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 |
addRateParameter() | bpp::AbstractSubstitutionModel | virtual |
alphabet_ | bpp::AbstractSubstitutionModel | protected |
clone() const | bpp::RE08 | inlinevirtual |
d2Pij_dt2(size_t i, size_t j, double d) const | bpp::RE08 | virtual |
d2pijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
dPij_dt(size_t i, size_t j, double d) const | bpp::RE08 | virtual |
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 |
exp_ | bpp::RE08 | mutableprivate |
fireParameterChanged(const ParameterList ¶meters) | bpp::RE08 | 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 d) const | bpp::RE08 | virtual |
getdPij_dt(double d) const | bpp::RE08 | 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::RE08 | virtual |
getModelStates(int code) const | bpp::AbstractSubstitutionModel | inlinevirtual |
getModelStates(const std::string &code) const | bpp::AbstractSubstitutionModel | inlinevirtual |
getName() const | bpp::RE08 | inlinevirtual |
getNestedModel() const | bpp::RE08 | inline |
getNumberOfStates() const | bpp::RE08 | inlinevirtual |
getPij_t(double d) const | bpp::RE08 | 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 |
lambda_ | bpp::RE08 | private |
leftEigenVectors_ | bpp::AbstractSubstitutionModel | protected |
mu_ | bpp::RE08 | private |
nestedPrefix_ | bpp::RE08 | private |
operator=(const RE08 &model) | bpp::RE08 | inline |
bpp::AbstractReversibleSubstitutionModel::operator=(const AbstractSubstitutionModel &model) | bpp::AbstractSubstitutionModel | inline |
p_ | bpp::RE08 | mutableprivate |
Pij_t(size_t i, size_t j, double d) const | bpp::RE08 | virtual |
pijt_ | bpp::AbstractSubstitutionModel | mutableprotected |
Qij(size_t i, size_t j) const | bpp::AbstractSubstitutionModel | inlinevirtual |
rate_ | bpp::AbstractSubstitutionModel | protected |
RE08(ReversibleSubstitutionModel *simpleModel, double lambda=0, double mu=0) | bpp::RE08 | |
RE08(const RE08 &model) | bpp::RE08 | inline |
ReversibleSubstitutionModel() | bpp::ReversibleSubstitutionModel | inline |
rightEigenVectors_ | bpp::AbstractSubstitutionModel | protected |
setFreq(std::map< int, double > &) | bpp::AbstractSubstitutionModel | virtual |
setFreqFromData(const SequenceContainer &data, double pseudoCount=0) | bpp::RE08 | inlinevirtual |
setNamespace(const std::string &prefix) | bpp::RE08 | |
setRate(double rate) | bpp::AbstractSubstitutionModel | virtual |
setScale(double scale) | bpp::AbstractSubstitutionModel | virtual |
Sij(size_t i, size_t j) const | bpp::AbstractSubstitutionModel | inlinevirtual |
simpleExchangeabilities_ | bpp::RE08 | private |
simpleGenerator_ | bpp::RE08 | private |
simpleModel_ | bpp::RE08 | private |
size_ | bpp::AbstractSubstitutionModel | protected |
stateMap_ | bpp::AbstractSubstitutionModel | protected |
SubstitutionModel() | bpp::SubstitutionModel | inline |
tmpMat_ | bpp::AbstractSubstitutionModel | mutableprotected |
updateMatrices() | bpp::RE08 | protectedvirtual |
vPowGen_ | bpp::AbstractSubstitutionModel | protected |
~AbstractReversibleSubstitutionModel() | bpp::AbstractReversibleSubstitutionModel | inlinevirtual |
~AbstractSubstitutionModel() | bpp::AbstractSubstitutionModel | inlinevirtual |
~RE08() | bpp::RE08 | inlinevirtual |
~ReversibleSubstitutionModel() | bpp::ReversibleSubstitutionModel | inlinevirtual |
~SubstitutionModel() | bpp::SubstitutionModel | inlinevirtual |