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

#include <Bpp/Phyl/Legacy/Model/SubstitutionModelSet.h>

Inheritance diagram for bpp::SubstitutionModelSet:

Collaboration diagram for bpp::SubstitutionModelSet:

Public Member Functions
	SubstitutionModelSet (std::shared_ptr< const Alphabet > alpha)
	Create a model set according to the specified alphabet. Stationarity is assumed. More...

	SubstitutionModelSet (std::shared_ptr< const Alphabet > alpha, std::shared_ptr< FrequencySetInterface > rootFreqs)
	Create a model set according to the specified alphabet and root frequencies. Stationarity is not assumed. More...

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

bool	isStationary () const

void	setRootFrequencies (std::shared_ptr< FrequencySetInterface > rootFreqs)
	Sets a given FrequencySet for root frequencies. More...

	SubstitutionModelSet (const SubstitutionModelSet &set)

SubstitutionModelSet &	operator= (const SubstitutionModelSet &set)

virtual	~SubstitutionModelSet ()

SubstitutionModelSet *	clone () const

size_t	getNumberOfStates () const
	Get the number of states associated to this model set. More...

virtual void	fireParameterChanged (const ParameterList &parameters)

size_t	getNumberOfModels () const

bool	hasMixedTransitionModel () const

std::shared_ptr< const TransitionModelInterface >	getModel (size_t i) const
	Get one model from the set knowing its index. More...

const TransitionModelInterface &	model (size_t i) const

std::shared_ptr< TransitionModelInterface >	getModel (size_t i)

TransitionModelInterface &	model (size_t i)

std::shared_ptr< const SubstitutionModelInterface >	getSubstitutionModel (size_t i) const
	Return a markovian substitution model (or null) More...

std::shared_ptr< SubstitutionModelInterface >	getSubstitutionModel (size_t i)

const SubstitutionModelInterface &	substitutionModel (size_t i) const

bool	hasOnlySubstitutionModels () const
	check if has only markovian substitution models More...

size_t	getModelIndexForNode (int nodeId) const
	Get the index in the set of the model associated to a particular node id. More...

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

std::shared_ptr< TransitionModelInterface >	getModelForNode (int nodeId)

std::shared_ptr< const SubstitutionModelInterface >	getSubstitutionModelForNode (int nodeId) const

std::shared_ptr< SubstitutionModelInterface >	getSubstitutionModelForNode (int nodeId)

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

std::vector< int >	getNodesWithParameter (const std::string &name) const

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

void	setNodeToModel (size_t modelIndex, int nodeId)
	Sets an assignment of a given model index to a given onde id. More...

void	resetModelToNodeIds ()
	Reset model indices to node ids assignment. More...

void	replaceModel (size_t modelIndex, std::shared_ptr< TransitionModelInterface > model)
	Replace a model in the set, and all corresponding parameters. The replaced model deleted. More...

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

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

const FrequencySetInterface &	rootFrequencySet () const

std::vector< double >	getRootFrequencies () const

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

ParameterList	getNodeParameters () const
	Get the parameters corresponding attached to the nodes of the tree. More...

ParameterList	getModelParameters (size_t modelIndex) const
	Get the parameters attached to a Model. More...

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

const Alphabet &	alphabet () const

const std::vector< int > &	getAlphabetStates () const

const StateMapInterface &	stateMap () const

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

std::vector< size_t >	getModelStates (int code) const

std::vector< size_t >	getModelStates (const std::string &code) const

int	getAlphabetStateAsInt (size_t index) const

std::string	getAlphabetStateAsChar (size_t index) const

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

void	setNamespace (const std::string &prefix)

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

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

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

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

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

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

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

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

const ParameterList &	getParameters () const override

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

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

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

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

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

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

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

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

Protected Member Functions
void	updateRootFrequencies ()

