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

Packages that use Organism

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 Organism in com.rubecula.darwin.domain.genetics

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

static Mating

MatingFactory.makeHaldanian(Genomic genomic, Organism female, Organism male, org.apache.commons.math.random.RandomGenerator random)

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

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

Organism

MateChoice.chooseMate(Organism female, Lek lek) Choose the best (male) mate for the given female, from among all of the organisms at the lek.

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

java.util.Collection<Organism>	Organism.getAsexualProgeny(int howMany)
java.util.Collection<Organism>	Colony.getOrganisms()

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

boolean	Colony.addOrganism(Organism organism)
Organism	MateChoice.chooseMate(Organism female, Lek lek) Choose the best (male) mate for the given female, from among all of the organisms at the lek.
Mate	Organism.createMate(MateChoice chooser, Organism female) Create a Mate object based on this (male) organism and its desirability to the given female.
Mating	MateChoice.createPairBond(Organism female, Lek lek, Lek alternativeLek) First, we call MateChoice.pairUp(Organism, Lek) for the female, lek and the appropriate genomic.
double	MateChoice.getDesirabilityIndex(Organism female, Organism male) Method to determine the desirability of a given male in the eyes, etc.
void	Colony.normalizeGenomes(Organism bestOrganism)
Mating	MateChoice.pairUp(Organism female, Lek lek) Method to create a Mating object based on the female given and a male chosen from the lek.

Method parameters in com.rubecula.darwin.domain.helper with type arguments of type Organism

java.util.Collection<Mating>	MateChoice.findPairs(java.util.Collection<Organism> organisms, Lek lek, Lek alternativeLek) Method to enumerate a set of mating pairs: females from this Colony and males from either the lek or the alternativeLek .
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)

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

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

class	Organism_ Abstract class defining the base methods and fields of an implementation of Organism interface.
class	Organism_Asexual This concrete class represents an individual organism within a Taxon .
class	Organism_Sexual This concrete class represents an individual organism within a Taxon .

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

protected java.util.List<Organism>

Colony_._organisms collection of organisms in this population.

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

Organism	MateChoice_.chooseMate(Organism female, Lek lek) Choose the best (male) mate for the given female, from among all of the organisms at the lek.
Organism	Mate.getMale()
static Organism	OrganismFactory.makeOrganism(java.lang.Class<? extends Organism> clazz, Nuclear nuclear, Population population, java.lang.String identifier)
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)
Organism	Organism_Asexual.reproduce(java.lang.String identifier, Genomic genomic)
Organism	Asexual.reproduce(java.lang.String identifier, Genomic genomic) Method to perform asexual reproduction.
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)

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

java.util.Collection<Organism>	Organism_Sexual.getAsexualProgeny(int howMany) This implementation of the method yields no progeny because we normally expect sexual organisms to reproduce only sexually.
java.util.Collection<Organism>	Organism_Asexual.getAsexualProgeny(int howMany)
java.util.Collection<Organism>	Colony_.getOrganisms()

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

boolean	Colony_.addOrganism(Organism organism) Note that this method does NOT invoke the populationChanged() method.
Organism	MateChoice_.chooseMate(Organism female, Lek lek) Choose the best (male) mate for the given female, from among all of the organisms at the lek.
Mate	Organism_Sexual.createMate(MateChoice chooser, Organism female) Create a Mate object based on this Organism [provided that this is male] and the given female.
Mate	Organism_Asexual.createMate(MateChoice chooser, Organism female)
static Mate	Mate.createMate(Organism male, double desirability) Factory method to create a new Mate object based on the given male Organism and his desirability.
Mating	MateChoice_.createPairBond(Organism female, Lek lek, Lek alternativeLek) First, we call MateChoice.pairUp(Organism, Lek) for the female, lek and the appropriate genomic.
protected double	MateChoice_.getAttraction(Organism female, Organism male)
protected double	MateChoice_Wrightian.getDesirability(Organism male)
protected double	MateChoice_Evaluator.getDesirability(Organism male) This implementation returns a value which is: d * g * h where d is the value of the desirability index defined by the superclass (see MateChoice_.getDesirabilityIndex(Organism, Organism) ; and g is one more than the age of the candidate male; TODO consider a different mechanism here: instead of passing in a random number to the desirability formula, we should divide the random space into several bands (or tranches), using Randomizer, and then cache the various desirability values for age/viability/tranche.
protected double	MateChoice_.getDesirability(Organism male)
double	MateChoice_.getDesirabilityIndex(Organism female, Organism male) Method to determine the desirability of a given male in the eyes, etc.
protected boolean	Best_Organism.isUnique(Organism candidate)
protected abstract void	Population_Managed.logBestFitness(Organism organism, Phenotype phenotype)
void	Colony_.normalizeGenomes(Organism bestOrganism)
void	Population_Managed.ProcessBestInEnvironment.onUpdate(Organism object) Callback method (see above).
Mating	MateChoice_.pairUp(Organism female, Lek lek)
boolean	Viability.resetViability(Organism organism)

Method parameters in com.rubecula.darwin.domain.world with type arguments of type Organism

java.util.Collection<Mating>	MateChoice_.findPairs(java.util.Collection<Organism> organisms, Lek lek, Lek alternativeLek) Method to enumerate a set of mating pairs: females from the given set of organisms and males from either the lek or the alternativeLek .
protected java.util.Map<java.lang.Object,java.lang.Integer>	Registry_.getOrganismFrequencyMap(java.util.Collection<Organism> organisms) TODO consider using FrequencyMap instead
static Organism	OrganismFactory.makeOrganism(java.lang.Class<? extends Organism> clazz, Nuclear nuclear, Population population, java.lang.String identifier)
protected boolean	Population_Managed.processBestFit(ProcessBest<Organism> bestOfGenerationProcessor) TODO this needs to be rewritten.
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

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

Best_Organism(java.lang.String identifier, Organism best, int generation, int convergence)

Best_Organism(java.lang.String identifier, Organism best, int generation, ProcessBest<Organism> processor, int convergence)

Constructor parameters in com.rubecula.darwin.domain.world with type arguments of type Organism

Best_Organism(java.lang.String identifier, int generation, java.util.Collection<Organism> candidates, ProcessBest<Organism> processor)

Best_Organism(java.lang.String identifier, int generation, java.util.Collection<Organism> candidates, ProcessBest<Organism> processor)

Best_Organism(java.lang.String identifier, int generation, ProcessBest<Organism> processor, int convergence)

Best_Organism(java.lang.String identifier, Organism best, int generation, ProcessBest<Organism> processor, int convergence)

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

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

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

static WingColor

VisualizationFactory_PepperedMoth.getWingColor(Organism organism) TODO Consider moving this somewhere else.

Method parameters in com.rubecula.darwin.examples.pepperedmoth with type arguments of type Organism

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

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

Classes in com.rubecula.darwin.examples.travelingsalesman that implement Organism

class

Organism_TS

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

static Organism	Organism_TS.createOrganism(int i, Colony colony) Method to create a new organism by seeding.
protected Organism	Population_TS.seedOrganism(Colony colony, int i)

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

protected void

Population_TS.logBestFitness(Organism organism, Phenotype phenotype)

Method parameters in com.rubecula.darwin.examples.travelingsalesman with type arguments of type Organism

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