#include <Bpp/Phyl/Likelihood/DataFlow/CollectionNodes.h>

Inheritance diagram for bpp::CollectionNodes:

Collaboration diagram for bpp::CollectionNodes:

Public Member Functions
	CollectionNodes (Context &context, std::shared_ptr< const SubstitutionProcessCollection > collection)

CollectionNodes *	clone () const

Context &	context ()

const SubstitutionProcessCollection &	collection () const

std::shared_ptr< const SubstitutionProcessCollection >	getCollection () const

ConfiguredModel &	model (size_t modelIndex)

std::shared_ptr< ConfiguredModel >	getModel (size_t modelIndex)

ParametrizableCollection< ConfiguredModel > &	getModelCollection ()

std::shared_ptr< ConfiguredFrequencySet >	getFrequencies (size_t freqIndex)

std::shared_ptr< ConfiguredDistribution >	getRateDistribution (size_t distIndex)

std::shared_ptr< ProcessTree >	getProcessTree (size_t treeIndex)

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

const ParameterList &	getParameters () const override

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

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

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

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

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

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

size_t	getNumberOfParameters () const override

void	setNamespace (const std::string &prefix) override

std::string	getNamespace () const override

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

virtual void	fireParameterChanged (const ParameterList &parameters)

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

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

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

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

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

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

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

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

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

ParameterList &	getParameters_ () override

Private Attributes
std::shared_ptr< const SubstitutionProcessCollection >	collection_

Context &	context_

ParametrizableCollection< ConfiguredModel >	modelColl_
	A collection of Branch Models. More...

ParametrizableCollection< ConfiguredFrequencySet >	freqColl_
	A collection of Frequencies Sets. More...

ParametrizableCollection< ConfiguredDistribution >	distColl_
	A collection of DiscreteDistributions. More...

ParametrizableCollection< ProcessTree >	treeColl_
	A collection of trees. More...

ParameterList	parameters_

std::string	prefix_

Detailed Description

Construction of all the DataFlow objects linked with objects in a SubstitutionProcessCollection.

Definition at line 23 of file CollectionNodes.h.

Constructor & Destructor Documentation

◆ CollectionNodes()

CollectionNodes::CollectionNodes	(	Context &	context,
		std::shared_ptr< const SubstitutionProcessCollection >	collection
	)

Definition at line 13 of file CollectionNodes.cpp.

References collection_, context(), context_, bpp::ConfiguredParameter::create(), distColl_, freqColl_, bpp::AbstractParametrizable::getParameters_(), modelColl_, bpp::AbstractParametrizable::parameter(), bpp::AbstractParametrizable::shareParameter_(), bpp::TextTools::toString(), and treeColl_.

Member Function Documentation

◆ clone()

CollectionNodes * bpp::CollectionNodes::clone ( ) const

inlinevirtual

Implements bpp::AbstractParametrizable.

Definition at line 56 of file CollectionNodes.h.

◆ collection()

const SubstitutionProcessCollection & bpp::CollectionNodes::collection ( ) const

inline

Definition at line 66 of file CollectionNodes.h.

References collection_.

Referenced by bpp::LikelihoodCalculationSingleProcess::makeProcessNodes_(), and bpp::ProcessTree::makeProcessTree().

◆ context()

Context & bpp::CollectionNodes::context ( )

inline

Definition at line 61 of file CollectionNodes.h.

References context_.

Referenced by CollectionNodes().

◆ getCollection()

std::shared_ptr< const SubstitutionProcessCollection > bpp::CollectionNodes::getCollection ( ) const

inline

Definition at line 71 of file CollectionNodes.h.

References collection_.

◆ getFrequencies()

std::shared_ptr< ConfiguredFrequencySet > bpp::CollectionNodes::getFrequencies ( size_t freqIndex )

inline

Definition at line 91 of file CollectionNodes.h.

References freqColl_.

Referenced by bpp::LikelihoodCalculationSingleProcess::makeProcessNodes_().

◆ getModel()

std::shared_ptr< ConfiguredModel > bpp::CollectionNodes::getModel ( size_t modelIndex )

inline

Definition at line 81 of file CollectionNodes.h.

References modelColl_.

◆ getModelCollection()

ParametrizableCollection< ConfiguredModel > & bpp::CollectionNodes::getModelCollection ( )

inline

Definition at line 86 of file CollectionNodes.h.

References modelColl_.

Referenced by bpp::ProcessTree::makeProcessTree().

◆ getProcessTree()

std::shared_ptr< ProcessTree > CollectionNodes::getProcessTree ( size_t treeIndex )

Definition at line 92 of file CollectionNodes.cpp.

References treeColl_.

Referenced by bpp::ProcessTree::makeProcessTree().

◆ getRateDistribution()

std::shared_ptr< ConfiguredDistribution > bpp::CollectionNodes::getRateDistribution ( size_t distIndex )

inline

Definition at line 96 of file CollectionNodes.h.

References distColl_.

Referenced by bpp::LikelihoodCalculationSingleProcess::makeProcessNodes_().

◆ model()

ConfiguredModel & bpp::CollectionNodes::model ( size_t modelIndex )

inline

Definition at line 76 of file CollectionNodes.h.

References modelColl_.

Member Data Documentation

◆ collection_

std::shared_ptr<const SubstitutionProcessCollection> bpp::CollectionNodes::collection_

private

Definition at line 27 of file CollectionNodes.h.

Referenced by collection(), CollectionNodes(), and getCollection().

◆ context_

Context& bpp::CollectionNodes::context_

private

Definition at line 29 of file CollectionNodes.h.

Referenced by CollectionNodes(), and context().

◆ distColl_

ParametrizableCollection<ConfiguredDistribution> bpp::CollectionNodes::distColl_

private

A collection of DiscreteDistributions.

Definition at line 44 of file CollectionNodes.h.

Referenced by CollectionNodes(), and getRateDistribution().

◆ freqColl_

ParametrizableCollection<ConfiguredFrequencySet> bpp::CollectionNodes::freqColl_

private

A collection of Frequencies Sets.

Definition at line 39 of file CollectionNodes.h.

Referenced by CollectionNodes(), and getFrequencies().

◆ modelColl_

ParametrizableCollection<ConfiguredModel> bpp::CollectionNodes::modelColl_

private

A collection of Branch Models.

Definition at line 34 of file CollectionNodes.h.

Referenced by CollectionNodes(), getModel(), getModelCollection(), and model().

◆ treeColl_

ParametrizableCollection<ProcessTree> bpp::CollectionNodes::treeColl_

private

A collection of trees.

Definition at line 49 of file CollectionNodes.h.

Referenced by CollectionNodes(), and getProcessTree().

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

Bpp/Phyl/Likelihood/DataFlow/CollectionNodes.h
Bpp/Phyl/Likelihood/DataFlow/CollectionNodes.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CollectionNodes()

Member Function Documentation

◆ clone()

◆ collection()

◆ context()

◆ getCollection()

◆ getFrequencies()

◆ getModel()

◆ getModelCollection()

◆ getProcessTree()

◆ getRateDistribution()

◆ model()

Member Data Documentation

◆ collection_

◆ context_

◆ distColl_

◆ freqColl_

◆ modelColl_

◆ treeColl_