bpp-phyl  2.1.0
Public Member Functions | Protected Attributes
bpp::SimpleMutationProcess Class Reference

Generally used mutation process model. More...

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

+ Inheritance diagram for bpp::SimpleMutationProcess:
+ Collaboration diagram for bpp::SimpleMutationProcess:

List of all members.

Public Member Functions

 SimpleMutationProcess (const SubstitutionModel *model)
 Build a new SimpleMutationProcess object.
virtual ~SimpleMutationProcess ()
int evolve (int initialState, double time) const
 Method redefinition for better performance.
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.
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.

Detailed Description

Generally used mutation process model.

This builds a MutationProcess according to a given SubstitutionModel. The underlying mutation process is the following:

  1. Draw a random time $ t $ from an exponential law with parameter $ - \lambda_i $,
  2. Mutate the initial state. The probability of mutating state $i$ to state $j$ is:

    \[ \frac{Q_{i,j}}{\sum_k Q_{i,k}}. \]

Definition at line 341 of file MutationProcess.h.

Constructor & Destructor Documentation

SimpleMutationProcess::SimpleMutationProcess ( const SubstitutionModel *  model)

Build a new SimpleMutationProcess object.

Parameters:
modelThe substitution model to use.

Definition at line 115 of file MutationProcess.cpp.

References bpp::SubstitutionModel::getGenerator(), bpp::SubstitutionModel::getNumberOfStates(), bpp::SubstitutionModel::Qij(), bpp::AbstractMutationProcess::repartition_, and bpp::AbstractMutationProcess::size_.

SimpleMutationProcess::~SimpleMutationProcess ( ) [virtual]

Definition at line 148 of file MutationProcess.cpp.

Member Function Documentation

MutationPath AbstractMutationProcess::detailedEvolve ( int  initialState,
double  time 
) const [virtual, inherited]

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:
initialStateThe state before beginning evolution.
timeThe 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(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractMutationProcess::model_, and bpp::AbstractMutationProcess::mutate().

int SimpleMutationProcess::evolve ( int  initialState,
double  time 
) const [virtual]

Method redefinition for better performance.

Parameters:
initialStateThe state before beginning evolution.
timeThe time during which evolution must occure.
Returns:
The resulting state after evolution is completed.

Reimplemented from bpp::AbstractMutationProcess.

Definition at line 151 of file MutationProcess.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), bpp::AbstractMutationProcess::model_, bpp::SubstitutionModel::Pij_t(), bpp::AbstractMutationProcess::size_, and bpp::TextTools::toString().

const SubstitutionModel* bpp::AbstractMutationProcess::getSubstitutionModel ( ) const [inline, virtual, inherited]

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 bpp::AbstractMutationProcess::model_.

double AbstractMutationProcess::getTimeBeforeNextMutationEvent ( int  state) const [virtual, inherited]

Get the time before next mutation event.

Parameters:
stateThe 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 bpp::AbstractMutationProcess::model_, bpp::SubstitutionModel::Qij(), and bpp::RandomTools::randExponential().

Referenced by bpp::AbstractMutationProcess::detailedEvolve(), and bpp::AbstractMutationProcess::evolve().

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

Mutate a character in state i.

Parameters:
stateThe current state of the character.

Implements bpp::MutationProcess.

Definition at line 48 of file MutationProcess.cpp.

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

Referenced by bpp::AbstractMutationProcess::detailedEvolve(), and bpp::AbstractMutationProcess::evolve().

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

Mutate a character in state i n times.

Parameters:
stateThe current state of the character.
nThe number of mutations to perform.

Implements bpp::MutationProcess.

Definition at line 59 of file MutationProcess.cpp.

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

Member Data Documentation

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

The substitution model to use:

Definition at line 285 of file MutationProcess.h.

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

VVdouble bpp::AbstractMutationProcess::repartition_ [protected, inherited]

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

size_t bpp::AbstractMutationProcess::size_ [protected, inherited]

The number of states allowed for the character to mutate.

Definition at line 290 of file MutationProcess.h.

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

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