bpp-phyl  2.1.0
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bpp::YNGKP_M1 Member List

This is the complete list of members for bpp::YNGKP_M1, including all inherited members.

AbstractBiblioMixedSubstitutionModel(const std::string &prefix)bpp::AbstractBiblioMixedSubstitutionModel
AbstractBiblioMixedSubstitutionModel(const AbstractBiblioMixedSubstitutionModel &model)bpp::AbstractBiblioMixedSubstitutionModel
AbstractBiblioSubstitutionModel(const std::string &prefix)bpp::AbstractBiblioSubstitutionModel
AbstractBiblioSubstitutionModel(const AbstractBiblioSubstitutionModel &model)bpp::AbstractBiblioSubstitutionModel
AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotected
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotected
bpp::addRateParameter()=0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::addRateParameter()bpp::AbstractBiblioSubstitutionModelvirtual
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
Clonable()bpp::Clonable
clone() const bpp::YNGKP_M1inlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotected
bpp::dPij_dt(size_t i, size_t j, double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::enableEigenDecomposition(bool yn)=0bpp::SubstitutionModelpure virtual
bpp::enableEigenDecomposition()=0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(bool yn)bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition()bpp::AbstractBiblioSubstitutionModelinlinevirtual
fireParameterChanged(const ParameterList &parameters)bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::freq(size_t i) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::freq(size_t i) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getAlias(const std::string &name) const =0bpp::ParameterAliasablepure virtual
bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getAlias(const std::string &name) const bpp::AbstractParameterAliasablevirtual
bpp::getAlphabet() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabet() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getAlphabetChar(size_t i) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(size_t i) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getAlphabetChars() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabetChars() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getColumnRightEigenVectors() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getd2Pij_dt2(double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(double t) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getdPij_dt(double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getdPij_dt(double t) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getEigenValues() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getEigenValues() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getExchangeabilityMatrix() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getFrequencies() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getFrequencies() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getFrequenciesSet() const bpp::SubstitutionModelinlinevirtual
bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getGenerator() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getGenerator() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getIEigenValues() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getIEigenValues() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getIndependentParameters() const =0bpp::ParameterAliasablepure virtual
bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getIndependentParameters() const bpp::AbstractParameterAliasablevirtual
bpp::getInitValue(size_t i, int state) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getInitValue(size_t i, int state) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
getMixedModel() const bpp::YNGKP_M1inlinevirtual
getMixedModel()bpp::YNGKP_M1inlineprivatevirtual
getModel() const bpp::YNGKP_M1inlinevirtual
getModel()bpp::YNGKP_M1inlineprivatevirtual
bpp::getModelStates(int i) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getModelStates(int i) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
getName() const bpp::YNGKP_M1inlinevirtual
getNamespace() const bpp::AbstractParameterAliasable
getNModel(size_t i) const bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
getNModel(size_t i)bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
getNProbability(size_t i) const bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
getNRate(size_t i) const bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
bpp::getNumberOfIndependentParameters() const =0bpp::ParameterAliasablepure virtual
bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() const bpp::AbstractParameterAliasablevirtual
getNumberOfModels() const bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
getNumberOfParameters() const bpp::AbstractParameterAliasable
bpp::getNumberOfStates() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getNumberOfStates() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
