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

computeCountsPerSitePerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &array)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerSitePerBranchPerType(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVVdouble &result)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerSitePerBranchPerType(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< SubstitutionModelInterface > nullModel, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVVdouble &result, bool perTime, bool perWord)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerSitePerBranchPerType(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< SubstitutionModelSet > nullModelSet, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVVdouble &result, bool perTime, bool perWord)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerSitePerType(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &result)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerSitePerType(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< SubstitutionModelInterface > nullModel, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &result, bool perTime, bool perWord)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerSitePerType(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< SubstitutionModelSet > nullModelSet, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &result, bool perTime, bool perWord)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerTypePerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &result, double threshold=-1, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerTypePerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< SubstitutionModelInterface > nullModel, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &result, bool perTime, bool perWord, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeCountsPerTypePerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< SubstitutionModelSet > nullModelSet, std::shared_ptr< const SubstitutionRegisterInterface > reg, VVdouble &result, bool perTime, bool perWord, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeNormForSite(const LegacySubstitutionMappingInterface &smap, size_t siteIndex)	bpp::LegacySubstitutionMappingTools	static
computeOneJumpProbabilityVectors(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, bool verbose=true)	bpp::LegacySubstitutionMappingTools	inlinestatic
computeSubstitutionVectors(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, std::shared_ptr< SubstitutionCountInterface > substitutionCount, bool verbose=true)	bpp::LegacySubstitutionMappingTools	inlinestatic
computeSubstitutionVectors(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, const std::vector< int > &nodeIds, std::shared_ptr< SubstitutionCountInterface > substitutionCount, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeSubstitutionVectors(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, const SubstitutionModelSet &modelSet, const std::vector< int > &nodeIds, std::shared_ptr< SubstitutionCountInterface > substitutionCount, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeSubstitutionVectorsMarginal(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, std::shared_ptr< SubstitutionCountInterface > substitutionCount, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeSubstitutionVectorsNoAveraging(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, std::shared_ptr< SubstitutionCountInterface > substitutionCount, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeSubstitutionVectorsNoAveragingMarginal(std::shared_ptr< const DRTreeLikelihoodInterface > drtl, std::shared_ptr< SubstitutionCountInterface > substitutionCount, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
computeSumForBranch(const LegacySubstitutionMappingInterface &smap, size_t branchIndex)	bpp::LegacySubstitutionMappingTools	static
computeSumForSite(const LegacySubstitutionMappingInterface &smap, size_t siteIndex)	bpp::LegacySubstitutionMappingTools	static
computeTotalSubstitutionVectorForSitePerBranch(const LegacySubstitutionMappingInterface &smap, size_t siteIndex)	bpp::LegacySubstitutionMappingTools	static
computeTotalSubstitutionVectorForSitePerType(const LegacySubstitutionMappingInterface &smap, size_t siteIndex)	bpp::LegacySubstitutionMappingTools	static
getCountsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, double threshold=-1, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
getCountsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, const SubstitutionModelSet &modelSet, std::shared_ptr< const SubstitutionRegisterInterface > reg, double threshold=-1, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
getNormalizationsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< const SubstitutionModelInterface > nullModel, const SubstitutionRegisterInterface &reg, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
getNormalizationsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< const SubstitutionModelSet > nullModelSet, const SubstitutionRegisterInterface &reg, bool verbose=true)	bpp::LegacySubstitutionMappingTools	static
getNormalizedCountsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< SubstitutionModelInterface > nullModel, std::shared_ptr< const SubstitutionRegisterInterface > reg, bool perTime, bool perWord, bool verbose=true)	bpp::LegacySubstitutionMappingTools	inlinestatic
getNormalizedCountsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< SubstitutionModelSet > nullModelSet, std::shared_ptr< const SubstitutionRegisterInterface > reg, bool perTime, bool perWord, bool verbose=true)	bpp::LegacySubstitutionMappingTools	inlinestatic
getRelativeCountsPerBranch(std::shared_ptr< DRTreeLikelihoodInterface > drtl, const std::vector< int > &ids, std::shared_ptr< SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, double threshold=-1, bool verbose=true)	bpp::LegacySubstitutionMappingTools	inlinestatic
LegacySubstitutionMappingTools()	bpp::LegacySubstitutionMappingTools	inline
outputPerSitePerBranch(const std::string &filename, const std::vector< int > &ids, const VVdouble &counts)	bpp::LegacySubstitutionMappingTools	static
outputPerSitePerBranchPerType(const std::string &filenamePrefix, const std::vector< int > &ids, const SubstitutionRegisterInterface &reg, const VVVdouble &counts)	bpp::LegacySubstitutionMappingTools	static
outputPerSitePerType(const std::string &filename, const SubstitutionRegisterInterface &reg, const VVdouble &counts)	bpp::LegacySubstitutionMappingTools	static
readFromStream(std::istream &in, LegacyProbabilisticSubstitutionMapping &substitutions, size_t type)	bpp::LegacySubstitutionMappingTools	static
writeToStream(const LegacyProbabilisticSubstitutionMapping &substitutions, const SiteContainerInterface &sites, size_t type, std::ostream &out)	bpp::LegacySubstitutionMappingTools	static
~LegacySubstitutionMappingTools()	bpp::LegacySubstitutionMappingTools	inlinevirtual