#include <Bpp/Phyl/Likelihood/SubstitutionProcessCollectionMember.h>

Inheritance diagram for bpp::SubstitutionProcessCollectionMember:

Collaboration diagram for bpp::SubstitutionProcessCollectionMember:

Classes
struct	Deleter

Public Member Functions
const SubstitutionProcessCollection &	collection () const

SubstitutionProcessCollection &	collection ()

void	clear ()

const SubstitutionProcessCollection *	getCollection () const

SubstitutionProcessCollection *	getCollection ()

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

size_t	getNumberOfProcesses () const

size_t	getNumberOfModels () const override

bool	hasMixedTransitionModel () const

bool	isStationary () const

const BranchModelInterface &	model (size_t n) const override

std::shared_ptr< const BranchModelInterface >	getModel (size_t n) const override

std::shared_ptr< BranchModelInterface >	getModel (size_t n)

std::vector< size_t >	getModelNumbers () const override

size_t	getModelNumberForNode (unsigned int nodeId) const override
	Get the number of the model associated to a particular node id. More...

std::shared_ptr< const BranchModelInterface >	getModelForNode (unsigned int nodeId) const override
	Get the model associated to a particular node id. More...

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

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

const DiscreteDistributionInterface &	rateDistribution () const override
	Get the rate distribution. More...

DiscreteDistributionInterface &	rateDistribution () override
	Get the rate distribution. More...

std::shared_ptr< const DiscreteDistributionInterface >	getRateDistribution () const override
	Get a pointer to the rate distribution (or null if there is no rate distribution). More...

std::shared_ptr< DiscreteDistributionInterface >	getRateDistribution () override
	Get a pointer to the rate distribution (or null if there is no rate distribution). More...

const size_t	getRateDistributionNumber () const

void	setRootFrequencies (size_t numFreq)
	Set the root Frequencies Set. More...

const size_t	getRootFrequenciesNumber () const

bool	hasRootFrequencySet () const override

const FrequencySetInterface &	rootFrequencySet () const override

FrequencySetInterface &	rootFrequencySet () override

std::shared_ptr< const FrequencySetInterface >	getRootFrequencySet () const override

std::shared_ptr< FrequencySetInterface >	getRootFrequencySet () override

void	setModelScenario (size_t numPath)

const size_t	getModelScenarioNumber () const

std::shared_ptr< const ModelScenario >	getModelScenario () const override
	Get the Model Scenario associated with this process, in case there are mixture models involved. More...

std::shared_ptr< ModelScenario >	getModelScenario ()

bool	matchParametersValues (const ParameterList &parameters) override
	AbsractParametrizable interface. More...

bool	isFullySetUp (bool throwEx=true) const
	Check if the model set is fully specified for a given tree. More...

const std::vector< double > &	getRootFrequencies () const override

const ParametrizablePhyloTree &	parametrizablePhyloTree () const override

std::shared_ptr< const ParametrizablePhyloTree >	getParametrizablePhyloTree () const override

ParametrizablePhyloTree &	parametrizablePhyloTree ()

std::shared_ptr< ParametrizablePhyloTree >	getParametrizablePhyloTree ()

void	setTreeNumber (size_t nTree, bool check=true)

size_t	getTreeNumber () const

const BranchModelInterface &	model (unsigned int nodeId, size_t classIndex) const override
	Get the substitution model corresponding to a certain branch, site pattern, and model class. More...

std::shared_ptr< const BranchModelInterface >	getModel (unsigned int nodeId, size_t classIndex) const override
	Get the substitution model corresponding to a certain branch, site pattern, and model class. More...

ParameterList	getSubstitutionModelParameters (bool independent) const override
	Get the parameters of the substitution models. More...

ParameterList	getRateDistributionParameters (bool independent) const override
	Get the parameters of the rate distribution. More...

ParameterList	getBranchLengthParameters (bool independent) const override
	Get the parameters of the tree. More...

ParameterList	getRootFrequenciesParameters (bool independent) const override
	Get the parameters of the root frequencies set. More...

