Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet. More...

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

Inheritance diagram for bpp::MixedSubstitutionModelSet:

Collaboration diagram for bpp::MixedSubstitutionModelSet:

Classes
class	HyperNode

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

	~MixedSubstitutionModelSet ()

	MixedSubstitutionModelSet (const MixedSubstitutionModelSet &set)

	MixedSubstitutionModelSet (const SubstitutionModelSet &set)

MixedSubstitutionModelSet &	operator= (const MixedSubstitutionModelSet &set)

MixedSubstitutionModelSet *	clone () const

void	clear ()
	Resets the list of the HyperNodes. More...

void	addEmptyHyperNode ()

void	addHyperNode (const HyperNode &hn)

bool	complete ()

void	addToHyperNode (size_t nM, const Vuint &vnS, int nH=-1)

size_t	getNumberOfHyperNodes () const

HyperNode &	getHyperNode (size_t i)

const HyperNode &	getHyperNode (size_t i) const

bool	hasExclusivePaths () const

void	fireParameterChanged (const ParameterList &parameters)

void	computeHyperNodesProbabilities ()

double	getHyperNodeProbability (const HyperNode &hn) const

bool	isStationary () const

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

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

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...

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

const TransitionModelInterface &	model (size_t i) const

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::vector< HyperNode * >	vpHyperNodes_

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 Mixed Substitution Models. This class inherits from SubstitutionModelSet.

This class is done to handle specific cases of choices among the submodels of mixed substitution models. Each branch of the tree is labelled by a mixed model, and a site may be restricted to a set of submodels it is allowed to follow. These sets are defined through an hypergrap, ie a list of hypernodes.

For example, suppose there are 3 mixed models (M1,M2 and M3), with 2, 3, 4 submodels (S1, S2, ...) each.

If the sites are allowed to follow any combination of submodels (12 combinations) the corresponding hypergraph has only one hypernode: (<1,2>,<1,2,3>,<1,2,3,4>).

The hypergraph with hypernodes ((<1>,<1,2>,<1,2>),(<2>,<3>,<3,4>)) means that a site either follows 6 combinations:

M1:S1, M2:S1 or M2:S2, and M3:S1 or M3:S2.

or

M1:S2, M2:S3, and M3:S3 or M3:S4.

Actually, additional coordinates are set when there are non mixed models, with no value in them, and not used in practice.

An hypernode is valid only if each mixed model is represented at least by one submodel.

Dependency of the submodels entails constraints in the probabilities of the submodels, and definition of the hypernodes must be taken with care for the whole modelling to be possible.

In this implementation, for sake of simplification (and for reason of time), all the submodels must belong to exactly one given hypernode, but in theory more complex dependencies are possible.

Concerning the probabilities of the submodels in each hypernode, the first coordinate (ie set of submodels inside a mixed model) in the list defines the probability of each hypernode. For each coordinate (the first included), when there are several submodels, their probabilities are conditional probabilities, which means that they sum 1 and their ratio are unchanged.

For instance, for hypergraph ((<1>,<1,2>,<1,2>),(<2>,<3>,<3,4>)), the probabilities of hypernodes are the probabilities of M1:S1 and M1:S2. In the first hypernode, the probabilities of M2:S1 and M2:S2 are P(M2:S1)/(P(M2:S1)+P(M2:S2)) and P(M2:S2)/(P(M2:S1)+P(M2:S2)).

We do not certify that the probability parameters of the mixed models are all useful, and then identifiability problems may be encountered.

There is a method ("complete") that creates an additional hypernode to ensure that all submodels belong to at least an hypernode.

Definition at line 85 of file MixedSubstitutionModelSet.h.

Constructor & Destructor Documentation

◆ MixedSubstitutionModelSet() [1/3]

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

inline

Create a model set according to the specified alphabet.

Parameters

alpha The alphabet to use for this set.

Definition at line 239 of file MixedSubstitutionModelSet.h.

Referenced by clone().

