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

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

Inheritance diagram for bpp::AbstractAutonomousSubstitutionProcess:

Collaboration diagram for bpp::AbstractAutonomousSubstitutionProcess:

Public Member Functions
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

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

FrequencySetInterface &	rootFrequencySet ()

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...

void	fireParameterChanged (const ParameterList &pl)
	AbsractParametrizable interface. More...

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

virtual void	setModelScenario (std::shared_ptr< ModelScenario > modelScenario)=0
	set the ModelScenario. More...

virtual SubstitutionProcessInterface *	clone () const =0

virtual const StateMapInterface &	stateMap () const =0

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

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

virtual size_t	getNumberOfClasses () const =0

virtual size_t	getNumberOfStates () 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 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	getBranchLengthParameters (bool independent) const =0

virtual ParameterList	getNonDerivableParameters () 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 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

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 Clonable *	clone () const=0

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)

const ParameterList &	getIndependentParameters () const

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

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

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

const ParameterList &	getParameters () const override

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

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

void	setNamespace (const std::string &prefix)

std::string	getNamespace () const override

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

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
	AbstractAutonomousSubstitutionProcess (std::shared_ptr< const PhyloTree > tree=0, std::shared_ptr< FrequencySetInterface > rootFrequencies=0, const std::string &prefix="")
	Builds using an optional pointer towards a PhyloTree. More...

	AbstractAutonomousSubstitutionProcess (std::shared_ptr< ParametrizablePhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFrequencies=0, const std::string &prefix="")
	Builds using a pointer towards a ParametrizablePhyloTree. This pointer will be owned by the AbstractAutonomousSubstitutionProcess. More...

	AbstractAutonomousSubstitutionProcess (const AbstractAutonomousSubstitutionProcess &asp)

AbstractAutonomousSubstitutionProcess &	operator= (const AbstractAutonomousSubstitutionProcess &asp)

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< 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

A partial implementation of the SubstitutionProcess interface.

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

Definition at line 23 of file AbstractAutonomousSubstitutionProcess.h.

Constructor & Destructor Documentation

◆ AbstractAutonomousSubstitutionProcess() [1/3]

AbstractAutonomousSubstitutionProcess::AbstractAutonomousSubstitutionProcess	(	std::shared_ptr< const PhyloTree >	tree = `0`,
		std::shared_ptr< FrequencySetInterface >	rootFrequencies = `0`,
		const std::string &	prefix = `""`
	)

protected

Builds using an optional pointer towards a PhyloTree.

If the pointer is non-null, a ParametrizablePhyloTree will be built from this PhyloTree, and owned by the AbstractAutonomousSubstitutionProcess.

Definition at line 10 of file AbstractAutonomousSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), rootFrequencies_, and setPhyloTree().

◆ AbstractAutonomousSubstitutionProcess() [2/3]

AbstractAutonomousSubstitutionProcess::AbstractAutonomousSubstitutionProcess	(	std::shared_ptr< ParametrizablePhyloTree >	tree,
		std::shared_ptr< FrequencySetInterface >	rootFrequencies = `0`,
		const std::string &	prefix = `""`
	)

protected

Builds using a pointer towards a ParametrizablePhyloTree. This pointer will be owned by the AbstractAutonomousSubstitutionProcess.

Definition at line 25 of file AbstractAutonomousSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), and rootFrequencies_.

◆ AbstractAutonomousSubstitutionProcess() [3/3]

AbstractAutonomousSubstitutionProcess::AbstractAutonomousSubstitutionProcess ( const AbstractAutonomousSubstitutionProcess & asp )

protected

Definition at line 39 of file AbstractAutonomousSubstitutionProcess.cpp.

Member Function Documentation

◆ clone()

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

pure virtualinherited

Implements bpp::ParameterAliasable.

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

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

◆ fireParameterChanged()

void AbstractAutonomousSubstitutionProcess::fireParameterChanged ( const ParameterList & pl )

virtual

AbsractParametrizable interface.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, and bpp::SimpleSubstitutionProcess.

Definition at line 56 of file AbstractAutonomousSubstitutionProcess.cpp.

References bpp::ParameterList::addParameters(), bpp::AbstractParameterAliasable::getAliasedParameters(), pTree_, and rootFrequencies_.

Referenced by bpp::NonHomogeneousSubstitutionProcess::fireParameterChanged(), bpp::RateAcrossSitesSubstitutionProcess::fireParameterChanged(), and bpp::SimpleSubstitutionProcess::fireParameterChanged().

◆ 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(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::SubstitutionProcessCollectionMember::setTreeNumber().

◆ getBranchLengthParameters()

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

pure virtualinherited

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

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

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

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

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

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

◆ getModelScenario()

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

inlinevirtual

get the ModelScenario.

Implements bpp::SubstitutionProcessInterface.

Definition at line 150 of file AbstractAutonomousSubstitutionProcess.h.

References modelScenario_.

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

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

◆ 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::AbstractParameterAliasable::getAliasedParameters(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::SubstitutionProcessInterface::getRateDistributionParameters(), bpp::SubstitutionProcessInterface::getRootFrequenciesParameters(), bpp::SubstitutionProcessInterface::getSubstitutionModelParameters(), and bpp::ParameterList::includeParameters().

◆ getNonDerivableParameters() [2/2]

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

pure virtualinherited

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

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()

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

pure virtualinherited

Returns: The current number of distinct models.

