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

Inheritance diagram for bpp::EvolutionSequenceSimulator:

Collaboration diagram for bpp::EvolutionSequenceSimulator:

Public Member Functions
	EvolutionSequenceSimulator (const SequenceEvolution &evol)

virtual	~EvolutionSequenceSimulator ()

	EvolutionSequenceSimulator (const EvolutionSequenceSimulator &ess)

EvolutionSequenceSimulator &	operator= (const EvolutionSequenceSimulator &ess)

EvolutionSequenceSimulator *	clone () const

void	resetSiteSimulators (size_t numberOfSites) const
	Reset the succession of site simulators (useful in case of HMM). More...

const SiteSimulatorInterface &	siteSimulator (size_t pos) const override

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

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

void	setMap (std::vector< size_t > vMap)
	reset the set of processes. More...

size_t	getNumberOfSites () const
	the number of mapped sites. More...

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

std::unique_ptr< SiteContainerInterface >	simulate (const std::vector< double > &rates) const

std::unique_ptr< SiteContainerInterface >	simulate (const std::vector< size_t > &states) const

std::unique_ptr< SiteContainerInterface >	simulate (const std::vector< double > &rates, const std::vector< size_t > &states) const

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

const Alphabet &	alphabet () const override

Protected Attributes
std::map< size_t, std::shared_ptr< SiteSimulatorInterface > >	mProcess_
	the map of the process simulators. More...

std::vector< size_t >	vMap_
	The vector of the site specific process in mProcess_; is mutable because can be changed for each simulation (for ex in case of HMM). More...

std::vector< std::string >	seqNames_
	all processes trees must have at least the same sequence names as the first process of the map. More...

std::map< size_t, std::vector< size_t > >	mvPosNames_
	correspondence map of seqNames positions of the several trees. Reference is the tree of the first process of the map. More...

Private Attributes
const SequenceEvolution *	seqEvol_

Detailed Description

Definition at line 14 of file EvolutionSequenceSimulator.h.

Constructor & Destructor Documentation

◆ EvolutionSequenceSimulator() [1/2]

EvolutionSequenceSimulator::EvolutionSequenceSimulator ( const SequenceEvolution & evol )

Definition at line 19 of file EvolutionSequenceSimulator.cpp.

Referenced by clone().

◆ ~EvolutionSequenceSimulator()

virtual bpp::EvolutionSequenceSimulator::~EvolutionSequenceSimulator ( )

inlinevirtual

Definition at line 23 of file EvolutionSequenceSimulator.h.

◆ EvolutionSequenceSimulator() [2/2]

bpp::EvolutionSequenceSimulator::EvolutionSequenceSimulator ( const EvolutionSequenceSimulator & ess )

inline

Definition at line 26 of file EvolutionSequenceSimulator.h.

Member Function Documentation

◆ alphabet()

const Alphabet & SubstitutionProcessSequenceSimulator::alphabet ( ) const

overridevirtualinherited

Implements bpp::SequenceSimulatorInterface.

Definition at line 278 of file SubstitutionProcessSequenceSimulator.cpp.

References bpp::SubstitutionProcessSequenceSimulator::mProcess_.

◆ clone()

EvolutionSequenceSimulator* bpp::EvolutionSequenceSimulator::clone ( ) const

inlinevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 39 of file EvolutionSequenceSimulator.h.

References EvolutionSequenceSimulator().

◆ getAlphabet()

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

overridevirtualinherited

Implements bpp::SequenceSimulatorInterface.

Definition at line 268 of file SubstitutionProcessSequenceSimulator.cpp.

References bpp::SubstitutionProcessSequenceSimulator::mProcess_.

Referenced by bpp::SubstitutionProcessSequenceSimulator::simulate().

◆ getNumberOfSites()

size_t bpp::SubstitutionProcessSequenceSimulator::getNumberOfSites ( ) const

inlineinherited

the number of mapped sites.

Definition at line 91 of file SubstitutionProcessSequenceSimulator.h.

References bpp::SubstitutionProcessSequenceSimulator::vMap_.

◆ getSequenceNames()

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

inlineoverridevirtualinherited

Implements bpp::SequenceSimulatorInterface.

Definition at line 70 of file SubstitutionProcessSequenceSimulator.h.

References bpp::SubstitutionProcessSequenceSimulator::seqNames_.

◆ operator=()

EvolutionSequenceSimulator& bpp::EvolutionSequenceSimulator::operator= ( const EvolutionSequenceSimulator & ess )

inline

Definition at line 31 of file EvolutionSequenceSimulator.h.

References bpp::SubstitutionProcessSequenceSimulator::operator=(), and seqEvol_.

◆ outputInternalSequences()

void SubstitutionProcessSequenceSimulator::outputInternalSequences ( bool yn )

overridevirtualinherited

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 124 of file SubstitutionProcessSequenceSimulator.cpp.

References bpp::SubstitutionProcessSequenceSimulator::mProcess_.

◆ resetSiteSimulators()

void EvolutionSequenceSimulator::resetSiteSimulators ( size_t numberOfSites ) const

Reset the succession of site simulators (useful in case of HMM).

Definition at line 26 of file EvolutionSequenceSimulator.cpp.

References bpp::PartitionSequenceEvolution::getNumberOfSites(), bpp::RandomTools::getSample(), bpp::MixtureSequenceEvolution::getSubProcessProbabilities(), bpp::PartitionSequenceEvolution::getSubstitutionProcessNumber(), bpp::SequenceEvolution::getSubstitutionProcessNumbers(), bpp::OneProcessSequenceEvolution::getSubstitutionProcessNumbers(), bpp::AutoCorrelationSequenceEvolution::hmmTransitionMatrix(), bpp::HmmSequenceEvolution::hmmTransitionMatrix(), bpp::AbstractHmmTransitionMatrix::sample(), seqEvol_, and bpp::SubstitutionProcessSequenceSimulator::vMap_.

◆ setMap()

void SubstitutionProcessSequenceSimulator::setMap ( std::vector< size_t > vMap )

inherited

reset the set of processes.

Definition at line 134 of file SubstitutionProcessSequenceSimulator.cpp.

References bpp::SubstitutionProcessSequenceSimulator::mProcess_, bpp::TextTools::toString(), and bpp::SubstitutionProcessSequenceSimulator::vMap_.

Referenced by bpp::SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator().

◆ simulate() [1/4]

unique_ptr< SiteContainerInterface > SubstitutionProcessSequenceSimulator::simulate ( const std::vector< double > & rates ) const

inherited

Definition at line 178 of file SubstitutionProcessSequenceSimulator.cpp.

References bpp::SubstitutionProcessSequenceSimulator::getAlphabet(), bpp::SubstitutionProcessSequenceSimulator::mProcess_, bpp::SubstitutionProcessSequenceSimulator::mvPosNames_, bpp::SubstitutionProcessSequenceSimulator::seqNames_, and bpp::SubstitutionProcessSequenceSimulator::vMap_.

◆ simulate() [2/4]

unique_ptr< SiteContainerInterface > SubstitutionProcessSequenceSimulator::simulate	(	const std::vector< double > &	rates,
		const std::vector< size_t > &	states
	)		const