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...

size_t	getParameterIndex (const std::string &name) const throw (ParameterNotFoundException)
	Get the index of a given parameter in the list of all parameters. More...

std::string	getParameterModelName (const std::string &name) const throw (ParameterNotFoundException, Exception)
	Get the model name of a given parameter in the list of all parameters. 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)

std::vector< size_t >	getModelsWithParameter (const std::string &name) const throw (ParameterNotFoundException)

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

void	setModel (SubstitutionModel *model, size_t modelIndex) throw (Exception, IndexOutOfBoundsException)
	Change a given model. More...

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

void	setParameterToModel (size_t parameterIndex, size_t modelIndex) throw (IndexOutOfBoundsException)
	Assign a parameter to a model. More...

void	unsetParameterToModel (size_t parameterIndex, size_t modelIndex) throw (IndexOutOfBoundsException, Exception)
	Unset a given parameter to the specified model. More...

void	addParameter (const Parameter &parameter, const std::vector< int > &nodesId) throw (Exception)
	Add a parameter to the list, and link it to specified existing nodes. More...

void	addParameters (const ParameterList &parameters, const std::vector< int > &nodesId) throw (Exception)
	Add several parameters to the list, and link them to specified existing nodes. More...

void	removeParameter (const std::string &name) throw (ParameterNotFoundException)
	Remove a parameter from the list, and unset it to all linked nodes and models. More...

void	removeModel (size_t modelIndex) throw (Exception)
	Remove a model from the set, and all corresponding parameters. 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

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

void	setNamespace (const std::string &prefix)

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

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

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

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

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

const ParameterList &	getParameters () const

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

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

void	setAllParametersValues (const ParameterList &parameters)

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

void	setParametersValues (const ParameterList &parameters)

bool	matchParametersValues (const ParameterList &parameters)

size_t	getNumberOfParameters () const

std::string	getNamespace () const

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

Protected Member Functions
void	updateRootFrequencies ()

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

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_ ()

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

bool	checkOrphanParameters (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< std::vector < size_t > >	paramToModels_
	Contains for each parameter in the list the indexes of the corresponding models in modelSet_ that share this parameter. More...

std::map< std::string, size_t >	paramNamesCount_

std::vector< std::string >	modelParameterNames_
	Contains for each parameter in the list the corresponding name in substitution models. More...

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 and an index which tells to which models these parameters apply to. Since parameters in a list must have unique names, duplicated names are numbered according to the order in the list. To track the relationships between names in the list and names in each model, the parameter list is duplicated in modelParameters_. The user only act on parameters_, the fireParameterChanged function, automatically called, will update the modelParameters_ field.

In the non-homogeneous and homogeneous non-reversible cases, the likelihood depends on the position of the root. The states frequencies at the root of the tree are hence distinct parameters. 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 99 of file SubstitutionModelSet.h.

Constructor & Destructor Documentation

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 157 of file SubstitutionModelSet.h.

Referenced by clone().

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 180 of file SubstitutionModelSet.h.

References setRootFrequencies().

SubstitutionModelSet::SubstitutionModelSet ( const SubstitutionModelSet & set )

Definition at line 49 of file SubstitutionModelSet.cpp.

References modelSet_.

virtual bpp::SubstitutionModelSet::~SubstitutionModelSet ( )

inlinevirtual

Definition at line 216 of file SubstitutionModelSet.h.

References modelSet_, and modelSet_.

Member Function Documentation

void SubstitutionModelSet::addModel	(	SubstitutionModel *	model,
		const std::vector< int > &	nodesId,
		const std::vector< std::string > &	newParams
	)		throw (Exception)

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.
newParams	The names of the parameters that have to be added to the global list. These parameters will only be affected to this susbstitution model. You can use the setParameterToModel function to assign this parameter to an additional model, and the unsetParameterToModel to remove the relationship with this model for instance. Parameters not specified in newParams will be ignored, unless you manually assign them to another parameter with setParameterToModel.

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 157 of file SubstitutionModelSet.cpp.

References bpp::Parameter::clone(), and bpp::TextTools::toString().

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

void SubstitutionModelSet::addParameter	(	const Parameter &	parameter,
		const std::vector< int > &	nodesId
	)		throw (Exception)

Add a parameter to the list, and link it to specified existing nodes.

Parameters

parameter	The parameter to add. Its name must match model parameter names.
nodesId	The list of ids of the nodes to link with these parameters. Nodes must have a corresponding model in the set.

Exceptions

Exception If one of the above requirement is not true.

Definition at line 288 of file SubstitutionModelSet.cpp.

References bpp::Parameter::clone(), bpp::TextTools::toString(), and bpp::TextTools::toString().

void SubstitutionModelSet::addParameters	(	const ParameterList &	parameters,
		const std::vector< int > &	nodesId
	)		throw (Exception)

Add several parameters to the list, and link them to specified existing nodes.

