(Legacy) Site and sequences simulation under non-homogeneous models. More...

#include <Bpp/Phyl/Legacy/Simulation/NonHomogeneousSequenceSimulator.h>

Inheritance diagram for bpp::NonHomogeneousSequenceSimulator:

Collaboration diagram for bpp::NonHomogeneousSequenceSimulator:

Public Member Functions
std::shared_ptr< const SubstitutionModelSet >	getSubstitutionModelSet () const
	Get the substitution model associated to this instance. More...

const SubstitutionModelSet &	substitutionModelSet () const
	Get the substitution model associated to this instance. More...

std::shared_ptr< const DiscreteDistributionInterface >	getRateDistribution () const
	Get the rate distribution associated to this instance. More...

const DiscreteDistributionInterface &	rateDistribution () const
	Get the rate distribution associated to this instance. More...

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

const Tree &	tree () 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	outputInternalSequences (bool yn) override
	Sets whether we will output the internal sequences or not. More...

void	outputInternalSites (bool yn) override

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

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

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

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

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

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

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

The SequenceSimulator interface
std::unique_ptr< SiteContainerInterface >	simulate (size_t numberOfSites) const override

const SiteSimulatorInterface &	siteSimulator (size_t pos) const override

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

const Alphabet &	alphabet () const override

Functions with rate classes instead of absolute rates.
virtual std::unique_ptr< Site >	simulateSite (size_t ancestralStateIndex, size_t rateClass) const

virtual std::unique_ptr< SiteSimulationResult >	dSimulateSite (size_t ancestralStateIndex, size_t rateClass) 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...

std::unique_ptr< SiteContainerInterface >	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

Private Attributes
std::shared_ptr< const SubstitutionModelSet >	modelSet_

std::shared_ptr< const Alphabet >	alphabet_

std::vector< int >	supportedStates_

std::shared_ptr< const DiscreteDistributionInterface >	rate_

std::shared_ptr< const Tree >	templateTree_

TreeTemplate< SNode >	tree_

std::shared_ptr< const ParametrizablePhyloTree >	phyloTree_

std::vector< SNode * >	leaves_
	This stores once for all all leaves in a given order. This order will be used during site creation. More...

std::vector< std::string >	seqNames_

size_t	nbNodes_

size_t	nbClasses_

size_t	nbStates_

bool	continuousRates_

bool	outputInternalSequences_

Stores intermediate results.
	NonHomogeneousSequenceSimulator (std::shared_ptr< const SubstitutionModelSet > modelSet, std::shared_ptr< const DiscreteDistributionInterface > rate, std::shared_ptr< const Tree > tree)

	NonHomogeneousSequenceSimulator (std::shared_ptr< const TransitionModelInterface > model, std::shared_ptr< const DiscreteDistributionInterface > rate, std::shared_ptr< const Tree > tree)

virtual	~NonHomogeneousSequenceSimulator ()

	NonHomogeneousSequenceSimulator (const NonHomogeneousSequenceSimulator &nhss)=default

NonHomogeneousSequenceSimulator &	operator= (const NonHomogeneousSequenceSimulator &nhss)=default

NonHomogeneousSequenceSimulator *	clone () const override

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

Detailed Description

(Legacy) Site and sequences simulation under non-homogeneous models.

Former class maintained for backward compatibility only. The old class has been ported to the new interfaces, but some methods are left unimplemented.

Rate across sites variation is supported, using a DiscreteDistribution object or by specifying explicitly the rate of the sites to simulate.

Definition at line 62 of file NonHomogeneousSequenceSimulator.h.

Constructor & Destructor Documentation

◆ NonHomogeneousSequenceSimulator() [1/3]

NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator	(	std::shared_ptr< const SubstitutionModelSet >	modelSet,
		std::shared_ptr< const DiscreteDistributionInterface >	rate,
		std::shared_ptr< const Tree >	tree
	)

Definition at line 22 of file NonHomogeneousSequenceSimulator.cpp.

References init(), and tree().

Referenced by clone().

