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:

Public Member Functions
	AbstractMutationProcess (const SubstitutionModel *model)
	AbstractMutationProcess (const AbstractMutationProcess &amp)
AbstractMutationProcess &	operator= (const AbstractMutationProcess &amp)
virtual	~AbstractMutationProcess ()
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...
const SubstitutionModel *	getSubstitutionModel () const
	Get the substitution model associated to the mutation process. More...

Protected Attributes
const SubstitutionModel *	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 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.

Constructor & Destructor Documentation

AbstractMutationProcess() [1/2]

bpp::AbstractMutationProcess::AbstractMutationProcess ( const SubstitutionModel *  model )

inline

Definition at line 301 of file MutationProcess.h.

AbstractMutationProcess() [2/2]

bpp::AbstractMutationProcess::AbstractMutationProcess ( const AbstractMutationProcess &  amp )

inline

Definition at line 305 of file MutationProcess.h.

~AbstractMutationProcess()

virtual bpp::AbstractMutationProcess::~AbstractMutationProcess ( )

inlinevirtual

Definition at line 317 of file MutationProcess.h.

Member Function Documentation

detailedEvolve()

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 occure.

Returns

The resulting mutation path.

Implements bpp::MutationProcess.

Definition at line 103 of file MutationProcess.cpp.

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

evolve()

size_t AbstractMutationProcess::evolve ( size_t  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 88 of file MutationProcess.cpp.

References getTimeBeforeNextMutationEvent(), and mutate().

getSubstitutionModel()

const SubstitutionModel* bpp::AbstractMutationProcess::getSubstitutionModel ( ) const

inlinevirtual

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_.

getTimeBeforeNextMutationEvent()

double AbstractMutationProcess::getTimeBeforeNextMutationEvent ( size_t  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 81 of file MutationProcess.cpp.

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

Referenced by detailedEvolve(), and evolve().

mutate() [1/2]

size_t AbstractMutationProcess::mutate ( size_t  state ) const

virtual

Mutate a character in state i.

Parameters

state

The current state of the character.

Implements bpp::MutationProcess.

Definition at line 49 of file MutationProcess.cpp.

References repartition_, and size_.

Referenced by detailedEvolve(), and evolve().

mutate() [2/2]

size_t AbstractMutationProcess::mutate ( size_t  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 61 of file MutationProcess.cpp.

References repartition_, and size_.

operator=()

AbstractMutationProcess& bpp::AbstractMutationProcess::operator= ( const AbstractMutationProcess &  amp )

inline

Definition at line 309 of file MutationProcess.h.

References model_, repartition_, and size_.

Member Data Documentation

model_

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=().

repartition_

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_

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