com.rubecula.darwin.domain.helper
Interface Colony

All Superinterfaces:

Censusible, java.lang.Cloneable, Countable, net.sf.tostring0.Identifiable, Insular, Theological, Visualizable

All Known Implementing Classes:

Colony_, Colony_Mayrian

public interface Colony
extends Visualizable, Countable, Theological, java.lang.Cloneable, Insular

This super-interface of Population addresses the more basic aspects of an Evolvable, Visualizable and Countable group. In particular, this interface knows nothing about Organisms. TODO consider switching names between this and Population.

Author:

Robin Hillyard

Method Summary

boolean	addOrganism(Organism organism)
void	cleanupGeneration() Cleanup (that's a euphemism) the organisms in this Colony.
java.lang.String	createIdentifier() Method to yield an unique identifier within this colony.
Environment	getEnvironment() Method to get the environment in which this colony thrives.
java.util.Collection<Organism>	getOrganisms()
Population	getPopulation()
double	getSaturation() Method to determine the population saturation.
double	grantPardons(double fittestOriginal, int pardonsPerColony)
void	markDeadOrganisms(Viability viability)
void	normalizeGenomes(Organism bestOrganism)
void	populationChanged(java.lang.Object context)
void	setIndex(int index) Set the index of this population within its parent Taxon System.
void	setIsolated(boolean isolated)
void	setNDaughters(int size) Set the number of daughter colonies we expect this colony to have.
void	setPopulation(Population population)
boolean	setupGeneration()
boolean	spin(int n)
void	thin(int thinFactor) Thin (decimate) the organisms of this colony by a factor of thinFactor.

Methods inherited from interface com.rubecula.darwin.foundation.Visualizable

getIndividuals, getRealm, getSink

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

Methods inherited from interface com.rubecula.darwin.foundation.Countable

getCount

Methods inherited from interface com.rubecula.darwin.domain.helper.Censusible

censusMe, getCensusibleChildren

Methods inherited from interface com.rubecula.darwin.foundation.Theological

cullMembers, seedMembers

Methods inherited from interface com.rubecula.darwin.domain.helper.Insular

isIsolated

Method Detail

addOrganism

boolean addOrganism(Organism organism)

Parameters:

organism -

Returns:

true if we added the organism

cleanupGeneration

void cleanupGeneration()

Cleanup (that's a euphemism) the organisms in this Colony. Normally, the cleanup consists of killing off all of the "marked" organisms. This method is called for each Colony of a population during the invocation of the Generational.nextGeneration() method.

createIdentifier

java.lang.String createIdentifier()

Method to yield an unique identifier within this colony.

Returns:

a string which represents the next integer in a sequence. TODO use the generation number for id TODO consider putting this in a factory class

getEnvironment

Environment getEnvironment()

Method to get the environment in which this colony thrives.

Returns:

the environment.

getOrganisms

java.util.Collection<Organism> getOrganisms()

Returns:

a collection of all the Organisms in this Population

getPopulation

Population getPopulation()

Returns:

the population to which this colony belongs

getSaturation

double getSaturation()

Method to determine the population saturation. One of the Eco Factors is the ideal population which the environment can support.

Returns:

current population divided by ideal population (unless the latter is undefined in which case the value 1 is returned).

grantPardons

double grantPardons(double fittestOriginal,
                    int pardonsPerColony)
                    throws FitnessException

Parameters:

fittestOriginal - the fitness value of the fittest we know of so far

pardonsPerColony -

Returns:

a new value of fitness

Throws:

FitnessException

markDeadOrganisms

void markDeadOrganisms(Viability viability)
                       throws FitnessException

Parameters:

viability - the viability which will determine whether an organism is viable or not.

Throws:

FitnessException

normalizeGenomes

void normalizeGenomes(Organism bestOrganism)

Parameters:

bestOrganism -

populationChanged

void populationChanged(java.lang.Object context)

Parameters:

context - something that characterizes what caused the population change

setIndex

void setIndex(int index)

Set the index of this population within its parent Taxon System. TODO consider removing this and always use List.indexOf(Object).

Parameters:

index -

setIsolated

void setIsolated(boolean isolated)

Parameters:

isolated - the isolated to set

setNDaughters

void setNDaughters(int size)

Set the number of daughter colonies we expect this colony to have.

Parameters:

size -

setPopulation

void setPopulation(Population population)

Parameters:

population - the population to set

setupGeneration

boolean setupGeneration()

Returns:

true if all OK

spin

boolean spin(int n)

Parameters:

n - the range of integers from which to choose (i.e. the odds against spin returning true).

Returns:

true if the random number source yields a zero

thin

void thin(int thinFactor)
          throws FitnessException

Thin (decimate) the organisms of this colony by a factor of thinFactor. Literal decimation would occur if the thinFactor was 10.

Parameters:

thinFactor - the factor by which the population is to be reduced.

Throws:

FitnessException