Parameters

parameters	The list of parameters to add. Its name must match model parameter names.
nodesId	The list of ids of the nodes to link with these parameters. Nodes must have a corresponding model in the set.

Exceptions

Exception If one of the above requirement is not true.

Definition at line 309 of file SubstitutionModelSet.cpp.

References bpp::ParameterList::size(), bpp::ParameterList::size(), bpp::TextTools::toString(), and bpp::TextTools::toString().

Referenced by bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet().

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

protected

Definition at line 396 of file SubstitutionModelSet.cpp.

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

Referenced by isFullySetUpFor().

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

protected

Definition at line 425 of file SubstitutionModelSet.cpp.

References bpp::TextTools::toString().

Referenced by isFullySetUpFor().

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

protected

Definition at line 411 of file SubstitutionModelSet.cpp.

Referenced by isFullySetUpFor().

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

protected

Definition at line 441 of file SubstitutionModelSet.cpp.

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

Referenced by isFullySetUpFor().

void SubstitutionModelSet::clear ( )

Resets all the information contained in this object.

Definition at line 96 of file SubstitutionModelSet.cpp.

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

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

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

inlinevirtual

Implements bpp::Clonable.

Definition at line 226 of file SubstitutionModelSet.h.

References SubstitutionModelSet().

void SubstitutionModelSet::fireParameterChanged ( const ParameterList & parameters )

virtual

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

Parameters

parameters The modified parameters.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::MixedSubstitutionModelSet.

Definition at line 366 of file SubstitutionModelSet.cpp.

References bpp::AbstractParameterAliasable::getNumberOfParameters(), bpp::AbstractParameterAliasable::getNumberOfParameters(), bpp::AbstractParameterAliasable::getParameter_(), modelParameterNames_, modelParameterNames_, modelParameterNames_, modelParameterNames_, modelParameters_, modelParameters_, modelParameters_, modelParameters_, modelSet_, paramToModels_, rootFrequencies_, stationarity_, and updateRootFrequencies().

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

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

inline

Definition at line 541 of file SubstitutionModelSet.h.

References alphabet_.

Referenced by bpp::NonHomogeneousSequenceSimulator::dSimulate().

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 301 of file SubstitutionModelSet.h.

References modelSet_, modelSet_, and modelSet_.

Referenced by bpp::MixedSubstitutionModelSet::complete(), bpp::MixedSubstitutionModelSet::complete(), bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator::ConstNonHomogeneousSiteModelIterator(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), bpp::HomogeneousSequenceSimulator::getSubstitutionModel(), hasMixedSubstitutionModel(), bpp::MixedSubstitutionModelSet::HyperNode::HyperNode(), bpp::PhylogeneticsApplicationTools::printParameters(), and bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

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

inline

Definition at line 307 of file SubstitutionModelSet.h.

References modelSet_, modelSet_, and modelSet_.

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 335 of file SubstitutionModelSet.h.

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

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

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

inline

Definition at line 342 of file SubstitutionModelSet.h.

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

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 320 of file SubstitutionModelSet.h.

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

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

ParameterList 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.

Definition at line 220 of file SubstitutionModelSet.cpp.

References bpp::ParameterList::addParameter(), modelParameterNames_, paramToModels_, rootFrequencies_, and stationarity_.

vector< size_t > SubstitutionModelSet::getModelsWithParameter ( const std::string & name ) const throw (ParameterNotFoundException)

Parameters

name	The name of the parameter to look for.

Returns: The list of model indices containing the specified parameter.

Exceptions

ParameterNotFoundException If no parameter with the specified name is found.

Definition at line 144 of file SubstitutionModelSet.cpp.

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

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 520 of file SubstitutionModelSet.h.

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

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

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 357 of file SubstitutionModelSet.h.

References modelSet_, modelSet_, and modelToNodes_.

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

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 124 of file SubstitutionModelSet.cpp.

References bpp::VectorTools::append().

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

size_t bpp::SubstitutionModelSet::getNumberOfModels ( ) const

inline

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

Definition at line 287 of file SubstitutionModelSet.h.

References modelSet_.

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

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 235 of file SubstitutionModelSet.h.

References nbStates_.

size_t bpp::SubstitutionModelSet::getParameterIndex ( const std::string & name ) const throw (ParameterNotFoundException)

inline

Get the index of a given parameter in the list of all parameters.

Parameters

name	The name of the parameter to look for.

Returns: The position of the parameter in the global parameter list.

Exceptions

ParameterNotFoundException If no parameter with this name is found.

Definition at line 247 of file SubstitutionModelSet.h.

References bpp::AbstractParameterAliasable::getNumberOfParameters(), and bpp::AbstractParameterAliasable::getParameter_().

Referenced by getParameterModelName(), and bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

std::string bpp::SubstitutionModelSet::getParameterModelName ( const std::string & name ) const throw (ParameterNotFoundException, Exception)

inline

Get the model name of a given parameter in the list of all parameters.

