Substitution process manager for non-homogeneous / non-reversible models of evolution. More...

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

Inheritance diagram for bpp::NonHomogeneousSubstitutionProcess:

Collaboration diagram for bpp::NonHomogeneousSubstitutionProcess:

Public Member Functions
	NonHomogeneousSubstitutionProcess (std::shared_ptr< DiscreteDistributionInterface > rdist, std::shared_ptr< const PhyloTree > tree=0, std::shared_ptr< FrequencySetInterface > rootFreqs=0)
	Create a model set according to the specified alphabet and root frequencies. Stationarity is not assumed. More...

	NonHomogeneousSubstitutionProcess (std::shared_ptr< DiscreteDistributionInterface > rdist, std::shared_ptr< ParametrizablePhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFreqs=0)
	Create a model set according to the specified alphabet and root frequencies. Stationarity is not assumed. More...

	NonHomogeneousSubstitutionProcess (const NonHomogeneousSubstitutionProcess &set)

NonHomogeneousSubstitutionProcess &	operator= (const NonHomogeneousSubstitutionProcess &set)

virtual	~NonHomogeneousSubstitutionProcess ()

NonHomogeneousSubstitutionProcess *	clone () const override

void	clear ()
	Resets all the information contained in this object. More...

void	fireParameterChanged (const ParameterList &parameters) override

const StateMapInterface &	stateMap () const override

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

size_t	getNumberOfModels () const override

bool	hasMixedTransitionModel () const

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

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

const BranchModelInterface &	model (size_t n) const override

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

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

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

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

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...

void	addModel (std::shared_ptr< BranchModelInterface > model, const std::vector< unsigned int > &nodesId)
	Add a new model to the set, and set relationships with nodes and params. More...

void	setModel (std::shared_ptr< BranchModelInterface > model, size_t modelIndex)
	Change a given model. More...

void	setModelToNode (size_t modelIndex, unsigned int nodeNumber)
	Associate an existing model with a given node. More...

void	listModelNames (std::ostream &out=std::cout) const
	list all model names. More...

ParameterList	getBranchLengthParameters (bool independent) const override

ParameterList	getRateDistributionParameters (bool independent) const override
	Get the parameters attached to the rate distribution. More...

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

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

ParameterList	getSubstitutionModelParameters (bool independent) const override
	Get the INDEPENDENT parameters corresponding to the models. More...

bool	isFullySetUp (bool throwEx=true) const
	Check if the model set is fully specified for a given tree. More...

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
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
std::vector< std::shared_ptr< BranchModelInterface > >	modelSet_
	Contains all models used in this tree. More...

std::shared_ptr< DiscreteDistributionInterface >	rDist_
	Rate Distribution. More...

std::map< unsigned int, size_t >	nodeToModel_
	Contains for each node in a tree the index of the corresponding model in modelSet_. More...

std::map< size_t, std::vector< unsigned int > >	modelToNodes_

std::vector< ParameterList >	modelParameters_
	Parameters for each model in the set. More...

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Check function.
const std::vector< double > &	getRootFrequencies () 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...

double	getProbabilityForModel (size_t classIndex) const override

Vdouble	getClassProbabilities () const override

double	getRateForModel (size_t classIndex) const override

bool	checkOrphanNodes (bool throwEx) const

bool	checkUnknownNodes (bool throwEx) const

static std::unique_ptr< AutonomousSubstitutionProcessInterface >	createHomogeneousSubstitutionProcess (std::shared_ptr< BranchModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rdist, std::shared_ptr< PhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFreqs=0, std::shared_ptr< ModelScenario > scenario=0)
	Create a NonHomogeneousSubstitutionProcess object, corresponding to the homogeneous case. More...

static std::unique_ptr< NonHomogeneousSubstitutionProcess >	createNonHomogeneousSubstitutionProcess (std::shared_ptr< BranchModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rdist, std::shared_ptr< PhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFreqs, const std::vector< std::string > &globalParameterNames, std::shared_ptr< ModelScenario > scenario=0)
	Create a NonHomogeneousSubstitutionProcess object, with one model per branch. More...

Detailed Description

Substitution process manager for non-homogeneous / non-reversible models of evolution.

This class contains a set of substitution models, and their assignment toward the branches of a phylogenetic tree. Each branch in the tree corresponds to a model in the set, but a susbstitution model may correspond to several branches. The particular case where all branches point toward a unique model is the homogeneous case.