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

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

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

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

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

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

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

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

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

ParameterList &	getParameters_ () override

Check function.
bool	checkOrphanModels (bool throwEx) const

bool	checkOrphanNodes (const Tree &tree, bool throwEx) const

bool	checkUnknownNodes (const Tree &tree, bool throwEx) const

Protected Attributes
std::shared_ptr< const Alphabet >	alphabet_
	A pointer toward the common alphabet to all models in the set. More...

size_t	nbStates_

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

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

std::map< 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< int > >	modelToNodes_

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

bool	stationarity_

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Substitution models 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. In the homogeneous case, the parameter list is the same as the list in susbstitution model. When two models at least are specified, these models may have their own parameters or share some of them. To deal with this issue, the SubstitutionModelSet class contains its own parameter list, where parameters are numbered according to the model they belong to.

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 SubstitutionModelSet 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 "asumme 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!

See also: SubstitutionModelSetTools for methods that provide instances of the SubstitutionModelSet for general cases.

Definition at line 67 of file SubstitutionModelSet.h.

Constructor & Destructor Documentation

◆ SubstitutionModelSet() [1/3]

bpp::SubstitutionModelSet::SubstitutionModelSet ( std::shared_ptr< const Alphabet > alpha )

inline

Create a model set according to the specified alphabet. Stationarity is assumed.

Parameters

alpha The alphabet to use for this set.

Definition at line 113 of file SubstitutionModelSet.h.

Referenced by clone().

◆ SubstitutionModelSet() [2/3]

bpp::SubstitutionModelSet::SubstitutionModelSet	(	std::shared_ptr< const Alphabet >	alpha,
		std::shared_ptr< FrequencySetInterface >	rootFreqs
	)

inline

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

Parameters

alpha	The alphabet to use for this set.
rootFreqs	The frequencies at root node. The underlying object will be owned by this instance.

Definition at line 132 of file SubstitutionModelSet.h.

References setRootFrequencies().

◆ SubstitutionModelSet() [3/3]

SubstitutionModelSet::SubstitutionModelSet ( const SubstitutionModelSet & set )

Definition at line 13 of file SubstitutionModelSet.cpp.

References modelSet_.

◆ ~SubstitutionModelSet()

virtual bpp::SubstitutionModelSet::~SubstitutionModelSet ( )

inlinevirtual

Definition at line 170 of file SubstitutionModelSet.h.

Member Function Documentation

◆ addModel()

void SubstitutionModelSet::addModel	(	std::shared_ptr< TransitionModelInterface >	model,
		const std::vector< 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 98 of file SubstitutionModelSet.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::BranchModelInterface::alphabet(), alphabet_, bpp::Alphabet::getAlphabetType(), bpp::BranchModelInterface::getNumberOfStates(), bpp::ParameterList::getParameterNames(), bpp::ParameterAliasable::getParameters(), model(), modelParameters_, modelSet_, modelToNodes_, nbStates_, nodeToModel_, bpp::ParameterList::parameter(), bpp::Parameter::setName(), and bpp::TextTools::toString().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ alphabet()

const Alphabet& bpp::SubstitutionModelSet::alphabet ( ) const

inline

Definition at line 467 of file SubstitutionModelSet.h.

References alphabet_.

◆ checkOrphanModels()

bool SubstitutionModelSet::checkOrphanModels ( bool throwEx ) const

protected

Definition at line 230 of file SubstitutionModelSet.cpp.

References bpp::VectorTools::contains(), bpp::MapTools::getValues(), modelSet_, nodeToModel_, and bpp::TextTools::toString().

Referenced by isFullySetUpFor().

◆ checkOrphanNodes()

bool SubstitutionModelSet::checkOrphanNodes	(	const Tree &	tree,
		bool	throwEx
	)		const

protected

Definition at line 245 of file SubstitutionModelSet.cpp.

References bpp::Tree::getNodesId(), bpp::Tree::getRootId(), nodeToModel_, and bpp::TextTools::toString().

Referenced by isFullySetUpFor().