getParameter(const std::string &name) const bpp::AbstractParameterAliasable
getParameter_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index) const bpp::AbstractParameterAliasableprotected
getParameterNameWithoutNamespace(const std::string &name) const bpp::AbstractParameterAliasable
getParameters() const bpp::AbstractParameterAliasable
getParameters_()bpp::AbstractParameterAliasableprotected
getParameterValue(const std::string &name) const bpp::AbstractParameterAliasable
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) const bpp::AbstractParameterAliasableprotected
bpp::getPij_t(double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getPij_t(double t) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
getProbabilities() const bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
bpp::getRate() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getRate() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getRowLeftEigenVectors() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::getScale() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::getScale() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
getSubmodelNumbers(std::string &desc) const bpp::AbstractBiblioMixedSubstitutionModelvirtual
getVRates() const bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
hasParameter(const std::string &name) const bpp::AbstractParameterAliasable
bpp::isDiagonalizable() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::isDiagonalizable() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::isNonSingular() const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::isNonSingular() const bpp::AbstractBiblioSubstitutionModelinlinevirtual
lParPmodel_bpp::AbstractBiblioSubstitutionModelprotected
mapParNamesFromPmodel_bpp::AbstractBiblioSubstitutionModelprotected
matchParametersValues(const ParameterList &parameters)bpp::AbstractParameterAliasable
MixedSubstitutionModel()bpp::MixedSubstitutionModelinline
normalizeVRates()bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
operator=(const YNGKP_M1 &)bpp::YNGKP_M1
bpp::AbstractBiblioMixedSubstitutionModel::operator=(const AbstractBiblioMixedSubstitutionModel &model)bpp::AbstractBiblioMixedSubstitutionModel
bpp::AbstractBiblioSubstitutionModel::operator=(const AbstractBiblioSubstitutionModel &model)bpp::AbstractBiblioSubstitutionModel
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
ParameterAliasable()bpp::ParameterAliasable
Parametrizable()bpp::Parametrizable
bpp::Pij_t(size_t i, size_t j, double t) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::Pij_t(size_t i, size_t j, double t) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
pmixmodel_bpp::YNGKP_M1private
bpp::Qij(size_t i, size_t j) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::Qij(size_t i, size_t j) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
ReversibleSubstitutionModel()bpp::ReversibleSubstitutionModelinline
setAllParametersValues(const ParameterList &parameters)bpp::AbstractParameterAliasable
bpp::setFreq(std::map< int, double > &frequencies)bpp::SubstitutionModelinlinevirtual
bpp::AbstractBiblioSubstitutionModel::setFreq(std::map< int, double > &frequ)bpp::AbstractBiblioSubstitutionModelvirtual
bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)bpp::AbstractBiblioSubstitutionModelvirtual
setNamespace(const std::string &prefix)bpp::AbstractParameterAliasable
setNProbability(size_t i, double prob)bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
setParametersValues(const ParameterList &parameters)bpp::AbstractParameterAliasable
setParameterValue(const std::string &name, double value)bpp::AbstractParameterAliasable
bpp::setRate(double rate)=0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::setRate(double rate)bpp::AbstractBiblioSubstitutionModelinlinevirtual
bpp::setScale(double scale)=0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::setScale(double scale)bpp::AbstractBiblioSubstitutionModelinlinevirtual
setVRates(const Vdouble &vd)bpp::AbstractBiblioMixedSubstitutionModelinlinevirtual
bpp::Sij(size_t i, size_t j) const =0bpp::SubstitutionModelpure virtual
bpp::AbstractBiblioSubstitutionModel::Sij(size_t i, size_t j) const bpp::AbstractBiblioSubstitutionModelinlinevirtual
SubstitutionModel()bpp::SubstitutionModelinline
synfrom_bpp::YNGKP_M1private
synto_bpp::YNGKP_M1private
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
updateMatrices()bpp::YNGKP_M1protectedvirtual
YNGKP_M1(const GeneticCode *gc, FrequenciesSet *codonFreqs)bpp::YNGKP_M1
YNGKP_M1(const YNGKP_M1 &)bpp::YNGKP_M1
~AbstractBiblioMixedSubstitutionModel()bpp::AbstractBiblioMixedSubstitutionModelvirtual
~AbstractBiblioSubstitutionModel()bpp::AbstractBiblioSubstitutionModelinlinevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~Clonable()bpp::Clonablevirtual
~MixedSubstitutionModel()bpp::MixedSubstitutionModelinlinevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~ReversibleSubstitutionModel()bpp::ReversibleSubstitutionModelinlinevirtual
~SubstitutionModel()bpp::SubstitutionModelinlinevirtual
~YNGKP_M1()bpp::YNGKP_M1virtual