This class also deals with the parameters associated to the models. The models may have their own parameters or share some of them. To deal with this issue, the NonHomogeneousSubstitutionProcess class contains its own parameter list and an index which tells to which models these parameters apply to. Since parameters in a list must have unique names, the names are suffixed with numbers according to the order of the model in the list.

To track the relationships between names in the list and names in each model, the parameter list is duplicated in modelParameters_. The user only act on parameters_, the fireParameterChanged function, automatically called, will update the modelParameters_ field.

In the non-homogeneous and homogeneous non-reversible cases, the likelihood depends on the position of the root. The states frequencies at the root of the tree are hence distinct parameters. These are accounted by a FrequencySet object, managed by the NonHomogeneousSubstitutionProcess class. The corresponding parameters, if any, are added at the beginning of the global parameter list.

If the heterogenity of the model does not affect the equilibrium frequencies, the model can be considered as stationary. In such a model, the process is supposed to be at equilibrium all along the trees, including at the root. Whether a model should be considered as stationary or not is left to the user. If the "assume stationarity" option is set when building the set, then no FrequencySet object is used, but the frequencies are taken to be the same as the one at the first model in the set. Nothing hence prevents you to build a "supposedly stationary model which actually is not", so be careful!!

This class provides several methods to specify which model and/or which parameter is associated to which branch/clade. Several check points are provided, but some are probably missing due to the large set of possible models that this class allows to build, so be careful!

Definition at line 78 of file NonHomogeneousSubstitutionProcess.h.

Constructor & Destructor Documentation

◆ NonHomogeneousSubstitutionProcess() [1/3]

bpp::NonHomogeneousSubstitutionProcess::NonHomogeneousSubstitutionProcess	(	std::shared_ptr< DiscreteDistributionInterface >	rdist,
		std::shared_ptr< const PhyloTree >	tree = `0`,
		std::shared_ptr< FrequencySetInterface >	rootFreqs = `0`
	)

inline

Create a model set according to the specified alphabet and root frequencies. Stationarity is not assumed.

Parameters

rdist	The DiscreteDistribution for the rates
tree	the phylo tree tree
rootFreqs	The frequencies at root node. The underlying object will be owned by this instance ( = 0 if stationary)

Definition at line 113 of file NonHomogeneousSubstitutionProcess.h.

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

Referenced by clone().

◆ NonHomogeneousSubstitutionProcess() [2/3]

bpp::NonHomogeneousSubstitutionProcess::NonHomogeneousSubstitutionProcess	(	std::shared_ptr< DiscreteDistributionInterface >	rdist,
		std::shared_ptr< ParametrizablePhyloTree >	tree,
		std::shared_ptr< FrequencySetInterface >	rootFreqs = `0`
	)

inline

Create a model set according to the specified alphabet and root frequencies. Stationarity is not assumed.

Parameters

rdist	The DiscreteDistribution for the rates
tree	the parametrizable tree
rootFreqs	The frequencies at root node. The underlying object will be owned by this instance ( = 0 if stationary)

Definition at line 137 of file NonHomogeneousSubstitutionProcess.h.

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

◆ NonHomogeneousSubstitutionProcess() [3/3]

NonHomogeneousSubstitutionProcess::NonHomogeneousSubstitutionProcess ( const NonHomogeneousSubstitutionProcess & set )

Definition at line 16 of file NonHomogeneousSubstitutionProcess.cpp.

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

◆ ~NonHomogeneousSubstitutionProcess()

virtual bpp::NonHomogeneousSubstitutionProcess::~NonHomogeneousSubstitutionProcess ( )

inlinevirtual

Definition at line 157 of file NonHomogeneousSubstitutionProcess.h.

References clear().

Member Function Documentation

◆ addModel()

void NonHomogeneousSubstitutionProcess::addModel	(	std::shared_ptr< BranchModelInterface >	model,
		const std::vector< unsigned int > &	nodesId
	)

Add a new model to the set, and set relationships with nodes and params.

Parameters

model	A pointer toward a susbstitution model, that will added to the set. Warning! The set will now be the owner of the pointer, and will destroy it if needed! Copy the model first if you don't want it to be lost!
nodesId	the set of nodes in the tree that points toward this model. This will override any previous affectation.

Exceptions

Exception

in case of error:

if the new model does not match the alphabet
if the new model does not have the same number of states than existing ones
etc.

