Site and sequences simulation under homogeneous models. More...

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

Inheritance diagram for bpp::HomogeneousSequenceSimulator:

Collaboration diagram for bpp::HomogeneousSequenceSimulator:

Public Member Functions
	HomogeneousSequenceSimulator (const SubstitutionModel model, const DiscreteDistribution rate, const Tree *tree)

virtual	~HomogeneousSequenceSimulator ()

const SubstitutionModel *	getSubstitutionModel () const

const SubstitutionModelSet *	getSubstitutionModelSet () const
	Get the substitution model associated to this instance. More...

const DiscreteDistribution *	getRateDistribution () const
	Get the rate distribution associated to this instance. More...

const Tree *	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...

Stores intermediate results.
NonHomogeneousSequenceSimulator *	clone () const

The SiteSimulator interface
Site *	simulateSite () const

Site *	simulateSite (size_t ancestralStateIndex) const

Site *	simulateSite (size_t ancestralStateIndex, double rate) const

Site *	simulateSite (double rate) const

std::vector< std::string >	getSequencesNames () const

Functions with rate classes instead of absolute rates.
virtual Site *	simulateSite (size_t ancestralStateIndex, size_t rateClass) const

virtual RASiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex, size_t rateClass) const

The DetailedSiteSimulator interface.
RASiteSimulationResult *	dSimulateSite () const
	Get a detailed simulation result for one site. More...

RASiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex) const

RASiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex, double rate) const

RASiteSimulationResult *	dSimulateSite (double rate) const

The SequenceSimulator interface
SiteContainer *	simulate (size_t numberOfSites) const

SiteSimulator and SequenceSimulator interface
const Alphabet *	getAlphabet () const

Protected Member Functions
size_t	evolve (const SNode *node, size_t initialStateIndex, size_t rateClass) const
	Evolve from an initial state along a branch, knowing the evolutionary rate class. More...

size_t	evolve (const SNode *node, size_t initialStateIndex, double rate) const
	Evolve from an initial state along a branch, knowing the evolutionary rate. More...

void	multipleEvolve (const SNode *node, const std::vector< size_t > &initialStateIndices, const std::vector< size_t > &rateClasses, std::vector< size_t > &finalStates) const
	The same as the evolve(initialState, rateClass) function, but for several sites at a time. More...

SiteContainer *	multipleEvolve (const std::vector< size_t > &initialStates, const std::vector< size_t > &rateClasses) const

void	dEvolve (size_t initialState, double rate, RASiteSimulationResult &rassr) const

The 'Internal' methods.
void	evolveInternal (SNode *node, size_t rateClass) const

void	evolveInternal (SNode *node, double rate) const

void	multipleEvolveInternal (SNode *node, const std::vector< size_t > &rateClasses) const

void	dEvolveInternal (SNode *node, double rate, RASiteSimulationResult &rassr) const

Detailed Description

Site and sequences simulation under homogeneous models.

This is an alias class, for clarity and backward compatibility.

Definition at line 53 of file HomogeneousSequenceSimulator.h.

Constructor & Destructor Documentation

◆ HomogeneousSequenceSimulator()

bpp::HomogeneousSequenceSimulator::HomogeneousSequenceSimulator	(	const SubstitutionModel *	model,
		const DiscreteDistribution *	rate,
		const Tree *	tree
	)

inline

Definition at line 58 of file HomogeneousSequenceSimulator.h.

◆ ~HomogeneousSequenceSimulator()

virtual bpp::HomogeneousSequenceSimulator::~HomogeneousSequenceSimulator ( )

inlinevirtual

Definition at line 64 of file HomogeneousSequenceSimulator.h.

Member Function Documentation

◆ clone()

NonHomogeneousSequenceSimulator* bpp::NonHomogeneousSequenceSimulator::clone ( ) const

inlinevirtualinherited

Implements bpp::SequenceSimulator.

Definition at line 185 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().

◆ dEvolve()

void NonHomogeneousSequenceSimulator::dEvolve	(	size_t	initialState,
		double	rate,
		RASiteSimulationResult &	rassr
	)		const

protectedinherited

Definition at line 515 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::NonHomogeneousSequenceSimulator::tree_.

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

◆ dEvolveInternal()

void NonHomogeneousSequenceSimulator::dEvolveInternal	(	SNode *	node,
		double	rate,
		RASiteSimulationResult &	rassr
	)		const

protectedinherited

This method uses the states_ variable for saving ancestral states.

Definition at line 528 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::SiteSimulationResult::addNode(), bpp::Node::getDistanceToFather(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::Node::getId(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::Node::hasFather().

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

◆ dSimulateSite() [1/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite ( ) const

virtualinherited

Get a detailed simulation result for one site.

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

Implements bpp::DetailedSiteSimulator.

Definition at line 300 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::SubstitutionModelSet::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::modelSet_, and bpp::NonHomogeneousSequenceSimulator::nbStates_.

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

◆ dSimulateSite() [2/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite ( size_t ancestralStateIndex ) const

virtualinherited

Implements bpp::DetailedSiteSimulator.

Definition at line 322 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::continuousRates_, bpp::NonHomogeneousSequenceSimulator::dSimulateSite(), and bpp::NonHomogeneousSequenceSimulator::rate_.

◆ dSimulateSite() [3/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite	(	size_t	ancestralStateIndex,
		double	rate
	)		const

virtualinherited

Implements bpp::DetailedSiteSimulator.

