bpp::SubstitutionProcessCollectionMember Class Reference

#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.

References bpp::SubstitutionProcessCollection::frequencySet(), getCollection(), isStationary(), bpp::SubstitutionProcessCollection::model(), modelToNodes_, nodeToModel_, nRoot_, and updateParameters().

checkOrphanNodes()

bool SubstitutionProcessCollectionMember::checkOrphanNodes ( bool  throwEx ) const

protected

Definition at line 294 of file SubstitutionProcessCollectionMember.cpp.

References getParametrizablePhyloTree(), nodeToModel_, and 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(), getParametrizablePhyloTree(), modelToNodes_, 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_.

Referenced by getBranchLengthParameters(), getModel(), getModelScenario(), getParametrizablePhyloTree(), getRateDistribution(), getRateDistributionParameters(), getRootFrequencies(), getRootFrequenciesParameters(), getRootFrequencySet(), hasMixedTransitionModel(), matchParametersValues(), model(), parametrizablePhyloTree(), rateDistribution(), rootFrequencySet(), and setTreeNumber().

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(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and setTreeNumber().

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.

References collection(), bpp::SubstitutionProcessCollection::getBranchLengthParameters(), and nTree_.

Referenced by setTreeNumber(), and updateParameters().

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.

References bpp::DiscreteDistributionInterface::getNumberOfCategories(), bpp::DiscreteDistributionInterface::getProbability(), and rateDistribution().

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_.

Referenced by addModel(), getNonDerivableParameters(), getRootFrequencies(), getSubstitutionModelParameters(), setModelScenario(), and setRootFrequencies().

getModel() [1/3]

std::shared_ptr< BranchModelInterface > SubstitutionProcessCollectionMember::getModel

(

size_t

n

)

Definition at line 35 of file SubstitutionProcessCollectionMember.cpp.

References collection(), and bpp::SubstitutionProcessCollection::getModel().

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.

References collection(), and bpp::SubstitutionProcessCollection::getModel().

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

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.

References modelToNodes_.

Referenced by bpp::PhylogeneticsApplicationTools::getSubstitutionProcess(), and setModelScenario().

getModelScenario() [1/2]

std::shared_ptr< ModelScenario > SubstitutionProcessCollectionMember::getModelScenario

(

)

Definition at line 45 of file SubstitutionProcessCollectionMember.cpp.

References collection(), bpp::SubstitutionProcessCollection::getModelScenario(), and nPath_.

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.

References collection(), bpp::SubstitutionProcessCollection::getModelScenario(), and nPath_.

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::AbstractParameterAliasable::getAliasedParameters(), getCollection(), bpp::AbstractParameterAliasable::getFromParameters(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), and 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.

References collection(), bpp::SubstitutionProcessCollection::getTree(), bpp::SubstitutionProcessCollection::hasTreeNumber(), and nTree_.

getParametrizablePhyloTree() [2/2]

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

overridevirtual

Implements bpp::SubstitutionProcessInterface.

Definition at line 211 of file SubstitutionProcessCollectionMember.cpp.

References collection(), bpp::SubstitutionProcessCollection::getTree(), bpp::SubstitutionProcessCollection::hasTreeNumber(), and nTree_.

Referenced by checkOrphanNodes(), checkUnknownNodes(), and 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.

References bpp::DiscreteDistributionInterface::getProbability(), getRateDistribution(), and rateDistribution().

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.

References collection(), bpp::SubstitutionProcessCollection::getRateDistribution(), and nDist_.

Referenced by getProbabilityForModel(), getRateForModel(), and 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.

References collection(), bpp::SubstitutionProcessCollection::getRateDistribution(), and nDist_.

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.

References collection(), bpp::SubstitutionProcessCollection::getRateDistributionParameters(), and nDist_.

Referenced by getNonDerivableParameters(), and updateParameters().

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.

References bpp::DiscreteDistributionInterface::getCategory(), getRateDistribution(), and rateDistribution().

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.

References collection(), bpp::SubstitutionProcessCollection::frequencySet(), getCollection(), bpp::FrequencySetInterface::getFrequencies(), getModel(), isStationary(), model(), modelToNodes_, and nRoot_.

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.

References collection(), bpp::SubstitutionProcessCollection::getRootFrequenciesParameters(), isStationary(), and nRoot_.

Referenced by getNonDerivableParameters(), and updateParameters().

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.

References collection(), bpp::SubstitutionProcessCollection::getFrequencySet(), isStationary(), and nRoot_.

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.

References collection(), bpp::SubstitutionProcessCollection::getFrequencySet(), isStationary(), and nRoot_.

