bpp::SubstitutionProcessCollection Member List

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

AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
addDistribution(std::shared_ptr< DiscreteDistributionInterface > distribution, size_t distributionIndex)	bpp::SubstitutionProcessCollection	inline
addFrequencies(std::shared_ptr< FrequencySetInterface > frequencies, size_t frequenciesIndex)	bpp::SubstitutionProcessCollection	inline
addModel(std::shared_ptr< BranchModelInterface > model, size_t modelIndex)	bpp::SubstitutionProcessCollection	inline
addOnePerBranchSubstitutionProcess(size_t nProc, size_t nMod, size_t nTree, size_t nRate, size_t nFreq, const std::vector< std::string > &sharedParameterNames)	bpp::SubstitutionProcessCollection
addOnePerBranchSubstitutionProcess(size_t nProc, size_t nMod, size_t nTree, size_t nRate, const std::vector< std::string > &sharedParameterNames)	bpp::SubstitutionProcessCollection
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
addParametrizable(std::shared_ptr< Parametrizable > parametrizable, size_t parametrizableIndex, bool withParameters=true)	bpp::SubstitutionProcessCollection
addScenario(std::shared_ptr< ModelScenario > scen, size_t scenIndex)	bpp::SubstitutionProcessCollection	inline
addSubstitutionProcess(size_t nProc, std::map< size_t, std::vector< unsigned int >> mModBr, size_t nTree, size_t nRate, size_t nFreq)	bpp::SubstitutionProcessCollection
addSubstitutionProcess(size_t nProc, std::map< size_t, std::vector< unsigned int >> mModBr, size_t nTree, size_t nRate)	bpp::SubstitutionProcessCollection
addTree(std::shared_ptr< ParametrizablePhyloTree > tree, size_t treeIndex)	bpp::SubstitutionProcessCollection	inline
aliasListenersRegister_	bpp::AbstractParameterAliasable	private
aliasParameters(const std::string &p1, const std::string &p2)	bpp::SubstitutionProcessCollection	virtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::SubstitutionProcessCollection	virtual
clear()	bpp::SubstitutionProcessCollection
clone() const	bpp::SubstitutionProcessCollection	inlinevirtual
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
distColl_	bpp::SubstitutionProcessCollection	private
fireParameterChanged(const ParameterList &parameters)	bpp::SubstitutionProcessCollection	virtual
freqColl_	bpp::SubstitutionProcessCollection	private
frequencySet(size_t frequenciesIndex)	bpp::SubstitutionProcessCollection	inline
frequencySet(size_t frequenciesIndex) const	bpp::SubstitutionProcessCollection	inline
getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getAliases() const	bpp::AbstractParameterAliasable	virtual
getBranchLengthParameters(bool independent) const	bpp::SubstitutionProcessCollection	inline
getBranchLengthParameters(size_t nTree, bool independent) const	bpp::SubstitutionProcessCollection	inline
getFrequenciesNumbers() const	bpp::SubstitutionProcessCollection	inline
getFrequencySet(size_t frequenciesIndex)	bpp::SubstitutionProcessCollection	inline
getFrequencySet(size_t frequenciesIndex) const	bpp::SubstitutionProcessCollection	inline
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getModel(size_t modelIndex)	bpp::SubstitutionProcessCollection	inline
getModel(size_t modelIndex) const	bpp::SubstitutionProcessCollection	inline
getModelIndex(std::shared_ptr< BranchModelInterface > model) const	bpp::SubstitutionProcessCollection	inline
getModelNumbers() const	bpp::SubstitutionProcessCollection	inline
getModelScenario(size_t numPath) const	bpp::SubstitutionProcessCollection	inline
getModelScenario(size_t numPath)	bpp::SubstitutionProcessCollection	inline
getNamespace() const override	bpp::AbstractParameterAliasable	virtual
getNonDerivableParameters() const	bpp::SubstitutionProcessCollection
getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
getNumberOfSubstitutionProcess() const	bpp::SubstitutionProcessCollection	inline
getParameter(const std::string &name) const	bpp::AbstractParameterAliasable
getParameter(size_t i) const	bpp::AbstractParameterAliasable	protected
getParameter(size_t i)	bpp::AbstractParameterAliasable	protected
getParameter_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index) const	bpp::AbstractParameterAliasable	protected
getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameters() const override	bpp::AbstractParameterAliasable	virtual
getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
getParameterValue(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParameterAliasable	protected
getRateDistribution(size_t distributionIndex)	bpp::SubstitutionProcessCollection	inline
getRateDistribution(size_t distributionIndex) const	bpp::SubstitutionProcessCollection	inline
getRateDistributionNumbers() const	bpp::SubstitutionProcessCollection	inline