◆ NonHomogeneousSequenceSimulator() [2/3]

NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator	(	std::shared_ptr< const TransitionModelInterface >	model,
		std::shared_ptr< const DiscreteDistributionInterface >	rate,
		std::shared_ptr< const Tree >	tree
	)

Definition at line 48 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::SubstitutionModelSetTools::createHomogeneousModelSet(), init(), modelSet_, and templateTree_.

◆ ~NonHomogeneousSequenceSimulator()

virtual bpp::NonHomogeneousSequenceSimulator::~NonHomogeneousSequenceSimulator ( )

inlinevirtual

Definition at line 111 of file NonHomogeneousSequenceSimulator.h.

◆ NonHomogeneousSequenceSimulator() [3/3]

bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator ( const NonHomogeneousSequenceSimulator & nhss )

default

Member Function Documentation

◆ alphabet()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 182 of file NonHomogeneousSequenceSimulator.h.

References alphabet_.

◆ clone()

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

inlineoverridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 117 of file NonHomogeneousSequenceSimulator.h.

References NonHomogeneousSequenceSimulator().

◆ dEvolve()

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

protected

Definition at line 585 of file NonHomogeneousSequenceSimulator.cpp.

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

Referenced by dSimulateSite().

◆ dEvolveInternal()

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

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 598 of file NonHomogeneousSequenceSimulator.cpp.

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

Referenced by dEvolve().

◆ dSimulateSite() [1/5]

std::unique_ptr< SiteSimulationResult > NonHomogeneousSequenceSimulator::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 332 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), modelSet_, and nbStates_.

Referenced by dSimulateSite().

◆ dSimulateSite() [2/5]

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

overridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 389 of file NonHomogeneousSequenceSimulator.cpp.

References dSimulateSite(), bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), modelSet_, and nbStates_.

◆ dSimulateSite() [3/5]

std::unique_ptr< SiteSimulationResult > NonHomogeneousSequenceSimulator::dSimulateSite ( size_t ancestralStateIndex ) const

overridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 354 of file NonHomogeneousSequenceSimulator.cpp.

References continuousRates_, dSimulateSite(), and rate_.

◆ dSimulateSite() [4/5]

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

overridevirtual

Implements bpp::DetailedSiteSimulatorInterface.

Definition at line 372 of file NonHomogeneousSequenceSimulator.cpp.

References dEvolve(), modelSet_, and phyloTree_.

◆ dSimulateSite() [5/5]

unique_ptr< SiteSimulationResult > NonHomogeneousSequenceSimulator::dSimulateSite	(	size_t	ancestralStateIndex,
		size_t	rateClass
	)		const

virtual

Definition at line 382 of file NonHomogeneousSequenceSimulator.cpp.

References dSimulateSite(), and rate_.

◆ enableContinuousRates()

void bpp::NonHomogeneousSequenceSimulator::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.

Parameters

yn	Tell if we should use continuous rates.

Definition at line 243 of file NonHomogeneousSequenceSimulator.h.

References continuousRates_.

◆ evolve() [1/2]

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

protected

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 424 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::Node::getDistanceToFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), nbStates_, bpp::MatrixTools::print(), and bpp::TextTools::toString().

◆ evolve() [2/2]

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

protected

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 410 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), nbStates_, and bpp::TextTools::toString().

Referenced by evolveInternal().

◆ evolveInternal() [1/2]

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

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 482 of file NonHomogeneousSequenceSimulator.cpp.

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

◆ evolveInternal() [2/2]

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

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 466 of file NonHomogeneousSequenceSimulator.cpp.

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

Referenced by evolveInternal(), and simulateSite().

◆ getAlphabet()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 180 of file NonHomogeneousSequenceSimulator.h.

References alphabet_.

◆ getRateDistribution()

std::shared_ptr<const DiscreteDistributionInterface> bpp::NonHomogeneousSequenceSimulator::getRateDistribution ( ) const

inline

Get the rate distribution associated to this instance.

Returns: The DiscreteDistribution object associated to this instance.

