A partial implementation of the SubstitutionProcess interface. More...

#include <Bpp/Phyl/Likelihood/AbstractSubstitutionProcess.h>

Inheritance diagram for bpp::AbstractSubstitutionProcess:

Collaboration diagram for bpp::AbstractSubstitutionProcess:

Public Member Functions
	AbstractSubstitutionProcess ()

size_t	getNumberOfClasses () const

size_t	getNumberOfStates () const

std::shared_ptr< const Alphabet >	getAlphabet () const

bool	isCompatibleWith (const AlignmentDataInterface &data) const

ParameterList	getNonDerivableParameters () const
	get NonDerivable parameters More...

virtual SubstitutionProcessInterface *	clone () const =0

virtual const StateMapInterface &	stateMap () const =0

virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0

virtual const ParametrizablePhyloTree &	parametrizablePhyloTree () const =0

virtual std::shared_ptr< const ParametrizablePhyloTree >	getParametrizablePhyloTree () const =0

virtual size_t	getNumberOfModels () const =0

virtual std::vector< size_t >	getModelNumbers () const =0

virtual const BranchModelInterface &	model (size_t i) const =0

virtual const BranchModelInterface &	model (unsigned int nodeId, size_t classIndex) const =0
	Get the substitution model corresponding to a certain branch, site pattern, and model class. More...

virtual std::shared_ptr< const BranchModelInterface >	getModel (size_t i) const =0

virtual std::shared_ptr< const BranchModelInterface >	getModel (unsigned int nodeId, size_t classIndex) const =0
	Get the substitution model corresponding to a certain branch, site pattern, and model class. More...

virtual std::shared_ptr< const ModelScenario >	getModelScenario () const =0
	Get the Model Scenario associated with this process, in case there are mixture models involved. More...

virtual const std::vector< unsigned int >	getNodesWithModel (size_t i) const =0
	Get a list of nodes id for which the given model is associated. More...

virtual size_t	getModelNumberForNode (unsigned int nodeId) const =0
	Get the number of the model associated to a particular node id. More...

virtual std::shared_ptr< const BranchModelInterface >	getModelForNode (unsigned int nodeId) const =0
	Get the model associated to a particular node id. More...

virtual const DiscreteDistributionInterface &	rateDistribution () const =0
	Get the rate distribution. More...

virtual DiscreteDistributionInterface &	rateDistribution ()=0
	Get the rate distribution. More...

virtual std::shared_ptr< const DiscreteDistributionInterface >	getRateDistribution () const =0
	Get a pointer to the rate distribution (or null if there is no rate distribution). More...

virtual std::shared_ptr< DiscreteDistributionInterface >	getRateDistribution ()=0
	Get a pointer to the rate distribution (or null if there is no rate distribution). More...

virtual ParameterList	getSubstitutionModelParameters (bool independent) const =0
	Methods to retrieve the parameters of specific objects. More...

virtual ParameterList	getRateDistributionParameters (bool independent) const =0

virtual ParameterList	getRootFrequenciesParameters (bool independent) const =0

virtual ParameterList	getBranchLengthParameters (bool independent) const =0

virtual const std::vector< double > &	getRootFrequencies () const =0
	Get the values of the frequencies for each state in the alphabet at the root node. More...

virtual bool	hasRootFrequencySet () const =0

virtual const FrequencySetInterface &	rootFrequencySet () const =0

virtual FrequencySetInterface &	rootFrequencySet ()=0

virtual std::shared_ptr< const FrequencySetInterface >	getRootFrequencySet () const =0

virtual std::shared_ptr< FrequencySetInterface >	getRootFrequencySet ()=0

virtual double	getProbabilityForModel (size_t classIndex) const =0

virtual Vdouble	getClassProbabilities () const =0

virtual double	getRateForModel (size_t classIndex) const =0

virtual size_t	getNumberOfIndependentParameters () const=0

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

virtual const ParameterList &	getIndependentParameters () const=0

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

virtual std::map< std::string, std::string >	getAliases () const=0

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

void	setNamespace (const std::string &prefix)

bool	hasIndependentParameter (const std::string &name) const

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

void	unaliasParameters (const std::string &p1, const std::string &p2)

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const

std::string	getFrom (const std::string &name) const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

virtual void	fireParameterChanged (const ParameterList &parameters)

virtual Clonable *	clone () const=0

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override

Private Attributes
ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Detailed Description

A partial implementation of the SubstitutionProcess interface.

