, 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::AbstractParameterAliasable | [protected] |
| addParameters_(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | [protected] |
| bpp::addRateParameter()=0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::addRateParameter() | bpp::AbstractBiblioSubstitutionModel | [virtual] |
| bpp::aliasParameters(const std::string &p1, const std::string &p2)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2) | bpp::AbstractParameterAliasable | [virtual] |
| Clonable() | bpp::Clonable | |
| clone() const | bpp::LLG08_EX2 | [inline, virtual] |
| bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| deleteParameter_(size_t index) | bpp::AbstractParameterAliasable | [protected] |
| bpp::dPij_dt(size_t i, size_t j, double t) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::enableEigenDecomposition(bool yn)=0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::enableEigenDecomposition()=0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(bool yn) | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition() | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| fireParameterChanged(const ParameterList ¶meters) | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::freq(size_t i) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::freq(size_t i) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getAlias(const std::string &name) const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getAlias(const std::string &name) const | bpp::AbstractParameterAliasable | [virtual] |
| bpp::getAlphabet() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getAlphabet() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getAlphabetChar(size_t i) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(size_t i) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getAlphabetChars() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getAlphabetChars() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getColumnRightEigenVectors() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getd2Pij_dt2(double t) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(double t) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getdPij_dt(double t) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getdPij_dt(double t) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getEigenValues() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getEigenValues() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getExchangeabilityMatrix() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getFrequencies() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getFrequencies() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getFrequenciesSet() const | bpp::SubstitutionModel | [inline, virtual] |
| bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| getFrom(const std::string &name) const | bpp::AbstractParameterAliasable | |
| bpp::getGenerator() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getGenerator() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getIEigenValues() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getIEigenValues() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getIndependentParameters() const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getIndependentParameters() const | bpp::AbstractParameterAliasable | [virtual] |
| bpp::getInitValue(size_t i, int state) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getInitValue(size_t i, int state) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| getMixedModel() const | bpp::LLG08_EX2 | [inline, virtual] |
| getMixedModel() | bpp::LLG08_EX2 | [inline, private, virtual] |
| getModel() const | bpp::LLG08_EX2 | [inline, virtual] |
| getModel() | bpp::LLG08_EX2 | [inline, private, virtual] |
| bpp::getModelStates(int i) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getModelStates(int i) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| getName() const | bpp::LLG08_EX2 | [inline, virtual] |
| bpp::getNamespace() const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getNamespace() const | bpp::AbstractParameterAliasable | [virtual] |
| getNModel(size_t i) const | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| getNModel(size_t i) | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| getNProbability(size_t i) const | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| getNRate(size_t i) const | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| bpp::getNumberOfIndependentParameters() const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() const | bpp::AbstractParameterAliasable | [virtual] |
| getNumberOfModels() const | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| bpp::getNumberOfParameters() const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getNumberOfParameters() const | bpp::AbstractParameterAliasable | [virtual] |
| bpp::getNumberOfStates() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getNumberOfStates() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getParameter(const std::string &name) const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getParameter(const std::string &name) const | bpp::AbstractParameterAliasable | [virtual] |
| getParameter_(const std::string &name) | bpp::AbstractParameterAliasable | [protected] |
| getParameter_(size_t index) | bpp::AbstractParameterAliasable | [protected] |
| getParameter_(size_t index) const | bpp::AbstractParameterAliasable | [protected] |
| bpp::getParameterNameWithoutNamespace(const std::string &name) const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const | bpp::AbstractParameterAliasable | [virtual] |
