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

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

Inheritance diagram for bpp::SubstitutionModelSet:

Collaboration diagram for bpp::SubstitutionModelSet:

Public Member Functions
	SubstitutionModelSet (const Alphabet *alpha)
	Create a model set according to the specified alphabet. Stationarity is assumed. More...

	SubstitutionModelSet (const Alphabet alpha, FrequenciesSet 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...

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

	SubstitutionModelSet (const SubstitutionModelSet &set)

SubstitutionModelSet &	operator= (const SubstitutionModelSet &set)

virtual	~SubstitutionModelSet ()

SubstitutionModelSet *	clone () const

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

virtual void	fireParameterChanged (const ParameterList &parameters)

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::auto_ptr< FrequenciesSet >	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_

Detailed Description

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

This class contains a set of substitution models, and their assigment 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. Theses are accounted by a FrequenciesSet objet, managed by the SubstitutionModelSet class. The corresponding parameters, if any, are added at the begining 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 FrequenciesSet 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 "supposingly 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 carefull!

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

Definition at line 104 of file SubstitutionModelSet.h.

Constructor & Destructor Documentation

◆ SubstitutionModelSet() [1/3]

bpp::SubstitutionModelSet::SubstitutionModelSet ( 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 150 of file SubstitutionModelSet.h.

Referenced by clone().

◆ SubstitutionModelSet() [2/3]

bpp::SubstitutionModelSet::SubstitutionModelSet	(	const Alphabet *	alpha,
		FrequenciesSet *	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 170 of file SubstitutionModelSet.h.

References setRootFrequencies().

◆ SubstitutionModelSet() [3/3]

SubstitutionModelSet::SubstitutionModelSet ( const SubstitutionModelSet & set )

Definition at line 49 of file SubstitutionModelSet.cpp.

References modelSet_.

◆ ~SubstitutionModelSet()

virtual bpp::SubstitutionModelSet::~SubstitutionModelSet ( )

inlinevirtual

Definition at line 203 of file SubstitutionModelSet.h.

References modelSet_.

Member Function Documentation

◆ addModel()

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

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

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

◆ checkOrphanModels()

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

protected

Definition at line 249 of file SubstitutionModelSet.cpp.

Referenced by isFullySetUpFor().

◆ checkOrphanNodes()

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

protected

Definition at line 264 of file SubstitutionModelSet.cpp.

Referenced by isFullySetUpFor().

◆ checkUnknownNodes()

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

protected

Definition at line 280 of file SubstitutionModelSet.cpp.

Referenced by isFullySetUpFor().

◆ clear()

void SubstitutionModelSet::clear ( )

Resets all the information contained in this object.

Definition at line 90 of file SubstitutionModelSet.cpp.

References modelParameters_, modelSet_, nbStates_, nodeToModel_, rootFrequencies_, and stationarity_.

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

◆ clone()

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

inline

Definition at line 213 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 in bpp::MixedSubstitutionModelSet.

Definition at line 231 of file SubstitutionModelSet.cpp.

References modelParameters_, modelSet_, and updateRootFrequencies().

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

◆ getAlphabet()

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

inline

Definition at line 410 of file SubstitutionModelSet.h.

References alphabet_.

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

◆ getAlphabetStateAsChar()

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

inlinevirtual

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 getModel().

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

◆ getAlphabetStateAsInt()

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

inlinevirtual

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 getModel().

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

◆ getAlphabetStates()

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

inlinevirtual

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 getModel().

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

◆ getModel() [1/2]

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

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 251 of file SubstitutionModelSet.h.

References modelSet_.

Referenced by bpp::MixedSubstitutionModelSet::complete(), bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator::ConstNonHomogeneousSiteModelIterator(), getAlphabetStateAsChar(), getAlphabetStateAsInt(), getAlphabetStates(), bpp::SubstitutionMappingTools::getCountsPerBranch(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), getModelStates(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::SubstitutionMappingTools::getNormalizedCountsPerBranch(), getStateMap(), bpp::HomogeneousSequenceSimulator::getSubstitutionModel(), hasMixedSubstitutionModel(), bpp::MixedSubstitutionModelSet::HyperNode::HyperNode(), and bpp::PhylogeneticsApplicationTools::printParameters().

◆ getModel() [2/2]

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

inline

Definition at line 257 of file SubstitutionModelSet.h.

References modelSet_.

◆ getModelForNode() [1/2]

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

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 285 of file SubstitutionModelSet.h.

References modelSet_, and 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
	)

inline

Definition at line 292 of file SubstitutionModelSet.h.

References modelSet_, and nodeToModel_.

◆ getModelIndexForNode()

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

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 270 of file SubstitutionModelSet.h.

References nodeToModel_.

