bpp::SiteSimulatorInterface Class Reference

The SiteSimulator interface. SiteSimulator classes can simulate single sites. More...

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

Inheritance diagram for bpp::SiteSimulatorInterface:

Collaboration diagram for bpp::SiteSimulatorInterface:

Public Member Functions
	SiteSimulatorInterface ()
virtual	~SiteSimulatorInterface ()
SiteSimulatorInterface *	clone () const override=0
virtual std::unique_ptr< Site >	simulateSite () const =0
virtual std::unique_ptr< Site >	simulateSite (size_t rateClass) const =0
virtual std::unique_ptr< Site >	simulateSite (double rate) const =0
virtual std::unique_ptr< Site >	simulateSite (size_t ancestralStateIndex, double rate) 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	outputInternalSites (bool yn)=0

Detailed Description

The SiteSimulator interface. SiteSimulator classes can simulate single sites.

See also

SequenceSimulator interface for simulating whole sequence sets.

Definition at line 22 of file SiteSimulator.h.

Constructor & Destructor Documentation

SiteSimulatorInterface()

bpp::SiteSimulatorInterface::SiteSimulatorInterface ( )

inline

Definition at line 26 of file SiteSimulator.h.

~SiteSimulatorInterface()

virtual bpp::SiteSimulatorInterface::~SiteSimulatorInterface ( )

inlinevirtual

Definition at line 27 of file SiteSimulator.h.

Member Function Documentation

alphabet()

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

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

clone()

SiteSimulatorInterface* bpp::SiteSimulatorInterface::clone ( ) const

overridepure virtual

Implements bpp::Clonable.

Implemented in bpp::DetailedSiteSimulatorInterface, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::GivenDataSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

getAlphabet()

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

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

getSequenceNames()

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

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

outputInternalSites()

virtual void bpp::SiteSimulatorInterface::outputInternalSites ( bool  yn )

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

simulateSite() [1/4]

virtual std::unique_ptr<Site> bpp::SiteSimulatorInterface::simulateSite ( ) const

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

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

simulateSite() [2/4]

virtual std::unique_ptr<Site> bpp::SiteSimulatorInterface::simulateSite ( double  rate ) const

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

simulateSite() [3/4]

virtual std::unique_ptr<Site> bpp::SiteSimulatorInterface::simulateSite ( size_t  ancestralStateIndex, double  rate  ) const

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

simulateSite() [4/4]

virtual std::unique_ptr<Site> bpp::SiteSimulatorInterface::simulateSite ( size_t  rateClass ) const

pure virtual

Implemented in bpp::SimpleSubstitutionProcessSiteSimulator, and bpp::NonHomogeneousSequenceSimulator.

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

• Bpp/Phyl/Simulation/SiteSimulator.h