ParameterList	getNonDerivableParameters () const override
	get all NonDerivable parameters. More...

double	getProbabilityForModel (size_t classIndex) const override

Vdouble	getClassProbabilities () const override

double	getRateForModel (size_t classIndex) const override

size_t	getNumberOfClasses () const

size_t	getNumberOfStates () const

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

bool	isCompatibleWith (const AlignmentDataInterface &data) const

virtual size_t	getNumberOfIndependentParameters () const=0

size_t	getNumberOfIndependentParameters () const

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

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

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

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

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

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

virtual std::map< std::string, std::string >	getAliases () const=0

virtual std::map< std::string, std::string >	getAliases () const

virtual bool	hasParameter (const std::string &name) const=0

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

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

virtual const Parameter &	parameter (const std::string &name) const=0

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

virtual double	getParameterValue (const std::string &name) const=0

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

virtual void	setParameterValue (const std::string &name, double value)=0

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

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual void	removeConstraint (const std::string &name)=0

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

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

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

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual void	setNamespace (const std::string &prefix)=0

void	setNamespace (const std::string &prefix)

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

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

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

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

virtual void	fireParameterChanged (const ParameterList &parameters)

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

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

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

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

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

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

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

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

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

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

Check function.
bool	checkOrphanNodes (bool throwEx) const

bool	checkUnknownNodes (bool throwEx) const

Private Member Functions
void	updateParameters ()
	sets the parameters as the independent parameters on the objects More...

	SubstitutionProcessCollectionMember (SubstitutionProcessCollection *pSubProColl, size_t nProc, size_t nTree, size_t nDist)
	Create a model set belonging to the specified SubstitutionProcessCollection. Stationarity is assumed. More...

	SubstitutionProcessCollectionMember (const SubstitutionProcessCollectionMember &set)
	Resets all the information contained in this object. More...

SubstitutionProcessCollectionMember &	operator= (const SubstitutionProcessCollectionMember &set)

virtual	~SubstitutionProcessCollectionMember ()

SubstitutionProcessCollectionMember *	clone () const override

Private Attributes
SubstitutionProcessCollection *	pSubProColl_
	A pointer towards the collection the SubstitutionProcessCollectionMember belongs to. More...

size_t	nProc_
	The number of the process in the collection. More...

std::map< unsigned 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< unsigned int > >	modelToNodes_

size_t	nTree_
	The number of the tree: 0 means no assigned tree. More...

size_t	nDist_
	The number of the rate distribution. More...

size_t	nRoot_
	The number of the root frequencies (0 if the process is stationary). More...

size_t	nPath_
	the number of the set of model path, if needed. More...

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Friends
class	SubstitutionProcessCollection

Detailed Description

Definition at line 21 of file SubstitutionProcessCollectionMember.h.

Constructor & Destructor Documentation

◆ SubstitutionProcessCollectionMember() [1/2]

bpp::SubstitutionProcessCollectionMember::SubstitutionProcessCollectionMember	(	SubstitutionProcessCollection *	pSubProColl,
		size_t	nProc,
		size_t	nTree,
		size_t	nDist
	)

inlineprivate

Create a model set belonging to the specified SubstitutionProcessCollection. Stationarity is assumed.

Parameters

pSubProColl	the SubstitutionProcessCollection.
nProc	Number of the process in the collection
nTree	Number of the tree
nDist	Number of the Discrete Distribution

Definition at line 85 of file SubstitutionProcessCollectionMember.h.

References updateParameters().

Referenced by clone().

◆ SubstitutionProcessCollectionMember() [2/2]

bpp::SubstitutionProcessCollectionMember::SubstitutionProcessCollectionMember ( const SubstitutionProcessCollectionMember & set )

inlineprivate

Resets all the information contained in this object.

Definition at line 106 of file SubstitutionProcessCollectionMember.h.

◆ ~SubstitutionProcessCollectionMember()

virtual bpp::SubstitutionProcessCollectionMember::~SubstitutionProcessCollectionMember ( )

inlineprivatevirtual

Definition at line 134 of file SubstitutionProcessCollectionMember.h.

