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

Packages that use Phenotype

com.rubecula.darwin.domain.environment
com.rubecula.darwin.domain.fitness	Math
com.rubecula.darwin.domain.genetics	Genetics
com.rubecula.darwin.domain.helper	Darwin
com.rubecula.darwin.domain.world	Darwin
com.rubecula.darwin.examples.travelingsalesman	Traveling Salesman Example

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

Classes in com.rubecula.darwin.domain.environment that implement Phenotype

class	Phenotype_ Abstract class to define the base methods and fields for an implementation of Phenotype.
class	Phenotype_Dawkinsian Lifespan: transient.

Methods in com.rubecula.darwin.domain.environment that return Phenotype

Phenotype	Trait_.getPhenotype()
static Phenotype	PhenotypeFactory.makeDawkinsian()
static Phenotype	PhenotypeFactory.makePhenotype(java.lang.Class<? extends Phenotype> clazz, java.lang.Class<? extends java.lang.Object>[] parameterClasses, java.lang.Object[] parameterValues)
static Phenotype	PhenotypeFactory.makePhenotype(java.lang.String classname, java.lang.Class<? extends java.lang.Object>[] parameterClasses, java.lang.Object[] parameterValues)

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

void	Trait_.setPhenotype(Phenotype phenotype)

Method parameters in com.rubecula.darwin.domain.environment with type arguments of type Phenotype

static Phenotype

PhenotypeFactory.makePhenotype(java.lang.Class<? extends Phenotype> clazz, java.lang.Class<? extends java.lang.Object>[] parameterClasses, java.lang.Object[] parameterValues)

Uses of Phenotype in com.rubecula.darwin.domain.fitness

Methods in com.rubecula.darwin.domain.fitness with parameters of type Phenotype

double

FitnessEngine_.calculateFitness(Phenotype phenotype, Environment environment) The base implementation of this method (which should normally be appropriate for all usage) simply goes through all possible pairings of trait/ecofactor (the traits belonging to the phenotype and the ecofactors belonging to the environment) and calculates the weighted product of all fitnesses.

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

Methods in com.rubecula.darwin.domain.genetics that return Phenotype

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.

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

void	Genomic_.express(Phenotype phenotype, Colony colony, Genes genes) Standard implementation of express for this Genomic.
void	Genomic_.express(Phenotype phenotype, Genes genes) Standard implementation of this method simply calls Genomic_.express(Phenotype, Colony, Genes) with null population.

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

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

Phenotype	Genome.express(Colony colony) Express the genes of this Genome in the context of population and return the result as a Phenotype.
Phenotype	Trait.getPhenotype() TODO consider renaming this method as getParent().
Phenotype	Organism.getPhenotype()
Phenotype	PhenotypeCache.getPhenotype(Basic genes, net.sf.tostring0.Identifiable identifiable)

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

void	PhenotypeCache.addPhenotype(Basic genes, net.sf.tostring0.Identifiable identifiable, Phenotype phenotype)
double	FitnessEngine.calculateFitness(Phenotype phenotype, Environment environment)
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.
void	Genomic.express(Phenotype phenotype, 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.
void	Trait.setPhenotype(Phenotype traits)

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

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

Phenotype

Organism_.getPhenotype() Get the phenotype by expressing the genome in the context of the colony.

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

protected abstract void

Population_Managed.logBestFitness(Organism organism, Phenotype phenotype)

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

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

class

Phenotype_TS

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

protected void

Population_TS.logBestFitness(Organism organism, Phenotype phenotype)