◆ checkUnknownNodes()

bool SubstitutionModelSet::checkUnknownNodes	(	const Tree &	tree,
		bool	throwEx
	)		const

protected

Definition at line 261 of file SubstitutionModelSet.cpp.

References bpp::VectorTools::contains(), bpp::Tree::getNodesId(), bpp::Tree::getRootId(), modelToNodes_, and bpp::TextTools::toString().

Referenced by isFullySetUpFor().

◆ clear()

void SubstitutionModelSet::clear ( )

Resets all the information contained in this object.

Definition at line 54 of file SubstitutionModelSet.cpp.

References modelParameters_, modelSet_, nbStates_, nodeToModel_, bpp::AbstractParameterAliasable::resetParameters_(), rootFrequencies_, and stationarity_.

Referenced by bpp::MixedSubstitutionModelSet::clear(), and bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ clone()

SubstitutionModelSet* bpp::SubstitutionModelSet::clone ( ) const

inlinevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 172 of file SubstitutionModelSet.h.

References SubstitutionModelSet().

◆ fireParameterChanged()

void SubstitutionModelSet::fireParameterChanged ( const ParameterList & parameters )

virtual

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

Parameters

parameters The modified parameters.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::MixedSubstitutionModelSet.

Definition at line 214 of file SubstitutionModelSet.cpp.

References bpp::AbstractParameterAliasable::getParameterValue(), modelParameters_, modelSet_, bpp::TextTools::toString(), and updateRootFrequencies().

Referenced by bpp::MixedSubstitutionModelSet::fireParameterChanged().

◆ getAlphabet()

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

inline

Definition at line 465 of file SubstitutionModelSet.h.

References alphabet_.

◆ getAlphabetStateAsChar()

std::string bpp::SubstitutionModelSet::getAlphabetStateAsChar ( size_t index ) const

inline

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Definition at line 512 of file SubstitutionModelSet.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and model().

◆ getAlphabetStateAsInt()

int bpp::SubstitutionModelSet::getAlphabetStateAsInt ( size_t index ) const

inline

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Definition at line 503 of file SubstitutionModelSet.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and model().

◆ getAlphabetStates()

const std::vector<int>& bpp::SubstitutionModelSet::getAlphabetStates ( ) const

inline

Returns: The supported states of the model set, as a vector of int codes.

See also: Alphabet

Definition at line 474 of file SubstitutionModelSet.h.

References bpp::BranchModelInterface::getAlphabetStates(), and model().

◆ getModel() [1/2]

std::shared_ptr<TransitionModelInterface> bpp::SubstitutionModelSet::getModel ( size_t i )

inline

Definition at line 222 of file SubstitutionModelSet.h.

References modelSet_.

◆ getModel() [2/2]

std::shared_ptr<const TransitionModelInterface> bpp::SubstitutionModelSet::getModel ( size_t i ) const

inline

Get one model from the set knowing its index.

Parameters

i	Index of the model in the set.

Returns: A pointer toward the corresponding model.

Definition at line 210 of file SubstitutionModelSet.h.

References modelSet_.

Referenced by bpp::LegacyPhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), getSubstitutionModel(), hasMixedTransitionModel(), and bpp::LegacyPhylogeneticsApplicationTools::printParameters().

◆ getModelForNode() [1/2]

std::shared_ptr<TransitionModelInterface> bpp::SubstitutionModelSet::getModelForNode ( int nodeId )

inline

Definition at line 308 of file SubstitutionModelSet.h.

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

◆ getModelForNode() [2/2]

std::shared_ptr<const TransitionModelInterface> bpp::SubstitutionModelSet::getModelForNode ( int nodeId ) const

inline

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.

Definition at line 301 of file SubstitutionModelSet.h.

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

Referenced by getSubstitutionModelForNode().

◆ getModelIndexForNode()

size_t bpp::SubstitutionModelSet::getModelIndexForNode ( int nodeId ) const

inline

Get the index in the set 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.

