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

Packages that use Trait

com.rubecula.darwin.domain.environment
com.rubecula.darwin.domain.fitness	Math
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 Trait in com.rubecula.darwin.domain.environment

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

class	Trait_ Base implementation of Trait.
class	Trait_Discrete Lifespan: transient.
class	Trait_Variable Concrete implementation of Trait which is based on a variable value.

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

protected Trait	Expresser_.createTrait(double value) TEST
protected static Trait	Expresser_.createTrait(Pharacter character, double value) TEST
protected static Trait	Expresser_.createTrait(Pharacter character, java.lang.String variant)
protected Trait	Expresser_.createTrait(java.lang.String key)
Trait	Expresser_Function.express(Gene... genes) TEST Express a gene by getting the allele's value and generating a new trait with value derived from the allele's value.
Trait	Expresser_Direct.express(Gene... genes) Express a gene by getting the allele's value and generating a new trait with value derived from the allele's value.
Trait	TraitMap_.getTrait(java.lang.String character) XXX
static Trait	TraitFactory.makeDiscrete(Pharacter character, java.lang.String variant) Factory method to create a discrete trait -- that is where the value is one of a finite set of variants, as opposed to the variable trait as in the case of TraitFactory.makeVariable(Pharacter, double).
static Trait	TraitFactory.makeTrait(java.lang.Class<? extends Trait> clazz, java.lang.Character character, java.lang.Object value) TEST
static Trait	TraitFactory.makeVariable(Pharacter character, double value) Factory method to create a variable trait -- that is where the value is infinitely (or relatively infinitely) variable (as opposed to one of a discrete set) as in the case of TraitFactory.makeDiscrete(Pharacter, String).

Methods in com.rubecula.darwin.domain.environment that return types with arguments of type Trait

java.util.Collection<Trait>

TraitMap_.getTraits() TEST

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

java.lang.String	Phenotype_.addTrait(java.lang.String key, Trait trait) Add a trait and set it to "belong" to this Phenotype.
java.lang.String	Phenotype_.addTrait(Trait trait) Add a trait using for its key the id of the character to which this trait belongs.
protected void	TraitMap_.put(java.lang.String key, Trait value)

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

void	Phenotype_.doCensus(Pharacter character, FrequencyMap<Trait> traitFrequencies)
static Trait	TraitFactory.makeTrait(java.lang.Class<? extends Trait> clazz, java.lang.Character character, java.lang.Object value) TEST

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

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

double

Fitness_Hamiltonian.getFitness(Trait trait, EcoFactor factor)

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

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

Trait	Expresser.express(Gene... genes) Express the genes.
Trait	TraitMap.getTrait(java.lang.String name) Accessor method to retrieve a trait from the map by name

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

java.util.Collection<Trait>

TraitMap.getTraits() TODO not required.

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

java.lang.String	Phenotype.addTrait(java.lang.String key, Trait trait)
java.lang.String	Phenotype.addTrait(Trait trait) Add the given trait to this Phenotype.
double	Fitness.getFitness(Trait trait, EcoFactor factor)

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

void	Phenotype.doCensus(Pharacter character, FrequencyMap<Trait> traitFrequencies)

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

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

Trait	Expresser_Mendelian.express(Gene... genes) Express (one) gene passed in [Note this class cannot handle calls to this method with multiple genes].
protected Trait	Expresser_Mendelian.expressDiploid(Gene gene)
protected Trait	Expresser_Sex.expressHaploid(Gene gene) We can express the sex of a (haploid) gamete
protected Trait	Expresser_Mendelian.expressHaploid(Gene gene)

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

FrequencyMap<Trait>

OrganismCensusContext.getTraitFrequencies()

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

void	TraitFrequencyMap.add(Trait key)
void	TraitFrequencyMap.add(Trait key, int increment)
boolean	TraitFrequencyMap.containsTrait(Trait trait)
int	TraitFrequencyMap.get(Trait trait)
int	TraitFrequencyMap.remove(Trait trait)

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

OrganismCensusContext(Pharacter character, FrequencyMap<Allele> alleleFrequencies, NumericFrequencyMap ageFrequencies, FrequencyMap<java.lang.String> sexFrequencies, FrequencyMap<Trait> traitFrequencies)

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

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

double

WcSdFitness.getFitness(Trait trait, EcoFactor factor)

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

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

Trait

Expresser_TS.express(Gene... genes)

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

double

RouteFitness.getFitness(Trait trait, EcoFactor factor) Calculate the fitness for the trait and the factor.