Space and time homogeneous substitution process, without mixture. More...

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

Inheritance diagram for bpp::SimpleSubstitutionProcess:

Collaboration diagram for bpp::SimpleSubstitutionProcess:

Public Member Functions
	SimpleSubstitutionProcess (std::shared_ptr< BranchModelInterface > model, std::shared_ptr< const PhyloTree > tree=nullptr, std::shared_ptr< FrequencySetInterface > rootFrequencies=nullptr)

	SimpleSubstitutionProcess (std::shared_ptr< BranchModelInterface > model, std::shared_ptr< ParametrizablePhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFrequencies=nullptr)

	SimpleSubstitutionProcess (const SimpleSubstitutionProcess &ssp)

SimpleSubstitutionProcess &	operator= (const SimpleSubstitutionProcess &ssp)

SimpleSubstitutionProcess *	clone () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

size_t	getNumberOfModels () const override

std::vector< size_t >	getModelNumbers () const override

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

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

const BranchModelInterface &	model (size_t n) const override

std::shared_ptr< const BranchModelInterface >	getModel (size_t n) const override

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

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

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

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

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

const DiscreteDistributionInterface &	rateDistribution () const override
	Get the rate distribution. More...

DiscreteDistributionInterface &	rateDistribution () override
	Get the rate distribution. More...

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

ParameterList	getRateDistributionParameters (bool independent) const override

ParameterList	getBranchLengthParameters (bool independent) const override

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

void	setModelScenario (std::shared_ptr< ModelScenario > modelpath) override
	Set the modelPath, after checking it is valid (ie modelpath has only the model of the process). More...

double	getProbabilityForModel (size_t classIndex) const override

Vdouble	getClassProbabilities () const override

double	getRateForModel (size_t classIndex) const override

void	setPhyloTree (const PhyloTree &phyloTree)
	sets the ParametrizablePhyloTree. More...

const ParametrizablePhyloTree &	parametrizablePhyloTree () const

std::shared_ptr< const ParametrizablePhyloTree >	getParametrizablePhyloTree () const

bool	hasRootFrequencySet () const

const FrequencySetInterface &	rootFrequencySet () const

FrequencySetInterface &	rootFrequencySet ()

std::shared_ptr< const FrequencySetInterface >	getRootFrequencySet () const

std::shared_ptr< FrequencySetInterface >	getRootFrequencySet ()

void	setRootFrequencySet (std::shared_ptr< FrequencySetInterface > rootfrequency)
	set the RootFrequency. More...

ParameterList	getRootFrequenciesParameters (bool independent) const
	Get the parameters corresponding to the root frequencies. More...

std::shared_ptr< const ModelScenario >	getModelScenario () const
	get the ModelScenario. More...

virtual bool	isCompatibleWith (const AlignmentDataInterface &data) const =0

bool	isCompatibleWith (const AlignmentDataInterface &data) const

virtual size_t	getNumberOfClasses () const =0

size_t	getNumberOfClasses () const

virtual size_t	getNumberOfStates () const =0

size_t	getNumberOfStates () const

virtual ParameterList	getNonDerivableParameters () const =0

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

virtual size_t	getNumberOfIndependentParameters () const=0

size_t	getNumberOfIndependentParameters () const

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

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

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

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

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

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

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

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

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

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

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

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

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

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

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

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

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

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

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

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

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

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

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

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

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

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

void	setNamespace (const std::string &prefix)

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

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

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

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

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

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

Protected Member Functions
void	fireParameterChanged (const ParameterList &pl) override
	AbsractParametrizable interface. More...

virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

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

Protected Attributes
std::shared_ptr< BranchModelInterface >	model_

std::shared_ptr< ParametrizablePhyloTree >	pTree_

std::shared_ptr< FrequencySetInterface >	rootFrequencies_
	Root frequencies. More...

std::shared_ptr< ModelScenario >	modelScenario_

Private Attributes
ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Space and time homogeneous substitution process, without mixture.

Definition at line 19 of file SimpleSubstitutionProcess.h.

Constructor & Destructor Documentation

◆ SimpleSubstitutionProcess() [1/3]

SimpleSubstitutionProcess::SimpleSubstitutionProcess	(	std::shared_ptr< BranchModelInterface >	model,
		std::shared_ptr< const PhyloTree >	tree = `nullptr`,
		std::shared_ptr< FrequencySetInterface >	rootFrequencies = `nullptr`
	)

Definition at line 25 of file SimpleSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::ParameterAliasable::getIndependentParameters(), and model().