Definition at line 286 of file SubstitutionModelSet.h.

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

◆ getModelParameters()

ParameterList bpp::SubstitutionModelSet::getModelParameters ( size_t modelIndex ) const

Get the parameters attached to a Model.

Parameters

modelIndex the index of the model in the set

Returns: The parameters attached to the model.

◆ getModelStates() [1/2]

std::vector<size_t> bpp::SubstitutionModelSet::getModelStates ( const std::string & code ) const

inline

Definition at line 494 of file SubstitutionModelSet.h.

References bpp::BranchModelInterface::getModelStates(), and model().

◆ getModelStates() [2/2]

std::vector<size_t> bpp::SubstitutionModelSet::getModelStates ( int code ) const

inline

Definition at line 489 of file SubstitutionModelSet.h.

References bpp::BranchModelInterface::getModelStates(), and model().

◆ getNodeParameters()

ParameterList bpp::SubstitutionModelSet::getNodeParameters ( ) const

inline

Get the parameters corresponding attached to the nodes of the tree.

That is, all the parameters without the root frequencies.

Returns: The parameters attached to the nodes of the tree.

Definition at line 444 of file SubstitutionModelSet.h.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::getNumberOfParameters(), bpp::AbstractParameterAliasable::getParameter_(), rootFrequencies_, and stationarity_.

Referenced by replaceModel().

◆ getNodesWithModel()

const std::vector<int>& bpp::SubstitutionModelSet::getNodesWithModel ( size_t i ) const

inline

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.

Definition at line 333 of file SubstitutionModelSet.h.

References modelSet_, and modelToNodes_.

Referenced by getNodesWithParameter(), and bpp::LegacyPhylogeneticsApplicationTools::printParameters().

◆ getNodesWithParameter()

std::vector< int > SubstitutionModelSet::getNodesWithParameter ( const std::string & name ) const

Parameters

name	The name of the parameter to look for.

Returns: The list of nodes with a model containing the specified parameter.

Exceptions

ParameterNotFoundException If no parameter with the specified name is found.

Definition at line 75 of file SubstitutionModelSet.cpp.

References bpp::AbstractParameterAliasable::getAlias(), getNodesWithModel(), and bpp::AbstractParameterAliasable::hasParameter().

◆ getNumberOfModels()

size_t bpp::SubstitutionModelSet::getNumberOfModels ( ) const

inline

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

Definition at line 196 of file SubstitutionModelSet.h.

References modelSet_.

Referenced by bpp::MixedSubstitutionModelSet::addToHyperNode(), bpp::MixedSubstitutionModelSet::complete(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), hasMixedTransitionModel(), and bpp::LegacyPhylogeneticsApplicationTools::printParameters().

◆ getNumberOfStates()

size_t bpp::SubstitutionModelSet::getNumberOfStates ( ) const

inline

Get the number of states associated to this model set.

Returns: The number of states.

Exceptions

Exception if no model is associated to the set.

Definition at line 181 of file SubstitutionModelSet.h.

References nbStates_.

◆ getRootFrequencies()

std::vector<double> bpp::SubstitutionModelSet::getRootFrequencies ( ) const

inline

Returns: The values of the root frequencies.

Definition at line 416 of file SubstitutionModelSet.h.

References modelSet_, rootFrequencies_, and stationarity_.

◆ getRootFrequenciesParameters()

ParameterList bpp::SubstitutionModelSet::getRootFrequenciesParameters ( ) const

inline

Get the parameters corresponding to the root frequencies.

Returns: The parameters corresponding to the root frequencies.

Definition at line 429 of file SubstitutionModelSet.h.

References rootFrequencies_, and stationarity_.

◆ getRootFrequencySet()

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

inline

Returns: The set of root frequencies.

Definition at line 396 of file SubstitutionModelSet.h.

References rootFrequencies_.

◆ getStateMap()

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

inline

Definition at line 484 of file SubstitutionModelSet.h.

