bpp-phyl3 3.0.0
bpp::SubstitutionProcessCollectionMember Member List

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

AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractSubstitutionProcess()bpp::AbstractSubstitutionProcessinline
addModel(size_t numModel, const std::vector< unsigned int > &nodesId)bpp::SubstitutionProcessCollectionMember
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
checkOrphanNodes(bool throwEx) constbpp::SubstitutionProcessCollectionMemberprotected
checkUnknownNodes(bool throwEx) constbpp::SubstitutionProcessCollectionMemberprotected
clear()bpp::SubstitutionProcessCollectionMemberinline
clone() const overridebpp::SubstitutionProcessCollectionMemberinlineprivatevirtual
collection() constbpp::SubstitutionProcessCollectionMemberinline
collection()bpp::SubstitutionProcessCollectionMemberinline
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::AbstractParameterAliasablevirtual
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
getAlphabet() constbpp::AbstractSubstitutionProcessinline
getBranchLengthParameters(bool independent) const overridebpp::SubstitutionProcessCollectionMembervirtual
getClassProbabilities() const overridebpp::SubstitutionProcessCollectionMembervirtual
getCollection() constbpp::SubstitutionProcessCollectionMemberinline
getCollection()bpp::SubstitutionProcessCollectionMemberinline
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getModel(size_t n) const overridebpp::SubstitutionProcessCollectionMembervirtual
getModel(size_t n)bpp::SubstitutionProcessCollectionMember
getModel(unsigned int nodeId, size_t classIndex) const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
getModelForNode(unsigned int nodeId) const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
getModelNumberForNode(unsigned int nodeId) const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
getModelNumbers() const overridebpp::SubstitutionProcessCollectionMembervirtual
getModelScenario() const overridebpp::SubstitutionProcessCollectionMembervirtual
getModelScenario()bpp::SubstitutionProcessCollectionMember
getModelScenarioNumber() constbpp::SubstitutionProcessCollectionMemberinline
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNodesWithModel(size_t i) const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
getNonDerivableParameters() const overridebpp::SubstitutionProcessCollectionMembervirtual
getNumberOfClasses() constbpp::AbstractSubstitutionProcessinlinevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfModels() const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfProcesses() constbpp::SubstitutionProcessCollectionMemberinline
getNumberOfStates() constbpp::AbstractSubstitutionProcessinlinevirtual
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
getParametrizablePhyloTree() const overridebpp::SubstitutionProcessCollectionMembervirtual
getParametrizablePhyloTree()bpp::SubstitutionProcessCollectionMember
getProbabilityForModel(size_t classIndex) const overridebpp::SubstitutionProcessCollectionMembervirtual
getRateDistribution() const overridebpp::SubstitutionProcessCollectionMembervirtual
getRateDistribution() overridebpp::SubstitutionProcessCollectionMembervirtual
getRateDistributionNumber() constbpp::SubstitutionProcessCollectionMemberinline
getRateDistributionParameters(bool independent) const overridebpp::SubstitutionProcessCollectionMembervirtual
getRateForModel(size_t classIndex) const overridebpp::SubstitutionProcessCollectionMembervirtual
getRootFrequencies() const overridebpp::SubstitutionProcessCollectionMembervirtual
getRootFrequenciesNumber() constbpp::SubstitutionProcessCollectionMemberinline
getRootFrequenciesParameters(bool independent) const overridebpp::SubstitutionProcessCollectionMembervirtual
getRootFrequencySet() const overridebpp::SubstitutionProcessCollectionMembervirtual
getRootFrequencySet() overridebpp::SubstitutionProcessCollectionMembervirtual
getStateMap() const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
getSubstitutionModelParameters(bool independent) const overridebpp::SubstitutionProcessCollectionMembervirtual
getTreeNumber() constbpp::SubstitutionProcessCollectionMemberinline
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
hasMixedTransitionModel() constbpp::SubstitutionProcessCollectionMember
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
hasRootFrequencySet() const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isCompatibleWith(const AlignmentDataInterface &data) constbpp::AbstractSubstitutionProcessinlinevirtual
isFullySetUp(bool throwEx=true) constbpp::SubstitutionProcessCollectionMemberinline
isStationary() constbpp::SubstitutionProcessCollectionMemberinline
matchParametersValues(const ParameterList &parameters) overridebpp::SubstitutionProcessCollectionMembervirtual
model(size_t n) const overridebpp::SubstitutionProcessCollectionMembervirtual
model(unsigned int nodeId, size_t classIndex) const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
modelToNodes_bpp::SubstitutionProcessCollectionMemberprivate
nDist_bpp::SubstitutionProcessCollectionMemberprivate
nodeToModel_bpp::SubstitutionProcessCollectionMemberprivate
nPath_bpp::SubstitutionProcessCollectionMemberprivate
nProc_bpp::SubstitutionProcessCollectionMemberprivate
nRoot_bpp::SubstitutionProcessCollectionMemberprivate
nTree_bpp::SubstitutionProcessCollectionMemberprivate
operator=(const SubstitutionProcessCollectionMember &set)bpp::SubstitutionProcessCollectionMemberinlineprivate
bpp::AbstractSubstitutionProcess::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
parametrizablePhyloTree() const overridebpp::SubstitutionProcessCollectionMembervirtual
parametrizablePhyloTree()bpp::SubstitutionProcessCollectionMember
prefix_bpp::AbstractParameterAliasableprivate
pSubProColl_bpp::SubstitutionProcessCollectionMemberprivate
rateDistribution() const overridebpp::SubstitutionProcessCollectionMembervirtual
rateDistribution() overridebpp::SubstitutionProcessCollectionMembervirtual
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
rootFrequencySet() const overridebpp::SubstitutionProcessCollectionMembervirtual
rootFrequencySet() overridebpp::SubstitutionProcessCollectionMembervirtual
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
setModelScenario(size_t numPath)bpp::SubstitutionProcessCollectionMember
bpp::setNamespace(const std::string &prefix)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
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
setRootFrequencies(size_t numFreq)bpp::SubstitutionProcessCollectionMember
setTreeNumber(size_t nTree, bool check=true)bpp::SubstitutionProcessCollectionMember
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
stateMap() const overridebpp::SubstitutionProcessCollectionMemberinlinevirtual
SubstitutionProcessCollectionbpp::SubstitutionProcessCollectionMemberfriend
SubstitutionProcessCollectionMember(SubstitutionProcessCollection *pSubProColl, size_t nProc, size_t nTree, size_t nDist)bpp::SubstitutionProcessCollectionMemberinlineprivate
SubstitutionProcessCollectionMember(const SubstitutionProcessCollectionMember &set)bpp::SubstitutionProcessCollectionMemberinlineprivate
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
updateParameters()bpp::SubstitutionProcessCollectionMemberprivate
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~Clonable()=defaultbpp::Clonablevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~SubstitutionProcessCollectionMember()bpp::SubstitutionProcessCollectionMemberinlineprivatevirtual