bpp-phyl3  3.0.0
bpp::SubstitutionMappingTools Member List

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

computeCounts(LikelihoodCalculationSingleProcess &rltc, SubstitutionCountInterface &substitutionCount, short unresolvedOption=UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
computeCounts(LikelihoodCalculationSingleProcess &rltc, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=0, std::shared_ptr< const AlphabetIndex2 > distances=0, short unresolvedOption=UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
computeCounts(LikelihoodCalculationSingleProcess &rltc, const std::vector< uint > &speciesIds, SubstitutionCountInterface &substitutionCount, short unresolvedOption=UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeCounts(LikelihoodCalculationSingleProcess &rltc, const std::vector< uint > &edgeIds, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=0, std::shared_ptr< const AlphabetIndex2 > distances=0, short unresolvedOption=UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeCountsPerTypePerBranch(LikelihoodCalculationSingleProcess &rltc, const std::vector< uint > &ids, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=0, std::shared_ptr< const AlphabetIndex2 > distances=0, short unresolvedOption=UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeNormalizations(LikelihoodCalculationSingleProcess &rltc, const std::vector< uint > &edgeIds, std::shared_ptr< const BranchedModelSet > nullModels, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > distances=0, short unresolvedOption=UNRESOLVED_ZERO, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeNormalizations(LikelihoodCalculationSingleProcess &rltc, std::shared_ptr< const BranchedModelSet > nullModels, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > distances=0, short unresolvedOption=UNRESOLVED_ZERO, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
computeNormalizedCounts(LikelihoodCalculationSingleProcess &rltc, const std::vector< uint > &edgeIds, std::shared_ptr< const BranchedModelSet > nullModels, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=0, std::shared_ptr< const AlphabetIndex2 > distances=0, bool perTimeUnit=false, uint siteSize=1, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeNormalizedCounts(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, const std::vector< uint > &edgeIds, bool perTimeUnit=false, uint siteSize=1)bpp::SubstitutionMappingToolsstatic
computeNormalizedCounts(LikelihoodCalculationSingleProcess &rltc, std::shared_ptr< const BranchedModelSet > nullModels, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=0, std::shared_ptr< const AlphabetIndex2 > distances=0, bool perTimeUnit=false, uint siteSize=1, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
computeNormalizedCounts(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, bool perTimeUnit, uint siteSize=1)bpp::SubstitutionMappingToolsinlinestatic
computeOneJumpCounts(LikelihoodCalculationSingleProcess &rltc, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
getCountsForBranchPerType(const ProbabilisticSubstitutionMapping &counts, uint branchId)bpp::SubstitutionMappingToolsstatic
getCountsForSitePerBranch(const ProbabilisticSubstitutionMapping &counts, size_t site)bpp::SubstitutionMappingToolsstatic
getCountsForSitePerBranch(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, size_t site)bpp::SubstitutionMappingToolsstatic
getCountsForSitePerType(const ProbabilisticSubstitutionMapping &counts, size_t site, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getCountsForSitePerType(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, size_t site, bool perTimeUnit, uint siteSize=1)bpp::SubstitutionMappingToolsstatic
getCountsForSitePerType(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, size_t site, const std::vector< uint > &ids, bool perTimeUnit, uint siteSize=1)bpp::SubstitutionMappingToolsstatic
getCountsPerBranchPerType(const ProbabilisticSubstitutionMapping &counts, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getCountsPerSitePerBranch(const ProbabilisticSubstitutionMapping &counts, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getCountsPerSitePerBranch(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getCountsPerSitePerBranchPerType(const ProbabilisticSubstitutionMapping &counts, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getCountsPerSitePerType(const ProbabilisticSubstitutionMapping &counts, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getCountsPerSitePerType(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, bool perTimeUnit, uint siteSize=1)bpp::SubstitutionMappingToolsstatic
getCountsPerSitePerType(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, const std::vector< uint > &ids, bool perTimeUnit, uint siteSize=1)bpp::SubstitutionMappingToolsstatic
getCountsPerTypePerBranch(const ProbabilisticSubstitutionMapping &counts, const std::vector< uint > &ids=Vuint(0))bpp::SubstitutionMappingToolsstatic
getNormForSite(const ProbabilisticSubstitutionMapping &counts, size_t site)bpp::SubstitutionMappingToolsstatic
getTreeForType(const ProbabilisticSubstitutionMapping &counts, size_t type)bpp::SubstitutionMappingToolsstatic
getTreeForType(const ProbabilisticSubstitutionMapping &counts, const ProbabilisticSubstitutionMapping &factors, size_t type)bpp::SubstitutionMappingToolsstatic
outputPerSitePerBranch(const std::string &filename, const std::vector< uint > &ids, const AlignmentDataInterface &sites, const VVdouble &counts)bpp::SubstitutionMappingToolsstatic
outputPerSitePerBranchPerType(const std::string &filenamePrefix, const std::vector< uint > &ids, const SubstitutionRegisterInterface &reg, const AlignmentDataInterface &sites, const VVVdouble &counts)bpp::SubstitutionMappingToolsstatic
outputPerSitePerType(const std::string &filename, const SubstitutionRegisterInterface &reg, const AlignmentDataInterface &sites, const VVdouble &counts)bpp::SubstitutionMappingToolsstatic
outputPerType(const std::string &filename, const SubstitutionRegisterInterface &reg, const AlignmentDataInterface &sites, const VVdouble &counts)bpp::SubstitutionMappingToolsstatic
readFromStream(std::istream &in, ProbabilisticSubstitutionMapping &substitutions, size_t type)bpp::SubstitutionMappingToolsstatic
SubstitutionMappingTools()bpp::SubstitutionMappingToolsinline
UNRESOLVED_AVERAGEbpp::SubstitutionMappingToolsstatic
UNRESOLVED_ONEbpp::SubstitutionMappingToolsstatic
UNRESOLVED_ZERObpp::SubstitutionMappingToolsstatic
writeToStream(const ProbabilisticSubstitutionMapping &substitutions, const AlignmentDataInterface &sites, size_t type, std::ostream &out)bpp::SubstitutionMappingToolsstatic
~SubstitutionMappingTools()bpp::SubstitutionMappingToolsinlinevirtual