bpp::SequenceSimulatorInterface Class Reference

The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets. More...

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

Inheritance diagram for bpp::SequenceSimulatorInterface:

Collaboration diagram for bpp::SequenceSimulatorInterface:

Public Member Functions
	SequenceSimulatorInterface ()
virtual	~SequenceSimulatorInterface ()
SequenceSimulatorInterface *	clone () const override=0
virtual std::unique_ptr< SiteContainerInterface >	simulate (size_t numberOfSites) const =0
virtual const SiteSimulatorInterface &	siteSimulator (size_t pos) const =0
virtual std::vector< std::string >	getSequenceNames () const =0
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
virtual const Alphabet &	alphabet () const =0
virtual void	outputInternalSequences (bool inter)=0

Detailed Description

The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets.

Definition at line 23 of file SequenceSimulator.h.

Constructor & Destructor Documentation

SequenceSimulatorInterface()

bpp::SequenceSimulatorInterface::SequenceSimulatorInterface ( )

inline

Definition at line 27 of file SequenceSimulator.h.

~SequenceSimulatorInterface()

virtual bpp::SequenceSimulatorInterface::~SequenceSimulatorInterface ( )

inlinevirtual

Definition at line 28 of file SequenceSimulator.h.

Member Function Documentation

alphabet()

virtual const Alphabet & bpp::SequenceSimulatorInterface::alphabet ( ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

clone()

SequenceSimulatorInterface * bpp::SequenceSimulatorInterface::clone ( ) const

overridepure virtual

Implements bpp::Clonable.

Implemented in bpp::EvolutionSequenceSimulator, bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

getAlphabet()

virtual std::shared_ptr< const Alphabet > bpp::SequenceSimulatorInterface::getAlphabet ( ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

Referenced by bpp::SequenceSimulationTools::simulateSites().

getSequenceNames()

virtual std::vector< std::string > bpp::SequenceSimulatorInterface::getSequenceNames ( ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

Referenced by bpp::SequenceSimulationTools::simulateSites().

outputInternalSequences()

virtual void bpp::SequenceSimulatorInterface::outputInternalSequences ( bool  inter )

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

simulate()

virtual std::unique_ptr< SiteContainerInterface > bpp::SequenceSimulatorInterface::simulate ( size_t  numberOfSites ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

siteSimulator()

virtual const SiteSimulatorInterface & bpp::SequenceSimulatorInterface::siteSimulator ( size_t  pos ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSequenceSimulator, and bpp::SubstitutionProcessSequenceSimulator.

Referenced by bpp::SequenceSimulationTools::simulateSites().

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

• Bpp/Phyl/Simulation/SequenceSimulator.h