Uses of Interface
com.rubecula.darwin.domain.helper.Colony

Packages that use Colony

com.rubecula.darwin.domain.environment
com.rubecula.darwin.domain.genetics	Genetics
com.rubecula.darwin.domain.helper	Darwin
com.rubecula.darwin.domain.world	Darwin
com.rubecula.darwin.examples.pepperedmoth	Peppered Moth Example
com.rubecula.darwin.examples.travelingsalesman	Traveling Salesman Example

Uses of Colony in com.rubecula.darwin.domain.environment

Methods in com.rubecula.darwin.domain.environment with parameters of type Colony

java.util.Collection<Expression>

Expresser_.express(Colony colony, Gene... genes) Default implementation of express simply ignores population and returns a collection of one Trait derived from invoking Expresser.express(Gene...).

Uses of Colony in com.rubecula.darwin.domain.genetics

Methods in com.rubecula.darwin.domain.genetics with parameters of type Colony

Phenotype	Genome_.express(Colony colony) Method to create a new phenotype from a collection of genes by expressing each and every gene, one at a time, using this Expresser.
void	Genomic_.express(Phenotype phenotype, Colony colony, Genes genes) Standard implementation of express for this Genomic.
int	Fecundity_Saturated.getFecundity(Colony colony) Get the fecundity for a population whose saturation is given by saturation.

Uses of Colony in com.rubecula.darwin.domain.helper

Methods in com.rubecula.darwin.domain.helper that return Colony

Colony	Organism.getColony() Method to determine to which population this organism currently belongs.
Colony	Population.getColony(int index) TODO consider using the id of the colony instead of the index.

Methods in com.rubecula.darwin.domain.helper that return types with arguments of type Colony

java.util.Collection<Colony>

Population.getColonies()

Methods in com.rubecula.darwin.domain.helper with parameters of type Colony

int	Population.addColony(Colony colony) Add a colony to this population.
Phenotype	Genome.express(Colony colony) Express the genes of this Genome in the context of population and return the result as a Phenotype.
java.util.Collection<Expression>	Expresser.express(Colony colony, Gene... genes) Express the gene in the context of the environment, potentially resulting in several expressions, each of which may be either a Trait or an ExPhen.
void	Genomic.express(Phenotype phenotype, Colony colony, Genes genes) Method to create a new phenotype from a collection of genes by expressing each and every gene, one at a time, using the appropriate Expresser.
int	Fecundity.getFecundity(Colony colony) Determine the number of progeny for each pair per generation.
Lek	MateChoice.getLek(Colony colony) Method to get a "lek", that is to say a population of breeding males.
void	Registry.registerBirths(Colony colony, java.util.Collection<Organism> neonates) TODO consider changing parameter to Colony
void	Registry.registerDeaths(Colony colony, java.util.Collection<Organism> deaths)
void	Registry.registerMarriages(Colony colony, java.util.Collection<Mating> marriages)
void	Organism.setColony(Colony colony) Mutating method to change the current population for this organism, as a result of migration.

Uses of Colony in com.rubecula.darwin.domain.world

Classes in com.rubecula.darwin.domain.world that implement Colony

class	Colony_
class	Colony_Mayrian Default implementation of a Colony.

Fields in com.rubecula.darwin.domain.world with type parameters of type Colony

java.util.List<Colony>

Population_._colonies A list of colonies.

Methods in com.rubecula.darwin.domain.world that return Colony

Colony	Organism_.getColony()
Colony	Lek.getColony()
Colony	Population_.getColony(int index)
protected abstract Colony	Population_Managed.makeDaughterColony(Colony founderColony, java.lang.Object addition, int pos) clone the founderColony to create a new colony with the newClient appropriately positioned in the new colony's environment.

