Tools for sites and sequences simulation. More...

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

Public Member Functions
	SequenceSimulationTools ()

	~SequenceSimulationTools ()

Static Public Member Functions
static SiteContainer *	simulateSites (const SiteSimulator &simulator, const std::vector< double > &rates)
	Simulate a set of sites knowing their rate. More...

static SiteContainer *	simulateSites (const SiteSimulator &simulator, const std::vector< double > &rates, const std::vector< size_t > &states) throw (Exception)
	Simulate a set of sites knowing their rate and ancestral state. More...

static SiteContainer *	simulateSites (const SiteSimulator &simulator, const std::vector< size_t > &states) throw (Exception)
	Simulate a set of sites knowing ancestral state. More...

Detailed Description

Tools for sites and sequences simulation.

Definition at line 57 of file SequenceSimulationTools.h.

Constructor & Destructor Documentation

◆ SequenceSimulationTools()

bpp::SequenceSimulationTools::SequenceSimulationTools ( )

inline

Definition at line 60 of file SequenceSimulationTools.h.

◆ ~SequenceSimulationTools()

bpp::SequenceSimulationTools::~SequenceSimulationTools ( )

inline

Definition at line 61 of file SequenceSimulationTools.h.

Member Function Documentation

◆ simulateSites() [1/3]

SiteContainer * SequenceSimulationTools::simulateSites	(	const SiteSimulator &	simulator,
		const std::vector< double > &	rates
	)

static

Simulate a set of sites knowing their rate.

This method is rather slow. consider using a discrete rate distribution and a SequenceSimulator, which is realy faster. This method should be used only for continuous rate distribution, or as estimated from posterior rates for instance.

See also: SequenceSimulator

Parameters

simulator	A SiteSimulator object to use to simulate sites.
rates	the rates to use, one for each site to simulate.

Returns: A container with all simulated sites.

Definition at line 48 of file SequenceSimulationTools.cpp.

References bpp::SiteSimulator::getAlphabet(), bpp::SiteSimulator::getSequencesNames(), and bpp::SiteSimulator::simulateSite().

◆ simulateSites() [2/3]

SiteContainer * SequenceSimulationTools::simulateSites	(	const SiteSimulator &	simulator,
		const std::vector< double > &	rates,
		const std::vector< size_t > &	states
	)
throw	(	Exception
	)

static

Simulate a set of sites knowing their rate and ancestral state.

This method is rather slow. consider using a discrete rate distribution and a SequenceSimulator, which is realy faster. This method should be used only for continuous rate distribution, or as estimated from posterior rates for instance.

See also: SequenceSimulator

Parameters

simulator	A SiteSimulator object to use to simulate sites.
rates	the rates to use, one for each site to simulate.
states	the ancestral states to use, one for each site to simulate.