbolListInterface &list, std::map< int, count_type > &counts)bpp::SymbolListToolsinlinestatic
getCounts(const ProbabilisticSymbolListInterface &list, std::map< int, double_t > &counts)bpp::SymbolListToolsinlinestatic
getCounts(const CruxSymbolListInterface &list, std::map< int, double > &counts, bool resolveUnknowns=false)bpp::SymbolListToolsinlinestatic
getCounts(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2, std::map< int, std::map< int, count_type >> &counts)bpp::SymbolListToolsinlinestatic
getCounts(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts)bpp::SymbolListToolsinlinestatic
getCounts(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts, bool resolveUnknowns)bpp::SymbolListToolsinlinestatic
getCountsResolveUnknowns(const IntSymbolListInterface &list, std::map< int, double > &counts)bpp::SymbolListToolsinlinestatic
getCountsResolveUnknowns(const ProbabilisticSymbolListInterface &list, std::map< int, double > &counts)bpp::SymbolListToolsinlinestatic
getCountsResolveUnknowns(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts)bpp::SymbolListToolsstatic
getCountsResolveUnknowns(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts)bpp::SymbolListToolsstatic
getFrequencies(const CruxSymbolListInterface &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)bpp::SymbolListToolsstatic
getFrequencies(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, std::map< int, std::map< int, double >> &frequencies, bool resolveUnknowns=false)bpp::SymbolListToolsstatic
getGCContent(const IntSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true)bpp::SymbolListToolsstatic
getGCContent(const ProbabilisticSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true)bpp::SymbolListToolsstatic
getGCContent(const CruxSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true)bpp::SymbolListToolsinlinestatic
getMajorAllele(const CruxSymbolListInterface &list)bpp::SymbolListToolsstatic
getMajorAlleleFrequency(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
getMinorAllele(const CruxSymbolListInterface &list)bpp::SymbolListToolsstatic
getMinorAlleleFrequency(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
getNumberOfDistinctCharacters(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
getNumberOfDistinctPositions(const IntSymbolListInterface &l1, const IntSymbolListInterface &l2)bpp::SymbolListToolsstatic
getNumberOfDistinctPositions(const ProbabilisticSymbolListInterface &l1, const ProbabilisticSymbolListInterface &l2)bpp::SymbolListToolsstatic
getNumberOfDistinctPositions(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2)bpp::SymbolListToolsinlinestatic
getNumberOfPositionsWithoutGap(const IntSymbolListInterface &l1, const IntSymbolListInterface &l2)bpp::SymbolListToolsstatic
getNumberOfPositionsWithoutGap(const ProbabilisticSymbolListInterface &l1, const ProbabilisticSymbolListInterface &l2)bpp::SymbolListToolsstatic
getNumberOfPositionsWithoutGap(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2)bpp::SymbolListToolsinlinestatic
hasGap(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
hasGap(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
hasGap(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
hasGapOrStop(const Site &site, const GeneticCode &gCode)bpp::CodonSiteToolsstatic
hasSingleton(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
hasStop(const Site &site, const GeneticCode &gCode)bpp::CodonSiteToolsstatic
hasUnknown(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
hasUnknown(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
hasUnknown(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
hasUnresolved(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
heterozygosity(const CruxSymbolListInterface &list)bpp::SymbolListToolsstatic
isComplete(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
isComplete(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
isComplete(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
isConstant(const IntSymbolListInterface &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true)bpp::SymbolListToolsstatic
isConstant(const ProbabilisticSymbolListInterface &site, bool unresolvedRaisesException=true)bpp::SymbolListToolsstatic
isConstant(const CruxSymbolListInterface &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true)bpp::SymbolListToolsinlinestatic
isDoubleton(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
isFourFoldDegenerated(const Site &site, const GeneticCode &gCode)bpp::CodonSiteToolsstatic
isGapOnly(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
isGapOnly(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
isGapOnly(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
isGapOrUnresolvedOnly(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
isGapOrUnresolvedOnly(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
isGapOrUnresolvedOnly(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
isMonoSitePolymorphic(const Site &site)bpp::CodonSiteToolsstatic
isParsimonyInformativeSite(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
isSynonymousPolymorphic(const Site &site, const GeneticCode &gCode)bpp::CodonSiteToolsstatic
isTriplet(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
jointEntropy(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, bool resolveUnknowns)bpp::SymbolListToolsstatic
meanNumberOfSynonymousPositions(const Site &site, const GeneticCode &gCode, double ratio=1)bpp::CodonSiteToolsstatic
mutualInformation(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, bool resolveUnknowns)bpp::SymbolListToolsstatic
numberOfDifferences(int i, int j, const CodonAlphabet &ca)bpp::CodonSiteToolsstatic
numberOfGaps(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
numberOfGaps(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
numberOfGaps(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
numberOfNonSynonymousSubstitutions(const Site &site, const GeneticCode &gCode, double freqmin=0.)bpp::CodonSiteToolsstatic
numberOfSubstitutions(const Site &site, const GeneticCode &gCode, double freqmin=0.)bpp::CodonSiteToolsstatic
numberOfSynonymousDifferences(int i, int j, const GeneticCode &gCode, bool minchange=false)bpp::CodonSiteToolsstatic
numberOfSynonymousPositions(int i, const GeneticCode &gCode, double ratio=1.0)bpp::CodonSiteToolsstatic
numberOfUnresolved(const IntSymbolListInterface &site)bpp::SymbolListToolsstatic
numberOfUnresolved(const ProbabilisticSymbolListInterface &site)bpp::SymbolListToolsstatic
numberOfUnresolved(const CruxSymbolListInterface &site)bpp::SymbolListToolsinlinestatic
piNonSynonymous(const Site &site, const GeneticCode &gCode, bool minchange=false)bpp::CodonSiteToolsstatic
piSynonymous(const Site &site, const GeneticCode &gCode, bool minchange=false)bpp::CodonSiteToolsstatic
SymbolListTools()bpp::SymbolListToolsinline
variabilityFactorial(const IntSymbolListInterface &list)bpp::SymbolListToolsstatic
variabilityShannon(const CruxSymbolListInterface &list, bool resolveUnknowns)bpp::SymbolListToolsstatic
~CodonSiteTools()bpp::CodonSiteToolsinlinevirtual
~SymbolListTools()bpp::SymbolListToolsinlinevirtual