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

Packages that use Gene

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.travelingsalesman	Traveling Salesman Example

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

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

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...).
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.

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

Classes in com.rubecula.darwin.domain.genetics that implement Gene

class	Gene_ This abstract class represents a particular gene at a locus of a genome.
class	Gene_Diploid Lifespan: transient.
class	Gene_Haploid Lifespan: transient.

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

Gene	Genotype_.getGene(int locus)
Gene	Genome_.getGene(java.lang.String id)
static Gene	GeneFactory.makeDiploid(Locus locus, java.lang.String allele1, java.lang.String allele2) Construct a new Gene_Diploid with the given allele indexes
static Gene	GeneFactory.makeGene(java.lang.Class<? extends Gene> clazz, Locus locus, java.lang.Object... parameters) TEST
Gene	Locus_.makeGene(java.lang.String... alleles) Make a gene with the alleles specified by the variable number of allele indexes.
static Gene	GeneFactory.makeHaploid(Locus locus, java.lang.String allele)
Gene	Gene_.mutate(Mutator mutator) Method to get a mutated copy of a Gene.

Methods in com.rubecula.darwin.domain.genetics that return types with arguments of type Gene

protected java.util.Collection<Gene>

Genotype_.getList()

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

boolean	Genotype_.addGene(Gene gene)
void	Genotype_.addGene(int locus, Gene gene)
java.lang.String	Meiosis_Clone.doMeiosis(Gene gene, int index)
java.lang.String	Meiosis_.doMeiosis(Gene gene, int index) Choose an allele at random for the given locus.
protected boolean	Mutator_.isComplementary(Gene prior, Gene gene) Method to test whether two genes are complimentary.

Method parameters in com.rubecula.darwin.domain.genetics with type arguments of type Gene

static Gene

GeneFactory.makeGene(java.lang.Class<? extends Gene> clazz, Locus locus, java.lang.Object... parameters) TEST

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

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

Gene	Genes.getGene(int locus)
Gene	Genome.getGene(java.lang.String id)
Gene	Locus.makeGene(java.lang.String... keys) Make a gene with the alleles specified by the variable number of allele indexes.
Gene	Gene.mutate(Mutator mutator) Method to get a mutated copy of a Gene.

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

boolean	Genotype.addGene(Gene gene) Add gene to this Genotype at its end.
void	Genotype.addGene(int locus, Gene gene) Add a Gene to this Genotype at a specific index.
java.lang.String	Meiosis.doMeiosis(Gene gene, int index) This method determines which allele will be chosen for a particular gene locus.
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.
Trait	Expresser.express(Gene... genes) Express the genes.

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

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

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)

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

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

java.util.Collection<Expression>	Expresser_TS.express(Colony colony, Gene... genes) TODO this is apparently called more often than necessary
Trait	Expresser_TS.express(Gene... genes)