Member Function Documentation

◆ addModel()

void SubstitutionProcessCollectionMember::addModel	(	size_t	numModel,
		const std::vector< unsigned int > &	nodesId
	)

Add a new model to the set, and set relationships with nodes.

Parameters

numModel	The number of a model in the SubstitutionProcessCollection.
nodesId	the set of nodes in the tree that points toward this model. This will override any previous affectation.

Definition at line 244 of file SubstitutionProcessCollectionMember.cpp.

◆ checkOrphanNodes()

bool SubstitutionProcessCollectionMember::checkOrphanNodes ( bool throwEx ) const

protected

Definition at line 294 of file SubstitutionProcessCollectionMember.cpp.

References bpp::TextTools::toString().

Referenced by isFullySetUp().

◆ checkUnknownNodes()

bool SubstitutionProcessCollectionMember::checkUnknownNodes ( bool throwEx ) const

protected

Definition at line 318 of file SubstitutionProcessCollectionMember.cpp.

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

Referenced by isFullySetUp().

◆ clear()

void bpp::SubstitutionProcessCollectionMember::clear ( )

inline

Definition at line 161 of file SubstitutionProcessCollectionMember.h.

References modelToNodes_, nodeToModel_, and nRoot_.

◆ clone()

SubstitutionProcessCollectionMember* bpp::SubstitutionProcessCollectionMember::clone ( ) const

inlineoverrideprivatevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 144 of file SubstitutionProcessCollectionMember.h.

References SubstitutionProcessCollectionMember().

Referenced by bpp::SubstitutionProcessCollection::SubstitutionProcessCollection().

◆ collection() [1/2]

SubstitutionProcessCollection& bpp::SubstitutionProcessCollectionMember::collection ( )

inline

Definition at line 154 of file SubstitutionProcessCollectionMember.h.

References pSubProColl_.

◆ collection() [2/2]

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

inline

Definition at line 147 of file SubstitutionProcessCollectionMember.h.

References pSubProColl_.

◆ getAlphabet()

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

inlineinherited

Definition at line 45 of file AbstractSubstitutionProcess.h.

References bpp::StateMapInterface::getAlphabet(), and bpp::SubstitutionProcessInterface::stateMap().

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::AbstractSubstitutionProcess::isCompatibleWith(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ getBranchLengthParameters()

ParameterList SubstitutionProcessCollectionMember::getBranchLengthParameters ( bool independent ) const

overridevirtual

Get the parameters of the tree.

Implements bpp::SubstitutionProcessInterface.

Definition at line 75 of file SubstitutionProcessCollectionMember.cpp.

◆ getClassProbabilities()

Vdouble SubstitutionProcessCollectionMember::getClassProbabilities ( ) const

overridevirtual

Returns: The vector of the probabilities associated to the classes.

Implements bpp::SubstitutionProcessInterface.

Definition at line 375 of file SubstitutionProcessCollectionMember.cpp.

◆ getCollection() [1/2]

SubstitutionProcessCollection* bpp::SubstitutionProcessCollectionMember::getCollection ( )

inline

Definition at line 173 of file SubstitutionProcessCollectionMember.h.

References pSubProColl_.

◆ getCollection() [2/2]

const SubstitutionProcessCollection* bpp::SubstitutionProcessCollectionMember::getCollection ( ) const

inline

Definition at line 168 of file SubstitutionProcessCollectionMember.h.

References pSubProColl_.

◆ getModel() [1/3]

std::shared_ptr< BranchModelInterface > SubstitutionProcessCollectionMember::getModel ( size_t n )

Definition at line 35 of file SubstitutionProcessCollectionMember.cpp.

◆ getModel() [2/3]

std::shared_ptr< const BranchModelInterface > SubstitutionProcessCollectionMember::getModel ( size_t i ) const

overridevirtual

Returns: A shared pointer toward the model with given index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 30 of file SubstitutionProcessCollectionMember.cpp.

Referenced by getModel(), getModelForNode(), and bpp::PhylogeneticsApplicationTools::getSubstitutionProcess().