Methods in com.rubecula.darwin.domain.world that return types with arguments of type Colony

java.util.Collection<Colony>

Population_.getColonies()

Methods in com.rubecula.darwin.domain.world with parameters of type Colony

int	Population_.addColony(Colony colony)
Lek	MateChoice_.getLek(Colony colony)
protected abstract void	Population_Managed.logBestOrganism(Colony colony)
protected abstract int	Population_Managed.makeDaughterColonies(Colony founderColony, Environment founderEnvironment)
protected int	Population_Managed.makeDaughterColonies(Colony founderColony, int size, java.lang.Object addition)
protected abstract Colony	Population_Managed.makeDaughterColony(Colony founderColony, java.lang.Object addition, int pos) clone the founderColony to create a new colony with the newClient appropriately positioned in the new colony's environment.
static Organism	OrganismFactory.makeOrganism(Nuclear nuclear, Colony colony, java.lang.String identifier) Factory method for a new Organism.
static Organism	Organism_Asexual.makeProgeny(java.lang.String identifier, Colony colony, Genome genome)
void	Taxon_.registerBirths(Colony colony, java.util.Collection<Organism> neonates)
void	Registry_.registerBirths(Colony colony, java.util.Collection<Organism> neonates) Do nothing
void	Taxon_.registerDeaths(Colony colony, java.util.Collection<Organism> deaths) TEST
void	Registry_.registerDeaths(Colony colony, java.util.Collection<Organism> deaths) Do nothing
void	Taxon_.registerMarriages(Colony colony, java.util.Collection<Mating> marriages)
void	Registry_.registerMarriages(Colony colony, java.util.Collection<Mating> marriages) Do nothing.
static Organism	Organism_Sexual.seed(Colony colony) Class method to create a new Organism_Sexual without parents (for seeding a population).
static Organism	Organism_Asexual.seed(Colony colony) Class method to create a new Organism without parents (for seeding a population).
protected abstract Organism	Population_Managed.seedOrganism(Colony colony, int i)
void	Organism_.setColony(Colony colony) Reset the owning colony of this organism.
boolean	Population_Managed.updateEnvironmentAndColonies(Colony founderColony, java.lang.Object source) This is a critical part of the evolutionary process for a Population_Managed and is called by the Population_Managed.ProcessBestInEnvironment.onUpdate(Organism), which in turn is invoked when there is a new best organism by Best_Organism#update(Organism, boolean).
boolean	Managed.updateEnvironmentAndColonies(Colony founderColony, java.lang.Object source) This method is responsible for updating the environment (from the given source) for the given colony in such a way that variations of the update are applied to a number of new daughter colonies.

Constructors in com.rubecula.darwin.domain.world with parameters of type Colony

Lek(java.util.Collection<Organism> organisms, org.apache.commons.math.random.RandomGenerator random, double sampleFraction, Colony colony)

Lek(Colony colony, org.apache.commons.math.random.RandomGenerator random)

Lek(Colony colony, org.apache.commons.math.random.RandomGenerator random, double sampleFraction)

MortalityStats(Colony colony)

Organism_(java.lang.String identifier, Colony colony, Nuclear nuclear)
Construct a new organism with the following attributes:

Uses of Colony in com.rubecula.darwin.examples.pepperedmoth

Methods in com.rubecula.darwin.examples.pepperedmoth with parameters of type Colony

void	Registry_PepperedMoth.registerBirths(Colony colony, java.util.Collection<Organism> neonates) Note the births

Uses of Colony in com.rubecula.darwin.examples.travelingsalesman

Methods in com.rubecula.darwin.examples.travelingsalesman that return Colony

protected Colony

Population_TS.makeDaughterColony(Colony founderColony, java.lang.Object newClient, int pos)

Methods in com.rubecula.darwin.examples.travelingsalesman with parameters of type Colony

static Organism	Organism_TS.createOrganism(int i, Colony colony) Method to create a new organism by seeding.
java.util.Collection<Expression>	Expresser_TS.express(Colony colony, Gene... genes) TODO this is apparently called more often than necessary
protected void	Population_TS.logBestOrganism(Colony colony)
protected int	Population_TS.makeDaughterColonies(Colony founderColony, Environment founderEnvironment) In this implementation, we get the client map from the founderEnvironment eco factor called EcoFactor_Clients.FACTOR_CLIENTS.
protected Colony	Population_TS.makeDaughterColony(Colony founderColony, java.lang.Object newClient, int pos)
void	Registry_TS.registerBirths(Colony colony, java.util.Collection<Organism> neonates) Note the births
protected Organism	Population_TS.seedOrganism(Colony colony, int i)