Referenced by clone().

◆ SimpleSubstitutionProcess() [2/3]

SimpleSubstitutionProcess::SimpleSubstitutionProcess	(	std::shared_ptr< BranchModelInterface >	model,
		std::shared_ptr< ParametrizablePhyloTree >	tree,
		std::shared_ptr< FrequencySetInterface >	rootFrequencies = `nullptr`
	)

Definition at line 10 of file SimpleSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::ParameterAliasable::getIndependentParameters(), and model().

◆ SimpleSubstitutionProcess() [3/3]

SimpleSubstitutionProcess::SimpleSubstitutionProcess ( const SimpleSubstitutionProcess & ssp )

Definition at line 40 of file SimpleSubstitutionProcess.cpp.

References model_, and bpp::AbstractAutonomousSubstitutionProcess::modelScenario_.

Member Function Documentation

◆ clone()

SimpleSubstitutionProcess* bpp::SimpleSubstitutionProcess::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 41 of file SimpleSubstitutionProcess.h.

References SimpleSubstitutionProcess().

◆ fireParameterChanged()

void SimpleSubstitutionProcess::fireParameterChanged ( const ParameterList & pl )

overrideprotectedvirtual

AbsractParametrizable interface.

Reimplemented from bpp::AbstractAutonomousSubstitutionProcess.

Definition at line 81 of file SimpleSubstitutionProcess.cpp.

References bpp::AbstractAutonomousSubstitutionProcess::fireParameterChanged(), and model_.

◆ getAlphabet()

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

inlineinherited

Definition at line 45 of file AbstractSubstitutionProcess.h.

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

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

◆ getBranchLengthParameters()

ParameterList bpp::SimpleSubstitutionProcess::getBranchLengthParameters ( bool independent ) const

inlineoverridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 126 of file SimpleSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::getParametrizablePhyloTree().

◆ getClassProbabilities()

Vdouble bpp::SimpleSubstitutionProcess::getClassProbabilities ( ) const

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 162 of file SimpleSubstitutionProcess.h.

◆ getModel() [1/2]

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

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 75 of file SimpleSubstitutionProcess.h.

References model_.

◆ getModel() [2/2]

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

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 65 of file SimpleSubstitutionProcess.h.

References model_.

◆ getModelForNode()

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

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 91 of file SimpleSubstitutionProcess.h.

References model_.

◆ getModelNumberForNode()

size_t bpp::SimpleSubstitutionProcess::getModelNumberForNode ( unsigned int nodeId ) const

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 86 of file SimpleSubstitutionProcess.h.

◆ getModelNumbers()

std::vector<size_t> bpp::SimpleSubstitutionProcess::getModelNumbers ( ) const

inlineoverridevirtual

Returns: The current indexes of models used in the process

Implements bpp::SubstitutionProcessInterface.

Definition at line 55 of file SimpleSubstitutionProcess.h.

◆ getModelScenario()

std::shared_ptr<const ModelScenario> bpp::AbstractAutonomousSubstitutionProcess::getModelScenario ( ) const

inlinevirtualinherited

get the ModelScenario.

Implements bpp::SubstitutionProcessInterface.

Definition at line 150 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::modelScenario_.

◆ getNodesWithModel()

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

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 80 of file SimpleSubstitutionProcess.h.

◆ getNonDerivableParameters() [1/2]

ParameterList AbstractSubstitutionProcess::getNonDerivableParameters ( ) const

virtualinherited

get NonDerivable parameters

Implements bpp::SubstitutionProcessInterface.

Reimplemented in bpp::SubstitutionProcessCollectionMember.

Definition at line 10 of file AbstractSubstitutionProcess.cpp.

References bpp::ParameterList::includeParameters().

◆ getNonDerivableParameters() [2/2]

virtual ParameterList bpp::SubstitutionProcessInterface::getNonDerivableParameters ( ) const

pure virtualinherited

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

Referenced by bpp::SingleProcessPhyloLikelihood::getNonDerivableParameters().

◆ getNumberOfClasses() [1/2]

size_t bpp::AbstractSubstitutionProcess::getNumberOfClasses ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 34 of file AbstractSubstitutionProcess.h.