References bpp::BranchModelInterface::getStateMap(), and model().

◆ getSubstitutionModel() [1/2]

std::shared_ptr<SubstitutionModelInterface> bpp::SubstitutionModelSet::getSubstitutionModel ( size_t i )

inline

Definition at line 245 of file SubstitutionModelSet.h.

References getModel(), and model().

◆ getSubstitutionModel() [2/2]

std::shared_ptr<const SubstitutionModelInterface> bpp::SubstitutionModelSet::getSubstitutionModel ( size_t i ) const

inline

Return a markovian substitution model (or null)

Definition at line 236 of file SubstitutionModelSet.h.

References getModel(), and model().

Referenced by bpp::LegacySubstitutionMappingTools::getCountsPerBranch().

◆ getSubstitutionModelForNode() [1/2]

std::shared_ptr<SubstitutionModelInterface> bpp::SubstitutionModelSet::getSubstitutionModelForNode ( int nodeId )

inline

Definition at line 321 of file SubstitutionModelSet.h.

References getModelForNode().

◆ getSubstitutionModelForNode() [2/2]

std::shared_ptr<const SubstitutionModelInterface> bpp::SubstitutionModelSet::getSubstitutionModelForNode ( int nodeId ) const

inline

Definition at line 316 of file SubstitutionModelSet.h.

References getModelForNode().

Referenced by bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors().

◆ hasMixedTransitionModel()

bool SubstitutionModelSet::hasMixedTransitionModel ( ) const

Returns: True iff there is a MixedTransitionModel in the SubstitutionModelSet

Definition at line 282 of file SubstitutionModelSet.cpp.

References getModel(), getNumberOfModels(), and modelToNodes_.

◆ hasOnlySubstitutionModels()

bool bpp::SubstitutionModelSet::hasOnlySubstitutionModels ( ) const

inline

check if has only markovian substitution models

Definition at line 269 of file SubstitutionModelSet.h.

References model(), and modelSet_.

◆ isFullySetUpFor()

bool bpp::SubstitutionModelSet::isFullySetUpFor	(	const Tree &	tree,
		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,
that each parameter in the set actually correspond to a model.
all nodes ids in the set refer to an existing node in the tree.

Parameters

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

Definition at line 529 of file SubstitutionModelSet.h.

References checkOrphanModels(), checkOrphanNodes(), and checkUnknownNodes().

◆ isStationary()

bool bpp::SubstitutionModelSet::isStationary ( ) const

inline

Definition at line 154 of file SubstitutionModelSet.h.

References stationarity_.

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

◆ listModelNames()

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

Definition at line 201 of file SubstitutionModelSet.cpp.

References modelSet_, and modelToNodes_.

◆ model() [1/2]

TransitionModelInterface& bpp::SubstitutionModelSet::model ( size_t i )

inline

Definition at line 228 of file SubstitutionModelSet.h.

References modelSet_.

◆ model() [2/2]

const TransitionModelInterface& bpp::SubstitutionModelSet::model ( size_t i ) const

inline

Definition at line 216 of file SubstitutionModelSet.h.

References modelSet_.

Referenced by addModel(), bpp::MixedSubstitutionModelSet::complete(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), getAlphabetStateAsChar(), getAlphabetStateAsInt(), getAlphabetStates(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), getModelStates(), getStateMap(), getSubstitutionModel(), hasOnlySubstitutionModels(), replaceModel(), stateMap(), and substitutionModel().

◆ operator=()

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

Definition at line 31 of file SubstitutionModelSet.cpp.

References alphabet_, modelParameters_, modelSet_, modelToNodes_, nbStates_, nodeToModel_, bpp::AbstractParameterAliasable::operator=(), rootFrequencies_, and stationarity_.

Referenced by bpp::MixedSubstitutionModelSet::operator=().

