Sequences simulation under position specific substitution process. More...

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

Inheritance diagram for bpp::SubstitutionProcessSequenceSimulator:

Collaboration diagram for bpp::SubstitutionProcessSequenceSimulator:

Public Member Functions
	SubstitutionProcessSequenceSimulator (const SequenceEvolution &evol)

	SubstitutionProcessSequenceSimulator (const SubstitutionProcessSequenceSimulator &)

SubstitutionProcessSequenceSimulator &	operator= (const SubstitutionProcessSequenceSimulator &)

SubstitutionProcessSequenceSimulator *	clone () const override

virtual	~SubstitutionProcessSequenceSimulator ()

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...

Detailed Description

Sequences simulation under position specific substitution process.

Definition at line 20 of file SubstitutionProcessSequenceSimulator.h.

Constructor & Destructor Documentation

◆ SubstitutionProcessSequenceSimulator() [1/2]

SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator ( const SequenceEvolution & evol )

Definition at line 22 of file SubstitutionProcessSequenceSimulator.cpp.

References bpp::VectorTools::contains(), bpp::SubstitutionProcessInterface::getParametrizablePhyloTree(), bpp::SequenceEvolution::getSubstitutionProcess(), bpp::SequenceEvolution::getSubstitutionProcessNumbers(), mProcess_, mvPosNames_, seqNames_, setMap(), bpp::SequenceEvolution::substitutionProcess(), and bpp::VectorTools::which().

Referenced by clone().

◆ SubstitutionProcessSequenceSimulator() [2/2]

SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator ( const SubstitutionProcessSequenceSimulator & spss )

Definition at line 76 of file SubstitutionProcessSequenceSimulator.cpp.

References mProcess_.

◆ ~SubstitutionProcessSequenceSimulator()

virtual bpp::SubstitutionProcessSequenceSimulator::~SubstitutionProcessSequenceSimulator ( )

inlinevirtual

Definition at line 61 of file SubstitutionProcessSequenceSimulator.h.

Member Function Documentation

◆ alphabet()

const Alphabet & SubstitutionProcessSequenceSimulator::alphabet ( ) const

overridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 278 of file SubstitutionProcessSequenceSimulator.cpp.

References mProcess_.

◆ clone()

SubstitutionProcessSequenceSimulator* bpp::SubstitutionProcessSequenceSimulator::clone ( ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 59 of file SubstitutionProcessSequenceSimulator.h.

References SubstitutionProcessSequenceSimulator().

◆ getAlphabet()

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

overridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 268 of file SubstitutionProcessSequenceSimulator.cpp.

References mProcess_.

Referenced by simulate().

◆ getNumberOfSites()

size_t bpp::SubstitutionProcessSequenceSimulator::getNumberOfSites ( ) const

inline

the number of mapped sites.

Definition at line 91 of file SubstitutionProcessSequenceSimulator.h.

References vMap_.

◆ getSequenceNames()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 70 of file SubstitutionProcessSequenceSimulator.h.

References seqNames_.

◆ operator=()

SubstitutionProcessSequenceSimulator & SubstitutionProcessSequenceSimulator::operator= ( const SubstitutionProcessSequenceSimulator & spss )

Definition at line 98 of file SubstitutionProcessSequenceSimulator.cpp.

References mProcess_, mvPosNames_, seqNames_, and vMap_.

Referenced by bpp::EvolutionSequenceSimulator::operator=().

◆ outputInternalSequences()

void SubstitutionProcessSequenceSimulator::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 124 of file SubstitutionProcessSequenceSimulator.cpp.

References mProcess_.

◆ setMap()

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

reset the set of processes.

Definition at line 134 of file SubstitutionProcessSequenceSimulator.cpp.

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

Referenced by SubstitutionProcessSequenceSimulator().

◆ simulate() [1/4]

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

Definition at line 178 of file SubstitutionProcessSequenceSimulator.cpp.

References getAlphabet(), mProcess_, mvPosNames_, seqNames_, and vMap_.

◆ simulate() [2/4]

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