bpp::AbstractMutationProcess Class Reference

Partial implmentation of the MutationProcess interface. More...

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

Inheritance diagram for bpp::AbstractMutationProcess:

Collaboration diagram for bpp::AbstractMutationProcess:

List of all members.

Public Member Functions
	AbstractMutationProcess (const SubstitutionModel *model)
	AbstractMutationProcess (const AbstractMutationProcess &amp)
AbstractMutationProcess &	operator= (const AbstractMutationProcess &amp)
virtual	~AbstractMutationProcess ()
int	mutate (int state) const
	Mutate a character in state i.
int	mutate (int state, unsigned int n) const
	Mutate a character in state i n times.
double	getTimeBeforeNextMutationEvent (int state) const
	Get the time before next mutation event.
int	evolve (int initialState, double time) const
	Simulation a character evolution during a specified time according to the given substitution model and send the final state.
MutationPath	detailedEvolve (int 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.
const SubstitutionModel *	getSubstitutionModel () const
	Get the substitution model associated to the mutation process.
Protected Attributes
const SubstitutionModel *	model_
	The substitution model to use:
size_t	size_
	The number of states allowed for the character to mutate.
VVdouble	repartition_
	The repartition function for states probabilities.

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Detailed Description

Partial implmentation 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 277 of file MutationProcess.h.

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Constructor & Destructor Documentation

bpp::AbstractMutationProcess::AbstractMutationProcess

(

const SubstitutionModel *

model

)

[inline]

Definition at line 301 of file MutationProcess.h.

bpp::AbstractMutationProcess::AbstractMutationProcess

(

const AbstractMutationProcess &

amp

)

[inline]

Definition at line 305 of file MutationProcess.h.

virtual bpp::AbstractMutationProcess::~AbstractMutationProcess

(

)

[inline, virtual]

Definition at line 317 of file MutationProcess.h.

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Member Function Documentation

MutationPath AbstractMutationProcess::detailedEvolve	(	int	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 occure.

Returns:

The resulting mutation path.

Implements bpp::MutationProcess.

Definition at line 98 of file MutationProcess.cpp.

References bpp::SubstitutionModel::getAlphabet(), getTimeBeforeNextMutationEvent(), model_, and mutate().

int AbstractMutationProcess::evolve	(	int	initialState,
		double	time
	)		const [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.

Implements bpp::MutationProcess.

Reimplemented in bpp::SimpleMutationProcess.

Definition at line 84 of file MutationProcess.cpp.

References getTimeBeforeNextMutationEvent(), and mutate().

const SubstitutionModel* bpp::AbstractMutationProcess::getSubstitutionModel

(

)

const [inline, virtual]

Get the substitution model associated to the mutation process.

Returns:

The SubstitutionModel associated to this instance.

Implements bpp::MutationProcess.

Definition at line 325 of file MutationProcess.h.

References model_.

double AbstractMutationProcess::getTimeBeforeNextMutationEvent

(

int

state

)

const [virtual]

Get the time before next mutation event.

Parameters:

state

The actual state of the chain;

Returns:

A random time before next mutation event.

Implements bpp::MutationProcess.

Definition at line 78 of file MutationProcess.cpp.

References model_, bpp::SubstitutionModel::Qij(), and bpp::RandomTools::randExponential().

Referenced by detailedEvolve(), and evolve().

int AbstractMutationProcess::mutate

(

int

state

)

const [virtual]

Mutate a character in state i.

Parameters:

state

The current state of the character.

Implements bpp::MutationProcess.

Definition at line 48 of file MutationProcess.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), repartition_, size_, and bpp::TextTools::toString().

Referenced by detailedEvolve(), and evolve().

int AbstractMutationProcess::mutate	(	int	state,
		unsigned int	n
	)		const [virtual]

Mutate a character in state i n times.

Parameters:

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

Implements bpp::MutationProcess.

Definition at line 59 of file MutationProcess.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), repartition_, and size_.

AbstractMutationProcess& bpp::AbstractMutationProcess::operator=

(

const AbstractMutationProcess &

amp

)

[inline]

Definition at line 309 of file MutationProcess.h.

References model_, repartition_, and size_.

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Member Data Documentation

const SubstitutionModel* bpp::AbstractMutationProcess::model_ [protected]

The substitution model to use:

Definition at line 285 of file MutationProcess.h.

Referenced by detailedEvolve(), bpp::SimpleMutationProcess::evolve(), getSubstitutionModel(), getTimeBeforeNextMutationEvent(), and operator=().

VVdouble bpp::AbstractMutationProcess::repartition_ [protected]

The repartition function for states probabilities.

repartition_[i][j] = probability that, being in state i at time t, we'll be in state <= j at time t+1.

Definition at line 298 of file MutationProcess.h.

Referenced by mutate(), operator=(), bpp::SelfMutationProcess::SelfMutationProcess(), and bpp::SimpleMutationProcess::SimpleMutationProcess().

size_t bpp::AbstractMutationProcess::size_ [protected]

The number of states allowed for the character to mutate.

Definition at line 290 of file MutationProcess.h.

Referenced by bpp::SimpleMutationProcess::evolve(), mutate(), operator=(), bpp::SelfMutationProcess::SelfMutationProcess(), and bpp::SimpleMutationProcess::SimpleMutationProcess().

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

• Bpp/Phyl/Simulation/MutationProcess.h
• Bpp/Phyl/Simulation/MutationProcess.cpp