◆ getModel() [3/3]

std::shared_ptr<const BranchModelInterface> bpp::SubstitutionProcessCollectionMember::getModel	(	unsigned int	nodeId,
		size_t	classIndex
	)		const

inlineoverridevirtual

Get the substitution model corresponding to a certain branch, site pattern, and model class.

Parameters

nodeId	The id of the node.
classIndex	The model class index.

Returns: A shared pointer toward the model with given index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 391 of file SubstitutionProcessCollectionMember.h.

References getModel(), and nodeToModel_.

◆ getModelForNode()

std::shared_ptr<const BranchModelInterface> bpp::SubstitutionProcessCollectionMember::getModelForNode ( unsigned int nodeId ) const

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 244 of file SubstitutionProcessCollectionMember.h.

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

◆ getModelNumberForNode()

size_t bpp::SubstitutionProcessCollectionMember::getModelNumberForNode ( unsigned int nodeId ) const

inlineoverridevirtual

Get the number of the model associated to a particular node id.

Parameters

nodeId The id of the query node.

Returns: The number of the model associated to the given node.

Exceptions

Exception If no model is found for this node.

Implements bpp::SubstitutionProcessInterface.

Definition at line 229 of file SubstitutionProcessCollectionMember.h.

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

◆ getModelNumbers()

std::vector< size_t > SubstitutionProcessCollectionMember::getModelNumbers ( ) const

overridevirtual

Returns: The current indexes of models used in the process

Implements bpp::SubstitutionProcessInterface.

Definition at line 14 of file SubstitutionProcessCollectionMember.cpp.

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

◆ getModelScenario() [1/2]

std::shared_ptr< ModelScenario > SubstitutionProcessCollectionMember::getModelScenario ( )

Definition at line 45 of file SubstitutionProcessCollectionMember.cpp.

◆ getModelScenario() [2/2]

std::shared_ptr< const ModelScenario > SubstitutionProcessCollectionMember::getModelScenario ( ) const

overridevirtual

Get the Model Scenario associated with this process, in case there are mixture models involved.

When a mixture model is not included in the ModelScenario, it is considered as non-mixed (transition probabilities are then computed as mixture of submodel transition probalities).

It returns 0 if there is no model path, which means that all mixture models are considered as non-mixed.

Implements bpp::SubstitutionProcessInterface.

Definition at line 40 of file SubstitutionProcessCollectionMember.cpp.

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

◆ getModelScenarioNumber()

const size_t bpp::SubstitutionProcessCollectionMember::getModelScenarioNumber ( ) const

inline

Definition at line 318 of file SubstitutionProcessCollectionMember.h.

References nPath_.

◆ getNodesWithModel()

const std::vector<unsigned int> bpp::SubstitutionProcessCollectionMember::getNodesWithModel ( size_t i ) const

inlineoverridevirtual

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.

Implements bpp::SubstitutionProcessInterface.

Definition at line 259 of file SubstitutionProcessCollectionMember.h.

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

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

◆ getNonDerivableParameters()

ParameterList SubstitutionProcessCollectionMember::getNonDerivableParameters ( ) const

overridevirtual

get all NonDerivable parameters.

Reimplemented from bpp::AbstractSubstitutionProcess.

Definition at line 100 of file SubstitutionProcessCollectionMember.cpp.

References bpp::ParameterList::includeParameters().

◆ getNumberOfClasses()

size_t bpp::AbstractSubstitutionProcess::getNumberOfClasses ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 34 of file AbstractSubstitutionProcess.h.

References bpp::SubstitutionProcessInterface::getRateDistribution().

◆ getNumberOfModels()

size_t bpp::SubstitutionProcessCollectionMember::getNumberOfModels ( ) const

inlineoverridevirtual

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

Implements bpp::SubstitutionProcessInterface.

Definition at line 199 of file SubstitutionProcessCollectionMember.h.

References modelToNodes_.

◆ getNumberOfProcesses()

size_t bpp::SubstitutionProcessCollectionMember::getNumberOfProcesses ( ) const

inline

Returns: the number of the process in the collection

Definition at line 191 of file SubstitutionProcessCollectionMember.h.

References nProc_.