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

◆ 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

inlinevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 78 of file AbstractAutonomousSubstitutionProcess.h.

References pTree_.

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

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

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

Referenced by bpp::AbstractSubstitutionProcess::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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

◆ getRateDistributionParameters()

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

pure virtualinherited

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

Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::OptimizationTools::estimateDistanceMatrix(), bpp::AbstractSubstitutionProcess::getNonDerivableParameters(), 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

◆ getRootFrequenciesParameters()

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

inlinevirtual

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 hasRootFrequencySet(), and rootFrequencies_.

◆ getRootFrequencySet() [1/2]

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

inlinevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 106 of file AbstractAutonomousSubstitutionProcess.h.

References rootFrequencies_.

◆ getRootFrequencySet() [2/2]

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

inlinevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 96 of file AbstractAutonomousSubstitutionProcess.h.

References rootFrequencies_.

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

◆ getStateMap()

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

pure virtualinherited

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

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

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

◆ hasRootFrequencySet()

bool bpp::AbstractAutonomousSubstitutionProcess::hasRootFrequencySet ( ) const

inlinevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 86 of file AbstractAutonomousSubstitutionProcess.h.

References rootFrequencies_.

Referenced by bpp::NonHomogeneousSubstitutionProcess::getRootFrequencies(), bpp::RateAcrossSitesSubstitutionProcess::getRootFrequencies(), bpp::SimpleSubstitutionProcess::getRootFrequencies(), and 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]

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

pure virtualinherited

Returns: the model with given index.

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

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

◆ operator=()

AbstractAutonomousSubstitutionProcess & AbstractAutonomousSubstitutionProcess::operator= ( const AbstractAutonomousSubstitutionProcess & asp )

protected

Definition at line 46 of file AbstractAutonomousSubstitutionProcess.cpp.

References modelScenario_, bpp::AbstractParameterAliasable::operator=(), pTree_, and rootFrequencies_.

Referenced by bpp::NonHomogeneousSubstitutionProcess::operator=(), bpp::RateAcrossSitesSubstitutionProcess::operator=(), and bpp::SimpleSubstitutionProcess::operator=().

◆ parametrizablePhyloTree()

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

inlinevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 73 of file AbstractAutonomousSubstitutionProcess.h.

References pTree_.

◆ 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::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, and bpp::SubstitutionProcessCollectionMember.

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

◆ rootFrequencySet() [1/2]

FrequencySetInterface & bpp::AbstractAutonomousSubstitutionProcess::rootFrequencySet ( )

inlinevirtual

Returns: The set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 101 of file AbstractAutonomousSubstitutionProcess.h.

References rootFrequencies_.

◆ rootFrequencySet() [2/2]

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

inlinevirtual

Returns: The set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 91 of file AbstractAutonomousSubstitutionProcess.h.

References rootFrequencies_.

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

◆ setModelScenario()

virtual void bpp::AbstractAutonomousSubstitutionProcess::setModelScenario ( std::shared_ptr< ModelScenario > modelScenario )

pure virtual

set the ModelScenario.

Implements bpp::AutonomousSubstitutionProcessInterface.

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

◆ setPhyloTree()

void AbstractAutonomousSubstitutionProcess::setPhyloTree ( const PhyloTree & phyloTree )

virtual

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 pTree_.

Referenced by AbstractAutonomousSubstitutionProcess().

◆ setRootFrequencySet()

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

inlinevirtual

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 rootFrequencies_.

◆ stateMap()

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

pure virtualinherited

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

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

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

Member Data Documentation

◆ modelScenario_

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

protected

Definition at line 35 of file AbstractAutonomousSubstitutionProcess.h.

Referenced by getModelScenario(), bpp::NonHomogeneousSubstitutionProcess::NonHomogeneousSubstitutionProcess(), operator=(), bpp::NonHomogeneousSubstitutionProcess::operator=(), bpp::RateAcrossSitesSubstitutionProcess::operator=(), bpp::SimpleSubstitutionProcess::operator=(), bpp::RateAcrossSitesSubstitutionProcess::RateAcrossSitesSubstitutionProcess(), bpp::RateAcrossSitesSubstitutionProcess::setModelScenario(), bpp::SimpleSubstitutionProcess::setModelScenario(), bpp::NonHomogeneousSubstitutionProcess::setModelScenario(), and bpp::SimpleSubstitutionProcess::SimpleSubstitutionProcess().

◆ pTree_

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

protected

Definition at line 28 of file AbstractAutonomousSubstitutionProcess.h.

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

◆ rootFrequencies_

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

protected

Root frequencies.

Definition at line 33 of file AbstractAutonomousSubstitutionProcess.h.

Referenced by AbstractAutonomousSubstitutionProcess(), fireParameterChanged(), getRootFrequenciesParameters(), getRootFrequencySet(), hasRootFrequencySet(), operator=(), rootFrequencySet(), and setRootFrequencySet().

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

Bpp/Phyl/Likelihood/AbstractAutonomousSubstitutionProcess.h
Bpp/Phyl/Likelihood/AbstractAutonomousSubstitutionProcess.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractAutonomousSubstitutionProcess() [1/3]

◆ AbstractAutonomousSubstitutionProcess() [2/3]

◆ AbstractAutonomousSubstitutionProcess() [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

◆ modelScenario_

◆ pTree_

◆ rootFrequencies_