bpp-phyl  2.4.0
bpp::SubstitutionMappingTools Member List

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

computeCountsPerSitePerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, VVdouble &array)bpp::SubstitutionMappingToolsstatic
computeCountsPerSitePerBranchPerType(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, VVVdouble &result)bpp::SubstitutionMappingToolsstatic
computeCountsPerSitePerBranchPerType(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, SubstitutionModel *nullModel, const SubstitutionRegister &reg, VVVdouble &result, bool perTime, bool perWord)bpp::SubstitutionMappingToolsstatic
computeCountsPerSitePerBranchPerType(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModelSet *modelSet, SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, VVVdouble &result, bool perTime, bool perWord)bpp::SubstitutionMappingToolsstatic
computeCountsPerSitePerType(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, VVdouble &result)bpp::SubstitutionMappingToolsstatic
computeCountsPerSitePerType(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, SubstitutionModel *nullModel, const SubstitutionRegister &reg, VVdouble &result, bool perTime, bool perWord)bpp::SubstitutionMappingToolsstatic
computeCountsPerSitePerType(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModelSet *modelSet, SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, VVdouble &result, bool perTime, bool perWord)bpp::SubstitutionMappingToolsstatic
computeCountsPerTypePerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, VVdouble &result, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeCountsPerTypePerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, SubstitutionModel *nullModel, const SubstitutionRegister &reg, VVdouble &result, bool perTime, bool perWord, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeCountsPerTypePerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModelSet *modelSet, SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, VVdouble &result, bool perTime, bool perWord, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeNormForSite(const SubstitutionMapping &smap, size_t siteIndex)bpp::SubstitutionMappingToolsstatic
computeOneJumpProbabilityVectors(const DRTreeLikelihood &drtl, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
computeSubstitutionVectors(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
computeSubstitutionVectors(const DRTreeLikelihood &drtl, const std::vector< int > &nodeIds, SubstitutionCount &substitutionCount, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeSubstitutionVectors(const DRTreeLikelihood &drtl, const SubstitutionModelSet &modelSet, const std::vector< int > &nodeIds, SubstitutionCount &substitutionCount, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeSubstitutionVectorsMarginal(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeSubstitutionVectorsNoAveraging(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeSubstitutionVectorsNoAveragingMarginal(const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true)bpp::SubstitutionMappingToolsstatic
computeSumForBranch(const SubstitutionMapping &smap, size_t branchIndex)bpp::SubstitutionMappingToolsstatic
computeSumForSite(const SubstitutionMapping &smap, size_t siteIndex)bpp::SubstitutionMappingToolsstatic
computeTotalSubstitutionVectorForSitePerBranch(const SubstitutionMapping &smap, size_t siteIndex)bpp::SubstitutionMappingToolsstatic
computeTotalSubstitutionVectorForSitePerType(const SubstitutionMapping &smap, size_t siteIndex)bpp::SubstitutionMappingToolsstatic
getCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
getCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModelSet &modelSet, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsstatic
getNormalizationsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModel *nullModel, const SubstitutionRegister &reg, bool verbose=true)bpp::SubstitutionMappingToolsstatic
getNormalizationsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, bool verbose=true)bpp::SubstitutionMappingToolsstatic
getNormalizedCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, SubstitutionModel *nullModel, const SubstitutionRegister &reg, bool perTime, bool perWord, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
getNormalizedCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModelSet *modelSet, SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, bool perTime, bool perWord, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
getRelativeCountsPerBranch(DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)bpp::SubstitutionMappingToolsinlinestatic
outputPerSitePerBranch(const std::string &filename, const std::vector< int > &ids, const VVdouble &counts)bpp::SubstitutionMappingToolsstatic
outputPerSitePerBranchPerType(const std::string &filenamePrefix, const std::vector< int > &ids, const SubstitutionRegister &reg, const VVVdouble &counts)bpp::SubstitutionMappingToolsstatic
outputPerSitePerType(const std::string &filename, const SubstitutionRegister &reg, const VVdouble &counts)bpp::SubstitutionMappingToolsstatic
readFromStream(std::istream &in, ProbabilisticSubstitutionMapping &substitutions, size_t type)bpp::SubstitutionMappingToolsstatic
SubstitutionMappingTools()bpp::SubstitutionMappingToolsinline
writeToStream(const ProbabilisticSubstitutionMapping &substitutions, const SiteContainer &sites, size_t type, std::ostream &out)bpp::SubstitutionMappingToolsstatic
~SubstitutionMappingTools()bpp::SubstitutionMappingToolsinlinevirtual