◆ ~MixedSubstitutionModelSet()

MixedSubstitutionModelSet::~MixedSubstitutionModelSet ( )

Definition at line 27 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

◆ MixedSubstitutionModelSet() [2/3]

MixedSubstitutionModelSet::MixedSubstitutionModelSet ( const MixedSubstitutionModelSet & set )

Definition at line 12 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

◆ MixedSubstitutionModelSet() [3/3]

MixedSubstitutionModelSet::MixedSubstitutionModelSet ( const SubstitutionModelSet & set )

Definition at line 22 of file MixedSubstitutionModelSet.cpp.

Member Function Documentation

◆ addEmptyHyperNode()

void MixedSubstitutionModelSet::addEmptyHyperNode ( )

Definition at line 62 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

Referenced by complete(), and bpp::LegacyPhylogeneticsApplicationTools::completeMixedSubstitutionModelSet().

◆ addHyperNode()

void MixedSubstitutionModelSet::addHyperNode ( const HyperNode & hn )

Definition at line 67 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

◆ addModel()

void SubstitutionModelSet::addModel	(	std::shared_ptr< TransitionModelInterface >	model,
		const std::vector< int > &	nodesId
	)

inherited

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

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

◆ addToHyperNode()

void MixedSubstitutionModelSet::addToHyperNode	(	size_t	nM,
		const Vuint &	vnS,
		int	nH = `-1`
	)

Definition at line 126 of file MixedSubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::getNumberOfModels(), and vpHyperNodes_.

Referenced by complete(), and bpp::LegacyPhylogeneticsApplicationTools::completeMixedSubstitutionModelSet().

◆ alphabet()

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

inlineinherited

Definition at line 467 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::alphabet_.

◆ checkOrphanModels()

bool SubstitutionModelSet::checkOrphanModels ( bool throwEx ) const

protectedinherited

Definition at line 230 of file SubstitutionModelSet.cpp.

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

Referenced by bpp::SubstitutionModelSet::isFullySetUpFor().

◆ checkOrphanNodes()

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

protectedinherited

Definition at line 245 of file SubstitutionModelSet.cpp.

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

Referenced by bpp::SubstitutionModelSet::isFullySetUpFor().

◆ checkUnknownNodes()

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

protectedinherited

Definition at line 261 of file SubstitutionModelSet.cpp.

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

Referenced by bpp::SubstitutionModelSet::isFullySetUpFor().

◆ clear()

void MixedSubstitutionModelSet::clear ( )

Resets the list of the HyperNodes.

Definition at line 35 of file MixedSubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::clear(), and vpHyperNodes_.

◆ clone()

MixedSubstitutionModelSet* bpp::MixedSubstitutionModelSet::clone ( ) const

inlinevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 251 of file MixedSubstitutionModelSet.h.

References MixedSubstitutionModelSet().

◆ complete()

bool MixedSubstitutionModelSet::complete ( )

Definition at line 72 of file MixedSubstitutionModelSet.cpp.

References addEmptyHyperNode(), addToHyperNode(), bpp::MixedSubstitutionModelSet::HyperNode::getNode(), bpp::SubstitutionModelSet::getNumberOfModels(), bpp::SubstitutionModelSet::model(), bpp::MixedSubstitutionModelSet::HyperNode::Node::size(), and vpHyperNodes_.

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

◆ computeHyperNodesProbabilities()

void MixedSubstitutionModelSet::computeHyperNodesProbabilities ( )

Definition at line 164 of file MixedSubstitutionModelSet.cpp.

References getHyperNode(), bpp::MixedSubstitutionModelSet::HyperNode::getNode(), bpp::MixedTransitionModelInterface::getNProbability(), getNumberOfHyperNodes(), bpp::SubstitutionModelSet::getNumberOfModels(), bpp::MixedSubstitutionModelSet::HyperNode::getProbability(), bpp::SubstitutionModelSet::model(), bpp::MixedTransitionModelInterface::normalizeVRates(), bpp::MixedTransitionModelInterface::setNProbability(), bpp::MixedSubstitutionModelSet::HyperNode::setProbability(), and bpp::MixedSubstitutionModelSet::HyperNode::Node::size().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), and fireParameterChanged().