References bpp::SubstitutionProcessInterface::getRateDistribution().

◆ getNumberOfClasses() [2/2]

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

pure virtualinherited

Implemented in bpp::AbstractSubstitutionProcess.

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

◆ getNumberOfModels()

size_t bpp::SimpleSubstitutionProcess::getNumberOfModels ( ) const

inlineoverridevirtual

Returns: The current number of distinct models.

Implements bpp::SubstitutionProcessInterface.

Definition at line 53 of file SimpleSubstitutionProcess.h.

◆ getNumberOfStates() [1/2]

size_t bpp::AbstractSubstitutionProcess::getNumberOfStates ( ) const

inlinevirtualinherited

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().

◆ getNumberOfStates() [2/2]

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

pure virtualinherited

Implemented in bpp::AbstractSubstitutionProcess.

◆ getParametrizablePhyloTree()

std::shared_ptr<const ParametrizablePhyloTree> bpp::AbstractAutonomousSubstitutionProcess::getParametrizablePhyloTree ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 78 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::pTree_.

Referenced by bpp::NonHomogeneousSubstitutionProcess::checkOrphanNodes(), bpp::NonHomogeneousSubstitutionProcess::checkUnknownNodes(), bpp::NonHomogeneousSubstitutionProcess::getBranchLengthParameters(), bpp::RateAcrossSitesSubstitutionProcess::getBranchLengthParameters(), and getBranchLengthParameters().

◆ getProbabilityForModel()

double bpp::SimpleSubstitutionProcess::getProbabilityForModel ( size_t classIndex ) const

inlineoverridevirtual

Returns: The probability associated to the given model class.

Parameters

classIndex The model class index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 155 of file SimpleSubstitutionProcess.h.

◆ getRateDistribution() [1/2]

std::shared_ptr<const DiscreteDistributionInterface> bpp::SimpleSubstitutionProcess::getRateDistribution ( ) const

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 96 of file SimpleSubstitutionProcess.h.

◆ getRateDistribution() [2/2]

std::shared_ptr<DiscreteDistributionInterface> bpp::SimpleSubstitutionProcess::getRateDistribution ( )

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 101 of file SimpleSubstitutionProcess.h.

◆ getRateDistributionParameters()

ParameterList bpp::SimpleSubstitutionProcess::getRateDistributionParameters ( bool independent ) const

inlineoverridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 121 of file SimpleSubstitutionProcess.h.

◆ getRateForModel()

double bpp::SimpleSubstitutionProcess::getRateForModel ( size_t classIndex ) const

inlineoverridevirtual

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

Parameters

classIndex The model class index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 167 of file SimpleSubstitutionProcess.h.

◆ getRootFrequencies()

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

inlineoverridevirtual

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;

Implements bpp::SubstitutionProcessInterface.

Definition at line 134 of file SimpleSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::getRootFrequencySet(), bpp::AbstractAutonomousSubstitutionProcess::hasRootFrequencySet(), and model_.

◆ getRootFrequenciesParameters()

ParameterList bpp::AbstractAutonomousSubstitutionProcess::getRootFrequenciesParameters ( bool independent ) const

inlinevirtualinherited

Get the parameters corresponding to the root frequencies.

Returns: The parameters corresponding to the root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 130 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::hasRootFrequencySet(), and bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

◆ getRootFrequencySet() [1/2]

std::shared_ptr<FrequencySetInterface> bpp::AbstractAutonomousSubstitutionProcess::getRootFrequencySet ( )

inlinevirtualinherited

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 106 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

◆ getRootFrequencySet() [2/2]

std::shared_ptr<const FrequencySetInterface> bpp::AbstractAutonomousSubstitutionProcess::getRootFrequencySet ( ) const

inlinevirtualinherited

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 96 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

Referenced by bpp::RateAcrossSitesSubstitutionProcess::getRootFrequencies(), getRootFrequencies(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::SimpleSubstitutionProcess::getStateMap ( ) const

inlineoverridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 48 of file SimpleSubstitutionProcess.h.

References model_.

◆ getSubstitutionModelParameters()

ParameterList bpp::SimpleSubstitutionProcess::getSubstitutionModelParameters ( bool independent ) const

inlineoverridevirtual

Methods to retrieve the parameters of specific objects.

