Site simulation under a unique substitution process. More...

#include <Bpp/Phyl/Simulation/SimpleSubstitutionProcessSiteSimulator.h>

Inheritance diagram for bpp::SimpleSubstitutionProcessSiteSimulator:

Collaboration diagram for bpp::SimpleSubstitutionProcessSiteSimulator:

Public Member Functions
std::shared_ptr< const SubstitutionProcessInterface >	getSubstitutionProcess () const
	Get the substitution process associated to this instance. More...

std::shared_ptr< const ParametrizablePhyloTree >	getTree () const
	Get the tree associated to this instance. More...

void	enableContinuousRates (bool yn)
	Enable the use of continuous rates instead of discrete rates. More...

void	outputInternalSites (bool yn) override
	Sets whether we will output the internal sequences or not. More...

The SiteSimulator interface
std::unique_ptr< Site >	simulateSite () const override

std::unique_ptr< Site >	simulateSite (size_t rateClass) const override

std::unique_ptr< Site >	simulateSite (double rate) const override

std::unique_ptr< Site >	simulateSite (size_t ancestralStateIndex, double rate) const override

std::vector< std::string >	getSequenceNames () const override

SiteSimulator interface
std::shared_ptr< const Alphabet >	getAlphabet () const override

const Alphabet &	alphabet () const override

The DetailedSiteSimulator interface.
std::unique_ptr< SiteSimulationResult >	dSimulateSite () const override
	Get a detailed simulation result for one site. More...

std::unique_ptr< SiteSimulationResult >	dSimulateSite (size_t rateClass) const override

std::unique_ptr< SiteSimulationResult >	dSimulateSite (double rate) const override

std::unique_ptr< SiteSimulationResult >	dSimulateSite (size_t ancestralStateIndex, double rate) const override

Protected Member Functions
The 'Internal' methods.
void	evolveInternal (std::shared_ptr< SimProcessNode > node, size_t rateClass, SiteSimulationResult *ssr=nullptr) const

void	evolveInternal (std::shared_ptr< SimProcessNode > node, double rate, SiteSimulationResult *ssr=nullptr) const

Protected Attributes
std::shared_ptr< const SubstitutionProcessInterface >	process_

std::shared_ptr< const ParametrizablePhyloTree >	phyloTree_

SPTree	tree_
	To store states & transition probabilities of the simulator. More...

Vdouble	qRates_
	cumsum probas of the substitution rates More...

VVdouble	qRoots_

std::vector< size_t >	seqIndexes_
	Vector of indexes of sequenced output species. More...

std::vector< std::string >	seqNames_
	Vector of names of sequenced output species. More...

std::map< size_t, std::shared_ptr< SimProcessNode > >	speciesNodes_
	Map between species Indexes & used nodes, may change at each simulation. More...

size_t	nbNodes_

size_t	nbClasses_

size_t	nbStates_

bool	continuousRates_

bool	outputInternalSites_

Stores intermediate results.
	SimpleSubstitutionProcessSiteSimulator (std::shared_ptr< const SubstitutionProcessInterface > process)

virtual	~SimpleSubstitutionProcessSiteSimulator ()

	SimpleSubstitutionProcessSiteSimulator (const SimpleSubstitutionProcessSiteSimulator &nhss)

SimpleSubstitutionProcessSiteSimulator &	operator= (const SimpleSubstitutionProcessSiteSimulator &nhss)

SimpleSubstitutionProcessSiteSimulator *	clone () const override

virtual void	init ()
	Init all probabilities. More...

Detailed Description

Site simulation under a unique substitution process.

Definition at line 69 of file SimpleSubstitutionProcessSiteSimulator.h.

Constructor & Destructor Documentation

◆ SimpleSubstitutionProcessSiteSimulator() [1/2]

SimpleSubstitutionProcessSiteSimulator::SimpleSubstitutionProcessSiteSimulator ( std::shared_ptr< const SubstitutionProcessInterface > process )

Definition at line 22 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References init().

Referenced by clone().

◆ ~SimpleSubstitutionProcessSiteSimulator()

virtual bpp::SimpleSubstitutionProcessSiteSimulator::~SimpleSubstitutionProcessSiteSimulator ( )

inlinevirtual

Definition at line 128 of file SimpleSubstitutionProcessSiteSimulator.h.

◆ SimpleSubstitutionProcessSiteSimulator() [2/2]

bpp::SimpleSubstitutionProcessSiteSimulator::SimpleSubstitutionProcessSiteSimulator ( const SimpleSubstitutionProcessSiteSimulator & nhss )

inline

Definition at line 130 of file SimpleSubstitutionProcessSiteSimulator.h.

Member Function Documentation

◆ alphabet()

const Alphabet& bpp::SimpleSubstitutionProcessSiteSimulator::alphabet ( ) const

inlineoverridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 207 of file SimpleSubstitutionProcessSiteSimulator.h.

References process_.

Referenced by simulateSite().

◆ clone()

SimpleSubstitutionProcessSiteSimulator* bpp::SimpleSubstitutionProcessSiteSimulator::clone ( ) const

inlineoverridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 165 of file SimpleSubstitutionProcessSiteSimulator.h.

References SimpleSubstitutionProcessSiteSimulator().

◆ dSimulateSite() [1/4]

unique_ptr< SiteSimulationResult > SimpleSubstitutionProcessSiteSimulator::dSimulateSite ( ) const

overridevirtual

Get a detailed simulation result for one site.