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 getCollection(), getSubstitutionModelParameters(), bpp::ParameterList::includeParameters(), and modelToNodes_.

Referenced by getNonDerivableParameters(), getSubstitutionModelParameters(), and updateParameters().

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.

References collection(), getModel(), and modelToNodes_.

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().

Referenced by setTreeNumber().

isStationary()

bool bpp::SubstitutionProcessCollectionMember::isStationary ( ) const

inline

Returns

True iff is stationary.

Definition at line 209 of file SubstitutionProcessCollectionMember.h.

References nRoot_.

Referenced by addModel(), getRootFrequencies(), getRootFrequenciesParameters(), getRootFrequencySet(), hasRootFrequencySet(), and rootFrequencySet().

matchParametersValues()

bool SubstitutionProcessCollectionMember::matchParametersValues ( const ParameterList &  parameters )

overridevirtual

AbsractParametrizable interface.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 359 of file SubstitutionProcessCollectionMember.cpp.

References collection(), and 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.

References collection(), and bpp::SubstitutionProcessCollection::model().

Referenced by getRootFrequencies(), getStateMap(), model(), setModelScenario(), 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.

References collection(), nTree_, and bpp::SubstitutionProcessCollection::tree().

parametrizablePhyloTree() [2/2]

const ParametrizablePhyloTree & SubstitutionProcessCollectionMember::parametrizablePhyloTree ( ) const

overridevirtual

Returns

the Tree

Implements bpp::SubstitutionProcessInterface.

Definition at line 203 of file SubstitutionProcessCollectionMember.cpp.

References collection(), nTree_, and bpp::SubstitutionProcessCollection::tree().

rateDistribution() [1/2]

const DiscreteDistributionInterface & SubstitutionProcessCollectionMember::rateDistribution ( ) const

overridevirtual

Get the rate distribution.

Implements bpp::SubstitutionProcessInterface.

Definition at line 60 of file SubstitutionProcessCollectionMember.cpp.

References collection(), nDist_, and bpp::SubstitutionProcessCollection::rateDistribution().

Referenced by getClassProbabilities(), getProbabilityForModel(), and getRateForModel().

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.

References collection(), nDist_, and bpp::SubstitutionProcessCollection::rateDistribution().

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.

References collection(), bpp::SubstitutionProcessCollection::frequencySet(), isStationary(), and nRoot_.

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.

References collection(), bpp::SubstitutionProcessCollection::frequencySet(), isStationary(), and nRoot_.

setModelScenario()

void SubstitutionProcessCollectionMember::setModelScenario

(

size_t

numPath

)

Definition at line 170 of file SubstitutionProcessCollectionMember.cpp.

References getCollection(), getModel(), getModelNumbers(), bpp::SubstitutionProcessCollection::getModelScenario(), bpp::BranchModelInterface::getName(), model(), nPath_, nProc_, and 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.

References bpp::SubstitutionProcessCollection::frequencySet(), getCollection(), bpp::SubstitutionProcessCollection::model(), modelToNodes_, nRoot_, and updateParameters().

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.

References bpp::AbstractParameterAliasable::addParameters_(), collection(), bpp::AbstractParameterAliasable::deleteParameters_(), bpp::AbstractSubstitutionProcess::getAlphabet(), getBranchLengthParameters(), isFullySetUp(), and nTree_.

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.

References bpp::AbstractParameterAliasable::addParameters_(), getBranchLengthParameters(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), and bpp::AbstractParameterAliasable::resetParameters_().

Referenced by addModel(), setRootFrequencies(), and 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 addModel(), checkUnknownNodes(), clear(), getModelNumbers(), getNodesWithModel(), getNumberOfModels(), getRootFrequencies(), getStateMap(), getSubstitutionModelParameters(), hasMixedTransitionModel(), operator=(), setRootFrequencies(), 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 getRateDistribution(), getRateDistributionNumber(), getRateDistributionParameters(), operator=(), and rateDistribution().

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 addModel(), checkOrphanNodes(), 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 getModelScenario(), getModelScenarioNumber(), operator=(), and setModelScenario().

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(), operator=(), and setModelScenario().

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 addModel(), clear(), getRootFrequencies(), getRootFrequenciesNumber(), getRootFrequenciesParameters(), getRootFrequencySet(), isStationary(), operator=(), rootFrequencySet(), and setRootFrequencies().

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 getBranchLengthParameters(), getParametrizablePhyloTree(), getTreeNumber(), operator=(), parametrizablePhyloTree(), and setTreeNumber().

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=().

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

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