◆ getNumberOfStates()

size_t bpp::AbstractSubstitutionProcess::getNumberOfStates ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 40 of file AbstractSubstitutionProcess.h.

References bpp::StateMapInterface::getNumberOfModelStates(), and bpp::SubstitutionProcessInterface::stateMap().

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ getParametrizablePhyloTree() [1/2]

std::shared_ptr< ParametrizablePhyloTree > SubstitutionProcessCollectionMember::getParametrizablePhyloTree ( )

Definition at line 224 of file SubstitutionProcessCollectionMember.cpp.

◆ getParametrizablePhyloTree() [2/2]

std::shared_ptr< const ParametrizablePhyloTree > SubstitutionProcessCollectionMember::getParametrizablePhyloTree ( ) const

overridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 211 of file SubstitutionProcessCollectionMember.cpp.

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

◆ getProbabilityForModel()

double SubstitutionProcessCollectionMember::getProbabilityForModel ( size_t classIndex ) const

overridevirtual

Inheriting from SubstitutionProcess

Implements bpp::SubstitutionProcessInterface.

Definition at line 368 of file SubstitutionProcessCollectionMember.cpp.

◆ getRateDistribution() [1/2]

std::shared_ptr< const DiscreteDistributionInterface > SubstitutionProcessCollectionMember::getRateDistribution ( ) const

overridevirtual

Get a pointer to the rate distribution (or null if there is no rate distribution).

Implements bpp::SubstitutionProcessInterface.

Definition at line 50 of file SubstitutionProcessCollectionMember.cpp.

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

◆ getRateDistribution() [2/2]

std::shared_ptr< DiscreteDistributionInterface > SubstitutionProcessCollectionMember::getRateDistribution ( )

overridevirtual

Get a pointer to the rate distribution (or null if there is no rate distribution).

Implements bpp::SubstitutionProcessInterface.

Definition at line 55 of file SubstitutionProcessCollectionMember.cpp.

◆ getRateDistributionNumber()

const size_t bpp::SubstitutionProcessCollectionMember::getRateDistributionNumber ( ) const

inline

Definition at line 288 of file SubstitutionProcessCollectionMember.h.

References nDist_.

◆ getRateDistributionParameters()

ParameterList SubstitutionProcessCollectionMember::getRateDistributionParameters ( bool independent ) const

overridevirtual

Get the parameters of the rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 70 of file SubstitutionProcessCollectionMember.cpp.

◆ getRateForModel()

double SubstitutionProcessCollectionMember::getRateForModel ( size_t classIndex ) const

overridevirtual

Returns: The substitution rate associated to the given model class.

Parameters

classIndex The model class index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 387 of file SubstitutionProcessCollectionMember.cpp.

◆ getRootFrequencies()

const std::vector< double > & SubstitutionProcessCollectionMember::getRootFrequencies ( ) const

overridevirtual

Returns: The values of the root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 160 of file SubstitutionProcessCollectionMember.cpp.

◆ getRootFrequenciesNumber()

const size_t bpp::SubstitutionProcessCollectionMember::getRootFrequenciesNumber ( ) const

inline

Definition at line 297 of file SubstitutionProcessCollectionMember.h.

References nRoot_.

◆ getRootFrequenciesParameters()

ParameterList SubstitutionProcessCollectionMember::getRootFrequenciesParameters ( bool independent ) const

overridevirtual

Get the parameters of the root frequencies set.

Implements bpp::SubstitutionProcessInterface.

Definition at line 83 of file SubstitutionProcessCollectionMember.cpp.

◆ getRootFrequencySet() [1/2]

std::shared_ptr< const FrequencySetInterface > SubstitutionProcessCollectionMember::getRootFrequencySet ( ) const

overridevirtual

Returns: A pointer toward rhe set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 128 of file SubstitutionProcessCollectionMember.cpp.

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

◆ getRootFrequencySet() [2/2]

std::shared_ptr< FrequencySetInterface > SubstitutionProcessCollectionMember::getRootFrequencySet ( )

overridevirtual

Returns: A pointer toward rhe set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 136 of file SubstitutionProcessCollectionMember.cpp.

