bpp::DetailedSiteSimulator Class Reference

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

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

Inheritance diagram for bpp::DetailedSiteSimulator:

Collaboration diagram for bpp::DetailedSiteSimulator:

Public Member Functions
	DetailedSiteSimulator ()
virtual	~DetailedSiteSimulator ()
virtual SiteSimulationResult *	dSimulateSite () const =0
	Get a detailed simulation result for one site. More...
virtual SiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex) const =0
virtual SiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex, double rate) const =0
virtual SiteSimulationResult *	dSimulateSite (double rate) const =0
virtual Site *	simulateSite () const =0
virtual Site *	simulateSite (size_t ancestralStateIndex) const =0
virtual Site *	simulateSite (size_t ancestralStateIndex, double rate) const =0
virtual Site *	simulateSite (double rate) const =0
virtual std::vector< std::string >	getSequencesNames () const =0
virtual const Alphabet *	getAlphabet () const =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 233 of file DetailedSiteSimulator.h.

Constructor & Destructor Documentation

DetailedSiteSimulator()

bpp::DetailedSiteSimulator::DetailedSiteSimulator ( )

inline

Definition at line 237 of file DetailedSiteSimulator.h.

~DetailedSiteSimulator()

virtual bpp::DetailedSiteSimulator::~DetailedSiteSimulator ( )

inlinevirtual

Definition at line 238 of file DetailedSiteSimulator.h.

Member Function Documentation

dSimulateSite() [1/4]

virtual SiteSimulationResult* bpp::DetailedSiteSimulator::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::NonHomogeneousSequenceSimulator.

dSimulateSite() [2/4]

virtual SiteSimulationResult* bpp::DetailedSiteSimulator::dSimulateSite ( size_t  ancestralStateIndex ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator.

dSimulateSite() [3/4]

virtual SiteSimulationResult* bpp::DetailedSiteSimulator::dSimulateSite ( size_t  ancestralStateIndex, double  rate  ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator.

dSimulateSite() [4/4]

virtual SiteSimulationResult* bpp::DetailedSiteSimulator::dSimulateSite ( double  rate ) const

pure virtual

Implemented in bpp::NonHomogeneousSequenceSimulator.

getAlphabet()

virtual const Alphabet* bpp::SiteSimulator::getAlphabet ( ) const

pure virtualinherited

Implemented in bpp::NonHomogeneousSequenceSimulator.

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

getSequencesNames()

virtual std::vector<std::string> bpp::SiteSimulator::getSequencesNames ( ) const

pure virtualinherited

Implemented in bpp::NonHomogeneousSequenceSimulator.

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

simulateSite() [1/4]

virtual Site* bpp::SiteSimulator::simulateSite ( ) const

pure virtualinherited

Implemented in bpp::NonHomogeneousSequenceSimulator.

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

simulateSite() [2/4]

virtual Site* bpp::SiteSimulator::simulateSite ( size_t  ancestralStateIndex ) const

pure virtualinherited

Implemented in bpp::NonHomogeneousSequenceSimulator.

simulateSite() [3/4]

virtual Site* bpp::SiteSimulator::simulateSite ( size_t  ancestralStateIndex, double  rate  ) const

pure virtualinherited

Implemented in bpp::NonHomogeneousSequenceSimulator.

simulateSite() [4/4]

virtual Site* bpp::SiteSimulator::simulateSite ( double  rate ) const

pure virtualinherited

Implemented in bpp::NonHomogeneousSequenceSimulator.

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

• Bpp/Phyl/Simulation/DetailedSiteSimulator.h