| bpp::getParameters() const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getParameters() const | bpp::AbstractParameterAliasable | [virtual] |
| getParameters_() | bpp::AbstractParameterAliasable | [protected] |
| bpp::getParameterValue(const std::string &name) const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const | bpp::AbstractParameterAliasable | [virtual] |
| getParameterWithNamespace_(const std::string &name) | bpp::AbstractParameterAliasable | [protected] |
| getParameterWithNamespace_(const std::string &name) const | bpp::AbstractParameterAliasable | [protected] |
| bpp::getPij_t(double t) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getPij_t(double t) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| getProbabilities() const | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| bpp::getRate() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getRate() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getRowLeftEigenVectors() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::getScale() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::getScale() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| getSubmodelNumbers(std::string &desc) const | bpp::AbstractBiblioMixedSubstitutionModel | [virtual] |
| getVRates() const | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| bpp::hasParameter(const std::string &name) const =0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const | bpp::AbstractParameterAliasable | [virtual] |
| bpp::isDiagonalizable() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::isDiagonalizable() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::isNonSingular() const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::isNonSingular() const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| LLG08_EX2(const ProteicAlphabet *alpha) | bpp::LLG08_EX2 | |
| LLG08_EX2(const LLG08_EX2 &) | bpp::LLG08_EX2 | |
| lParPmodel_ | bpp::AbstractBiblioSubstitutionModel | [protected] |
| mapParNamesFromPmodel_ | bpp::AbstractBiblioSubstitutionModel | [protected] |
| bpp::matchParametersValues(const ParameterList ¶meters)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | [virtual] |
| MixedSubstitutionModel() | bpp::MixedSubstitutionModel | [inline] |
| normalizeVRates() | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| operator=(const LLG08_EX2 &) | bpp::LLG08_EX2 | |
| 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 =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::Pij_t(size_t i, size_t j, double t) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| pmixmodel_ | bpp::LLG08_EX2 | [private] |
| bpp::Qij(size_t i, size_t j) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::Qij(size_t i, size_t j) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| resetParameters_() | bpp::AbstractParameterAliasable | [protected] |
| bpp::setAllParametersValues(const ParameterList ¶meters)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | [virtual] |
| bpp::setFreq(std::map< int, double > &frequencies) | bpp::SubstitutionModel | [inline, virtual] |
| bpp::AbstractBiblioSubstitutionModel::setFreq(std::map< int, double > &frequ) | bpp::AbstractBiblioSubstitutionModel | [virtual] |
| bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0) | bpp::AbstractBiblioSubstitutionModel | [virtual] |
| bpp::setNamespace(const std::string &prefix)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::setNamespace(const std::string &prefix) | bpp::AbstractParameterAliasable | [virtual] |
| setNProbability(size_t i, double prob) | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| bpp::setParametersValues(const ParameterList ¶meters)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::setParametersValues(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | [virtual] |
| bpp::setParameterValue(const std::string &name, double value)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) | bpp::AbstractParameterAliasable | [virtual] |
| bpp::setRate(double rate)=0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::setRate(double rate) | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| bpp::setScale(double scale)=0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::setScale(double scale) | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| setVRates(const Vdouble &vd) | bpp::AbstractBiblioMixedSubstitutionModel | [inline, virtual] |
| bpp::Sij(size_t i, size_t j) const =0 | bpp::SubstitutionModel | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::Sij(size_t i, size_t j) const | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| SubstitutionModel() | bpp::SubstitutionModel | [inline] |
| bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0 | bpp::ParameterAliasable | [pure virtual] |
| bpp::AbstractBiblioSubstitutionModel::bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2) | bpp::AbstractParameterAliasable | [virtual] |
| updateMatrices() | bpp::AbstractBiblioSubstitutionModel | [protected, virtual] |
| ~AbstractBiblioMixedSubstitutionModel() | bpp::AbstractBiblioMixedSubstitutionModel | [virtual] |
| ~AbstractBiblioSubstitutionModel() | bpp::AbstractBiblioSubstitutionModel | [inline, virtual] |
| ~AbstractParameterAliasable() | bpp::AbstractParameterAliasable | [virtual] |
| ~AbstractParametrizable() | bpp::AbstractParametrizable | [virtual] |
| ~Clonable() | bpp::Clonable | [virtual] |
| ~LLG08_EX2() | bpp::LLG08_EX2 | |
| ~MixedSubstitutionModel() | bpp::MixedSubstitutionModel | [inline, virtual] |
| ~ParameterAliasable() | bpp::ParameterAliasable | [virtual] |
| ~Parametrizable() | bpp::Parametrizable | [virtual] |
| ~SubstitutionModel() | bpp::SubstitutionModel | [inline, virtual] |
1.7.6.1 