Implements bpp::SubstitutionProcessInterface.

Definition at line 116 of file SimpleSubstitutionProcess.h.

References model_.

◆ hasRootFrequencySet()

bool bpp::AbstractAutonomousSubstitutionProcess::hasRootFrequencySet ( ) const

inlinevirtualinherited

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 86 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

Referenced by bpp::NonHomogeneousSubstitutionProcess::getRootFrequencies(), bpp::RateAcrossSitesSubstitutionProcess::getRootFrequencies(), getRootFrequencies(), and bpp::AbstractAutonomousSubstitutionProcess::getRootFrequenciesParameters().

◆ isCompatibleWith() [1/2]

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

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 50 of file AbstractSubstitutionProcess.h.

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

◆ isCompatibleWith() [2/2]

virtual bool bpp::SubstitutionProcessInterface::isCompatibleWith ( const AlignmentDataInterface & data ) const

pure virtualinherited

Implemented in bpp::AbstractSubstitutionProcess.

◆ model() [1/2]

const BranchModelInterface& bpp::SimpleSubstitutionProcess::model ( size_t i ) const

inlineoverridevirtual

Returns: the model with given index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 70 of file SimpleSubstitutionProcess.h.

References model_.

◆ model() [2/2]

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

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 60 of file SimpleSubstitutionProcess.h.

References model_.

Referenced by SimpleSubstitutionProcess().

◆ operator=()

SimpleSubstitutionProcess & SimpleSubstitutionProcess::operator= ( const SimpleSubstitutionProcess & ssp )

Definition at line 49 of file SimpleSubstitutionProcess.cpp.

References model_, bpp::AbstractAutonomousSubstitutionProcess::modelScenario_, bpp::AbstractAutonomousSubstitutionProcess::operator=(), and bpp::AbstractParameterAliasable::operator=().

◆ parametrizablePhyloTree()

const ParametrizablePhyloTree& bpp::AbstractAutonomousSubstitutionProcess::parametrizablePhyloTree ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 73 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::pTree_.

◆ rateDistribution() [1/2]

const DiscreteDistributionInterface& bpp::SimpleSubstitutionProcess::rateDistribution ( ) const

inlineoverridevirtual

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 106 of file SimpleSubstitutionProcess.h.

◆ rateDistribution() [2/2]

DiscreteDistributionInterface& bpp::SimpleSubstitutionProcess::rateDistribution ( )

inlineoverridevirtual

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 111 of file SimpleSubstitutionProcess.h.

◆ rootFrequencySet() [1/2]

FrequencySetInterface& bpp::AbstractAutonomousSubstitutionProcess::rootFrequencySet ( )

inlinevirtualinherited

Returns: The set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 101 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

◆ rootFrequencySet() [2/2]

const FrequencySetInterface& bpp::AbstractAutonomousSubstitutionProcess::rootFrequencySet ( ) const

inlinevirtualinherited

Returns: The set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 91 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

Referenced by bpp::NonHomogeneousSubstitutionProcess::getRootFrequencies(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ setModelScenario()

void SimpleSubstitutionProcess::setModelScenario ( std::shared_ptr< ModelScenario > modelpath )

overridevirtual

Set the modelPath, after checking it is valid (ie modelpath has only the model of the process).

Implements bpp::AbstractAutonomousSubstitutionProcess.

Definition at line 61 of file SimpleSubstitutionProcess.cpp.

References model_, and bpp::AbstractAutonomousSubstitutionProcess::modelScenario_.

◆ setPhyloTree()

void AbstractAutonomousSubstitutionProcess::setPhyloTree ( const PhyloTree & phyloTree )

virtualinherited

sets the ParametrizablePhyloTree.

Will build a unique_ptr<ParametrizablePhyloTree> from the given PhyloTree

Implements bpp::AutonomousSubstitutionProcessInterface.

Definition at line 67 of file AbstractAutonomousSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::ParameterList::deleteParameters(), bpp::AbstractParameterAliasable::getParameters_(), and bpp::AbstractAutonomousSubstitutionProcess::pTree_.

Referenced by bpp::AbstractAutonomousSubstitutionProcess::AbstractAutonomousSubstitutionProcess().

◆ setRootFrequencySet()

void bpp::AbstractAutonomousSubstitutionProcess::setRootFrequencySet ( std::shared_ptr< FrequencySetInterface > rootfrequency )

inlinevirtualinherited

set the RootFrequency.

