bpp::SequenceStatistics Member List

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

dvh(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
dvk(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
fayWu2000(const PolymorphismSequenceContainer &psc, const Sequence &ancestralSites)	bpp::SequenceStatistics	static
fixedDifferences(const PolymorphismSequenceContainer &pscin, const PolymorphismSequenceContainer &pscout, PolymorphismSequenceContainer &psccons, const GeneticCode &gc)	bpp::SequenceStatistics	static
fstHudson92(const PolymorphismSequenceContainer &psc, size_t id1, size_t id2)	bpp::SequenceStatistics
fuLiD(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, bool original=true)	bpp::SequenceStatistics	static
fuLiDStar(const PolymorphismSequenceContainer &group)	bpp::SequenceStatistics	static
fuLiF(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, bool original=true)	bpp::SequenceStatistics	static
fuLiFStar(const PolymorphismSequenceContainer &group)	bpp::SequenceStatistics	static
gcContent(const PolymorphismSequenceContainer &psc)	bpp::SequenceStatistics	static
gcPolymorphism(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
generateLdContainer(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
getNumberOfDerivedSingletons_(const Site &site_in, const Site &site_out)	bpp::SequenceStatistics	privatestatic
getNumberOfMutations_(const Site &site)	bpp::SequenceStatistics	privatestatic
getNumberOfSingletons_(const Site &site)	bpp::SequenceStatistics	privatestatic
getUD_(double a1, double vD)	bpp::SequenceStatistics	privatestatic
getUDstar_(size_t n, double a1, double vDs)	bpp::SequenceStatistics	privatestatic
getUsefulValues_(size_t n)	bpp::SequenceStatistics	privatestatic
getVD_(size_t n, double a1, double a2, double cn)	bpp::SequenceStatistics	privatestatic
getVDstar_(size_t n, double a1, double a2, double dn)	bpp::SequenceStatistics	privatestatic
heterozygosity(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
hudson87(const PolymorphismSequenceContainer &psc, double precision=0.000001, double cinf=0.001, double csup=10000.)	bpp::SequenceStatistics	static
inverseRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
leftHandHudson_(const PolymorphismSequenceContainer &psc)	bpp::SequenceStatistics	privatestatic
linearRegressionD(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
linearRegressionDprime(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
linearRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
meanD(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
meanDistance1(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
meanDistance2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
meanDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
meanNumberOfNonSynonymousSites(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double ratio=1.)	bpp::SequenceStatistics	static
meanNumberOfSynonymousSites(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double ratio=1.)	bpp::SequenceStatistics	static
meanR2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
mkTable(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, const GeneticCode &gc, double freqmin=0.)	bpp::SequenceStatistics	static
neutralityIndex(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, const GeneticCode &gc, double freqmin=0.)	bpp::SequenceStatistics	static
numberOfMonoSitePolymorphicCodons(const PolymorphismSequenceContainer &psc, bool stopflag=true, bool gapflag=true)	bpp::SequenceStatistics	static
numberOfNonSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.)	bpp::SequenceStatistics	static
numberOfParsimonyInformativeSites(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
numberOfPolymorphicSites(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)	bpp::SequenceStatistics	static
numberOfSingletons(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
numberOfSitesWithStopCodon(const PolymorphismSequenceContainer &psc, const GeneticCode &gCode, bool gapflag=true)	bpp::SequenceStatistics	static
numberOfSynonymousPolymorphicCodons(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)	bpp::SequenceStatistics	static
numberOfSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.)	bpp::SequenceStatistics	static
numberOfTransitions(const PolymorphismSequenceContainer &psc)	bpp::SequenceStatistics	static
numberOfTransversions(const PolymorphismSequenceContainer &psc)	bpp::SequenceStatistics	static
numberOfTriplets(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
originRegressionD(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
originRegressionDprime(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
originRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
pairwiseD(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
pairwiseDistances1(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
pairwiseDistances2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
pairwiseDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
pairwiseR2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)	bpp::SequenceStatistics	static
piNonSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false)	bpp::SequenceStatistics	static
piSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false)	bpp::SequenceStatistics	static
ratioOfTransitionsTransversions(const PolymorphismSequenceContainer &psc)	bpp::SequenceStatistics	static
rightHandHudson_(double c, size_t n)	bpp::SequenceStatistics	privatestatic
squaredHeterozygosity(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
tajima83(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
tajimaDss(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
tajimaDtnm(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
testUsefulValues(std::ostream &s, size_t n)	bpp::SequenceStatistics	static
totalNumberOfMutations(const PolymorphismSequenceContainer &psc, bool gapflag=true)	bpp::SequenceStatistics	static
totalNumberOfMutationsOnExternalBranches(const PolymorphismSequenceContainer &ing, const PolymorphismSequenceContainer &outg)	bpp::SequenceStatistics	static
watterson75(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)	bpp::SequenceStatistics	static
watterson75NonSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)	bpp::SequenceStatistics	static
watterson75Synonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)	bpp::SequenceStatistics	static