Returns: A SiteSimulationResult object with all ancestral states for all nodes and branches.

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 249 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References continuousRates_, bpp::RandomTools::pickFromCumSum(), process_, and qRates_.

◆ dSimulateSite() [2/4]

unique_ptr< SiteSimulationResult > SimpleSubstitutionProcessSiteSimulator::dSimulateSite ( double rate ) const

overridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 264 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References evolveInternal(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getRoot(), phyloTree_, bpp::RandomTools::pickFromCumSum(), process_, qRoots_, and tree_.

◆ dSimulateSite() [3/4]

unique_ptr< SiteSimulationResult > SimpleSubstitutionProcessSiteSimulator::dSimulateSite	(	size_t	ancestralStateIndex,
		double	rate
	)		const

overridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 298 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References evolveInternal(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getRoot(), phyloTree_, process_, and tree_.

◆ dSimulateSite() [4/4]

unique_ptr< SiteSimulationResult > SimpleSubstitutionProcessSiteSimulator::dSimulateSite ( size_t rateClass ) const

overridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 281 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References evolveInternal(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getRoot(), phyloTree_, bpp::RandomTools::pickFromCumSum(), process_, qRoots_, and tree_.

◆ enableContinuousRates()

void bpp::SimpleSubstitutionProcessSiteSimulator::enableContinuousRates ( bool yn )

inline

Enable the use of continuous rates instead of discrete rates.

To work, the DiscreteDistribution object used should implement the randC method.

In this case, sampling is done jointly on the process classes and on the continuous rate.

Parameters

yn	Tell if we should use continuous rates.

Definition at line 257 of file SimpleSubstitutionProcessSiteSimulator.h.

References continuousRates_.

◆ evolveInternal() [1/2]

void SimpleSubstitutionProcessSiteSimulator::evolveInternal	(	std::shared_ptr< SimProcessNode >	node,
		double	rate,
		SiteSimulationResult *	ssr = `nullptr`
	)		const

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 380 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References bpp::SiteSimulationResult::addNode(), bpp::AbstractMutationProcess::detailedEvolve(), evolveInternal(), bpp::MutationPath::getFinalState(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getOutgoingEdges(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSon(), bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), nbStates_, phyloTree_, bpp::RandomTools::pickFromCumSum(), process_, speciesNodes_, bpp::TextTools::toString(), and tree_.

◆ evolveInternal() [2/2]

void SimpleSubstitutionProcessSiteSimulator::evolveInternal	(	std::shared_ptr< SimProcessNode >	node,
		size_t	rateClass,
		SiteSimulationResult *	ssr = `nullptr`
	)		const

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 313 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References bpp::SiteSimulationResult::addNode(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::MutationPath::getFinalState(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getOutgoingEdges(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSon(), phyloTree_, bpp::RandomTools::pickFromCumSum(), process_, speciesNodes_, bpp::TextTools::toString(), and tree_.

Referenced by dSimulateSite(), evolveInternal(), and simulateSite().

◆ getAlphabet()

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

inlineoverridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 205 of file SimpleSubstitutionProcessSiteSimulator.h.

References process_.

Referenced by simulateSite().

◆ getSequenceNames()

std::vector<std::string> bpp::SimpleSubstitutionProcessSiteSimulator::getSequenceNames ( ) const

inlineoverridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 193 of file SimpleSubstitutionProcessSiteSimulator.h.

References seqNames_.

◆ getSubstitutionProcess()

std::shared_ptr<const SubstitutionProcessInterface> bpp::SimpleSubstitutionProcessSiteSimulator::getSubstitutionProcess ( ) const

inline

Get the substitution process associated to this instance.

Returns: The substitution process associated to this instance.

Definition at line 231 of file SimpleSubstitutionProcessSiteSimulator.h.

References process_.

◆ getTree()

std::shared_ptr<const ParametrizablePhyloTree> bpp::SimpleSubstitutionProcessSiteSimulator::getTree ( ) const

inline

Get the tree associated to this instance.

Returns: The Tree object associated to this instance.

Definition at line 241 of file SimpleSubstitutionProcessSiteSimulator.h.

References phyloTree_.

◆ init()

void SimpleSubstitutionProcessSiteSimulator::init ( )

privatevirtual

Init all probabilities.

Method called by constructors.

Reimplemented in bpp::GivenDataSubstitutionProcessSiteSimulator.

Definition at line 43 of file SimpleSubstitutionProcessSiteSimulator.cpp.

References bpp::VectorTools::cumSum(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllEdges(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllNodes(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getOutgoingEdges(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSon(), nbClasses_, nbStates_, outputInternalSites(), outputInternalSites_, phyloTree_, process_, qRates_, qRoots_, bpp::Matrix< class >::resize(), bpp::VectorTools::sum(), bpp::TextTools::toString(), and tree_.

Referenced by SimpleSubstitutionProcessSiteSimulator().

◆ operator=()

SimpleSubstitutionProcessSiteSimulator& bpp::SimpleSubstitutionProcessSiteSimulator::operator= ( const SimpleSubstitutionProcessSiteSimulator & nhss )

inline

Definition at line 146 of file SimpleSubstitutionProcessSiteSimulator.h.

References continuousRates_, nbClasses_, nbNodes_, nbStates_, outputInternalSites_, phyloTree_, process_, qRates_, qRoots_, seqIndexes_, seqNames_, speciesNodes_, and tree_.