◆ getStateMap()

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

inlineoverridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 183 of file SubstitutionProcessCollectionMember.h.

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

◆ getSubstitutionModelParameters()

ParameterList SubstitutionProcessCollectionMember::getSubstitutionModelParameters ( bool independent ) const

overridevirtual

Get the parameters of the substitution models.

Implements bpp::SubstitutionProcessInterface.

Definition at line 113 of file SubstitutionProcessCollectionMember.cpp.

References bpp::ParameterList::includeParameters().

◆ getTreeNumber()

size_t bpp::SubstitutionProcessCollectionMember::getTreeNumber ( ) const

inline

Definition at line 384 of file SubstitutionProcessCollectionMember.h.

References nTree_.

◆ hasMixedTransitionModel()

bool SubstitutionProcessCollectionMember::hasMixedTransitionModel ( ) const

Returns: True iff there is a MixedTransitionModel in the SubstitutionProcessCollectionMember

Definition at line 347 of file SubstitutionProcessCollectionMember.cpp.

◆ hasRootFrequencySet()

bool bpp::SubstitutionProcessCollectionMember::hasRootFrequencySet ( ) const

inlineoverridevirtual

Returns: true if the process has parametrized root frequencies (non-stationary model)

Implements bpp::SubstitutionProcessInterface.

Definition at line 299 of file SubstitutionProcessCollectionMember.h.

References isStationary().

◆ isCompatibleWith()

bool bpp::AbstractSubstitutionProcess::isCompatibleWith ( const AlignmentDataInterface & data ) const

inlinevirtualinherited

Implements bpp::SubstitutionProcessInterface.

Definition at line 50 of file AbstractSubstitutionProcess.h.

References bpp::AbstractSubstitutionProcess::getAlphabet(), and bpp::TemplateAlignmentDataInterface< class >::getAlphabet().

◆ isFullySetUp()

bool bpp::SubstitutionProcessCollectionMember::isFullySetUp ( bool throwEx = true ) const

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,
all nodes ids in the set refer to an existing node in the tree.

Parameters

throwEx Tell if an exception have to be thrown in case of test not passed.

Definition at line 339 of file SubstitutionProcessCollectionMember.h.

References checkOrphanNodes(), and checkUnknownNodes().

◆ isStationary()

bool bpp::SubstitutionProcessCollectionMember::isStationary ( ) const

inline

Returns: True iff is stationary.

Definition at line 209 of file SubstitutionProcessCollectionMember.h.

References nRoot_.

Referenced by hasRootFrequencySet().

◆ matchParametersValues()

bool SubstitutionProcessCollectionMember::matchParametersValues ( const ParameterList & parameters )

overridevirtual

AbsractParametrizable interface.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 359 of file SubstitutionProcessCollectionMember.cpp.

References bpp::AbstractParameterAliasable::matchParametersValues().

◆ model() [1/2]

const BranchModelInterface & SubstitutionProcessCollectionMember::model ( size_t i ) const

overridevirtual

Returns: the model with given index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 25 of file SubstitutionProcessCollectionMember.cpp.

Referenced by getStateMap(), model(), and stateMap().

◆ model() [2/2]

const BranchModelInterface& bpp::SubstitutionProcessCollectionMember::model	(	unsigned int	nodeId,
		size_t	classIndex
	)		const

inlineoverridevirtual

Get the substitution model corresponding to a certain branch, site pattern, and model class.

Parameters

nodeId	The id of the node.
classIndex	The model class index.

Returns: the model with given index.

Implements bpp::SubstitutionProcessInterface.

Definition at line 386 of file SubstitutionProcessCollectionMember.h.

References model(), and nodeToModel_.

◆ operator=()

SubstitutionProcessCollectionMember& bpp::SubstitutionProcessCollectionMember::operator= ( const SubstitutionProcessCollectionMember & set )

inlineprivate

Definition at line 118 of file SubstitutionProcessCollectionMember.h.

References modelToNodes_, nDist_, nodeToModel_, nPath_, nProc_, nRoot_, nTree_, bpp::AbstractParameterAliasable::operator=(), and pSubProColl_.