◆ replaceModel()

void SubstitutionModelSet::replaceModel	(	size_t	modelIndex,
		std::shared_ptr< TransitionModelInterface >	model
	)

Replace a model in the set, and all corresponding parameters. The replaced model deleted.

Parameters

modelIndex	The index of the model in the set.
model	the new model. This model will be owned by the Set.

Exceptions

Exception if a parameter becomes orphan because of the removal.

Definition at line 149 of file SubstitutionModelSet.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::clone(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParameterAliasable::getAlias(), getNodeParameters(), bpp::ParameterList::getParameterNames(), bpp::ParameterAliasable::getParameters(), model(), modelParameters_, modelSet_, bpp::ParameterList::parameter(), bpp::Parameter::setName(), bpp::ParameterList::size(), bpp::TextTools::toInt(), bpp::TextTools::toString(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ resetModelToNodeIds()

void SubstitutionModelSet::resetModelToNodeIds ( )

Reset model indices to node ids assignment.

Definition at line 132 of file SubstitutionModelSet.cpp.

References modelToNodes_, and nodeToModel_.

◆ rootFrequencySet()

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

inline

Returns: The set of root frequencies.

Definition at line 401 of file SubstitutionModelSet.h.

References rootFrequencies_.

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

◆ setNodeToModel()

void SubstitutionModelSet::setNodeToModel	(	size_t	modelIndex,
		int	nodeId
	)

Sets an assignment of a given model index to a given onde id.

Parameters

modelIndex	The index of the model in the set.
nodeId	The node ID

Exceptions

Exception if the model index doesn't correspond to an existing model in the modelSet

Definition at line 140 of file SubstitutionModelSet.cpp.

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

◆ setRootFrequencies()

void SubstitutionModelSet::setRootFrequencies ( std::shared_ptr< FrequencySetInterface > rootFreqs )

Sets a given FrequencySet for root frequencies.

Parameters

rootFreqs The FrequencySet for root frequencies.

Definition at line 65 of file SubstitutionModelSet.cpp.

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

Referenced by bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet(), and SubstitutionModelSet().

◆ stateMap()

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

inline

Definition at line 479 of file SubstitutionModelSet.h.

References model(), and bpp::BranchModelInterface::stateMap().

◆ substitutionModel()

const SubstitutionModelInterface& bpp::SubstitutionModelSet::substitutionModel ( size_t i ) const

inline

Definition at line 253 of file SubstitutionModelSet.h.

References model().

◆ updateRootFrequencies()

void bpp::SubstitutionModelSet::updateRootFrequencies ( )

inlineprotected

Set rootFrequencies_ from parameters.

Definition at line 541 of file SubstitutionModelSet.h.

References bpp::AbstractParameterAliasable::getParameters(), rootFrequencies_, and stationarity_.

Referenced by fireParameterChanged().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::SubstitutionModelSet::alphabet_

protected

A pointer toward the common alphabet to all models in the set.

Definition at line 74 of file SubstitutionModelSet.h.

Referenced by addModel(), alphabet(), getAlphabet(), and operator=().

◆ modelParameters_

std::vector<ParameterList> bpp::SubstitutionModelSet::modelParameters_

private

Parameters for each model in the set.

The parameters_ field, inherited from AbstractSubstitutionModel contains all parameters, with unique names. To make the correspondence with parameters for each model in the set, we duplicate them in this array. In most cases, this is something like 'theta_1 <=> theta', 'theta_2 <=> theta', etc.

Definition at line 102 of file SubstitutionModelSet.h.

Referenced by addModel(), clear(), fireParameterChanged(), operator=(), and replaceModel().

◆ modelSet_

std::vector< std::shared_ptr<TransitionModelInterface> > bpp::SubstitutionModelSet::modelSet_

protected

Contains all models used in this tree.

Definition at line 81 of file SubstitutionModelSet.h.

