bpp::MutationProcess Class Reference

Interface for simulations. More...

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

Inheritance diagram for bpp::MutationProcess:

List of all members.

Public Member Functions
	MutationProcess ()
virtual	~MutationProcess ()
virtual int	mutate (int state) const =0
	Mutate a character in state i.
virtual int	mutate (int state, unsigned int n) const =0
	Mutate a character in state i n times.
virtual double	getTimeBeforeNextMutationEvent (int state) const =0
	Get the time before next mutation event.
virtual int	evolve (int initialState, double time) const =0
	Simulation a character evolution during a specified time according to the given substitution model and send the final state.
virtual MutationPath	detailedEvolve (int initialState, double time) const =0
	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.
virtual const SubstitutionModel *	getSubstitutionModel () const =0
	Get the substitution model associated to the mutation process.

---

Detailed Description

Interface for simulations.

A mutation process defines the rules for mutations to occure. The MutationProcess interface provides two methods, one for mutating a character in state i in another character, another for achieving this task n times.

Definition at line 204 of file MutationProcess.h.

---

Constructor & Destructor Documentation

bpp::MutationProcess::MutationProcess

(

)

[inline]

Definition at line 207 of file MutationProcess.h.

virtual bpp::MutationProcess::~MutationProcess

(

)

[inline, virtual]

Definition at line 208 of file MutationProcess.h.

---

Member Function Documentation

virtual MutationPath bpp::MutationProcess::detailedEvolve	(	int	initialState,
		double	time
	)		const [pure 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 occure.

Returns:

The resulting mutation path.

Implemented in bpp::AbstractMutationProcess.

virtual int bpp::MutationProcess::evolve	(	int	initialState,
		double	time
	)		const [pure virtual]

Simulation a character evolution during a specified time according to the given substitution model and send the final state.

Parameters:

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

Returns:

The resulting state after evolution is completed.

Implemented in bpp::SimpleMutationProcess, and bpp::AbstractMutationProcess.

virtual const SubstitutionModel* bpp::MutationProcess::getSubstitutionModel

(

)

const [pure virtual]

Get the substitution model associated to the mutation process.

Returns:

The SubstitutionModel associated to this instance.

Implemented in bpp::AbstractMutationProcess.

virtual double bpp::MutationProcess::getTimeBeforeNextMutationEvent

(

int

state

)

const [pure virtual]

Get the time before next mutation event.

Parameters:

state

The actual state of the chain;

Returns:

A random time before next mutation event.

Implemented in bpp::AbstractMutationProcess.

virtual int bpp::MutationProcess::mutate

(

int

state

)

const [pure virtual]

Mutate a character in state i.

Parameters:

state

The current state of the character.

Implemented in bpp::AbstractMutationProcess.

virtual int bpp::MutationProcess::mutate	(	int	state,
		unsigned int	n
	)		const [pure virtual]

Mutate a character in state i n times.

Parameters:

state	The current state of the character.
n	The number of mutations to perform.

Implemented in bpp::AbstractMutationProcess.

---

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

• Bpp/Phyl/Simulation/MutationProcess.h