bpp-phyl3  3.0.0
Public Member Functions | List of all members
bpp::DetailedSiteSimulatorInterface Class Referenceabstract

This interface adds the dSimulate method to the SiteSimulator interface. More...

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

+ Inheritance diagram for bpp::DetailedSiteSimulatorInterface:
+ Collaboration diagram for bpp::DetailedSiteSimulatorInterface:

Public Member Functions

 DetailedSiteSimulatorInterface ()
 
virtual ~DetailedSiteSimulatorInterface ()
 
DetailedSiteSimulatorInterface * clone () const override=0
 
virtual std::unique_ptr< SiteSimulationResult > dSimulateSite () const =0
 Get a detailed simulation result for one site. More...
 
virtual std::unique_ptr< SiteSimulationResult > dSimulateSite (size_t rateClass) const =0
 
virtual std::unique_ptr< SiteSimulationResult > dSimulateSite (double rate) const =0
 
virtual std::unique_ptr< SiteSimulationResult > dSimulateSite (size_t ancestralStateIndex, double rate) const =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

This interface adds the dSimulate method to the SiteSimulator interface.

Instances of this class should be used when a detailed output of the simulation is needed.

Definition at line 216 of file DetailedSiteSimulator.h.

Constructor & Destructor Documentation

◆ DetailedSiteSimulatorInterface()

bpp::DetailedSiteSimulatorInterface::DetailedSiteSimulatorInterface ( )
inline

Definition at line 220 of file DetailedSiteSimulator.h.

◆ ~DetailedSiteSimulatorInterface()

virtual bpp::DetailedSiteSimulatorInterface::~DetailedSiteSimulatorInterface ( )
inlinevirtual

Definition at line 221 of file DetailedSiteSimulator.h.

Member Function Documentation

◆ alphabet()

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

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

◆ clone()

DetailedSiteSimulatorInterface* bpp::DetailedSiteSimulatorInterface::clone ( ) const
overridepure virtual

Implements bpp::SiteSimulatorInterface.

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

◆ dSimulateSite() [1/4]

virtual std::unique_ptr<SiteSimulationResult> bpp::DetailedSiteSimulatorInterface::dSimulateSite ( ) const
pure virtual

Get a detailed simulation result for one site.

Returns
A SiteSimulationResult object with all ancestral states for all nodes and branches.

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

◆ dSimulateSite() [2/4]

virtual std::unique_ptr<SiteSimulationResult> bpp::DetailedSiteSimulatorInterface::dSimulateSite ( double  rate) const
pure virtual

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

◆ dSimulateSite() [3/4]

virtual std::unique_ptr<SiteSimulationResult> bpp::DetailedSiteSimulatorInterface::dSimulateSite ( size_t  ancestralStateIndex,
double  rate 
) const
pure virtual

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

◆ dSimulateSite() [4/4]

virtual std::unique_ptr<SiteSimulationResult> bpp::DetailedSiteSimulatorInterface::dSimulateSite ( size_t  rateClass) const
pure virtual

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

◆ getAlphabet()

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

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

◆ getSequenceNames()

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

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

◆ outputInternalSites()

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

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

◆ simulateSite() [1/4]

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

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 virtualinherited

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 virtualinherited

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

◆ simulateSite() [4/4]

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

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

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