Controller Class Reference

Controls a coalescent simulation. More...

#include <Controller.hpp>

Public Member Functions
	Controller ()
	Default constructor. More...
	~Controller ()
	Destructor. More...
	Controller (const ParamSet *paramSet, Random *random)
	Standard constructor. More...
void	reset ()
	Reset for a new simulation. More...
unsigned int	step ()
	Increments the coalescent model. More...
Arg *	getArg ()
	Gets the Ancestral Recombination Graph. More...
void	bottleneck (unsigned int populationIndex, double strength)
	Applies a bottleneck to a given population. More...
void	moveAllLineages (unsigned int source, unsigned int dest)
	Migrate a complete population. More...
void	moveSomeLineages (unsigned int source, unsigned int dest, double probability)
	Migrate a complete population. More...
void	addPopulation ()
	Adds an empty population.

Detailed Description

Controls a coalescent simulation.

This class generates the gene genealogy, based on the parameters stocked in a ParamSet object.

Constructor & Destructor Documentation

Controller

(

)

Default constructor.

Uses a default ParamSet object that will not allow performing simulations.

~Controller

(

)

Destructor.

Controller	(	const ParamSet *	paramSet,
		Random *	random
	)

Standard constructor.

Parameters

paramSet	a ParamSet object containing run parameters (it is taken as a reference and stored as this so it must not be modified during simulations).
random	the address of the random number generator.

Member Function Documentation

void bottleneck	(	unsigned int	populationIndex,
		double	strength
	)

Applies a bottleneck to a given population.

The bottleneck is applied following Galtier, Depaulis and Barton (Genetics, 2000): the general time counter is stopped, and coalescence events are performed during a time (of normal coalescent process) given by the parameter strength. All coalescent events are instantaneous.

Parameters

populationIndex	index of the population concerned by the event.
strength	strength of the bottleneck given by a number of time units (2N generations times the size of the population).

Arg * getArg

(

)

Gets the Ancestral Recombination Graph.

Returns

The address of the ARG contained in the object.

void moveAllLineages	(	unsigned int	source,
		unsigned int	dest
	)

Migrate a complete population.

Takes all the lineages currently present in the population source to the population dest.

void moveSomeLineages	(	unsigned int	source,
		unsigned int	dest,
		double	probability
	)

Migrate a complete population.

Takes all the lineages currently present in the population source to the population dest.

Parameters

source	source population.
dest	destination population.
probability	the probability that a lineage of source migrates to dest.

void reset

(

)

Reset for a new simulation.

Object is reinitiliazed for a new simulation.

unsigned int step

(

)

Increments the coalescent model.

Returns

The number of lineages.

---

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

• /home/stephane/Documents/devel/egglib2/egglib-cpp/Controller.hpp
• /home/stephane/Documents/devel/egglib2/egglib-cpp/Controller.cpp