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

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

Inheritance diagram for bpp::MixedSubstitutionModelSet:

Collaboration diagram for bpp::MixedSubstitutionModelSet:

Classes
class	HyperNode

Public Member Functions
	MixedSubstitutionModelSet (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 Vint &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

void	setRootFrequencies (FrequenciesSet *rootFreqs)
	Sets a given FrequenciesSet for root frequencies. More...

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

size_t	getNumberOfModels () const

bool	hasMixedSubstitutionModel () const

const SubstitutionModel *	getModel (size_t i) const throw (IndexOutOfBoundsException)
	Get one model from the set knowing its index. More...

SubstitutionModel *	getModel (size_t i) throw (IndexOutOfBoundsException)

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

const SubstitutionModel *	getModelForNode (int nodeId) const throw (Exception)
	Get the model associated to a particular node id. More...

SubstitutionModel *	getModelForNode (int nodeId) throw (Exception)

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

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

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

void	replaceModel (size_t modelIndex, SubstitutionModel *model) throw (Exception)
	Replace a model in the set, and all corresponding parameters. The replaced model deleted. More...

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

const FrequenciesSet *	getRootFrequenciesSet () 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...

const Alphabet *	getAlphabet () const

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

virtual const StateMap &	getStateMap () const

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

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

virtual int	getAlphabetStateAsInt (size_t index) const

virtual std::string	getAlphabetStateAsChar (size_t index) const

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

Protected Member Functions
void	updateRootFrequencies ()

Check function.
bool	checkOrphanModels (bool throwEx) const throw (Exception)

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

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

Protected Attributes
const Alphabet *	alphabet_
	A pointer toward the common alphabet to all models in the set. More...

size_t	nbStates_

std::vector< SubstitutionModel * >	modelSet_
	Contains all models used in this tree. More...

Private Attributes
std::vector< HyperNode * >	vpHyperNodes_

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 121 of file MixedSubstitutionModelSet.h.

Constructor & Destructor Documentation

◆ MixedSubstitutionModelSet() [1/3]

bpp::MixedSubstitutionModelSet::MixedSubstitutionModelSet ( 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 286 of file MixedSubstitutionModelSet.h.

Referenced by clone().

◆ ~MixedSubstitutionModelSet()

MixedSubstitutionModelSet::~MixedSubstitutionModelSet ( )

Definition at line 62 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

◆ MixedSubstitutionModelSet() [2/3]

MixedSubstitutionModelSet::MixedSubstitutionModelSet ( const MixedSubstitutionModelSet & set )

Definition at line 47 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

◆ MixedSubstitutionModelSet() [3/3]

MixedSubstitutionModelSet::MixedSubstitutionModelSet ( const SubstitutionModelSet & set )

Definition at line 57 of file MixedSubstitutionModelSet.cpp.

Member Function Documentation

◆ addEmptyHyperNode()

void MixedSubstitutionModelSet::addEmptyHyperNode ( )

Definition at line 97 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

Referenced by complete(), bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), and bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet().

◆ addHyperNode()

void MixedSubstitutionModelSet::addHyperNode ( const HyperNode & hn )

Definition at line 102 of file MixedSubstitutionModelSet.cpp.

References vpHyperNodes_.

◆ addModel()

void SubstitutionModelSet::addModel	(	SubstitutionModel *	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 135 of file SubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::alphabet_, bpp::SubstitutionModel::clone(), bpp::SubstitutionModel::getAlphabet(), bpp::SubstitutionModel::getNumberOfStates(), bpp::SubstitutionModelSet::modelParameters_, bpp::SubstitutionModelSet::modelSet_, bpp::SubstitutionModelSet::modelToNodes_, bpp::SubstitutionModelSet::nbStates_, and bpp::SubstitutionModelSet::nodeToModel_.

Referenced by bpp::SubstitutionModelSetTools::createHomogeneousModelSet(), bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet(), and bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ addToHyperNode()

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

Definition at line 157 of file MixedSubstitutionModelSet.cpp.

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

Referenced by complete(), bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), and bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet().

◆ checkOrphanModels()

bool SubstitutionModelSet::checkOrphanModels	(	bool	throwEx	)	const
throw	(	Exception
	)

protectedinherited

Definition at line 249 of file SubstitutionModelSet.cpp.

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

◆ checkOrphanNodes()

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

protectedinherited

Definition at line 264 of file SubstitutionModelSet.cpp.