Referenced by addModel(), checkOrphanModels(), clear(), fireParameterChanged(), getModel(), getModelForNode(), getNodesWithModel(), getNumberOfModels(), getRootFrequencies(), hasOnlySubstitutionModels(), listModelNames(), model(), operator=(), replaceModel(), setNodeToModel(), and SubstitutionModelSet().

◆ modelToNodes_

std::map<size_t, std::vector<int> > bpp::SubstitutionModelSet::modelToNodes_

mutableprivate

Definition at line 93 of file SubstitutionModelSet.h.

Referenced by addModel(), checkUnknownNodes(), getNodesWithModel(), hasMixedTransitionModel(), listModelNames(), operator=(), resetModelToNodeIds(), and setNodeToModel().

◆ nbStates_

size_t bpp::SubstitutionModelSet::nbStates_

protected

Definition at line 76 of file SubstitutionModelSet.h.

Referenced by addModel(), clear(), getNumberOfStates(), and operator=().

◆ nodeToModel_

std::map<int, size_t> bpp::SubstitutionModelSet::nodeToModel_

mutableprivate

Contains for each node in a tree the index of the corresponding model in modelSet_.

Definition at line 92 of file SubstitutionModelSet.h.

Referenced by addModel(), checkOrphanModels(), checkOrphanNodes(), clear(), getModelForNode(), getModelIndexForNode(), operator=(), resetModelToNodeIds(), and setNodeToModel().

◆ rootFrequencies_

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

private

Root frequencies.

Definition at line 87 of file SubstitutionModelSet.h.

Referenced by clear(), getNodeParameters(), getRootFrequencies(), getRootFrequenciesParameters(), getRootFrequencySet(), operator=(), rootFrequencySet(), setRootFrequencies(), and updateRootFrequencies().

◆ stationarity_

bool bpp::SubstitutionModelSet::stationarity_

private

Definition at line 104 of file SubstitutionModelSet.h.

Referenced by clear(), getNodeParameters(), getRootFrequencies(), getRootFrequenciesParameters(), isStationary(), operator=(), setRootFrequencies(), and updateRootFrequencies().

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

Bpp/Phyl/Legacy/Model/SubstitutionModelSet.h
Bpp/Phyl/Legacy/Model/SubstitutionModelSet.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SubstitutionModelSet() [1/3]

◆ SubstitutionModelSet() [2/3]

◆ SubstitutionModelSet() [3/3]

◆ ~SubstitutionModelSet()

Member Function Documentation

◆ addModel()

◆ alphabet()

◆ checkOrphanModels()

◆ checkOrphanNodes()

◆ checkUnknownNodes()

◆ clear()

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getModel() [1/2]

◆ getModel() [2/2]

◆ getModelForNode() [1/2]

◆ getModelForNode() [2/2]

◆ getModelIndexForNode()

◆ getModelParameters()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getNodeParameters()

◆ getNodesWithModel()

◆ getNodesWithParameter()

◆ getNumberOfModels()

◆ getNumberOfStates()

◆ getRootFrequencies()

◆ getRootFrequenciesParameters()

◆ getRootFrequencySet()

◆ getStateMap()

◆ getSubstitutionModel() [1/2]

◆ getSubstitutionModel() [2/2]

◆ getSubstitutionModelForNode() [1/2]

◆ getSubstitutionModelForNode() [2/2]

◆ hasMixedTransitionModel()

◆ hasOnlySubstitutionModels()

◆ isFullySetUpFor()

◆ isStationary()

◆ listModelNames()

◆ model() [1/2]

◆ model() [2/2]

◆ operator=()

◆ replaceModel()

◆ resetModelToNodeIds()

◆ rootFrequencySet()

◆ setNodeToModel()

◆ setRootFrequencies()

◆ stateMap()

◆ substitutionModel()

◆ updateRootFrequencies()

Member Data Documentation

◆ alphabet_

◆ modelParameters_

◆ modelSet_

◆ modelToNodes_

◆ nbStates_

◆ nodeToModel_

◆ rootFrequencies_

◆ stationarity_