| AbstractReversibleSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix) | bpp::AbstractReversibleSubstitutionModel | inline |
| AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix) | bpp::AbstractSubstitutionModel | |
| AbstractSubstitutionModel(const AbstractSubstitutionModel &model) | bpp::AbstractSubstitutionModel | inline |
| bpp::addRateParameter()=0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::addRateParameter() | bpp::AbstractSubstitutionModel | virtual |
| alphabet_ | bpp::AbstractSubstitutionModel | protected |
| clone() const | bpp::HKY85 | inlinevirtual |
| d2Pij_dt2(size_t i, size_t j, double d) const | bpp::HKY85 | virtual |
| d2pijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
| dPij_dt(size_t i, size_t j, double d) const | bpp::HKY85 | virtual |
| dpijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
| eigenDecompose_ | bpp::AbstractSubstitutionModel | protected |
| eigenValues_ | bpp::AbstractSubstitutionModel | protected |
| bpp::enableEigenDecomposition(bool yn)=0 | bpp::SubstitutionModel | pure virtual |
| bpp::enableEigenDecomposition()=0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::enableEigenDecomposition(bool yn) | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::AbstractReversibleSubstitutionModel::enableEigenDecomposition() | bpp::AbstractSubstitutionModel | inlinevirtual |
| exchangeability_ | bpp::AbstractSubstitutionModel | protected |
| exp1_ | bpp::HKY85 | mutableprivate |
| exp21_ | bpp::HKY85 | mutableprivate |
| exp22_ | bpp::HKY85 | mutableprivate |
| fireParameterChanged(const ParameterList ¶meters) | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::freq(size_t i) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::freq(size_t i) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| freq_ | bpp::AbstractSubstitutionModel | protected |
| generator_ | bpp::AbstractSubstitutionModel | protected |
| bpp::getAlphabet() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getAlphabet() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getAlphabetStateAsChar(size_t index) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getAlphabetStateAsChar(size_t index) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getAlphabetStateAsInt(size_t index) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getAlphabetStateAsInt(size_t index) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getAlphabetStates() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getAlphabetStates() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getColumnRightEigenVectors() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getColumnRightEigenVectors() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getd2Pij_dt2(double d) const | bpp::HKY85 | virtual |
| getdPij_dt(double d) const | bpp::HKY85 | virtual |
| bpp::getEigenValues() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getEigenValues() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getExchangeabilityMatrix() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getExchangeabilityMatrix() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getFrequencies() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getFrequencies() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getFrequenciesSet() const | bpp::SubstitutionModel | inlinevirtual |
| bpp::getGenerator() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getGenerator() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getIEigenValues() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getIEigenValues() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getInitValue(size_t i, int state) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getInitValue(size_t i, int state) const | bpp::AbstractSubstitutionModel | virtual |
| bpp::getModelStates(int code) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::getModelStates(const std::string &code) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getModelStates(int code) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::AbstractReversibleSubstitutionModel::getModelStates(const std::string &code) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| getName() const | bpp::HKY85 | inlinevirtual |
| getNumberOfStates() const | bpp::NucleotideSubstitutionModel | inlinevirtual |
| getPij_t(double d) const | bpp::HKY85 | virtual |
| bpp::getRate() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getRate() const | bpp::AbstractSubstitutionModel | virtual |
| bpp::getRowLeftEigenVectors() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getRowLeftEigenVectors() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| bpp::getScale() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getScale() const | bpp::AbstractSubstitutionModel | virtual |
| bpp::getStateMap() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::getStateMap() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| HKY85(const NucleicAlphabet *alpha, double kappa=1., double piA=0.25, double piC=0.25, double piG=0.25, double piT=0.25) | bpp::HKY85 | |
| iEigenValues_ | bpp::AbstractSubstitutionModel | protected |
| bpp::isDiagonalizable() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::isDiagonalizable() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| isDiagonalizable_ | bpp::AbstractSubstitutionModel | protected |
| bpp::isNonSingular() const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::isNonSingular() const | bpp::AbstractSubstitutionModel | inlinevirtual |
| isNonSingular_ | bpp::AbstractSubstitutionModel | protected |
| k1_ | bpp::HKY85 | private |
| k2_ | bpp::HKY85 | private |
| kappa_ | bpp::HKY85 | private |
| l_ | bpp::HKY85 | mutableprivate |
| leftEigenVectors_ | bpp::AbstractSubstitutionModel | protected |
| operator=(const AbstractSubstitutionModel &model) | bpp::AbstractSubstitutionModel | inline |
| p_ | bpp::HKY85 | mutableprivate |
| piA_ | bpp::HKY85 | private |
| piC_ | bpp::HKY85 | private |
| piG_ | bpp::HKY85 | private |
| Pij_t(size_t i, size_t j, double d) const | bpp::HKY85 | virtual |
| pijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
| piR_ | bpp::HKY85 | private |
| piT_ | bpp::HKY85 | private |
| piY_ | bpp::HKY85 | private |
| bpp::Qij(size_t i, size_t j) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::Qij(size_t i, size_t j) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| r_ | bpp::HKY85 | private |
| rate_ | bpp::AbstractSubstitutionModel | protected |
| ReversibleSubstitutionModel() | bpp::ReversibleSubstitutionModel | inline |
| rightEigenVectors_ | bpp::AbstractSubstitutionModel | protected |
| setFreq(std::map< int, double > &freqs) | bpp::HKY85 | virtual |
| bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0) | bpp::AbstractSubstitutionModel | virtual |
| bpp::setRate(double rate)=0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::setRate(double rate) | bpp::AbstractSubstitutionModel | virtual |
| bpp::setScale(double scale)=0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::setScale(double scale) | bpp::AbstractSubstitutionModel | virtual |
| bpp::Sij(size_t i, size_t j) const =0 | bpp::SubstitutionModel | pure virtual |
| bpp::AbstractReversibleSubstitutionModel::Sij(size_t i, size_t j) const | bpp::AbstractSubstitutionModel | inlinevirtual |
| size_ | bpp::AbstractSubstitutionModel | protected |
| stateMap_ | bpp::AbstractSubstitutionModel | protected |
| SubstitutionModel() | bpp::SubstitutionModel | inline |
| theta1_ | bpp::HKY85 | private |
| theta2_ | bpp::HKY85 | private |
| theta_ | bpp::HKY85 | private |
| tmpMat_ | bpp::AbstractSubstitutionModel | mutableprotected |
| updateMatrices() | bpp::HKY85 | virtual |
| vPowGen_ | bpp::AbstractSubstitutionModel | protected |
| ~AbstractReversibleSubstitutionModel() | bpp::AbstractReversibleSubstitutionModel | inlinevirtual |
| ~AbstractSubstitutionModel() | bpp::AbstractSubstitutionModel | inlinevirtual |
| ~HKY85() | bpp::HKY85 | inlinevirtual |
| ~NucleotideSubstitutionModel() | bpp::NucleotideSubstitutionModel | inlinevirtual |
| ~ReversibleSubstitutionModel() | bpp::ReversibleSubstitutionModel | inlinevirtual |
| ~SubstitutionModel() | bpp::SubstitutionModel | inlinevirtual |
1.8.14