Parameters

rootfrequency The root frequencies to be associated with this instance.

Implements bpp::AutonomousSubstitutionProcessInterface.

Definition at line 116 of file AbstractAutonomousSubstitutionProcess.h.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::ParameterList::deleteParameters(), bpp::AbstractParameterAliasable::getParameters_(), and bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_.

◆ stateMap()

const StateMapInterface& bpp::SimpleSubstitutionProcess::stateMap ( ) const

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 43 of file SimpleSubstitutionProcess.h.

References model_.

Member Data Documentation

◆ model_

std::shared_ptr<BranchModelInterface> bpp::SimpleSubstitutionProcess::model_

protected

Definition at line 23 of file SimpleSubstitutionProcess.h.

Referenced by fireParameterChanged(), getModel(), getModelForNode(), getRootFrequencies(), getStateMap(), getSubstitutionModelParameters(), model(), operator=(), setModelScenario(), SimpleSubstitutionProcess(), and stateMap().

◆ modelScenario_

std::shared_ptr<ModelScenario> bpp::AbstractAutonomousSubstitutionProcess::modelScenario_

protectedinherited

Definition at line 35 of file AbstractAutonomousSubstitutionProcess.h.

◆ pTree_

std::shared_ptr<ParametrizablePhyloTree> bpp::AbstractAutonomousSubstitutionProcess::pTree_

protectedinherited

Definition at line 28 of file AbstractAutonomousSubstitutionProcess.h.

Referenced by bpp::AbstractAutonomousSubstitutionProcess::fireParameterChanged(), bpp::AbstractAutonomousSubstitutionProcess::getParametrizablePhyloTree(), bpp::AbstractAutonomousSubstitutionProcess::operator=(), bpp::AbstractAutonomousSubstitutionProcess::parametrizablePhyloTree(), and bpp::AbstractAutonomousSubstitutionProcess::setPhyloTree().

◆ rootFrequencies_

std::shared_ptr<FrequencySetInterface> bpp::AbstractAutonomousSubstitutionProcess::rootFrequencies_

protectedinherited

Root frequencies.

Definition at line 33 of file AbstractAutonomousSubstitutionProcess.h.

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

Bpp/Phyl/Likelihood/SimpleSubstitutionProcess.h
Bpp/Phyl/Likelihood/SimpleSubstitutionProcess.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SimpleSubstitutionProcess() [1/3]

◆ SimpleSubstitutionProcess() [2/3]

◆ SimpleSubstitutionProcess() [3/3]

Member Function Documentation

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getClassProbabilities()

◆ getModel() [1/2]

◆ getModel() [2/2]

◆ getModelForNode()

◆ getModelNumberForNode()

◆ getModelNumbers()

◆ getModelScenario()

◆ getNodesWithModel()

◆ getNonDerivableParameters() [1/2]

◆ getNonDerivableParameters() [2/2]

◆ getNumberOfClasses() [1/2]

◆ getNumberOfClasses() [2/2]

◆ getNumberOfModels()

◆ getNumberOfStates() [1/2]

◆ getNumberOfStates() [2/2]

◆ getParametrizablePhyloTree()

◆ getProbabilityForModel()

◆ getRateDistribution() [1/2]

◆ getRateDistribution() [2/2]

◆ getRateDistributionParameters()

◆ getRateForModel()

◆ getRootFrequencies()

◆ getRootFrequenciesParameters()

◆ getRootFrequencySet() [1/2]

◆ getRootFrequencySet() [2/2]

◆ getStateMap()

◆ getSubstitutionModelParameters()

◆ hasRootFrequencySet()

◆ isCompatibleWith() [1/2]

◆ isCompatibleWith() [2/2]

◆ model() [1/2]

◆ model() [2/2]

◆ operator=()

◆ parametrizablePhyloTree()

◆ rateDistribution() [1/2]

◆ rateDistribution() [2/2]

◆ rootFrequencySet() [1/2]

◆ rootFrequencySet() [2/2]

◆ setModelScenario()

◆ setPhyloTree()

◆ setRootFrequencySet()

◆ stateMap()

Member Data Documentation

◆ model_

◆ modelScenario_

◆ pTree_

◆ rootFrequencies_