| _nestedPrefix | bpp::YpR | protected |
| AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix) | bpp::AbstractSubstitutionModel | |
| AbstractSubstitutionModel(const AbstractSubstitutionModel &model) | bpp::AbstractSubstitutionModel | inline |
| addRateParameter() | bpp::AbstractSubstitutionModel | virtual |
| alphabet_ | bpp::AbstractSubstitutionModel | protected |
| check_model(SubstitutionModel *const) const | bpp::YpR | protected |
| clone() const | bpp::YpR_Gen | inlinevirtual |
| d2Pij_dt2(size_t i, size_t j, double t) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| d2pijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
| dPij_dt(size_t i, size_t j, double t) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| dpijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
| eigenDecompose_ | bpp::AbstractSubstitutionModel | protected |
| eigenValues_ | bpp::AbstractSubstitutionModel | protected |
| enableEigenDecomposition(bool yn) | bpp::AbstractSubstitutionModel | inlinevirtual |
| enableEigenDecomposition() | bpp::AbstractSubstitutionModel | inlinevirtual |
| exchangeability_ | bpp::AbstractSubstitutionModel | protected |
| fireParameterChanged(const ParameterList ¶meters) | bpp::YpR | inlinevirtual |
| freq(size_t i) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| freq_ | bpp::AbstractSubstitutionModel | protected |
| generator_ | bpp::AbstractSubstitutionModel | protected |
| getAlphabet() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getAlphabetStateAsChar(size_t index) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getAlphabetStateAsInt(size_t index) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getAlphabetStates() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getColumnRightEigenVectors() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getd2Pij_dt2(double t) const | bpp::AbstractSubstitutionModel | virtual |
| getdPij_dt(double t) const | bpp::AbstractSubstitutionModel | virtual |
| getEigenValues() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getExchangeabilityMatrix() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getFrequencies() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getFrequenciesSet() const | bpp::SubstitutionModel | inlinevirtual |
| getGenerator() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getIEigenValues() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getInitValue(size_t i, int state) const | bpp::AbstractSubstitutionModel | virtual |
| getModelStates(int code) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getModelStates(const std::string &code) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getName() const | bpp::YpR_Gen | virtual |
| getNestedModel() const | bpp::YpR | inline |
| getNestedPrefix() const | bpp::YpR | inlineprotected |
| getNumberOfStates() const | bpp::YpR | inlinevirtual |
| getPij_t(double t) const | bpp::AbstractSubstitutionModel | virtual |
| getRate() const | bpp::AbstractSubstitutionModel | virtual |
| getRowLeftEigenVectors() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getScale() const | bpp::AbstractSubstitutionModel | virtual |
| getStateMap() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| iEigenValues_ | bpp::AbstractSubstitutionModel | protected |
| isDiagonalizable() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| isDiagonalizable_ | bpp::AbstractSubstitutionModel | protected |
| isNonSingular() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| isNonSingular_ | bpp::AbstractSubstitutionModel | protected |
| leftEigenVectors_ | bpp::AbstractSubstitutionModel | protected |
| operator=(const YpR &ypr) | bpp::YpR | inlineprotected |
| bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model) | bpp::AbstractSubstitutionModel | inline |
| Pij_t(size_t i, size_t j, double t) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| pijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
| pmodel_ | bpp::YpR | protected |
| Qij(size_t i, size_t j) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| rate_ | bpp::AbstractSubstitutionModel | protected |
| rightEigenVectors_ | bpp::AbstractSubstitutionModel | protected |
| setFreq(std::map< int, double > &) | bpp::AbstractSubstitutionModel | virtual |
| setFreqFromData(const SequenceContainer &data, double pseudoCount=0) | bpp::AbstractSubstitutionModel | virtual |
| setNamespace(const std::string &) | bpp::YpR | virtual |
| setRate(double rate) | bpp::AbstractSubstitutionModel | virtual |
| setScale(double scale) | bpp::AbstractSubstitutionModel | virtual |
| Sij(size_t i, size_t j) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| size_ | bpp::AbstractSubstitutionModel | protected |
| stateMap_ | bpp::AbstractSubstitutionModel | protected |
| SubstitutionModel() | bpp::SubstitutionModel | inline |
| tmpMat_ | bpp::AbstractSubstitutionModel | mutableprotected |
| updateMatrices() | bpp::YpR_Gen | virtual |
| bpp::YpR::updateMatrices(double, double, double, double, double, double, double, double) | bpp::YpR | protected |
| vPowGen_ | bpp::AbstractSubstitutionModel | protected |
| YpR(const RNY *, SubstitutionModel *const, const std::string &prefix) | bpp::YpR | protected |
| YpR(const YpR &, const std::string &prefix) | bpp::YpR | protected |
| YpR(const YpR &ypr) | bpp::YpR | protected |
| YpR_Gen(const RNY *alph, SubstitutionModel *pm, double CgT=0., double cGA=0., double TgC=0., double tGA=0., double CaT=0., double cAG=0., double TaC=0., double tAG=0.) | bpp::YpR_Gen | |
| YpR_Gen(const YpR_Gen &) | bpp::YpR_Gen | |
| ~AbstractSubstitutionModel() | bpp::AbstractSubstitutionModel | inlinevirtual |
| ~SubstitutionModel() | bpp::SubstitutionModel | inlinevirtual |
| ~YpR() | bpp::YpR | inlinevirtual |
| ~YpR_Gen() | bpp::YpR_Gen | inlinevirtual |
1.8.14