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

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

Inheritance diagram for bpp::SimpleSubstitutionProcessSequenceSimulator:

Collaboration diagram for bpp::SimpleSubstitutionProcessSequenceSimulator:

Public Member Functions
	SimpleSubstitutionProcessSequenceSimulator (std::shared_ptr< const SubstitutionProcessInterface > process)

	SimpleSubstitutionProcessSequenceSimulator (std::shared_ptr< LikelihoodCalculationSingleProcess > calcul, size_t pos, bool shrunked=false, std::vector< uint > vPrior=std::vector< uint >())
	A posterior simulation, from a position in an alignment. More...

	SimpleSubstitutionProcessSequenceSimulator (std::shared_ptr< SiteSimulatorInterface > simul)

virtual	~SimpleSubstitutionProcessSequenceSimulator ()

	SimpleSubstitutionProcessSequenceSimulator (const SimpleSubstitutionProcessSequenceSimulator &nhss)

SimpleSubstitutionProcessSequenceSimulator *	clone () const override

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

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

const SiteSimulatorInterface &	siteSimulator (size_t pos) const override

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

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

const Alphabet &	alphabet () const override

Private Attributes
std::shared_ptr< SiteSimulatorInterface >	siteSim_

Detailed Description

Sequences simulation under a unique substitution process.

Definition at line 20 of file SimpleSubstitutionProcessSequenceSimulator.h.

Constructor & Destructor Documentation

◆ SimpleSubstitutionProcessSequenceSimulator() [1/4]

bpp::SimpleSubstitutionProcessSequenceSimulator::SimpleSubstitutionProcessSequenceSimulator ( std::shared_ptr< const SubstitutionProcessInterface > process )

inline

Definition at line 27 of file SimpleSubstitutionProcessSequenceSimulator.h.

Referenced by clone().

◆ SimpleSubstitutionProcessSequenceSimulator() [2/4]

bpp::SimpleSubstitutionProcessSequenceSimulator::SimpleSubstitutionProcessSequenceSimulator	(	std::shared_ptr< LikelihoodCalculationSingleProcess >	calcul,
		size_t	pos,
		bool	shrunked = `false`,
		std::vector< uint >	vPrior = `std::vector<uint>()`
	)

inline

A posterior simulation, from a position in an alignment.

Definition at line 34 of file SimpleSubstitutionProcessSequenceSimulator.h.

◆ SimpleSubstitutionProcessSequenceSimulator() [3/4]

bpp::SimpleSubstitutionProcessSequenceSimulator::SimpleSubstitutionProcessSequenceSimulator ( std::shared_ptr< SiteSimulatorInterface > simul )

inline

Definition at line 42 of file SimpleSubstitutionProcessSequenceSimulator.h.

◆ ~SimpleSubstitutionProcessSequenceSimulator()

virtual bpp::SimpleSubstitutionProcessSequenceSimulator::~SimpleSubstitutionProcessSequenceSimulator ( )

inlinevirtual

Definition at line 46 of file SimpleSubstitutionProcessSequenceSimulator.h.

◆ SimpleSubstitutionProcessSequenceSimulator() [4/4]

bpp::SimpleSubstitutionProcessSequenceSimulator::SimpleSubstitutionProcessSequenceSimulator ( const SimpleSubstitutionProcessSequenceSimulator & nhss )

inline

Definition at line 48 of file SimpleSubstitutionProcessSequenceSimulator.h.