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

◆ 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]

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

inlinevirtual

Definition at line 425 of file SubstitutionModelSet.h.

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

◆ getModelStates() [2/2]

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

inlinevirtual

Definition at line 429 of file SubstitutionModelSet.h.

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

◆ 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 389 of file SubstitutionModelSet.h.

References rootFrequencies_, and 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
	)

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 307 of file SubstitutionModelSet.h.

References modelSet_, and 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
	)

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().

◆ getNumberOfModels()

size_t bpp::SubstitutionModelSet::getNumberOfModels ( ) const

inline

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

Definition at line 237 of file SubstitutionModelSet.h.

References modelSet_.

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

◆ getNumberOfStates()

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

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 222 of file SubstitutionModelSet.h.

References nbStates_.

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

◆ getRootFrequencies()

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

inline

Returns: The values of the root frequencies.

Definition at line 361 of file SubstitutionModelSet.h.

References modelSet_, rootFrequencies_, and 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

inline

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 rootFrequencies_, and stationarity_.

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

◆ getRootFrequenciesSet()

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

inline

Returns: The set of root frequencies.

Definition at line 356 of file SubstitutionModelSet.h.

References rootFrequencies_.

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

◆ getStateMap()

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

inlinevirtual

Definition at line 421 of file SubstitutionModelSet.h.

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

◆ hasMixedSubstitutionModel()

bool SubstitutionModelSet::hasMixedSubstitutionModel ( ) const

Returns: True iff there is a MixedSubstitutionModel in the SubstitutionModelSet

Definition at line 301 of file SubstitutionModelSet.cpp.

References getModel(), and getNumberOfModels().

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

◆ isFullySetUpFor()

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

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 461 of file SubstitutionModelSet.h.

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

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

◆ listModelNames()

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

Definition at line 218 of file SubstitutionModelSet.cpp.

References modelSet_, and modelToNodes_.

◆ operator=()

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

Definition at line 67 of file SubstitutionModelSet.cpp.

References alphabet_, modelParameters_, modelSet_, modelToNodes_, nbStates_, nodeToModel_, rootFrequencies_, and stationarity_.

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

◆ replaceModel()

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

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 )

Sets a given FrequenciesSet for root frequencies.

Parameters

rootFreqs The FrequenciesSet for root frequencies.

Definition at line 106 of file SubstitutionModelSet.cpp.

References rootFrequencies_, and stationarity_.

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

◆ updateRootFrequencies()

void bpp::SubstitutionModelSet::updateRootFrequencies ( )

inlineprotected

Set rootFrequencies_ from parameters.

Definition at line 473 of file SubstitutionModelSet.h.

References rootFrequencies_, and stationarity_.

Referenced by fireParameterChanged().

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::SubstitutionModelSet::alphabet_

protected

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

Definition at line 111 of file SubstitutionModelSet.h.

Referenced by addModel(), 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 correspondance 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 139 of file SubstitutionModelSet.h.

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

◆ modelSet_

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

protected

Contains all models used in this tree.

Definition at line 118 of file SubstitutionModelSet.h.

Referenced by addModel(), clear(), fireParameterChanged(), getModel(), getModelForNode(), getNodesWithModel(), getNumberOfModels(), getRootFrequencies(), listModelNames(), operator=(), SubstitutionModelSet(), and ~SubstitutionModelSet().

◆ modelToNodes_

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

mutableprivate

Definition at line 130 of file SubstitutionModelSet.h.

Referenced by addModel(), getNodesWithModel(), listModelNames(), and operator=().

◆ nbStates_

size_t bpp::SubstitutionModelSet::nbStates_

protected

Definition at line 113 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 129 of file SubstitutionModelSet.h.

Referenced by addModel(), clear(), getModelForNode(), getModelIndexForNode(), and operator=().

◆ rootFrequencies_

std::auto_ptr<FrequenciesSet> bpp::SubstitutionModelSet::rootFrequencies_

private

Root frequencies.

Definition at line 124 of file SubstitutionModelSet.h.

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

◆ stationarity_

bool bpp::SubstitutionModelSet::stationarity_

private

Definition at line 141 of file SubstitutionModelSet.h.

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

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

Bpp/Phyl/Model/SubstitutionModelSet.h
Bpp/Phyl/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()

◆ 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()

◆ getRootFrequenciesSet()

◆ getStateMap()

◆ hasMixedSubstitutionModel()

◆ isFullySetUpFor()

◆ listModelNames()

◆ operator=()

◆ replaceModel()

◆ setRootFrequencies()

◆ updateRootFrequencies()

Member Data Documentation

◆ alphabet_

◆ modelParameters_

◆ modelSet_

◆ modelToNodes_

◆ nbStates_

◆ nodeToModel_

◆ rootFrequencies_

◆ stationarity_