Definition at line 89 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::clone(), bpp::AbstractSubstitutionProcess::getAlphabet(), bpp::BranchModelInterface::getAlphabet(), bpp::ParameterAliasable::getIndependentParameters(), bpp::Parameter::getName(), bpp::AbstractSubstitutionProcess::getNumberOfStates(), bpp::BranchModelInterface::getNumberOfStates(), model(), modelParameters_, modelSet_, modelToNodes_, nodeToModel_, bpp::Parameter::setName(), bpp::ParameterList::size(), and bpp::TextTools::toString().

◆ checkOrphanNodes()

bool NonHomogeneousSubstitutionProcess::checkOrphanNodes ( bool throwEx ) const

protected

Definition at line 206 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::AbstractAutonomousSubstitutionProcess::getParametrizablePhyloTree(), nodeToModel_, and bpp::TextTools::toString().

Referenced by isFullySetUp().

◆ checkUnknownNodes()

bool NonHomogeneousSubstitutionProcess::checkUnknownNodes ( bool throwEx ) const

protected

Definition at line 229 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::VectorTools::contains(), bpp::AbstractAutonomousSubstitutionProcess::getParametrizablePhyloTree(), modelToNodes_, and bpp::TextTools::toString().

Referenced by isFullySetUp().

◆ clear()

void NonHomogeneousSubstitutionProcess::clear ( )

Resets all the information contained in this object.

Definition at line 68 of file NonHomogeneousSubstitutionProcess.cpp.

References modelParameters_, modelSet_, nodeToModel_, rDist_, and bpp::AbstractParameterAliasable::resetParameters_().

Referenced by operator=(), and ~NonHomogeneousSubstitutionProcess().

◆ clone()

NonHomogeneousSubstitutionProcess* bpp::NonHomogeneousSubstitutionProcess::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 162 of file NonHomogeneousSubstitutionProcess.h.

References NonHomogeneousSubstitutionProcess().

◆ createHomogeneousSubstitutionProcess()

unique_ptr< AutonomousSubstitutionProcessInterface > NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess	(	std::shared_ptr< BranchModelInterface >	model,
		std::shared_ptr< DiscreteDistributionInterface >	rdist,
		std::shared_ptr< PhyloTree >	tree,
		std::shared_ptr< FrequencySetInterface >	rootFreqs = `0`,
		std::shared_ptr< ModelScenario >	scenario = `0`
	)

static

Create a NonHomogeneousSubstitutionProcess object, corresponding to the homogeneous case.

Static methods to create "simply" NonHomogeneousSubstitutionProcess.

This class is mainly for testing purpose.

Parameters

model	The model to use.
rdist	The rate distribution
tree	The tree to use for the construction of the set.
rootFreqs	A FrequencySet object to parametrize root frequencies (0 if stationary).
scenario	(optional) the scenario used (in case of Mixed Models)

Definition at line 284 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::BranchModelInterface::alphabet(), bpp::BranchModelInterface::getAlphabet(), bpp::Alphabet::getAlphabetType(), and model().

◆ createNonHomogeneousSubstitutionProcess()

unique_ptr< NonHomogeneousSubstitutionProcess > NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess	(	std::shared_ptr< BranchModelInterface >	model,
		std::shared_ptr< DiscreteDistributionInterface >	rdist,
		std::shared_ptr< PhyloTree >	tree,
		std::shared_ptr< FrequencySetInterface >	rootFreqs,
		const std::vector< std::string > &	globalParameterNames,
		std::shared_ptr< ModelScenario >	scenario = `0`
	)

static

Create a NonHomogeneousSubstitutionProcess object, with one model per branch.

All branches share the same type of model, but allow one set of parameters per branch. This is also possible to specify some parameters to be common to all branches.

Parameters

model	The model to use.
rdist	The rate distribution
rootFreqs	A FrequencySet object to parametrize root frequencies.
tree	The tree to use for the construction of the set.
globalParameterNames	Common parameters for all branches. All other parameters will be considered distinct for all branches.
scenario	(optional) the scenario used (in case of Mixed Models)

Definition at line 314 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::ParameterList::addParameter(), bpp::BranchModelInterface::alphabet(), bpp::BranchModelInterface::clone(), bpp::ParameterList::deleteParameter(), bpp::BranchModelInterface::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::ParameterAliasable::getIndependentParameters(), bpp::StringTokenizer::hasMoreToken(), bpp::ParameterList::hasParameter(), model(), bpp::StringTokenizer::nextToken(), bpp::ParameterList::size(), and bpp::TextTools::toString().

◆ fireParameterChanged()

void NonHomogeneousSubstitutionProcess::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

To be called when a parameter has changed. Depending on parameters, this will actualize the rootFrequencies_ vector or the corresponding models in the set.

