bpp::SimpleSubstitutionProcessSequenceSimulator Class Reference

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)
	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  )

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 40 of file SimpleSubstitutionProcessSequenceSimulator.h.

~SimpleSubstitutionProcessSequenceSimulator()

virtual bpp::SimpleSubstitutionProcessSequenceSimulator::~SimpleSubstitutionProcessSequenceSimulator ( )

inlinevirtual

Definition at line 44 of file SimpleSubstitutionProcessSequenceSimulator.h.

SimpleSubstitutionProcessSequenceSimulator() [4/4]

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

inline

Definition at line 46 of file SimpleSubstitutionProcessSequenceSimulator.h.

Member Function Documentation

alphabet()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 84 of file SimpleSubstitutionProcessSequenceSimulator.h.

References siteSim_.

clone()

SimpleSubstitutionProcessSequenceSimulator* bpp::SimpleSubstitutionProcessSequenceSimulator::clone ( ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 50 of file SimpleSubstitutionProcessSequenceSimulator.h.

References SimpleSubstitutionProcessSequenceSimulator().

getAlphabet()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 82 of file SimpleSubstitutionProcessSequenceSimulator.h.

References siteSim_.

getSequenceNames()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 70 of file SimpleSubstitutionProcessSequenceSimulator.h.

References siteSim_.

outputInternalSequences()

void bpp::SimpleSubstitutionProcessSequenceSimulator::outputInternalSequences ( bool  yn )

inlineoverridevirtual

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 93 of file SimpleSubstitutionProcessSequenceSimulator.h.

References siteSim_.

simulate()

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

overridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 15 of file SimpleSubstitutionProcessSequenceSimulator.cpp.

siteSimulator()

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

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 65 of file SimpleSubstitutionProcessSequenceSimulator.h.

References siteSim_.

Member Data Documentation

siteSim_

std::shared_ptr<SiteSimulatorInterface> bpp::SimpleSubstitutionProcessSequenceSimulator::siteSim_

private

Definition at line 24 of file SimpleSubstitutionProcessSequenceSimulator.h.

Referenced by alphabet(), getAlphabet(), getSequenceNames(), outputInternalSequences(), and siteSimulator().

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

• Bpp/Phyl/Simulation/SimpleSubstitutionProcessSequenceSimulator.h
• Bpp/Phyl/Simulation/SimpleSubstitutionProcessSequenceSimulator.cpp