Uses of Interface
com.rubecula.darwin.core.Organism

Packages that use Organism

com.rubecula.darwin.core	Darwin
com.rubecula.darwin.examples.pepperedmoth	Peppered Moth Example
com.rubecula.darwin.visualization	Display Package

Uses of Organism in com.rubecula.darwin.core

Classes in com.rubecula.darwin.core that implement Organism

class	Organism_Abstract 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 Darwinian System.
class	Organism_Sexual This concrete class represents an individual organism within a Darwinian System.

Methods in com.rubecula.darwin.core that return Organism

Organism	Sexual.birth(String identifier, Genotype genotype, boolean female) Method to construct a new organism in the given population, with the given identifier, the given genotype and the given sex (female).
Organism	Organism_Sexual.birth(String identifier, Genotype genotype, boolean female) Method to construct a new organism in the given population, with the given identifier, the given genotype and the given sex (female).
Organism	Factory.makeOrganism(Population population, Genotype genotype) Factory method to instantiate a new organism of the appropriate class, with a population-specific auto-generated identifier.
Organism	Factory_Abstract.makeOrganism(Population population, Genotype genotype)
Organism	Factory.makeOrganism(Population population, Genotype genotype, Map<String,Object> properties) Factory method to instantiate a new organism of the appropriate class, with a population-specific auto-generated identifier.
Organism	Factory_Abstract.makeOrganism(Population population, Genotype genotype, Map<String,Object> properties)
Organism	Factory.makeOrganism(String identifier, Population population, Genotype genotype) Factory method to instantiate a new organism of the appropriate class.
Organism	Factory_Abstract.makeOrganism(String identifier, Population population, Genotype genotype)
Organism	Factory.makeOrganism(String identifier, Population population, Genotype genotype, Map<String,Object> properties) Factory method to instantiate a new organism of the appropriate class.
Organism	Factory_Default.makeOrganism(String identifier, Population population, Genotype genotype, Map<String,Object> properties)
Organism	Mating.progeny(String identifier) Method to create progeny for this mating.
Organism	Mating_Abstract.progeny(String identifier) Each of the parents in this Mating object produce a gamete.
Organism	Asexual.reproduce(String identifier, Genome genome) Method to perform asexual reproduction.
Organism	Organism_Asexual.reproduce(String identifier, Genome genome)
static Organism	Organism_Sexual.Seed(Population population, boolean female, Map<String,Object> paramsGenotype, Map<String,Object> paramsGene) Class method to create a new Organism_Sexual without parents (for seeding a population).
static Organism	Organism_Asexual.Seed(Population population, Map<String,Object> paramsGenotype, Map<String,Object> paramsGene) Class method to create a new Organism without parents (for seeding a population).

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

Iterator<Organism>	Population.iterator()
Iterator<Organism>	Population_Abstract.iterator()

Methods in com.rubecula.darwin.core with parameters of type Organism

boolean	Population.add(Organism organism)
boolean	Population_Abstract.add(Organism organism) Note that this method does NOT invoke the populationChanged() method.
double	MateChoice.getDesirabilityIndex(Organism female, Organism male) Method to determine the desirability of a given male in the eyes, etc.
double	MateChoice_Default.getDesirabilityIndex(Organism female, Organism male)
double	MateChoice_Abstract.getDesirabilityIndex(Organism female, Organism male)

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

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

double	MateChoice_PepperedMoth.getDesirabilityIndex(Organism female, 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_Abstract.getDesirabilityIndex(Organism, Organism); and g is one more than the age of the candidate male;
static String	ApplicationDefinitions.getWingColor(Organism organism)
Color	VisualizationFactory_PepperedMoth.makeColor(Organism organism)
Individual	VisualizationFactory_PepperedMoth.makeIndividual(Organism organism, Map<String,Object> properties)
Point	VisualizationFactory_PepperedMoth.makeLocation(Organism organism)

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

Individual_PepperedMoth(Organism organism, Point location, Color color)
Public constructor.

Uses of Organism in com.rubecula.darwin.visualization

Methods in com.rubecula.darwin.visualization that return Organism

Organism	Individual_Abstract.getOrganism()
Organism	Individual.getOrganism()

Methods in com.rubecula.darwin.visualization with parameters of type Organism

Individual	VisualizationModel_Abstract.findIndividual(Organism organism)
Individual	VisualizationModel.findIndividual(Organism organism)
Color	VisualizationFactory.makeColor(Organism organism) Method to determine a suitable color for visualizing the organism
Individual	VisualizationFactory.makeIndividual(Organism organism, Map<String,Object> properties) Method to create a new Individual, based on an organism.
Point	VisualizationFactory.makeLocation(Organism organism) Method to determine a suitable location for visualizing the organism

Constructors in com.rubecula.darwin.visualization with parameters of type Organism

Individual_Abstract(Organism organism)
Protected constructor which creates a new instance of Individual at the point [0,0] and with color black.

Individual_Abstract(Organism organism, Color color)
Protected constructor which creates a new instance of Individual at the point [0,0] and with given color.

Individual_Abstract(Organism organism, Point location)
Protected constructor which creates a new instance of Individual at the given point and with color black.

Individual_Abstract(Organism organism, Point location, Color color)
Protected constructor which creates a new instance of Individual at the given point and with given color.

Individual_Default(Organism organism)
Public constructor which invokes Individual_Abstract.Individual_Abstract(Organism)

Individual_Default(Organism organism, Color color)
Public constructor which invokes Individual_Abstract.Individual_Abstract(Organism, Color)

Individual_Default(Organism organism, Point location)
Public constructor which invokes Individual_Abstract.Individual_Abstract(Organism, Point)

Individual_Default(Organism organism, Point location, Color color)
Public constructor which invokes Individual_Abstract.Individual_Abstract(Organism, Point, Color)