bpp-phyl3  3.0.0
bpp::HmmSequenceEvolution Member List

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

AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
bpp::AbstractParameterAliasable::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
clone() constbpp::HmmSequenceEvolutioninlinevirtual
collection() constbpp::MultiProcessSequenceEvolutioninline
collection()bpp::MultiProcessSequenceEvolutioninline
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
fireParameterChanged(const ParameterList &parameters)bpp::HmmSequenceEvolutionvirtual
bpp::getAlias(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getAliases() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getAliases() constbpp::AbstractParameterAliasablevirtual
getBranchLengthParameters(bool independent) constbpp::MultiProcessSequenceEvolutionvirtual
getCollection() constbpp::MultiProcessSequenceEvolutioninline
getCollection()bpp::MultiProcessSequenceEvolutioninline
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getHmmProcessAlphabet()bpp::HmmSequenceEvolutioninline
getHmmTransitionMatrix()bpp::HmmSequenceEvolutioninline
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNonDerivableParameters() constbpp::MultiProcessSequenceEvolutionvirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfSubstitutionProcess() constbpp::MultiProcessSequenceEvolutioninline
getParameter(const std::string &name) constbpp::AbstractParameterAliasable
getParameter(size_t i) constbpp::AbstractParameterAliasableprotected
getParameter(size_t i)bpp::AbstractParameterAliasableprotected
getParameter_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index) constbpp::AbstractParameterAliasableprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters_()=0bpp::ParameterAliasableprotectedpure virtual
bpp::AbstractParameterAliasable::getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
getRateDistributionParameters(bool independent) constbpp::MultiProcessSequenceEvolutionvirtual
getRootFrequenciesParameters(bool independent) constbpp::MultiProcessSequenceEvolutionvirtual
getStateMap() constbpp::SequenceEvolutioninline
getSubstitutionModelParameters(bool independent) constbpp::MultiProcessSequenceEvolutionvirtual
getSubstitutionProcess(size_t number) constbpp::MultiProcessSequenceEvolutioninlinevirtual
getSubstitutionProcessNumbers() constbpp::MultiProcessSequenceEvolutioninlinevirtual
getSubstitutionProcessParameters(bool independent) constbpp::MultiProcessSequenceEvolutionvirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
hmmAlph_bpp::HmmSequenceEvolutionprivate
hmmProcessAlphabet() constbpp::HmmSequenceEvolutioninline
hmmProcessAlphabet()bpp::HmmSequenceEvolutioninline
HmmSequenceEvolution(std::shared_ptr< SubstitutionProcessCollection > processColl, std::vector< size_t > &nProc)bpp::HmmSequenceEvolution
HmmSequenceEvolution(const HmmSequenceEvolution &mlc)bpp::HmmSequenceEvolutioninline
hmmTransitionMatrix() constbpp::HmmSequenceEvolutioninline
hmmTransitionMatrix()bpp::HmmSequenceEvolutioninline
hmmTransMat_bpp::HmmSequenceEvolutionprivate
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isCompatibleWith(const AlignmentDataInterface &data) constbpp::MultiProcessSequenceEvolutionvirtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
MultiProcessSequenceEvolution(std::shared_ptr< SubstitutionProcessCollection > processColl, std::vector< size_t > nProc, const std::string &prefix="")bpp::MultiProcessSequenceEvolution
MultiProcessSequenceEvolution(const MultiProcessSequenceEvolution &lik)bpp::MultiProcessSequenceEvolutioninline
nProc_bpp::MultiProcessSequenceEvolutionprotected
operator=(const HmmSequenceEvolution &mlc)bpp::HmmSequenceEvolutioninline
bpp::MultiProcessSequenceEvolution::operator=(const MultiProcessSequenceEvolution &lik)bpp::MultiProcessSequenceEvolutioninline
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
prefix_bpp::AbstractParameterAliasableprivate
processColl_bpp::MultiProcessSequenceEvolutionprotected
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setNamespace(const std::string &nameSpace)bpp::HmmSequenceEvolutionvirtual
setParameters(const ParameterList &parameters)bpp::MultiProcessSequenceEvolution
bpp::setParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
stateMap() constbpp::SequenceEvolutioninline
substitutionProcess(size_t number) constbpp::MultiProcessSequenceEvolutioninlinevirtual
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~Clonable()=defaultbpp::Clonablevirtual
~HmmSequenceEvolution()bpp::HmmSequenceEvolutioninlinevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual