Partial implementation of the MutationProcess interface. More...

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

Inheritance diagram for bpp::AbstractMutationProcess:

Collaboration diagram for bpp::AbstractMutationProcess:

Public Member Functions
	AbstractMutationProcess (std::shared_ptr< const SubstitutionModelInterface > model)

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

Partial implementation of the MutationProcess interface.

This class provides an implementation of the MutationProcess interface. It assumes that there are size_ states allowed for the character of interest, and that the distribution of probabilities are in repartition_. As a matter of facts, probabilities must be cumulative, so that repartition_ contains values of the repartition function. The mutate function hence draws a random number between 0 and 1 and gives the corresponding character using the bijection of the repartition function.

All derived classes must initialize the repartition_ and size_ fields.

Definition at line 275 of file MutationProcess.h.

Constructor & Destructor Documentation

◆ AbstractMutationProcess()

bpp::AbstractMutationProcess::AbstractMutationProcess ( std::shared_ptr< const SubstitutionModelInterface > model )

inline

Definition at line 298 of file MutationProcess.h.

Member Function Documentation

◆ detailedEvolve() [1/2]

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

virtual

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(), getTimeBeforeNextMutationEvent(), model_, and mutate().

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

◆ detailedEvolve() [2/2]

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

virtual

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