Parameters

name	The name of the parameter to look for.

Returns: The model name of the parameter in the global parameter list.

Exceptions

ParameterNotFoundException	If no parameter with this name is found.
Exception	If the parameter is not a 'model' parameter (that is, it is a root frequency parameter).

Definition at line 264 of file SubstitutionModelSet.h.

References getParameterIndex(), modelParameterNames_, modelParameterNames_, rootFrequencies_, and stationarity_.

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

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

inline

Returns: The values of the root frequencies.

Definition at line 492 of file SubstitutionModelSet.h.

References modelSet_, rootFrequencies_, and stationarity_.

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

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 505 of file SubstitutionModelSet.h.

References rootFrequencies_, and stationarity_.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters(), and bpp::PhylogeneticsApplicationTools::printParameters().

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

inline

Returns: The set of root frequencies.

Definition at line 487 of file SubstitutionModelSet.h.

References rootFrequencies_.

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

bool SubstitutionModelSet::hasMixedSubstitutionModel ( ) const

Returns: True iff there is a MixedSubstitutionModel in the SubstitutionModelSet

Definition at line 462 of file SubstitutionModelSet.cpp.

References getModel(), and getNumberOfModels().

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

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 555 of file SubstitutionModelSet.h.

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

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

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

Definition at line 240 of file SubstitutionModelSet.cpp.

References modelSet_, modelSet_, modelToNodes_, and modelToNodes_.

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

Definition at line 70 of file SubstitutionModelSet.cpp.

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

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

void SubstitutionModelSet::removeModel ( size_t modelIndex ) throw (Exception)

Remove a model from the set, and all corresponding parameters.

Parameters

modelIndex The index of the model in the set.

Exceptions

Exception if a parameter becomes orphan because of the removal.

Definition at line 201 of file SubstitutionModelSet.cpp.

void SubstitutionModelSet::removeParameter ( const std::string & name ) throw (ParameterNotFoundException)

Remove a parameter from the list, and unset it to all linked nodes and models.

Parameters

name	The name of the parameter to remove.

Exceptions

ParameterNotFoundException If no parameter with the given name is found in the list.

Definition at line 342 of file SubstitutionModelSet.cpp.

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

Change a given model.

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

Parameters

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

Definition at line 191 of file SubstitutionModelSet.cpp.

void bpp::SubstitutionModelSet::setModelToNode	(	size_t	modelIndex,
		int	nodeNumber
	)		throw (IndexOutOfBoundsException)

inline

Associate an existing model with a given node.

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

Parameters

modelIndex	The position of the model in the set.
nodeNumber	The id of the corresponding node.

Definition at line 421 of file SubstitutionModelSet.h.

References nodeToModel_, nodeToModel_, and nodeToModel_.

void SubstitutionModelSet::setParameterToModel	(	size_t	parameterIndex,
		size_t	modelIndex
	)		throw (IndexOutOfBoundsException)

Assign a parameter to a model.

Parameters

parameterIndex	The index of the parameter in the list.
modelIndex	The index of the model in the list.

Exceptions

IndexOutOfBoundsException If one of the index is not valid.

Definition at line 253 of file SubstitutionModelSet.cpp.

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

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

void SubstitutionModelSet::setRootFrequencies ( FrequenciesSet * rootFreqs )

Sets a given FrequenciesSet for root frequencies.

Parameters

rootFreqs The FrequenciesSet for root frequencies.

Definition at line 115 of file SubstitutionModelSet.cpp.

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

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

void SubstitutionModelSet::unsetParameterToModel	(	size_t	parameterIndex,
		size_t	modelIndex
	)		throw (IndexOutOfBoundsException, Exception)

Unset a given parameter to the specified model.

Parameters

parameterIndex	The index of the parameter in the list.
modelIndex	The index of the model in the list.

Exceptions

IndexOutOfBoundsException	If one of the index is not valid.
Exception	If the pseicified parameter is not currently associated to the specified model.

Definition at line 271 of file SubstitutionModelSet.cpp.

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

void bpp::SubstitutionModelSet::updateRootFrequencies ( )

inlineprotected

Set rootFrequencies_ from parameters.

Definition at line 567 of file SubstitutionModelSet.h.

References rootFrequencies_, and stationarity_.

Referenced by fireParameterChanged().

Member Data Documentation

const Alphabet* bpp::SubstitutionModelSet::alphabet_

protected

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

Definition at line 106 of file SubstitutionModelSet.h.

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

std::vector<std::string> bpp::SubstitutionModelSet::modelParameterNames_

private

Contains for each parameter in the list the corresponding name in substitution models.

Definition at line 137 of file SubstitutionModelSet.h.

Referenced by clear(), fireParameterChanged(), fireParameterChanged(), fireParameterChanged(), fireParameterChanged(), getModelParameters(), getParameterModelName(), getParameterModelName(), and operator=().

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 146 of file SubstitutionModelSet.h.

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