◆ fireParameterChanged()

void MixedSubstitutionModelSet::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::SubstitutionModelSet.

Definition at line 155 of file MixedSubstitutionModelSet.cpp.

References computeHyperNodesProbabilities(), and bpp::SubstitutionModelSet::fireParameterChanged().

◆ getAlphabet()

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

inlineinherited

Definition at line 465 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::alphabet_.

◆ getAlphabetStateAsChar()

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

inlineinherited

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 bpp::SubstitutionModelSet::model().

◆ getAlphabetStateAsInt()

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

inlineinherited

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 bpp::SubstitutionModelSet::model().

◆ getAlphabetStates()

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

inlineinherited

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 bpp::SubstitutionModelSet::model().

◆ getHyperNode() [1/2]

HyperNode& bpp::MixedSubstitutionModelSet::getHyperNode ( size_t i )

inline

Definition at line 299 of file MixedSubstitutionModelSet.h.

References vpHyperNodes_.

Referenced by bpp::LegacyPhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), computeHyperNodesProbabilities(), and hasExclusivePaths().

◆ getHyperNode() [2/2]

const HyperNode& bpp::MixedSubstitutionModelSet::getHyperNode ( size_t i ) const

inline

Definition at line 301 of file MixedSubstitutionModelSet.h.

References vpHyperNodes_.

◆ getHyperNodeProbability()

double MixedSubstitutionModelSet::getHyperNodeProbability ( const HyperNode & hn ) const

Definition at line 242 of file MixedSubstitutionModelSet.cpp.

References bpp::MixedSubstitutionModelSet::HyperNode::getNode(), bpp::MixedTransitionModelInterface::getNProbability(), bpp::SubstitutionModelSet::getNumberOfModels(), bpp::SubstitutionModelSet::model(), and bpp::MixedSubstitutionModelSet::HyperNode::Node::size().

◆ getModel() [1/2]

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

inlineinherited

Definition at line 222 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

◆ getModel() [2/2]

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

inlineinherited

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 bpp::SubstitutionModelSet::modelSet_.

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

◆ getModelForNode() [1/2]

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

inlineinherited

Definition at line 308 of file SubstitutionModelSet.h.

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

◆ getModelForNode() [2/2]

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

inlineinherited

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

Referenced by bpp::SubstitutionModelSet::getSubstitutionModelForNode().

◆ getModelIndexForNode()

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

inlineinherited

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

◆ getModelParameters()

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

inherited

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

inlineinherited

Definition at line 494 of file SubstitutionModelSet.h.

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

◆ getModelStates() [2/2]

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

inlineinherited

Definition at line 489 of file SubstitutionModelSet.h.

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

◆ getNodeParameters()

ParameterList bpp::SubstitutionModelSet::getNodeParameters ( ) const

inlineinherited

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_(), bpp::SubstitutionModelSet::rootFrequencies_, and bpp::SubstitutionModelSet::stationarity_.

Referenced by bpp::SubstitutionModelSet::replaceModel().

◆ getNodesWithModel()

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

inlineinherited

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 bpp::SubstitutionModelSet::modelSet_, and bpp::SubstitutionModelSet::modelToNodes_.

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

◆ getNodesWithParameter()

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

inherited

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(), bpp::SubstitutionModelSet::getNodesWithModel(), and bpp::AbstractParameterAliasable::hasParameter().

◆ getNumberOfHyperNodes()

size_t bpp::MixedSubstitutionModelSet::getNumberOfHyperNodes ( ) const

inline

Definition at line 297 of file MixedSubstitutionModelSet.h.

References vpHyperNodes_.

Referenced by bpp::LegacyPhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), computeHyperNodesProbabilities(), and hasExclusivePaths().

◆ getNumberOfModels()

size_t bpp::SubstitutionModelSet::getNumberOfModels ( ) const

inlineinherited

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

Definition at line 196 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

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

◆ getNumberOfStates()

size_t bpp::SubstitutionModelSet::getNumberOfStates ( ) const

inlineinherited

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 bpp::SubstitutionModelSet::nbStates_.