This class handles a pointer toward a ParametrizableTree object, as well as convenient arrays for storing previously computed probabilities.

Definition at line 25 of file AbstractSubstitutionProcess.h.

Constructor & Destructor Documentation

◆ AbstractSubstitutionProcess()

bpp::AbstractSubstitutionProcess::AbstractSubstitutionProcess ( )

inline

Definition at line 30 of file AbstractSubstitutionProcess.h.

Member Function Documentation

◆ clone()

virtual SubstitutionProcessInterface* bpp::SubstitutionProcessInterface::clone ( ) const

pure virtualinherited

Implements bpp::ParameterAliasable.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::OptimizationTools::buildDistanceTree().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractSubstitutionProcess::getAlphabet ( ) const

inline

Definition at line 45 of file AbstractSubstitutionProcess.h.

References bpp::StateMapInterface::getAlphabet(), and bpp::SubstitutionProcessInterface::stateMap().

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), isCompatibleWith(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ getBranchLengthParameters()

virtual ParameterList bpp::SubstitutionProcessInterface::getBranchLengthParameters ( bool independent ) const

pure virtualinherited

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::SingleProcessPhyloLikelihood::getBranchLengthParameters(), and bpp::SingleProcessPhyloLikelihood::getDerivableParameters().

◆ getClassProbabilities()

virtual Vdouble bpp::SubstitutionProcessInterface::getClassProbabilities ( ) const

pure virtualinherited

Returns: The vector of the probabilities associated to the classes.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getModel() [1/2]

virtual std::shared_ptr<const BranchModelInterface> bpp::SubstitutionProcessInterface::getModel ( size_t i ) const

pure virtualinherited

Returns: A shared pointer toward the model with given index.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::makeConfiguredModelCollection().

◆ getModel() [2/2]

virtual std::shared_ptr<const BranchModelInterface> bpp::SubstitutionProcessInterface::getModel	(	unsigned int	nodeId,
		size_t	classIndex
	)		const

pure virtualinherited

Get the substitution model corresponding to a certain branch, site pattern, and model class.

Parameters

nodeId	The id of the node.
classIndex	The model class index.

Returns: A shared pointer toward the model with given index.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getModelForNode()

virtual std::shared_ptr<const BranchModelInterface> bpp::SubstitutionProcessInterface::getModelForNode ( unsigned int nodeId ) const

pure virtualinherited

Get the model associated to a particular node id.

Parameters

nodeId The id of the query node.

Returns: A pointer toward the corresponding model.

Exceptions

Exception If no model is found for this node.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getModelNumberForNode()

virtual size_t bpp::SubstitutionProcessInterface::getModelNumberForNode ( unsigned int nodeId ) const

pure virtualinherited

Get the number of the model associated to a particular node id.

Parameters

nodeId The id of the query node.

Returns: The number of the model associated to the given node.

Exceptions

Exception If no model is found for this node.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getModelNumbers()

virtual std::vector<size_t> bpp::SubstitutionProcessInterface::getModelNumbers ( ) const

pure virtualinherited

Returns: The current indexes of models used in the process

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::makeConfiguredModelCollection(), bpp::OneProcessSequenceSubstitutionMapping::setBranchedModelSet_(), and bpp::SingleProcessSubstitutionMapping::setBranchedModelSet_().

◆ getModelScenario()

virtual std::shared_ptr<const ModelScenario> bpp::SubstitutionProcessInterface::getModelScenario ( ) const

pure virtualinherited

Get the Model Scenario associated with this process, in case there are mixture models involved.

When a mixture model is not included in the ModelScenario, it is considered as non-mixed (transition probabilities are then computed as mixture of submodel transition probalities).

It returns 0 if there is no model path, which means that all mixture models are considered as non-mixed.

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

◆ getNodesWithModel()

virtual const std::vector<unsigned int> bpp::SubstitutionProcessInterface::getNodesWithModel ( size_t i ) const

pure virtualinherited

Get a list of nodes id for which the given model is associated.

Parameters

i	The index of the model in the set.

Returns: A vector with the ids of the node associated to this model.

Exceptions

IndexOutOfBoundsException If the index is not valid.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::OneProcessSequenceSubstitutionMapping::setBranchedModelSet_(), and bpp::SingleProcessSubstitutionMapping::setBranchedModelSet_().

◆ getNonDerivableParameters()

ParameterList AbstractSubstitutionProcess::getNonDerivableParameters ( ) const

virtual

get NonDerivable parameters

Implements bpp::SubstitutionProcessInterface.