Definition at line 213 of file NonHomogeneousSequenceSimulator.h.

References rate_.

◆ getSequenceNames()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 144 of file NonHomogeneousSequenceSimulator.h.

References seqNames_.

◆ getSubstitutionModelSet()

std::shared_ptr<const SubstitutionModelSet> bpp::NonHomogeneousSequenceSimulator::getSubstitutionModelSet ( ) const

inline

Get the substitution model associated to this instance.

Returns: The substitution model associated to this instance.

Definition at line 199 of file NonHomogeneousSequenceSimulator.h.

References modelSet_.

◆ getTree()

std::shared_ptr<const Tree> bpp::NonHomogeneousSequenceSimulator::getTree ( ) const

inline

Get the tree associated to this instance.

Returns: The Tree object associated to this instance.

Definition at line 227 of file NonHomogeneousSequenceSimulator.h.

References templateTree_.

◆ init()

void NonHomogeneousSequenceSimulator::init ( )

private

Init all probabilities.

Method called by constructors.

Definition at line 75 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getId(), bpp::NodeTemplate< NodeInfos >::getInfos(), leaves_, modelSet_, nbClasses_, nbNodes_, nbStates_, outputInternalSequences_, rate_, seqNames_, bpp::TextTools::toString(), and tree_.

Referenced by NonHomogeneousSequenceSimulator().

◆ 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

protected

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 442 of file NonHomogeneousSequenceSimulator.cpp.

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

Referenced by multipleEvolveInternal(), and simulate().

◆ multipleEvolve() [2/2]

unique_ptr< SiteContainerInterface > NonHomogeneousSequenceSimulator::multipleEvolve	(	const std::vector< size_t > &	initialStates,
		const std::vector< size_t > &	rateClasses
	)		const

protected

Definition at line 517 of file NonHomogeneousSequenceSimulator.cpp.

References alphabet_, bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), leaves_, multipleEvolveInternal(), nbNodes_, outputInternalSequences_, bpp::TextTools::toString(), and tree_.

◆ multipleEvolveInternal()

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

protected

This method uses the multipleStates_ variable for saving ancestral states.

Definition at line 498 of file NonHomogeneousSequenceSimulator.cpp.

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

Referenced by multipleEvolve().

◆ operator=()

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

default

◆ outputInternalSequences()

void NonHomogeneousSequenceSimulator::outputInternalSequences ( bool yn )

overridevirtual

Sets whether we will output the internal sequences or not.

Parameters

yn	Tell if we should output internal sequences.

Implements bpp::SequenceSimulatorInterface.

Definition at line 626 of file NonHomogeneousSequenceSimulator.cpp.

References leaves_, outputInternalSequences_, seqNames_, bpp::TextTools::toString(), and tree_.

◆ outputInternalSites()

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

inlineoverridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 252 of file NonHomogeneousSequenceSimulator.h.

◆ rateDistribution()

const DiscreteDistributionInterface& bpp::NonHomogeneousSequenceSimulator::rateDistribution ( ) const

inline

Get the rate distribution associated to this instance.

Returns: The DiscreteDistribution object associated to this instance.

Definition at line 220 of file NonHomogeneousSequenceSimulator.h.

References rate_.

◆ simulate()

unique_ptr< SiteContainerInterface > NonHomogeneousSequenceSimulator::simulate ( size_t numberOfSites ) const

overridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 285 of file NonHomogeneousSequenceSimulator.cpp.

References alphabet_, continuousRates_, bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), modelSet_, multipleEvolve(), nbStates_, rate_, seqNames_, and simulateSite().

◆ simulateSite() [1/5]

unique_ptr< Site > NonHomogeneousSequenceSimulator::simulateSite ( ) const

overridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 134 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), modelSet_, and nbStates_.

Referenced by simulate(), and simulateSite().

◆ simulateSite() [2/5]

unique_ptr< Site > NonHomogeneousSequenceSimulator::simulateSite ( double rate ) const

overridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 263 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), modelSet_, nbStates_, and simulateSite().

