bpp-phyl  2.2.0
bpp::AbstractMixedSubstitutionModel Member List

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

AbstractMixedSubstitutionModel(const Alphabet *, StateMap *stateMap, const std::string &prefix)bpp::AbstractMixedSubstitutionModel
AbstractMixedSubstitutionModel(const AbstractMixedSubstitutionModel &)bpp::AbstractMixedSubstitutionModel
AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
bpp::addRateParameter()=0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::addRateParameter()bpp::AbstractSubstitutionModelvirtual
alphabet_bpp::AbstractSubstitutionModelprotected
clone() const =0bpp::AbstractMixedSubstitutionModelpure virtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) constbpp::AbstractSubstitutionModelinlinevirtual
d2pijt_bpp::AbstractSubstitutionModelmutableprotected
bpp::dPij_dt(size_t i, size_t j, double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::dPij_dt(size_t i, size_t j, double t) constbpp::AbstractSubstitutionModelinlinevirtual
dpijt_bpp::AbstractSubstitutionModelmutableprotected
eigenDecompose_bpp::AbstractSubstitutionModelprotected
eigenValues_bpp::AbstractSubstitutionModelprotected
bpp::enableEigenDecomposition(bool yn)=0bpp::SubstitutionModelpure virtual
bpp::enableEigenDecomposition()=0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::enableEigenDecomposition(bool yn)bpp::AbstractSubstitutionModelinlinevirtual
bpp::AbstractSubstitutionModel::enableEigenDecomposition()bpp::AbstractSubstitutionModelinlinevirtual
exchangeability_bpp::AbstractSubstitutionModelprotected
fireParameterChanged(const ParameterList &parameters)bpp::AbstractSubstitutionModelinlinevirtual
bpp::freq(size_t i) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::freq(size_t i) constbpp::AbstractSubstitutionModelinlinevirtual
freq_bpp::AbstractSubstitutionModelprotected
generator_bpp::AbstractSubstitutionModelprotected
bpp::getAlphabet() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getAlphabet() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getAlphabetStateAsChar(size_t index) constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(size_t index) constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getAlphabetStates() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getAlphabetStates() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getColumnRightEigenVectors() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getColumnRightEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
getd2Pij_dt2(double t) constbpp::AbstractMixedSubstitutionModelvirtual
getdPij_dt(double t) constbpp::AbstractMixedSubstitutionModelvirtual
bpp::getEigenValues() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getExchangeabilityMatrix() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getExchangeabilityMatrix() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getFrequencies() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getFrequencies() constbpp::AbstractSubstitutionModelinlinevirtual
getFrequenciesSet() constbpp::SubstitutionModelinlinevirtual
bpp::getGenerator() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getGenerator() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getIEigenValues() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getIEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getInitValue(size_t i, int state) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getInitValue(size_t i, int state) constbpp::AbstractSubstitutionModelvirtual
bpp::getModelStates(int code) const =0bpp::SubstitutionModelpure virtual
bpp::getModelStates(const std::string &code) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getModelStates(int code) constbpp::AbstractSubstitutionModelinlinevirtual
bpp::AbstractSubstitutionModel::getModelStates(const std::string &code) constbpp::AbstractSubstitutionModelinlinevirtual
getName() const =0bpp::SubstitutionModelpure virtual
getNModel(size_t i) constbpp::AbstractMixedSubstitutionModelinlinevirtual
getNModel(size_t i)bpp::AbstractMixedSubstitutionModelinlinevirtual
getNProbability(size_t i) constbpp::AbstractMixedSubstitutionModelinlinevirtual
getNRate(size_t i) constbpp::AbstractMixedSubstitutionModelinlinevirtual
getNumberOfModels() constbpp::AbstractMixedSubstitutionModelinlinevirtual
getNumberOfStates() constbpp::AbstractMixedSubstitutionModelvirtual
getPij_t(double t) constbpp::AbstractMixedSubstitutionModelvirtual
getProbabilities() constbpp::AbstractMixedSubstitutionModelinlinevirtual
bpp::getRate() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getRate() constbpp::AbstractSubstitutionModelvirtual
bpp::getRowLeftEigenVectors() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getRowLeftEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getScale() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getScale() constbpp::AbstractSubstitutionModelvirtual
bpp::getStateMap() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::getStateMap() constbpp::AbstractSubstitutionModelinlinevirtual
getSubmodelNumbers(std::string &desc) const =0bpp::MixedSubstitutionModelpure virtual
getVRates() constbpp::AbstractMixedSubstitutionModelinlinevirtual
iEigenValues_bpp::AbstractSubstitutionModelprotected
bpp::isDiagonalizable() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::isDiagonalizable() constbpp::AbstractSubstitutionModelinlinevirtual
isDiagonalizable_bpp::AbstractSubstitutionModelprotected
bpp::isNonSingular() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::isNonSingular() constbpp::AbstractSubstitutionModelinlinevirtual
isNonSingular_bpp::AbstractSubstitutionModelprotected
leftEigenVectors_bpp::AbstractSubstitutionModelprotected
MixedSubstitutionModel()bpp::MixedSubstitutionModelinline
modelsContainer_bpp::AbstractMixedSubstitutionModelprotected
normalizeVRates()bpp::AbstractMixedSubstitutionModelvirtual
operator=(const AbstractMixedSubstitutionModel &)bpp::AbstractMixedSubstitutionModel
bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
bpp::Pij_t(size_t i, size_t j, double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::Pij_t(size_t i, size_t j, double t) constbpp::AbstractSubstitutionModelinlinevirtual
pijt_bpp::AbstractSubstitutionModelmutableprotected
Qij(size_t i, size_t j) constbpp::AbstractMixedSubstitutionModelinlinevirtual
rate_bpp::AbstractSubstitutionModelprotected
rightEigenVectors_bpp::AbstractSubstitutionModelprotected
bpp::setFreq(std::map< int, double > &frequencies)bpp::SubstitutionModelinlinevirtual
bpp::AbstractSubstitutionModel::setFreq(std::map< int, double > &)bpp::AbstractSubstitutionModelvirtual
bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)bpp::AbstractSubstitutionModelvirtual
setNProbability(size_t i, double prob)bpp::AbstractMixedSubstitutionModelinlinevirtual
setRate(double rate)bpp::AbstractMixedSubstitutionModelvirtual
bpp::setScale(double scale)=0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::setScale(double scale)bpp::AbstractSubstitutionModelvirtual
setVRates(const Vdouble &vd)bpp::AbstractMixedSubstitutionModelvirtual
bpp::Sij(size_t i, size_t j) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractSubstitutionModel::Sij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
size_bpp::AbstractSubstitutionModelprotected
stateMap_bpp::AbstractSubstitutionModelprotected
SubstitutionModel()bpp::SubstitutionModelinline
tmpMat_bpp::AbstractSubstitutionModelmutableprotected
updateMatrices()bpp::AbstractSubstitutionModelprotectedvirtual
vPowGen_bpp::AbstractSubstitutionModelprotected
vProbas_bpp::AbstractMixedSubstitutionModelprotected
vRates_bpp::AbstractMixedSubstitutionModelprotected
~AbstractMixedSubstitutionModel()bpp::AbstractMixedSubstitutionModelvirtual
~AbstractSubstitutionModel()bpp::AbstractSubstitutionModelinlinevirtual
~MixedSubstitutionModel()bpp::MixedSubstitutionModelinlinevirtual
~SubstitutionModel()bpp::SubstitutionModelinlinevirtual