Reimplemented in bpp::SubstitutionProcessCollectionMember.

Definition at line 10 of file AbstractSubstitutionProcess.cpp.

References bpp::ParameterList::includeParameters().

◆ getNumberOfClasses()

size_t bpp::AbstractSubstitutionProcess::getNumberOfClasses ( ) const

inlinevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 34 of file AbstractSubstitutionProcess.h.

References bpp::SubstitutionProcessInterface::getRateDistribution().

◆ getNumberOfModels()

virtual size_t bpp::SubstitutionProcessInterface::getNumberOfModels ( ) const

pure virtualinherited

Returns: The current number of distinct models.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getNumberOfStates()

size_t bpp::AbstractSubstitutionProcess::getNumberOfStates ( ) const

inlinevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 40 of file AbstractSubstitutionProcess.h.

References bpp::StateMapInterface::getNumberOfModelStates(), and bpp::SubstitutionProcessInterface::stateMap().

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ getParametrizablePhyloTree()

virtual std::shared_ptr<const ParametrizablePhyloTree> bpp::SubstitutionProcessInterface::getParametrizablePhyloTree ( ) const

pure virtualinherited

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

Referenced by bpp::RewardMappingTools::computeRewardVectors(), bpp::SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator(), and bpp::SingleProcessPhyloLikelihood::tree().

◆ getProbabilityForModel()

virtual double bpp::SubstitutionProcessInterface::getProbabilityForModel ( size_t classIndex ) const

pure virtualinherited

Returns: The probability associated to the given model class.

Parameters

classIndex The model class index.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::RewardMappingTools::computeRewardVectors().

◆ getRateDistribution() [1/2]

virtual std::shared_ptr<const DiscreteDistributionInterface> bpp::SubstitutionProcessInterface::getRateDistribution ( ) const

pure virtualinherited

Get a pointer to the rate distribution (or null if there is no rate distribution).

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by getNumberOfClasses().

◆ getRateDistribution() [2/2]

virtual std::shared_ptr<DiscreteDistributionInterface> bpp::SubstitutionProcessInterface::getRateDistribution ( )

pure virtualinherited

Get a pointer to the rate distribution (or null if there is no rate distribution).

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getRateDistributionParameters()

virtual ParameterList bpp::SubstitutionProcessInterface::getRateDistributionParameters ( bool independent ) const

pure virtualinherited

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::OptimizationTools::estimateDistanceMatrix(), and bpp::SingleProcessPhyloLikelihood::getRateDistributionParameters().

◆ getRateForModel()

virtual double bpp::SubstitutionProcessInterface::getRateForModel ( size_t classIndex ) const

pure virtualinherited

Returns: The substitution rate associated to the given model class.

Parameters

classIndex The model class index.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getRootFrequencies()

virtual const std::vector<double>& bpp::SubstitutionProcessInterface::getRootFrequencies ( ) const

pure virtualinherited

Get the values of the frequencies for each state in the alphabet at the root node.

For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.

Returns: A vector with ancestral frequencies for each state in the alphabet;

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ getRootFrequenciesParameters()

virtual ParameterList bpp::SubstitutionProcessInterface::getRootFrequenciesParameters ( bool independent ) const

pure virtualinherited

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::OptimizationTools::estimateDistanceMatrix(), and bpp::SingleProcessPhyloLikelihood::getRootFrequenciesParameters().

◆ getRootFrequencySet() [1/2]

virtual std::shared_ptr<const FrequencySetInterface> bpp::SubstitutionProcessInterface::getRootFrequencySet ( ) const

pure virtualinherited

Returns: A pointer toward rhe set of parametrized root frequencies.

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

◆ getRootFrequencySet() [2/2]

virtual std::shared_ptr<FrequencySetInterface> bpp::SubstitutionProcessInterface::getRootFrequencySet ( )

pure virtualinherited

Returns: A pointer toward rhe set of parametrized root frequencies.

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

◆ getStateMap()

virtual std::shared_ptr<const StateMapInterface> bpp::SubstitutionProcessInterface::getStateMap ( ) const

pure virtualinherited

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::SequenceEvolution::getStateMap().

◆ getSubstitutionModelParameters()

virtual ParameterList bpp::SubstitutionProcessInterface::getSubstitutionModelParameters ( bool independent ) const

pure virtualinherited

Methods to retrieve the parameters of specific objects.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::OptimizationTools::estimateDistanceMatrix(), and bpp::SingleProcessPhyloLikelihood::getSubstitutionModelParameters().