◆ simulateSite() [3/5]

unique_ptr< Site > NonHomogeneousSequenceSimulator::simulateSite ( size_t ancestralStateIndex ) const

overridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 155 of file NonHomogeneousSequenceSimulator.cpp.

References continuousRates_, rate_, and simulateSite().

◆ simulateSite() [4/5]

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

overridevirtual

Implements bpp::SiteSimulatorInterface.

Definition at line 219 of file NonHomogeneousSequenceSimulator.cpp.

References alphabet_, evolveInternal(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), leaves_, nbNodes_, outputInternalSequences_, and tree_.

◆ simulateSite() [5/5]

std::unique_ptr< Site > NonHomogeneousSequenceSimulator::simulateSite	(	size_t	ancestralStateIndex,
		size_t	rateClass
	)		const

virtual

Definition at line 175 of file NonHomogeneousSequenceSimulator.cpp.

References alphabet_, evolveInternal(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), leaves_, nbNodes_, outputInternalSequences_, and tree_.

◆ siteSimulator()

const SiteSimulatorInterface& bpp::NonHomogeneousSequenceSimulator::siteSimulator ( size_t pos ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 169 of file NonHomogeneousSequenceSimulator.h.

◆ substitutionModelSet()

const SubstitutionModelSet& bpp::NonHomogeneousSequenceSimulator::substitutionModelSet ( ) const

inline

Get the substitution model associated to this instance.

Returns: The substitution model associated to this instance.

Definition at line 206 of file NonHomogeneousSequenceSimulator.h.

References modelSet_.

◆ tree()

const Tree& bpp::NonHomogeneousSequenceSimulator::tree ( ) const

inline

Get the tree associated to this instance.

Returns: The Tree object associated to this instance.

Definition at line 234 of file NonHomogeneousSequenceSimulator.h.

References templateTree_.

Referenced by NonHomogeneousSequenceSimulator().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::NonHomogeneousSequenceSimulator::alphabet_

mutableprivate

Definition at line 68 of file NonHomogeneousSequenceSimulator.h.

Referenced by alphabet(), getAlphabet(), multipleEvolve(), simulate(), and simulateSite().

◆ continuousRates_

bool bpp::NonHomogeneousSequenceSimulator::continuousRates_

private

Definition at line 87 of file NonHomogeneousSequenceSimulator.h.

Referenced by dSimulateSite(), enableContinuousRates(), simulate(), and simulateSite().

◆ leaves_

std::vector<SNode*> bpp::NonHomogeneousSequenceSimulator::leaves_

private

This stores once for all all leaves in a given order. This order will be used during site creation.

Definition at line 79 of file NonHomogeneousSequenceSimulator.h.

Referenced by init(), multipleEvolve(), outputInternalSequences(), and simulateSite().

◆ modelSet_

std::shared_ptr<const SubstitutionModelSet> bpp::NonHomogeneousSequenceSimulator::modelSet_

private

Definition at line 67 of file NonHomogeneousSequenceSimulator.h.

Referenced by dSimulateSite(), getSubstitutionModelSet(), init(), NonHomogeneousSequenceSimulator(), simulate(), simulateSite(), and substitutionModelSet().

◆ nbClasses_

size_t bpp::NonHomogeneousSequenceSimulator::nbClasses_

private

Definition at line 84 of file NonHomogeneousSequenceSimulator.h.

Referenced by init().

◆ nbNodes_

size_t bpp::NonHomogeneousSequenceSimulator::nbNodes_

private

Definition at line 83 of file NonHomogeneousSequenceSimulator.h.

Referenced by init(), multipleEvolve(), and simulateSite().

◆ nbStates_

size_t bpp::NonHomogeneousSequenceSimulator::nbStates_

private

Definition at line 85 of file NonHomogeneousSequenceSimulator.h.

Referenced by dSimulateSite(), evolve(), init(), multipleEvolve(), simulate(), and simulateSite().