Parameters

parameters The modified parameters.

Reimplemented from bpp::AbstractAutonomousSubstitutionProcess.

Definition at line 164 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::AbstractAutonomousSubstitutionProcess::fireParameterChanged(), bpp::AbstractParameterAliasable::getParameterValue(), modelParameters_, modelSet_, rDist_, and bpp::TextTools::toString().

◆ 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 addModel(), bpp::AbstractSubstitutionProcess::isCompatibleWith(), and setModel().

◆ getBranchLengthParameters()

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

inlineoverridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 329 of file NonHomogeneousSubstitutionProcess.h.

References bpp::AbstractAutonomousSubstitutionProcess::getParametrizablePhyloTree().

◆ getClassProbabilities()

Vdouble bpp::NonHomogeneousSubstitutionProcess::getClassProbabilities ( ) const

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 434 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ getModel() [1/3]

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

inline

Definition at line 234 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_.

◆ getModel() [2/3]

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

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 228 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_.

Referenced by hasMixedTransitionModel(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ getModel() [3/3]

std::shared_ptr<const BranchModelInterface> bpp::NonHomogeneousSubstitutionProcess::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 422 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_, and nodeToModel_.

◆ getModelForNode()

std::shared_ptr<const BranchModelInterface> bpp::NonHomogeneousSubstitutionProcess::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 263 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_, nodeToModel_, and bpp::TextTools::toString().

◆ getModelNumberForNode()

size_t bpp::NonHomogeneousSubstitutionProcess::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 index of the model associated to the given node.

Exceptions

Exception If no model is found for this node.

Implements bpp::SubstitutionProcessInterface.

Definition at line 248 of file NonHomogeneousSubstitutionProcess.h.

References nodeToModel_, and bpp::TextTools::toString().

◆ getModelNumbers()

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

inlineoverridevirtual

Returns: The current indexes of models used in the process

Implements bpp::SubstitutionProcessInterface.

Definition at line 215 of file NonHomogeneousSubstitutionProcess.h.

References getNumberOfModels().

◆ 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::NonHomogeneousSubstitutionProcess::getNodesWithModel ( size_t i ) const

inlineoverridevirtual

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

Parameters

i	The number of the model in the set (ie the index in the set, plus 1).

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 278 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_, and modelToNodes_.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters().

◆ 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::NonHomogeneousSubstitutionProcess::getNumberOfModels ( ) const

inlineoverridevirtual

Returns: The current number of distinct substitution models in this set.

Implements bpp::SubstitutionProcessInterface.

Definition at line 199 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_.

Referenced by getModelNumbers(), hasMixedTransitionModel(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ 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 addModel(), and 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 checkOrphanNodes(), checkUnknownNodes(), getBranchLengthParameters(), bpp::RateAcrossSitesSubstitutionProcess::getBranchLengthParameters(), and bpp::SimpleSubstitutionProcess::getBranchLengthParameters().

◆ getProbabilityForModel()

double bpp::NonHomogeneousSubstitutionProcess::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 427 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ getRateDistribution() [1/2]

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

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 359 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ getRateDistribution() [2/2]

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

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 364 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ getRateDistributionParameters()

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

inlineoverridevirtual

Get the parameters attached to the rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 340 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ getRateForModel()

double bpp::NonHomogeneousSubstitutionProcess::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 449 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ getRootFrequencies()

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

inlineoverridevirtual

Returns: The values of the root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 404 of file NonHomogeneousSubstitutionProcess.h.

References bpp::FrequencySetInterface::getFrequencies(), bpp::AbstractAutonomousSubstitutionProcess::hasRootFrequencySet(), modelSet_, and bpp::AbstractAutonomousSubstitutionProcess::rootFrequencySet().

◆ 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(), bpp::SimpleSubstitutionProcess::getRootFrequencies(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ getStateMap()

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

inlineoverridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 188 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_.

◆ getSubstitutionModelParameters()

ParameterList NonHomogeneousSubstitutionProcess::getSubstitutionModelParameters ( bool independent ) const

overridevirtual

Get the INDEPENDENT parameters corresponding to the models.

Implements bpp::SubstitutionProcessInterface.

Definition at line 185 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::ParameterList::addParameter(), bpp::Parameter::getName(), bpp::AbstractParameterAliasable::hasIndependentParameter(), modelParameters_, bpp::Parameter::setName(), and bpp::TextTools::toString().