◆ hasRootFrequencySet()

virtual bool bpp::SubstitutionProcessInterface::hasRootFrequencySet ( ) const

pure virtualinherited

Returns: true if the process has parametrized root frequencies (non-stationary model)

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

◆ isCompatibleWith()

bool bpp::AbstractSubstitutionProcess::isCompatibleWith ( const AlignmentDataInterface & data ) const

inlinevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 50 of file AbstractSubstitutionProcess.h.

References getAlphabet(), and bpp::TemplateAlignmentDataInterface< class >::getAlphabet().

◆ model() [1/2]

virtual const BranchModelInterface& bpp::SubstitutionProcessInterface::model ( size_t i ) const

pure virtualinherited

Returns: the model with given index.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters(), bpp::OneProcessSequenceSubstitutionMapping::setBranchedModelSet_(), and bpp::SingleProcessSubstitutionMapping::setBranchedModelSet_().

◆ model() [2/2]

virtual const BranchModelInterface& bpp::SubstitutionProcessInterface::model	(	unsigned int	nodeId,
		size_t	classIndex
	)		const

pure virtualinherited

Get the substitution model corresponding to a certain branch, site pattern, and model class.

Parameters

nodeId	The id of the node.
classIndex	The model class index.

Returns: the model with given index.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ parametrizablePhyloTree()

virtual const ParametrizablePhyloTree& bpp::SubstitutionProcessInterface::parametrizablePhyloTree ( ) const

pure virtualinherited

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::SubstitutionMappingTools::computeNormalizedCounts(), and bpp::RewardMappingTools::computeRewardVectors().

◆ rateDistribution() [1/2]

virtual const DiscreteDistributionInterface& bpp::SubstitutionProcessInterface::rateDistribution ( ) const

pure virtualinherited

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite().

◆ rateDistribution() [2/2]

virtual DiscreteDistributionInterface& bpp::SubstitutionProcessInterface::rateDistribution ( )

pure virtualinherited

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

◆ rootFrequencySet() [1/2]

virtual const FrequencySetInterface& bpp::SubstitutionProcessInterface::rootFrequencySet ( ) const

pure virtualinherited

Returns: The set of parametrized root frequencies.

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

◆ rootFrequencySet() [2/2]

virtual FrequencySetInterface& bpp::SubstitutionProcessInterface::rootFrequencySet ( )

pure virtualinherited

Returns: The set of parametrized root frequencies.

Implemented in bpp::SubstitutionProcessCollectionMember, and bpp::AbstractAutonomousSubstitutionProcess.

◆ stateMap()

virtual const StateMapInterface& bpp::SubstitutionProcessInterface::stateMap ( ) const

pure virtualinherited

Returns: The state map associated with the models of this process

Implemented in bpp::SubstitutionProcessCollectionMember, bpp::SimpleSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::NonHomogeneousSubstitutionProcess.

Referenced by getAlphabet(), getNumberOfStates(), and bpp::SequenceEvolution::stateMap().

The documentation for this class was generated from the following files:

Bpp/Phyl/Likelihood/AbstractSubstitutionProcess.h
Bpp/Phyl/Likelihood/AbstractSubstitutionProcess.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractSubstitutionProcess()

Member Function Documentation

◆ clone()

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getClassProbabilities()

◆ getModel() [1/2]

◆ getModel() [2/2]

◆ getModelForNode()

◆ getModelNumberForNode()

◆ getModelNumbers()

◆ getModelScenario()

◆ getNodesWithModel()

◆ getNonDerivableParameters()

◆ getNumberOfClasses()

◆ getNumberOfModels()

◆ getNumberOfStates()

◆ getParametrizablePhyloTree()

◆ getProbabilityForModel()

◆ getRateDistribution() [1/2]

◆ getRateDistribution() [2/2]

◆ getRateDistributionParameters()

◆ getRateForModel()

◆ getRootFrequencies()

◆ getRootFrequenciesParameters()

◆ getRootFrequencySet() [1/2]

◆ getRootFrequencySet() [2/2]

◆ getStateMap()

◆ getSubstitutionModelParameters()

◆ hasRootFrequencySet()

◆ isCompatibleWith()

◆ model() [1/2]

◆ model() [2/2]

◆ parametrizablePhyloTree()

◆ rateDistribution() [1/2]

◆ rateDistribution() [2/2]

◆ rootFrequencySet() [1/2]

◆ rootFrequencySet() [2/2]

◆ stateMap()