This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;. More...

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

Inheritance diagram for bpp::SelfMutationProcess:

Collaboration diagram for bpp::SelfMutationProcess:

Public Member Functions
	SelfMutationProcess (size_t alphabetSize)

virtual	~SelfMutationProcess ()

size_t	mutate (size_t state) const
	Mutate a character in state i. More...

size_t	mutate (size_t state, unsigned int n) const
	Mutate a character in state i n times. More...

double	getTimeBeforeNextMutationEvent (size_t state) const
	Get the time before next mutation event. More...

size_t	evolve (size_t initialState, double time) const
	Simulation a character evolution during a specified time according to the given substitution model and send the final state. More...

MutationPath	detailedEvolve (size_t initialState, double time) const
	Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events. More...

MutationPath	detailedEvolve (size_t initialState, size_t finalState, double time) const
	Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events, conditional to the final state.q. More...

std::shared_ptr< const SubstitutionModelInterface >	getSubstitutionModel () const
	Get the substitution model associated to the mutation process. More...

Protected Attributes
std::shared_ptr< const SubstitutionModelInterface >	model_
	The substitution model to use: More...

size_t	size_
	The number of states allowed for the character to mutate. More...

VVdouble	repartition_
	The repartition function for states probabilities. More...

Detailed Description

This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;.

Definition at line 354 of file MutationProcess.h.

Constructor & Destructor Documentation

◆ SelfMutationProcess()

SelfMutationProcess::SelfMutationProcess ( size_t alphabetSize )

Definition at line 202 of file MutationProcess.cpp.

References bpp::AbstractMutationProcess::repartition_, and bpp::AbstractMutationProcess::size_.

◆ ~SelfMutationProcess()

SelfMutationProcess::~SelfMutationProcess ( )

virtual

Definition at line 222 of file MutationProcess.cpp.

Member Function Documentation

◆ detailedEvolve() [1/2]

MutationPath AbstractMutationProcess::detailedEvolve	(	size_t	initialState,
		double	time
	)		const

virtualinherited

Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events.

Parameters

initialState	The state before beginning evolution.
time	The time during which evolution must occur.

Returns: The resulting mutation path.

Implements bpp::MutationProcess.

Definition at line 70 of file MutationProcess.cpp.

References bpp::MutationPath::addEvent().

Referenced by bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), and bpp::SimpleSubstitutionProcessSiteSimulator::evolveInternal().

◆ detailedEvolve() [2/2]

MutationPath AbstractMutationProcess::detailedEvolve	(	size_t	initialState,
		size_t	finalState,
		double	time
	)		const

virtualinherited

Simulation a character evolution during a specified time according to the given substitution model and send the total path with all intermediate states and times between mutation events, conditional to the final state.q.

Parameters