bpp-phyl3 3.0.0
bpp::CodonFromIndependentFrequencySet Member List

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

AbstractFrequencySet(std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix, const std::string &name)bpp::AbstractFrequencySetinline
AbstractFrequencySet(const AbstractFrequencySet &af)bpp::AbstractFrequencySetinline
AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractWordFrequencySet(std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix="", const std::string &name="")bpp::AbstractWordFrequencySet
AbstractWordFrequencySet(const AbstractWordFrequencySet &af)bpp::AbstractWordFrequencySetinline
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::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::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
bpp::alphabet() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::alphabet() const overridebpp::AbstractFrequencySetinlinevirtual
alphabet_bpp::AbstractFrequencySetprivate
clone() const overridebpp::CodonFromIndependentFrequencySetinlinevirtual
CodonFromIndependentFrequencySet(std::shared_ptr< const GeneticCode > gCode, std::vector< std::unique_ptr< FrequencySetInterface > > &freqvector, const std::string &name="Codon", const std::string &mgmtStopCodon="quadratic")bpp::CodonFromIndependentFrequencySet
CodonFromIndependentFrequencySet(const CodonFromIndependentFrequencySet &iwfs)bpp::CodonFromIndependentFrequencySet
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
F0bpp::CodonFrequencySetInterfacestatic
F1X4bpp::CodonFrequencySetInterfacestatic
F3X4bpp::CodonFrequencySetInterfacestatic
F61bpp::CodonFrequencySetInterfacestatic
fireParameterChanged(const ParameterList &pl) overridebpp::WordFromIndependentFrequencySetvirtual
freq_bpp::AbstractFrequencySetprivate
FREQUENCE_CONSTRAINT_CENTIbpp::FrequencySetInterfacestatic
FREQUENCE_CONSTRAINT_MILLIbpp::FrequencySetInterfacestatic
FREQUENCE_CONSTRAINT_SMALLbpp::FrequencySetInterfacestatic
frequencySetForLetter(size_t i) const overridebpp::WordFromIndependentFrequencySetinlinevirtual
bpp::getAlias(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getAliases() const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getAliases() constbpp::AbstractParameterAliasablevirtual
bpp::getAlphabet() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::getAlphabet() const overridebpp::AbstractFrequencySetinlinevirtual
bpp::getAlphabetStatesFrequencies() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::getAlphabetStatesFrequencies() const overridebpp::AbstractFrequencySetvirtual
getCodonAlphabet() const overridebpp::CodonFromIndependentFrequencySetvirtual
getDescription() constbpp::WordFromIndependentFrequencySet
getFreq_(size_t i)bpp::AbstractFrequencySetinlineprotected
getFreq_(size_t i) constbpp::AbstractFrequencySetinlineprotected
bpp::getFrequencies() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::getFrequencies() const overridebpp::AbstractFrequencySetinlinevirtual
getFrequencies_()bpp::AbstractFrequencySetinlineprotected
getFrequencySetForCodons(short option, std::shared_ptr< const GeneticCode > gCode, const std::string &mgmtStopCodon="quadratic", unsigned short method=1)bpp::CodonFrequencySetInterfacestatic
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getGeneticCode() const overridebpp::CodonFromIndependentFrequencySetinlinevirtual
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getLength() const overridebpp::WordFromIndependentFrequencySetvirtual
getMgmtStopCodon() constbpp::CodonFromIndependentFrequencySetinline
bpp::getName() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::getName() const overridebpp::AbstractFrequencySetinlinevirtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
bpp::getNumberOfFrequencies() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::getNumberOfFrequencies() const overridebpp::AbstractFrequencySetinlinevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
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::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters() const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters_()=0bpp::ParameterAliasableprotectedpure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
getSizeFromVector(const std::vector< std::unique_ptr< FrequencySetInterface > > &freqVector) overridebpp::AbstractWordFrequencySetprotectedvirtual
bpp::getStateMap() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::getStateMap() const overridebpp::AbstractFrequencySetinlinevirtual
getWordAlphabet() const overridebpp::AbstractWordFrequencySetinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
mgmtStopCodon_bpp::CodonFromIndependentFrequencySetprivate
mStopNeigh_bpp::CodonFromIndependentFrequencySetprivate
name_bpp::AbstractFrequencySetprivate
normalize()bpp::AbstractFrequencySetinline
operator=(const CodonFromIndependentFrequencySet &iwfs)bpp::CodonFromIndependentFrequencySet
bpp::WordFromIndependentFrequencySet::operator=(const WordFromIndependentFrequencySet &iwfs)bpp::WordFromIndependentFrequencySet
bpp::AbstractWordFrequencySet::operator=(const AbstractWordFrequencySet &af)bpp::AbstractWordFrequencySetinline
bpp::AbstractFrequencySet::operator=(const AbstractFrequencySet &af)bpp::AbstractFrequencySetinline
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
pgc_bpp::CodonFromIndependentFrequencySetprivate
prefix_bpp::AbstractParameterAliasableprivate
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
bpp::setFrequencies(const std::vector< double > &frequencies)=0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::setFrequencies(const std::vector< double > &frequencies) overridebpp::WordFromIndependentFrequencySetvirtual
setFrequencies_(const std::vector< double > &frequencies)bpp::AbstractFrequencySetinlineprotected
bpp::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies) overridebpp::AbstractFrequencySetvirtual
bpp::setNamespace(const std::string &prefix)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::setNamespace(const std::string &prefix) overridebpp::WordFromIndependentFrequencySetvirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::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
bpp::stateMap() const =0bpp::FrequencySetInterfacepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::stateMap() const overridebpp::AbstractFrequencySetinlinevirtual
stateMap_bpp::AbstractFrequencySetprivate
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::WordFromIndependentFrequencySet::bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
updateFrequencies() overridebpp::CodonFromIndependentFrequencySetvirtual
vFreq_bpp::WordFromIndependentFrequencySetprotected
vNestedPrefix_bpp::WordFromIndependentFrequencySetprotected
WordFromIndependentFrequencySet(std::shared_ptr< const WordAlphabet > pWA, std::vector< std::unique_ptr< FrequencySetInterface > > &freqVector, const std::string &prefix="", const std::string &name="WordFromIndependent")bpp::WordFromIndependentFrequencySet
WordFromIndependentFrequencySet(std::shared_ptr< const CodonAlphabet > pWA, std::vector< std::unique_ptr< FrequencySetInterface > > &freqVector, const std::string &prefix="", const std::string &name="WordFromIndependent")bpp::WordFromIndependentFrequencySet
WordFromIndependentFrequencySet(const WordFromIndependentFrequencySet &iwfs)bpp::WordFromIndependentFrequencySet
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractWordFrequencySet()bpp::AbstractWordFrequencySetvirtual
~Clonable()=defaultbpp::Clonablevirtual
~CodonFromIndependentFrequencySet()bpp::CodonFromIndependentFrequencySetinlinevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~WordFromIndependentFrequencySet()bpp::WordFromIndependentFrequencySetvirtual