◆ parametrizablePhyloTree() [1/2]

ParametrizablePhyloTree & SubstitutionProcessCollectionMember::parametrizablePhyloTree ( )

Definition at line 216 of file SubstitutionProcessCollectionMember.cpp.

◆ parametrizablePhyloTree() [2/2]

const ParametrizablePhyloTree & SubstitutionProcessCollectionMember::parametrizablePhyloTree ( ) const

overridevirtual

Returns: the Tree

Implements bpp::SubstitutionProcessInterface.

Definition at line 203 of file SubstitutionProcessCollectionMember.cpp.

◆ rateDistribution() [1/2]

const DiscreteDistributionInterface & SubstitutionProcessCollectionMember::rateDistribution ( ) const

overridevirtual

Get the rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 60 of file SubstitutionProcessCollectionMember.cpp.

◆ rateDistribution() [2/2]

DiscreteDistributionInterface & SubstitutionProcessCollectionMember::rateDistribution ( )

overridevirtual

Get the rate distribution.

Exceptions

NullPointerException if there is no associated rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 65 of file SubstitutionProcessCollectionMember.cpp.

◆ rootFrequencySet() [1/2]

const FrequencySetInterface & SubstitutionProcessCollectionMember::rootFrequencySet ( ) const

overridevirtual

Returns: The set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 144 of file SubstitutionProcessCollectionMember.cpp.

◆ rootFrequencySet() [2/2]

FrequencySetInterface & SubstitutionProcessCollectionMember::rootFrequencySet ( )

overridevirtual

Returns: The set of parametrized root frequencies.

Implements bpp::SubstitutionProcessInterface.

Definition at line 152 of file SubstitutionProcessCollectionMember.cpp.

◆ setModelScenario()

void SubstitutionProcessCollectionMember::setModelScenario ( size_t numPath )

Definition at line 170 of file SubstitutionProcessCollectionMember.cpp.

References bpp::TextTools::toString().

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

◆ setRootFrequencies()

void SubstitutionProcessCollectionMember::setRootFrequencies ( size_t numFreq )

Set the root Frequencies Set.

Parameters

numFreq the index of the frequencies in the collection.

Definition at line 276 of file SubstitutionProcessCollectionMember.cpp.

Referenced by bpp::SubstitutionProcessCollection::addOnePerBranchSubstitutionProcess(), and bpp::SubstitutionProcessCollection::addSubstitutionProcess().

◆ setTreeNumber()

void SubstitutionProcessCollectionMember::setTreeNumber	(	size_t	nTree,
		bool	check = `true`
	)

Definition at line 229 of file SubstitutionProcessCollectionMember.cpp.

◆ stateMap()

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

inlineoverridevirtual

Returns: The state map associated with the models of this process

Implements bpp::SubstitutionProcessInterface.

Definition at line 178 of file SubstitutionProcessCollectionMember.h.

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

◆ updateParameters()

void SubstitutionProcessCollectionMember::updateParameters ( )

private

sets the parameters as the independent parameters on the objects

Definition at line 91 of file SubstitutionProcessCollectionMember.cpp.

Referenced by SubstitutionProcessCollectionMember().

Friends And Related Function Documentation

◆ SubstitutionProcessCollection

friend class SubstitutionProcessCollection

friend

Definition at line 428 of file SubstitutionProcessCollectionMember.h.

Member Data Documentation

◆ modelToNodes_

std::map<size_t, std::vector<unsigned int> > bpp::SubstitutionProcessCollectionMember::modelToNodes_

private

Definition at line 49 of file SubstitutionProcessCollectionMember.h.

Referenced by clear(), getNodesWithModel(), getNumberOfModels(), getStateMap(), operator=(), and stateMap().

◆ nDist_

size_t bpp::SubstitutionProcessCollectionMember::nDist_

private

The number of the rate distribution.

Definition at line 59 of file SubstitutionProcessCollectionMember.h.

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

◆ nodeToModel_

std::map<unsigned int, size_t> bpp::SubstitutionProcessCollectionMember::nodeToModel_

private

Contains for each node in a tree the index of the corresponding model in modelSet_.