◆ outputInternalSequences_

bool bpp::NonHomogeneousSequenceSimulator::outputInternalSequences_

private

Definition at line 90 of file NonHomogeneousSequenceSimulator.h.

Referenced by init(), multipleEvolve(), outputInternalSequences(), and simulateSite().

◆ phyloTree_

std::shared_ptr<const ParametrizablePhyloTree> bpp::NonHomogeneousSequenceSimulator::phyloTree_

mutableprivate

Definition at line 73 of file NonHomogeneousSequenceSimulator.h.

Referenced by dSimulateSite().

◆ rate_

std::shared_ptr<const DiscreteDistributionInterface> bpp::NonHomogeneousSequenceSimulator::rate_

private

Definition at line 70 of file NonHomogeneousSequenceSimulator.h.

Referenced by dSimulateSite(), getRateDistribution(), init(), rateDistribution(), simulate(), and simulateSite().

◆ seqNames_

std::vector<std::string> bpp::NonHomogeneousSequenceSimulator::seqNames_

private

Definition at line 81 of file NonHomogeneousSequenceSimulator.h.

Referenced by getSequenceNames(), init(), outputInternalSequences(), and simulate().

◆ supportedStates_

std::vector<int> bpp::NonHomogeneousSequenceSimulator::supportedStates_

private

Definition at line 69 of file NonHomogeneousSequenceSimulator.h.

◆ templateTree_

std::shared_ptr<const Tree> bpp::NonHomogeneousSequenceSimulator::templateTree_

private

Definition at line 71 of file NonHomogeneousSequenceSimulator.h.

Referenced by getTree(), NonHomogeneousSequenceSimulator(), and tree().

◆ tree_

TreeTemplate<SNode> bpp::NonHomogeneousSequenceSimulator::tree_

mutableprivate

Definition at line 72 of file NonHomogeneousSequenceSimulator.h.

Referenced by dEvolve(), init(), multipleEvolve(), outputInternalSequences(), and simulateSite().

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

Bpp/Phyl/Legacy/Simulation/NonHomogeneousSequenceSimulator.h
Bpp/Phyl/Legacy/Simulation/NonHomogeneousSequenceSimulator.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Stores intermediate results.

Detailed Description

Constructor & Destructor Documentation

◆ NonHomogeneousSequenceSimulator() [1/3]

◆ NonHomogeneousSequenceSimulator() [2/3]

◆ ~NonHomogeneousSequenceSimulator()

◆ NonHomogeneousSequenceSimulator() [3/3]

Member Function Documentation

◆ alphabet()

◆ clone()

◆ dEvolve()

◆ dEvolveInternal()

◆ dSimulateSite() [1/5]

◆ dSimulateSite() [2/5]

◆ dSimulateSite() [3/5]

◆ dSimulateSite() [4/5]

◆ dSimulateSite() [5/5]

◆ enableContinuousRates()

◆ evolve() [1/2]

◆ evolve() [2/2]

◆ evolveInternal() [1/2]

◆ evolveInternal() [2/2]

◆ getAlphabet()

◆ getRateDistribution()

◆ getSequenceNames()

◆ getSubstitutionModelSet()

◆ getTree()

◆ init()

◆ multipleEvolve() [1/2]

◆ multipleEvolve() [2/2]

◆ multipleEvolveInternal()

◆ operator=()

◆ outputInternalSequences()

◆ outputInternalSites()

◆ rateDistribution()

◆ simulate()

◆ simulateSite() [1/5]

◆ simulateSite() [2/5]

◆ simulateSite() [3/5]

◆ simulateSite() [4/5]

◆ simulateSite() [5/5]

◆ siteSimulator()

◆ substitutionModelSet()

◆ tree()

Member Data Documentation

◆ alphabet_

◆ continuousRates_

◆ leaves_

◆ modelSet_

◆ nbClasses_

◆ nbNodes_

◆ nbStates_

◆ outputInternalSequences_

◆ phyloTree_

◆ rate_

◆ seqNames_

◆ supportedStates_

◆ templateTree_

◆ tree_