◆ getRootFrequencies()

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

inlineinherited

Returns: The values of the root frequencies.

Definition at line 416 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_, bpp::SubstitutionModelSet::rootFrequencies_, and bpp::SubstitutionModelSet::stationarity_.

◆ getRootFrequenciesParameters()

ParameterList bpp::SubstitutionModelSet::getRootFrequenciesParameters ( ) const

inlineinherited

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 bpp::SubstitutionModelSet::rootFrequencies_, and bpp::SubstitutionModelSet::stationarity_.

◆ getRootFrequencySet()

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

inlineinherited

Returns: The set of root frequencies.

Definition at line 396 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::rootFrequencies_.

◆ getStateMap()

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

inlineinherited

Definition at line 484 of file SubstitutionModelSet.h.

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

◆ getSubstitutionModel() [1/2]

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

inlineinherited

Definition at line 245 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModel(), and bpp::SubstitutionModelSet::model().

◆ getSubstitutionModel() [2/2]

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

inlineinherited

Return a markovian substitution model (or null)

Definition at line 236 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModel(), and bpp::SubstitutionModelSet::model().

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

◆ getSubstitutionModelForNode() [1/2]

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

inlineinherited

Definition at line 321 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModelForNode().

◆ getSubstitutionModelForNode() [2/2]

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

inlineinherited

Definition at line 316 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModelForNode().

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

◆ hasExclusivePaths()

bool MixedSubstitutionModelSet::hasExclusivePaths ( ) const

Definition at line 139 of file MixedSubstitutionModelSet.cpp.

References getHyperNode(), getNumberOfHyperNodes(), and bpp::MixedSubstitutionModelSet::HyperNode::intersects().

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

◆ hasMixedTransitionModel()

bool SubstitutionModelSet::hasMixedTransitionModel ( ) const

inherited

Returns: True iff there is a MixedTransitionModel in the SubstitutionModelSet

Definition at line 282 of file SubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::getModel(), bpp::SubstitutionModelSet::getNumberOfModels(), and bpp::SubstitutionModelSet::modelToNodes_.

◆ hasOnlySubstitutionModels()

bool bpp::SubstitutionModelSet::hasOnlySubstitutionModels ( ) const

inlineinherited

check if has only markovian substitution models

Definition at line 269 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::model(), and bpp::SubstitutionModelSet::modelSet_.

◆ isFullySetUpFor()

bool bpp::SubstitutionModelSet::isFullySetUpFor	(	const Tree &	tree,
		bool	throwEx = `true`
	)		const

inlineinherited

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 bpp::SubstitutionModelSet::checkOrphanModels(), bpp::SubstitutionModelSet::checkOrphanNodes(), and bpp::SubstitutionModelSet::checkUnknownNodes().

◆ isStationary()

bool bpp::SubstitutionModelSet::isStationary ( ) const

inlineinherited

Definition at line 154 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::stationarity_.

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

◆ listModelNames()

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

inherited

Definition at line 201 of file SubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::modelSet_, and bpp::SubstitutionModelSet::modelToNodes_.

◆ model() [1/2]

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

inlineinherited

Definition at line 228 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

◆ model() [2/2]

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

inlineinherited

Definition at line 216 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

◆ operator=()

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

Definition at line 44 of file MixedSubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::operator=(), and vpHyperNodes_.

◆ replaceModel()

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

inherited

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

◆ resetModelToNodeIds()

void SubstitutionModelSet::resetModelToNodeIds ( )

inherited

Reset model indices to node ids assignment.

Definition at line 132 of file SubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::modelToNodes_, and bpp::SubstitutionModelSet::nodeToModel_.

◆ rootFrequencySet()

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

inlineinherited

Returns: The set of root frequencies.

Definition at line 401 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::rootFrequencies_.

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

◆ setNodeToModel()

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

inherited

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

◆ setRootFrequencies()

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

inherited

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_(), bpp::SubstitutionModelSet::rootFrequencies_, and bpp::SubstitutionModelSet::stationarity_.

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

◆ stateMap()

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

inlineinherited

Definition at line 479 of file SubstitutionModelSet.h.