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

◆ checkUnknownNodes()

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

protectedinherited

Definition at line 280 of file SubstitutionModelSet.cpp.

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

◆ clear()

void MixedSubstitutionModelSet::clear ( )

Resets the list of the HyperNodes.

Definition at line 70 of file MixedSubstitutionModelSet.cpp.

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

◆ clone()

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

inline

Definition at line 303 of file MixedSubstitutionModelSet.h.

References MixedSubstitutionModelSet().

◆ complete()

bool MixedSubstitutionModelSet::complete ( )

Definition at line 107 of file MixedSubstitutionModelSet.cpp.

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

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

◆ computeHyperNodesProbabilities()

void MixedSubstitutionModelSet::computeHyperNodesProbabilities ( )

Definition at line 195 of file MixedSubstitutionModelSet.cpp.

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

Referenced by bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet(), 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 186 of file MixedSubstitutionModelSet.cpp.

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

◆ getAlphabet()

const Alphabet* bpp::SubstitutionModelSet::getAlphabet ( ) const

inlineinherited

Definition at line 410 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::alphabet_.

Referenced by bpp::NonHomogeneousSequenceSimulator::dSimulateSite(), and bpp::SubstitutionMappingTools::getNormalizationsPerBranch().

◆ getAlphabetStateAsChar()

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

inlinevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Definition at line 445 of file SubstitutionModelSet.h.

References bpp::SubstitutionModel::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getModel().

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

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

inlinevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Definition at line 437 of file SubstitutionModelSet.h.

References bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::SubstitutionModelSet::getModel().

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsInt().

◆ getAlphabetStates()

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

inlinevirtualinherited

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

See also: Alphabet

Definition at line 417 of file SubstitutionModelSet.h.

References bpp::SubstitutionModel::getAlphabetStates(), and bpp::SubstitutionModelSet::getModel().

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStates().

◆ getHyperNode() [1/2]

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

inline

Definition at line 351 of file MixedSubstitutionModelSet.h.

References vpHyperNodes_.

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

◆ getHyperNode() [2/2]

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

inline

Definition at line 353 of file MixedSubstitutionModelSet.h.

References vpHyperNodes_.

◆ getHyperNodeProbability()

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

Definition at line 275 of file MixedSubstitutionModelSet.cpp.

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

◆ getModel() [1/2]

const SubstitutionModel* bpp::SubstitutionModelSet::getModel	(	size_t	i	)	const
throw	(	IndexOutOfBoundsException
	)

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 251 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

◆ getModel() [2/2]

SubstitutionModel* bpp::SubstitutionModelSet::getModel	(	size_t	i	)
throw	(	IndexOutOfBoundsException
	)

inlineinherited

Definition at line 257 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

◆ getModelForNode() [1/2]

const SubstitutionModel* bpp::SubstitutionModelSet::getModelForNode	(	int	nodeId	)	const
throw	(	Exception
	)

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 285 of file SubstitutionModelSet.h.

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

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelForNode(), and bpp::NonHomogeneousSequenceSimulator::init().

◆ getModelForNode() [2/2]

SubstitutionModel* bpp::SubstitutionModelSet::getModelForNode	(	int	nodeId	)
throw	(	Exception
	)

inlineinherited

Definition at line 292 of file SubstitutionModelSet.h.

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

◆ getModelIndexForNode()

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

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 270 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::nodeToModel_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode().

◆ 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]

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

inlinevirtualinherited

Definition at line 425 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModel(), and bpp::SubstitutionModel::getModelStates().

◆ getModelStates() [2/2]

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

inlinevirtualinherited

Definition at line 429 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModel(), and bpp::SubstitutionModel::getModelStates().

◆ 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 389 of file SubstitutionModelSet.h.

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

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged().

◆ getNodesWithModel()

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

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 307 of file SubstitutionModelSet.h.

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

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator::ConstNonHomogeneousSiteModelIterator(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ getNodesWithParameter()

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

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 115 of file SubstitutionModelSet.cpp.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged().

◆ getNumberOfHyperNodes()

size_t bpp::MixedSubstitutionModelSet::getNumberOfHyperNodes ( ) const

inline

Definition at line 349 of file MixedSubstitutionModelSet.h.

References vpHyperNodes_.

Referenced by bpp::PhylogeneticsApplicationTools::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 237 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::modelSet_.