◆ hasMixedTransitionModel()

bool NonHomogeneousSubstitutionProcess::hasMixedTransitionModel ( ) const

Returns: True iff there is a MixedTransitionModel in the NonHomogeneousSubstitutionProcess

Definition at line 259 of file NonHomogeneousSubstitutionProcess.cpp.

References getModel(), and getNumberOfModels().

◆ 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 getRootFrequencies(), bpp::RateAcrossSitesSubstitutionProcess::getRootFrequencies(), bpp::SimpleSubstitutionProcess::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.

◆ isFullySetUp()

bool bpp::NonHomogeneousSubstitutionProcess::isFullySetUp ( bool throwEx = true ) const

inline

Check if the model set is fully specified for a given tree.

This include:

that each node as a model set up,
that each model in the set is attributed to a node,
all nodes ids in the set refer to an existing node in the tree.

Parameters

throwEx Tell if an exception have to be thrown in case of test not passed.

Definition at line 384 of file NonHomogeneousSubstitutionProcess.h.

References checkOrphanNodes(), and checkUnknownNodes().

◆ listModelNames()

void NonHomogeneousSubstitutionProcess::listModelNames ( std::ostream & out = std::cout ) const

list all model names.

Definition at line 151 of file NonHomogeneousSubstitutionProcess.cpp.

References modelSet_, and modelToNodes_.

◆ model() [1/2]

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

inlineoverridevirtual

Returns: the model with given index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 222 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_.

Referenced by addModel(), createHomogeneousSubstitutionProcess(), createNonHomogeneousSubstitutionProcess(), and setModel().

◆ model() [2/2]

const BranchModelInterface& bpp::NonHomogeneousSubstitutionProcess::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 417 of file NonHomogeneousSubstitutionProcess.h.

References modelSet_, and nodeToModel_.

◆ operator=()

NonHomogeneousSubstitutionProcess & NonHomogeneousSubstitutionProcess::operator= ( const NonHomogeneousSubstitutionProcess & set )

Definition at line 38 of file NonHomogeneousSubstitutionProcess.cpp.

References clear(), modelParameters_, bpp::AbstractAutonomousSubstitutionProcess::modelScenario_, modelSet_, modelToNodes_, nodeToModel_, bpp::AbstractAutonomousSubstitutionProcess::operator=(), bpp::AbstractParameterAliasable::operator=(), and rDist_.

◆ 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::NonHomogeneousSubstitutionProcess::rateDistribution ( ) const

inlineoverridevirtual

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 345 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters().

◆ rateDistribution() [2/2]

DiscreteDistributionInterface& bpp::NonHomogeneousSubstitutionProcess::rateDistribution ( )

inlineoverridevirtual

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 352 of file NonHomogeneousSubstitutionProcess.h.

References rDist_.

◆ 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 getRootFrequencies(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ setModel()

void NonHomogeneousSubstitutionProcess::setModel	(	std::shared_ptr< BranchModelInterface >	model,
		size_t	modelIndex
	)

Change a given model.

The new model will be copied and will replace the old one. All previous associations will be kept the same.

Parameters

model	A pointer toward a susbstitution model, that will added to the set. Warning! The set will now be the owner of the pointer, and will destroy it if needed! Copy the model first if you don't want it to be lost!
modelIndex	The index of the existing model to replace.

Definition at line 120 of file NonHomogeneousSubstitutionProcess.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::clone(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractSubstitutionProcess::getAlphabet(), bpp::BranchModelInterface::getAlphabet(), bpp::ParameterAliasable::getIndependentParameters(), bpp::Parameter::getName(), bpp::AbstractSubstitutionProcess::getNumberOfStates(), bpp::BranchModelInterface::getNumberOfStates(), model(), modelParameters_, modelSet_, bpp::Parameter::setName(), bpp::ParameterList::size(), and bpp::TextTools::toString().

◆ setModelScenario()

void NonHomogeneousSubstitutionProcess::setModelScenario ( std::shared_ptr< ModelScenario > modelscenario )

overridevirtual

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

Implements bpp::AbstractAutonomousSubstitutionProcess.

Definition at line 270 of file NonHomogeneousSubstitutionProcess.cpp.

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

◆ setModelToNode()

void NonHomogeneousSubstitutionProcess::setModelToNode	(	size_t	modelIndex,
		unsigned int	nodeNumber
	)

Associate an existing model with a given node.

If the node was was previously associated to a model, the old association is deleted. If other nodes are associated to this model, the association is conserved.

Parameters