bpp::SubstitutionMappingTools Member List

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

computeNormForSite(const SubstitutionMapping &smap, size_t siteIndex)	bpp::SubstitutionMappingTools	static
computeOneJumpProbabilityVectors(const DRTreeLikelihood &drtl, bool verbose=true)	bpp::SubstitutionMappingTools	inlinestatic
computeSubstitutionVectors(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)	bpp::SubstitutionMappingTools	inlinestatic
computeSubstitutionVectors(const DRTreeLikelihood &drtl, const std::vector< int > &nodeIds, SubstitutionCount &substitutionCount, bool verbose=true)	bpp::SubstitutionMappingTools	static
computeSubstitutionVectors(const DRTreeLikelihood &drtl, const SubstitutionModelSet &modelSet, const std::vector< int > &nodeIds, SubstitutionCount &substitutionCount, bool verbose=true)	bpp::SubstitutionMappingTools	static
computeSubstitutionVectorsMarginal(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)	bpp::SubstitutionMappingTools	static
computeSubstitutionVectorsNoAveraging(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)	bpp::SubstitutionMappingTools	static
computeSubstitutionVectorsNoAveragingMarginal(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)	bpp::SubstitutionMappingTools	static
computeSumForBranch(const SubstitutionMapping &smap, size_t branchIndex)	bpp::SubstitutionMappingTools	static
computeSumForSite(const SubstitutionMapping &smap, size_t siteIndex)	bpp::SubstitutionMappingTools	static
computeTotalSubstitutionVectorForSite(const SubstitutionMapping &smap, size_t siteIndex)	bpp::SubstitutionMappingTools	static
getCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)	bpp::SubstitutionMappingTools	static
getCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModelSet &modelSet, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)	bpp::SubstitutionMappingTools	static
getNormalizationsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModel *nullModel, const SubstitutionRegister &reg, bool verbose=true)	bpp::SubstitutionMappingTools	static
getNormalizationsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, bool verbose=true)	bpp::SubstitutionMappingTools	static
getNormalizedCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, SubstitutionModel *nullModel, const SubstitutionRegister &reg, bool verbose=true)	bpp::SubstitutionMappingTools	static
getNormalizedCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModelSet *modelSet, SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, bool verbose=true)	bpp::SubstitutionMappingTools	static
getRelativeCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, bool stationarity=true, double threshold=-1)	bpp::SubstitutionMappingTools	static
outputIndividualCountsPerBranchPerSite(const std::string &filenamePrefix, DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg)	bpp::SubstitutionMappingTools	static
outputTotalCountsPerBranchPerSite(std::string &filename, DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg)	bpp::SubstitutionMappingTools	static
readFromStream(std::istream &in, ProbabilisticSubstitutionMapping &substitutions, size_t type)	bpp::SubstitutionMappingTools	static
SubstitutionMappingTools()	bpp::SubstitutionMappingTools	inline
writeToStream(const ProbabilisticSubstitutionMapping &substitutions, const SiteContainer &sites, size_t type, std::ostream &out)	bpp::SubstitutionMappingTools	static
~SubstitutionMappingTools()	bpp::SubstitutionMappingTools	inlinevirtual