Definition at line 340 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::dEvolve(), bpp::SubstitutionModelSet::getAlphabet(), bpp::NonHomogeneousSequenceSimulator::modelSet_, and bpp::NonHomogeneousSequenceSimulator::templateTree_.

◆ dSimulateSite() [4/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite ( double rate ) const

virtualinherited

Implements bpp::DetailedSiteSimulator.

Definition at line 357 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::dSimulateSite(), bpp::SubstitutionModelSet::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::modelSet_, and bpp::NonHomogeneousSequenceSimulator::nbStates_.

◆ dSimulateSite() [5/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite	(	size_t	ancestralStateIndex,
		size_t	rateClass
	)		const

virtualinherited

Definition at line 350 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::dSimulateSite(), and bpp::NonHomogeneousSequenceSimulator::rate_.

◆ enableContinuousRates()

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

inlineinherited

Enable the use of continuous rates instead of discrete rates.

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

Parameters

yn	Tell if we should use continuous rates.

Definition at line 280 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::continuousRates_.

◆ evolve() [1/2]

size_t NonHomogeneousSequenceSimulator::evolve	(	const SNode *	node,
		size_t	initialStateIndex,
		size_t	rateClass
	)		const

protectedinherited

Evolve from an initial state along a branch, knowing the evolutionary rate class.

This method is fast since all pijt have been computed in the constructor of the class. This method is used for the implementation of the SiteSimulator interface.

Definition at line 378 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NodeTemplate< NodeInfos >::getInfos(), and bpp::NonHomogeneousSequenceSimulator::nbStates_.

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

◆ evolve() [2/2]

size_t NonHomogeneousSequenceSimulator::evolve	(	const SNode *	node,
		size_t	initialStateIndex,
		double	rate
	)		const

protectedinherited

Evolve from an initial state along a branch, knowing the evolutionary rate.

This method is slower than the previous one since exponential terms must be computed. This method is used for the implementation of the SiteSimulator interface.

Definition at line 391 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::Node::getDistanceToFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::SubstitutionModel::getPij_t(), bpp::NonHomogeneousSequenceSimulator::nbStates_, and bpp::SubstitutionModel::Pij_t().

◆ evolveInternal() [1/2]

void NonHomogeneousSequenceSimulator::evolveInternal	(	SNode *	node,
		size_t	rateClass
	)		const

protectedinherited

This method uses the states_ variable for saving ancestral states.

Definition at line 432 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::Node::hasFather().

Referenced by bpp::NonHomogeneousSequenceSimulator::evolveInternal(), and bpp::NonHomogeneousSequenceSimulator::simulateSite().

◆ evolveInternal() [2/2]

void NonHomogeneousSequenceSimulator::evolveInternal	(	SNode *	node,
		double	rate
	)		const

protectedinherited

This method uses the states_ variable for saving ancestral states.

Definition at line 448 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::Node::hasFather().

◆ getAlphabet()

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

inlinevirtualinherited

Implements bpp::SequenceSimulator.

Definition at line 240 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::alphabet_.

◆ getRateDistribution()

const DiscreteDistribution* bpp::NonHomogeneousSequenceSimulator::getRateDistribution ( ) const

inlineinherited

Get the rate distribution associated to this instance.

Returns: The DiscreteDistribution object associated to this instance.

Definition at line 264 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::rate_.

◆ getSequencesNames()

std::vector<std::string> bpp::NonHomogeneousSequenceSimulator::getSequencesNames ( ) const

inlinevirtualinherited

Implements bpp::SiteSimulator.

Definition at line 210 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::seqNames_.

◆ getSubstitutionModel()

const SubstitutionModel* bpp::HomogeneousSequenceSimulator::getSubstitutionModel ( ) const

inline

Definition at line 67 of file HomogeneousSequenceSimulator.h.

References bpp::SubstitutionModelSet::getModel(), and bpp::NonHomogeneousSequenceSimulator::getSubstitutionModelSet().

◆ getSubstitutionModelSet()

const SubstitutionModelSet* bpp::NonHomogeneousSequenceSimulator::getSubstitutionModelSet ( ) const

inlineinherited

Get the substitution model associated to this instance.

Returns: The substitution model associated to this instance.

Definition at line 257 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::modelSet_.

Referenced by getSubstitutionModel().

◆ getTree()

const Tree* bpp::NonHomogeneousSequenceSimulator::getTree ( ) const

inlineinherited

Get the tree associated to this instance.

Returns: The Tree object associated to this instance.

Definition at line 271 of file NonHomogeneousSequenceSimulator.h.

References bpp::NonHomogeneousSequenceSimulator::templateTree_.

◆ multipleEvolve() [1/2]

void NonHomogeneousSequenceSimulator::multipleEvolve	(	const SNode *	node,
		const std::vector< size_t > &	initialStateIndices,
		const std::vector< size_t > &	rateClasses,
		std::vector< size_t > &	finalStates
	)		const

protectedinherited

The same as the evolve(initialState, rateClass) function, but for several sites at a time.

This method is used for the implementation of the SequenceSimulator interface.

Definition at line 408 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NodeTemplate< NodeInfos >::getInfos(), and bpp::NonHomogeneousSequenceSimulator::nbStates_.

Referenced by bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), and bpp::NonHomogeneousSequenceSimulator::simulate().

◆ multipleEvolve() [2/2]

SiteContainer * NonHomogeneousSequenceSimulator::multipleEvolve	(	const std::vector< size_t > &	initialStates,
		const std::vector< size_t > &	rateClasses
	)		const