Definition at line 48 of file SubstitutionProcessCollectionMember.h.

Referenced by clear(), getModel(), getModelForNode(), getModelNumberForNode(), model(), and operator=().

◆ nPath_

size_t bpp::SubstitutionProcessCollectionMember::nPath_

private

the number of the set of model path, if needed.

Definition at line 69 of file SubstitutionProcessCollectionMember.h.

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

◆ nProc_

size_t bpp::SubstitutionProcessCollectionMember::nProc_

private

The number of the process in the collection.

Definition at line 34 of file SubstitutionProcessCollectionMember.h.

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

◆ nRoot_

size_t bpp::SubstitutionProcessCollectionMember::nRoot_

private

The number of the root frequencies (0 if the process is stationary).

Definition at line 64 of file SubstitutionProcessCollectionMember.h.

Referenced by clear(), getRootFrequenciesNumber(), isStationary(), and operator=().

◆ nTree_

size_t bpp::SubstitutionProcessCollectionMember::nTree_

private

The number of the tree: 0 means no assigned tree.

Definition at line 54 of file SubstitutionProcessCollectionMember.h.

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

◆ pSubProColl_

SubstitutionProcessCollection* bpp::SubstitutionProcessCollectionMember::pSubProColl_

private

A pointer towards the collection the SubstitutionProcessCollectionMember belongs to.

Definition at line 29 of file SubstitutionProcessCollectionMember.h.

Referenced by collection(), getCollection(), and operator=().

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

Bpp/Phyl/Likelihood/SubstitutionProcessCollectionMember.h
Bpp/Phyl/Likelihood/SubstitutionProcessCollectionMember.cpp

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ SubstitutionProcessCollectionMember() [1/2]

◆ SubstitutionProcessCollectionMember() [2/2]

◆ ~SubstitutionProcessCollectionMember()

Member Function Documentation

◆ addModel()

◆ checkOrphanNodes()

◆ checkUnknownNodes()

◆ clear()

◆ clone()

◆ collection() [1/2]

◆ collection() [2/2]

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getClassProbabilities()

◆ getCollection() [1/2]

◆ getCollection() [2/2]

◆ getModel() [1/3]

◆ getModel() [2/3]

◆ getModel() [3/3]

◆ getModelForNode()

◆ getModelNumberForNode()

◆ getModelNumbers()

◆ getModelScenario() [1/2]

◆ getModelScenario() [2/2]

◆ getModelScenarioNumber()

◆ getNodesWithModel()

◆ getNonDerivableParameters()

◆ getNumberOfClasses()

◆ getNumberOfModels()

◆ getNumberOfProcesses()

◆ getNumberOfStates()

◆ getParametrizablePhyloTree() [1/2]

◆ getParametrizablePhyloTree() [2/2]

◆ getProbabilityForModel()

◆ getRateDistribution() [1/2]

◆ getRateDistribution() [2/2]

◆ getRateDistributionNumber()

◆ getRateDistributionParameters()

◆ getRateForModel()

◆ getRootFrequencies()

◆ getRootFrequenciesNumber()

◆ getRootFrequenciesParameters()

◆ getRootFrequencySet() [1/2]

◆ getRootFrequencySet() [2/2]

◆ getStateMap()

◆ getSubstitutionModelParameters()

◆ getTreeNumber()

◆ hasMixedTransitionModel()

◆ hasRootFrequencySet()

◆ isCompatibleWith()

◆ isFullySetUp()

◆ isStationary()

◆ matchParametersValues()

◆ model() [1/2]

◆ model() [2/2]

◆ operator=()

◆ parametrizablePhyloTree() [1/2]

◆ parametrizablePhyloTree() [2/2]

◆ rateDistribution() [1/2]

◆ rateDistribution() [2/2]

◆ rootFrequencySet() [1/2]

◆ rootFrequencySet() [2/2]

◆ setModelScenario()

◆ setRootFrequencies()

◆ setTreeNumber()

◆ stateMap()

◆ updateParameters()

Friends And Related Function Documentation

◆ SubstitutionProcessCollection

Member Data Documentation

◆ modelToNodes_

◆ nDist_