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

◆ substitutionModel()

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

inlineinherited

Definition at line 253 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::model().

◆ updateRootFrequencies()

void bpp::SubstitutionModelSet::updateRootFrequencies ( )

inlineprotectedinherited

Set rootFrequencies_ from parameters.

Definition at line 541 of file SubstitutionModelSet.h.

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

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

Member Data Documentation

◆ alphabet_

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

protectedinherited

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

Definition at line 74 of file SubstitutionModelSet.h.

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

◆ modelParameters_

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

privateinherited

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 bpp::SubstitutionModelSet::addModel(), bpp::SubstitutionModelSet::clear(), bpp::SubstitutionModelSet::fireParameterChanged(), bpp::SubstitutionModelSet::operator=(), and bpp::SubstitutionModelSet::replaceModel().

◆ modelSet_

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

protectedinherited

Contains all models used in this tree.

Definition at line 81 of file SubstitutionModelSet.h.

◆ modelToNodes_

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

mutableprivateinherited

Definition at line 93 of file SubstitutionModelSet.h.

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

◆ nbStates_

size_t bpp::SubstitutionModelSet::nbStates_

protectedinherited

Definition at line 76 of file SubstitutionModelSet.h.

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

◆ nodeToModel_

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

mutableprivateinherited

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 bpp::SubstitutionModelSet::addModel(), bpp::SubstitutionModelSet::checkOrphanModels(), bpp::SubstitutionModelSet::checkOrphanNodes(), bpp::SubstitutionModelSet::clear(), bpp::SubstitutionModelSet::getModelForNode(), bpp::SubstitutionModelSet::getModelIndexForNode(), bpp::SubstitutionModelSet::operator=(), bpp::SubstitutionModelSet::resetModelToNodeIds(), and bpp::SubstitutionModelSet::setNodeToModel().

◆ rootFrequencies_

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

privateinherited

Root frequencies.

Definition at line 87 of file SubstitutionModelSet.h.

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

◆ stationarity_

bool bpp::SubstitutionModelSet::stationarity_

privateinherited

Definition at line 104 of file SubstitutionModelSet.h.

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

◆ vpHyperNodes_

std::vector<HyperNode*> bpp::MixedSubstitutionModelSet::vpHyperNodes_

private

Definition at line 231 of file MixedSubstitutionModelSet.h.

Referenced by addEmptyHyperNode(), addHyperNode(), addToHyperNode(), clear(), complete(), getHyperNode(), getNumberOfHyperNodes(), MixedSubstitutionModelSet(), operator=(), and ~MixedSubstitutionModelSet().

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

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MixedSubstitutionModelSet() [1/3]

◆ ~MixedSubstitutionModelSet()

◆ MixedSubstitutionModelSet() [2/3]

◆ MixedSubstitutionModelSet() [3/3]

Member Function Documentation

◆ addEmptyHyperNode()

◆ addHyperNode()

◆ addModel()

◆ addToHyperNode()

◆ alphabet()

◆ checkOrphanModels()

◆ checkOrphanNodes()

◆ checkUnknownNodes()

◆ clear()

◆ clone()

◆ complete()

◆ computeHyperNodesProbabilities()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getHyperNode() [1/2]

◆ getHyperNode() [2/2]

◆ getHyperNodeProbability()

◆ getModel() [1/2]

◆ getModel() [2/2]

◆ getModelForNode() [1/2]

◆ getModelForNode() [2/2]

◆ getModelIndexForNode()

◆ getModelParameters()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getNodeParameters()

◆ getNodesWithModel()

◆ getNodesWithParameter()

◆ getNumberOfHyperNodes()

◆ getNumberOfModels()

◆ getNumberOfStates()

◆ getRootFrequencies()

◆ getRootFrequenciesParameters()

◆ getRootFrequencySet()

◆ getStateMap()

◆ getSubstitutionModel() [1/2]

◆ getSubstitutionModel() [2/2]

◆ getSubstitutionModelForNode() [1/2]

◆ getSubstitutionModelForNode() [2/2]

◆ hasExclusivePaths()

◆ 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_