Referenced by addToHyperNode(), complete(), computeHyperNodesProbabilities(), getHyperNodeProbability(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::SubstitutionModelSet::hasMixedSubstitutionModel(), bpp::MixedSubstitutionModelSet::HyperNode::HyperNode(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ getNumberOfStates()

size_t bpp::SubstitutionModelSet::getNumberOfStates	(		)	const
throw	(	Exception
	)

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 222 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::nbStates_.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getNumberOfStates().

◆ getRootFrequencies()

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

inlineinherited

Returns: The values of the root frequencies.

Definition at line 361 of file SubstitutionModelSet.h.

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

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::NonHomogeneousSequenceSimulator::dSimulateSite(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::NonHomogeneousSequenceSimulator::simulate(), and bpp::NonHomogeneousSequenceSimulator::simulateSite().

◆ 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 374 of file SubstitutionModelSet.h.

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

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters().

◆ getRootFrequenciesSet()

const FrequenciesSet* bpp::SubstitutionModelSet::getRootFrequenciesSet ( ) const

inlineinherited

Returns: The set of root frequencies.

Definition at line 356 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::rootFrequencies_.

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

◆ getStateMap()

virtual const StateMap& bpp::SubstitutionModelSet::getStateMap ( ) const

inlinevirtualinherited

Definition at line 421 of file SubstitutionModelSet.h.

References bpp::SubstitutionModelSet::getModel(), and bpp::SubstitutionModel::getStateMap().

◆ hasExclusivePaths()

bool MixedSubstitutionModelSet::hasExclusivePaths ( ) const

Definition at line 170 of file MixedSubstitutionModelSet.cpp.

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

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

◆ hasMixedSubstitutionModel()

bool SubstitutionModelSet::hasMixedSubstitutionModel ( ) const

inherited

Returns: True iff there is a MixedSubstitutionModel in the SubstitutionModelSet

Definition at line 301 of file SubstitutionModelSet.cpp.

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

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

◆ isFullySetUpFor()

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

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 461 of file SubstitutionModelSet.h.

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

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood().

◆ listModelNames()

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

inherited

Definition at line 218 of file SubstitutionModelSet.cpp.

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

◆ operator=()

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

Definition at line 79 of file MixedSubstitutionModelSet.cpp.

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

◆ replaceModel()

void SubstitutionModelSet::replaceModel	(	size_t	modelIndex,
		SubstitutionModel *	model
	)
throw	(	Exception
	)

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 169 of file SubstitutionModelSet.cpp.

◆ setRootFrequencies()

void SubstitutionModelSet::setRootFrequencies ( FrequenciesSet * rootFreqs )

inherited

Sets a given FrequenciesSet for root frequencies.

Parameters

rootFreqs The FrequenciesSet for root frequencies.

Definition at line 106 of file SubstitutionModelSet.cpp.

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

Referenced by bpp::SubstitutionModelSetTools::createHomogeneousModelSet(), bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet(), bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet(), and bpp::SubstitutionModelSet::SubstitutionModelSet().

◆ updateRootFrequencies()

void bpp::SubstitutionModelSet::updateRootFrequencies ( )

inlineprotectedinherited

Set rootFrequencies_ from parameters.

Definition at line 473 of file SubstitutionModelSet.h.

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

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

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::SubstitutionModelSet::alphabet_

protectedinherited

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

Definition at line 111 of file SubstitutionModelSet.h.

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

◆ modelSet_

std::vector<SubstitutionModel*> bpp::SubstitutionModelSet::modelSet_

protectedinherited

Contains all models used in this tree.

Definition at line 118 of file SubstitutionModelSet.h.

◆ nbStates_

size_t bpp::SubstitutionModelSet::nbStates_

protectedinherited

Definition at line 113 of file SubstitutionModelSet.h.

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

◆ vpHyperNodes_

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

private

Definition at line 278 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/Model/MixedSubstitutionModelSet.h
Bpp/Phyl/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()

◆ 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()

◆ getRootFrequenciesSet()

◆ getStateMap()

◆ hasExclusivePaths()

◆ hasMixedSubstitutionModel()

◆ isFullySetUpFor()

◆ listModelNames()

◆ operator=()

◆ replaceModel()

◆ setRootFrequencies()

◆ updateRootFrequencies()

Member Data Documentation

◆ alphabet_

◆ modelSet_

◆ nbStates_

◆ vpHyperNodes_