ParamSet Class Reference

Set of parameters. More...

#include <ParamSet.hpp>

Public Member Functions
	ParamSet ()
	Default constructor. More...
	~ParamSet ()
	Destructor. More...
	ParamSet (const ParamSet &)
	Copy constructor. More...
ParamSet &	operator= (const ParamSet &)
	Assignment operator. More...
void	reset ()
	Restores default value of all parameters. More...
unsigned int	numberOfPopulations () const
	Gets the number of populations. More...
double	pairwiseMigrationRate (unsigned int source, unsigned int dest) const
	Gets a pairwise migration rate. More...
void	pairwiseMigrationRate (unsigned int source, unsigned int dest, double value)
	Sets a pairwise migration rate. More...
void	migrationRate (double value)
	Sets the migration rate for all matrix. More...
double	populationSize (unsigned int populationIndex) const
	Gets a population size. More...
void	populationSize (unsigned int populationIndex, double value)
	Sets a population size. More...
double	growthRate (unsigned int populationIndex) const
	Gets a growth rate. More...
void	growthRate (unsigned int populationIndex, double value)
	Sets a growth rate. More...
double	recombinationRate () const
	Gets the recombination rate. More...
void	recombinationRate (double value)
	Sets the recombination rate. More...
unsigned int	numberOfSegments () const
	Gets the number of recombining segments. More...
void	numberOfSegments (unsigned int value)
	Sets the number of recombining segments. More...
double	selfingRate () const
	Gets the selfing rate. More...
void	selfingRate (double value)
	Sets the selfing rate. More...
void	addPopulation (double migr)
	Adds a population to the model. More...
void	addChange (const Change *change)
	Adds a change. More...
double	nextChangeDate () const
	Gets the date of the next change. More...
void	nextChangeDo (Controller *controller)
	Applies the next change event. More...
unsigned int	singles (unsigned int populationIndex) const
	Gets the number of single sample from a population. More...
void	singles (unsigned int populationIndex, unsigned int value)
	Sets the number of single sample from a population. More...
unsigned int	doubles (unsigned int populationIndex) const
	Gets the number of double sample from a population. More...
void	doubles (unsigned int populationIndex, unsigned int value)
	Sets the number of double sample from a population. More...
unsigned int	numberOfSamples () const
	Computes the total number of samples. More...
double	dateOfLastChange (unsigned int populationIndex) const
	Gives the date of the last size change. More...
void	dateOfLastChange (unsigned int populationIndex, double date) const
	Sets the date of the last size change. More...
void	setGroups (DataMatrix &dataMatrix, bool labelIndividuals=false)
	Set groups labels. More...

Detailed Description

Set of parameters.

Constructor & Destructor Documentation

ParamSet

(

)

Default constructor.

Initializes all parameters to reasonnable values (except that the sample size is null: 1 population, 0 samples, selfing rate of 0, recombination rate of 0, growth rate of 0, population size of 1 and no changes.

~ParamSet

(

)

Destructor.

ParamSet

(

const ParamSet &

source

)

Copy constructor.

Member Function Documentation

void addChange

(

const Change *

change

)

Adds a change.

The change can be of any type derived from Change. A const Change* must be passed, so ParamSet will neither modify or delete the object itself. All passed Change object must be kept available for use by ParamSet.

void addPopulation

(

double

migr

)

Adds a population to the model.

Parameters

migr	pairwise migration rate between other population and the new one.

The parameters for the new population are equivalent to the default parameters.

double dateOfLastChange

(

unsigned int

populationIndex

)

const

Gives the date of the last size change.

Parameters

populationIndex

the index of the population.

Returns

The date where the last change occurred, or 0. if no change occurred during the simulation.

void dateOfLastChange	(	unsigned int	populationIndex,
		double	date
	)		const

Sets the date of the last size change.

Parameters

populationIndex	the index of the population.
date	the date where the last change occurred, or 0. if no change occurred during the simulation.

unsigned int doubles

(

unsigned int

populationIndex

)

const

Gets the number of double sample from a population.

void doubles	(	unsigned int	populationIndex,
		unsigned int	value
	)

Sets the number of double sample from a population.

double growthRate

(

unsigned int

populationIndex

)

const

Gets a growth rate.

void growthRate	(	unsigned int	populationIndex,
		double	value
	)

Sets a growth rate.

void migrationRate

(

double

value

)

Sets the migration rate for all matrix.

double nextChangeDate

(

)

const

Gets the date of the next change.

Returns -1 if no change is planned.

void nextChangeDo

(

Controller *

controller

)

Applies the next change event.

Parameters

controller

the Change event might need to have access to simulation controller (to trigger coalescent events, for example).

unsigned int numberOfPopulations

(

)

const

Gets the number of populations.

unsigned int numberOfSamples

(

)

const

Computes the total number of samples.

unsigned int numberOfSegments

(

)

const

Gets the number of recombining segments.

void numberOfSegments

(

unsigned int

value

)

Sets the number of recombining segments.

ParamSet & operator=

(

const ParamSet &

source

)

Assignment operator.

double pairwiseMigrationRate	(	unsigned int	source,
		unsigned int	dest
	)		const

Gets a pairwise migration rate.

It is allowed to access a diagonal value. Diagonal values contain the sum of values of the corresponding line (diagonal cell excepted, of course).

void pairwiseMigrationRate	(	unsigned int	source,
		unsigned int	dest,
		double	value
	)

Sets a pairwise migration rate.

It is not allowed to set a value on the diagonal (this would raise an exception). The method takes care of modifying the diagonal accordingly (still this is not relevant for the client);

double populationSize

(

unsigned int

populationIndex

)

const

Gets a population size.

void populationSize	(	unsigned int	populationIndex,
		double	value
	)

Sets a population size.

The size must be strictly positive.

double recombinationRate

(

)

const

Gets the recombination rate.

void recombinationRate

(

double

value

)

Sets the recombination rate.

void reset

(

)

Restores default value of all parameters.

double selfingRate

(

)

const

Gets the selfing rate.

void selfingRate

(

double

value

)

Sets the selfing rate.

void setGroups	(	DataMatrix &	dataMatrix,
		bool	labelIndividuals = false
	)

Set groups labels.

Sets the group labels of the DataMatrix, according to the current state of population structure, and assuming that the DataMatrix was generated by the class Arg.

Parameters

dataMatrix	the DataMatrix object to modify. The number of sequences must match the total number of samples defined by the ParamSet object this method is called on.
labelIndividuals	by default, labels the different samples depending on the population they come from (0 being the label of the first population). If this flag is set to true, then the samples are labelled depending on the individual they come from, regardless of populations. In that case there can be only one or two genes for a given group label.

unsigned int singles

(

unsigned int

populationIndex

)

const

Gets the number of single sample from a population.

void singles	(	unsigned int	populationIndex,
		unsigned int	value
	)

Sets the number of single sample from a population.

---

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

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