bpp-phyl  2.2.0
bpp::TripletSubstitutionModel Member List

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

AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
AbstractWordSubstitutionModel(const std::vector< SubstitutionModel *> &modelVector, const std::string &prefix)bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(SubstitutionModel *pmodel, unsigned int num, const std::string &prefix)bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const AbstractWordSubstitutionModel &)bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const Alphabet *alph, StateMap *stateMap, const std::string &prefix)bpp::AbstractWordSubstitutionModelprotected
addRateParameter()bpp::AbstractSubstitutionModelvirtual
alphabet_bpp::AbstractSubstitutionModelprotected
clone() constbpp::TripletSubstitutionModelinlinevirtual
completeMatrices()bpp::WordSubstitutionModelprotectedvirtual
d2Pij_dt2(size_t i, size_t j, double t) constbpp::AbstractSubstitutionModelinlinevirtual
d2pijt_bpp::AbstractSubstitutionModelmutableprotected
dPij_dt(size_t i, size_t j, double t) constbpp::AbstractSubstitutionModelinlinevirtual
dpijt_bpp::AbstractSubstitutionModelmutableprotected
eigenDecompose_bpp::AbstractSubstitutionModelprotected
eigenValues_bpp::AbstractSubstitutionModelprotected
enableEigenDecomposition(bool yn)bpp::AbstractSubstitutionModelinlinevirtual
enableEigenDecomposition()bpp::AbstractSubstitutionModelinlinevirtual
exchangeability_bpp::AbstractSubstitutionModelprotected
extractAlph(const std::vector< SubstitutionModel *> &modelVector)bpp::AbstractWordSubstitutionModelprotectedstatic
fireParameterChanged(const ParameterList &parameters)bpp::AbstractSubstitutionModelinlinevirtual
freq(size_t i) constbpp::AbstractSubstitutionModelinlinevirtual
freq_bpp::AbstractSubstitutionModelprotected
generator_bpp::AbstractSubstitutionModelprotected
getAlphabet() constbpp::AbstractSubstitutionModelinlinevirtual
getAlphabetStateAsChar(size_t index) constbpp::AbstractSubstitutionModelinlinevirtual
getAlphabetStateAsInt(size_t index) constbpp::AbstractSubstitutionModelinlinevirtual
getAlphabetStates() constbpp::AbstractSubstitutionModelinlinevirtual
getColumnRightEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
getd2Pij_dt2(double d) constbpp::WordSubstitutionModelvirtual
getdPij_dt(double d) constbpp::WordSubstitutionModelvirtual
getEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
getExchangeabilityMatrix() constbpp::AbstractSubstitutionModelinlinevirtual
getFrequencies() constbpp::AbstractSubstitutionModelinlinevirtual
getFrequenciesSet() constbpp::SubstitutionModelinlinevirtual
getGenerator() constbpp::AbstractSubstitutionModelinlinevirtual
getIEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
getInitValue(size_t i, int state) constbpp::AbstractSubstitutionModelvirtual
getModelStates(int code) constbpp::AbstractSubstitutionModelinlinevirtual
getModelStates(const std::string &code) constbpp::AbstractSubstitutionModelinlinevirtual
getName() constbpp::TripletSubstitutionModelvirtual
getNModel(size_t i) constbpp::AbstractWordSubstitutionModelinline
getNumberOfModels() constbpp::AbstractWordSubstitutionModelinline
getNumberOfStates() constbpp::AbstractWordSubstitutionModelvirtual
getPij_t(double d) constbpp::WordSubstitutionModelvirtual
getRate() constbpp::AbstractSubstitutionModelvirtual
getRowLeftEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
getScale() constbpp::AbstractSubstitutionModelvirtual
getStateMap() constbpp::AbstractSubstitutionModelinlinevirtual
iEigenValues_bpp::AbstractSubstitutionModelprotected
isDiagonalizable() constbpp::AbstractSubstitutionModelinlinevirtual
isDiagonalizable_bpp::AbstractSubstitutionModelprotected
isNonSingular() constbpp::AbstractSubstitutionModelinlinevirtual
isNonSingular_bpp::AbstractSubstitutionModelprotected
leftEigenVectors_bpp::AbstractSubstitutionModelprotected
operator=(const AbstractWordSubstitutionModel &)bpp::AbstractWordSubstitutionModel
bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
Pij_t(size_t i, size_t j, double t) constbpp::AbstractSubstitutionModelinlinevirtual
pijt_bpp::AbstractSubstitutionModelmutableprotected
Qij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
rate_bpp::AbstractSubstitutionModelprotected
rightEigenVectors_bpp::AbstractSubstitutionModelprotected
setFreq(std::map< int, double > &freqs)bpp::AbstractWordSubstitutionModelvirtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)bpp::AbstractSubstitutionModelvirtual
setNamespace(const std::string &prefix)bpp::AbstractWordSubstitutionModel
setRate(double rate)bpp::AbstractSubstitutionModelvirtual
setScale(double scale)bpp::AbstractSubstitutionModelvirtual
Sij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
size_bpp::AbstractSubstitutionModelprotected
stateMap_bpp::AbstractSubstitutionModelprotected
SubstitutionModel()bpp::SubstitutionModelinline
tmpMat_bpp::AbstractSubstitutionModelmutableprotected
TripletSubstitutionModel(const CodonAlphabet *palph, NucleotideSubstitutionModel *pmod)bpp::TripletSubstitutionModel
TripletSubstitutionModel(const CodonAlphabet *palph, NucleotideSubstitutionModel *pmod1, NucleotideSubstitutionModel *pmod2, NucleotideSubstitutionModel *pmod3)bpp::TripletSubstitutionModel
updateMatrices()bpp::WordSubstitutionModelprotectedvirtual
VnestedPrefix_bpp::AbstractWordSubstitutionModelprotected
vPowGen_bpp::AbstractSubstitutionModelprotected
Vrate_bpp::AbstractWordSubstitutionModelprotected
VSubMod_bpp::AbstractWordSubstitutionModelprotected
WordSubstitutionModel(const std::vector< SubstitutionModel *> &modelVector, const std::string &prefix="")bpp::WordSubstitutionModel
WordSubstitutionModel(SubstitutionModel *pmodel, unsigned int num, const std::string &prefix="")bpp::WordSubstitutionModel
WordSubstitutionModel(const Alphabet *alph, StateMap *stateMap, const std::string &prefix="")bpp::WordSubstitutionModelprotected
~AbstractSubstitutionModel()bpp::AbstractSubstitutionModelinlinevirtual
~AbstractWordSubstitutionModel()bpp::AbstractWordSubstitutionModelvirtual
~SubstitutionModel()bpp::SubstitutionModelinlinevirtual
~TripletSubstitutionModel()bpp::TripletSubstitutionModelinline
~WordSubstitutionModel()bpp::WordSubstitutionModelinlinevirtual