getRateDistributionParameters(size_t nRate, bool independent) const	bpp::SubstitutionProcessCollection	inline
getRateDistributionParameters(bool independent) const	bpp::SubstitutionProcessCollection	inline
getRootFrequenciesParameters(size_t nFreq, bool independent) const	bpp::SubstitutionProcessCollection	inline
getRootFrequenciesParameters(bool independent) const	bpp::SubstitutionProcessCollection	inline
getScenarioNumbers() const	bpp::SubstitutionProcessCollection	inline
getSubstitutionModelParameters(size_t nMod, bool independent) const	bpp::SubstitutionProcessCollection	inline
getSubstitutionModelParameters(bool independent) const	bpp::SubstitutionProcessCollection	inline
getSubstitutionProcess(size_t i)	bpp::SubstitutionProcessCollection	inline
getSubstitutionProcess(size_t i) const	bpp::SubstitutionProcessCollection	inline
getSubstitutionProcessNumbers() const	bpp::SubstitutionProcessCollection	inline
getSubstitutionProcessParameters(size_t nProc, bool independent) const	bpp::SubstitutionProcessCollection	inline
getSubstitutionProcessParameters() const	bpp::SubstitutionProcessCollection
getTree(size_t treeIndex)	bpp::SubstitutionProcessCollection	inline
getTree(size_t treeIndex) const	bpp::SubstitutionProcessCollection	inline
getTreeNumbers() const	bpp::SubstitutionProcessCollection	inline
hasDistributionNumber(size_t n) const	bpp::SubstitutionProcessCollection	inline
hasFrequenciesNumber(size_t n) const	bpp::SubstitutionProcessCollection	inline
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
hasModel(std::shared_ptr< BranchModelInterface > model) const	bpp::SubstitutionProcessCollection	inline
hasModelNumber(size_t n) const	bpp::SubstitutionProcessCollection	inline
hasModelScenario(size_t numPath) const	bpp::SubstitutionProcessCollection	inline
hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
hasSubstitutionProcessNumber(size_t n) const	bpp::SubstitutionProcessCollection	inline
hasTreeNumber(size_t n) const	bpp::SubstitutionProcessCollection	inline
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
mDistToSubPro_	bpp::SubstitutionProcessCollection	private
mFreqToSubPro_	bpp::SubstitutionProcessCollection	private
mModelScenario_	bpp::SubstitutionProcessCollection	private
mModelToSubPro_	bpp::SubstitutionProcessCollection	private
model(size_t modelIndex)	bpp::SubstitutionProcessCollection	inline
model(size_t modelIndex) const	bpp::SubstitutionProcessCollection	inline
modelColl_	bpp::SubstitutionProcessCollection	private
mSubProcess_	bpp::SubstitutionProcessCollection	private
mTreeToSubPro_	bpp::SubstitutionProcessCollection	private
mVConstDist_	bpp::SubstitutionProcessCollection	private
operator=(const SubstitutionProcessCollection &set)	bpp::SubstitutionProcessCollection
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
prefix_	bpp::AbstractParameterAliasable	private
rateDistribution(size_t distributionIndex)	bpp::SubstitutionProcessCollection	inline
rateDistribution(size_t distributionIndex) const	bpp::SubstitutionProcessCollection	inline
removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
replaceFrequencies(std::shared_ptr< FrequencySetInterface > frequencies, size_t frequenciesIndex)	bpp::SubstitutionProcessCollection	inline
replaceModel(std::shared_ptr< BranchModelInterface > model, size_t modelIndex)	bpp::SubstitutionProcessCollection	inline
replaceParametrizable(std::shared_ptr< Parametrizable > parametrizable, size_t parametrizableIndex, bool withParameters=true)	bpp::SubstitutionProcessCollection
replaceTree(std::shared_ptr< ParametrizablePhyloTree > tree, size_t treeIndex)	bpp::SubstitutionProcessCollection	inline
resetParameters_()	bpp::AbstractParameterAliasable	protected
setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
setNamespace(const std::string &prefix)	bpp::SubstitutionProcessCollection	virtual
setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
substitutionProcess(size_t i)	bpp::SubstitutionProcessCollection	inline
substitutionProcess(size_t i) const	bpp::SubstitutionProcessCollection	inline
SubstitutionProcessCollection()	bpp::SubstitutionProcessCollection	inline
SubstitutionProcessCollection(const SubstitutionProcessCollection &set)	bpp::SubstitutionProcessCollection
tree(size_t treeIndex)	bpp::SubstitutionProcessCollection	inline
tree(size_t treeIndex) const	bpp::SubstitutionProcessCollection	inline
treeColl_	bpp::SubstitutionProcessCollection	private
unaliasParameters(const std::string &p1, const std::string &p2)	bpp::SubstitutionProcessCollection	virtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~Clonable()=default	bpp::Clonable	virtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~SubstitutionProcessCollection()	bpp::SubstitutionProcessCollection	inlinevirtual