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

Packages that use Genomic

com.rubecula.darwin.domain.genetics	Genetics
com.rubecula.darwin.domain.helper	Darwin
com.rubecula.darwin.domain.world	Darwin

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

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

class	Genomic_ Abstract class implementing base methods for the Genomic interface.
class	Genomic_Diploid Lifespan: permanent.
class	Genomic_Haploid Lifespan: permanent.

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

Genomic	Genome_.getGenomic()
Genomic	Chromosome_.getGenomic()

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

Genome	Meiosis_Locus.doMeiosis(Genomic genomic, Genes genes, Chromosome chromosome) This method does meiosis for a set of genes.
Genome	Meiosis_Clone.doMeiosis(Genomic genomic, Genes genes, Chromosome chromosome) This method essentially clones the existing set of genes.
Genome	Meiosis_Chromosome.doMeiosis(Genomic genomic, Genes genes, Chromosome chromosome) This method does meiosis for a set of genes.
protected Genome	Meiosis_.doMeiosisChromosome(Genomic genomic, Genes genes, Chromosome chromosome, int index)
static Genome	GenomeFactory.makeGamete(Genomic genomic) Factory method to create a haploid genome which conforms to the given Genomic and with genes where the alleles have been picked for each locus according to the Locus.pickAllele() method.
static Genome	GenomeFactory.makeGenome(java.lang.Class<? extends Genome> clazz, Genomic genomic, java.lang.Object... parameters) TEST
static Mating	MatingFactory.makeHaldanian(Genomic genomic, Organism female, Organism male, org.apache.commons.math.random.RandomGenerator random)
static Genome	GenomeFactory.makeLinear(Genomic genomic, int ploidy) Factory method to create an empty genome which conforms to the given Genomic and is diploid or haploid according to the ploidy parameter.
static Genome	GenomeFactory.makeZygote(Genomic genomic) Method to create (from "whole cloth") a new diploid Genome, by creating two gametes (using GenomeFactory.makeGamete(com.rubecula.darwin.domain.helper.Genomic) and then fertilizing them.
void	Chromosome_.setGenomic(Genomic genomic)

Constructors in com.rubecula.darwin.domain.genetics with parameters of type Genomic

Genome_(Genomic genomic, int ploidy)

Mating_(Nuclear parent1, Nuclear parent2, org.apache.commons.math.random.RandomGenerator random, Genomic genomic)
Protected primary constructor for a new instance of Mating_.

Mating_Haldanian(Nuclear parent1, Nuclear parent2, org.apache.commons.math.random.RandomGenerator random, Genomic genomic)
Primary constructor.

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

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

Genomic	Taxon.getGenomic()
Genomic	Genome.getGenomic()
Genomic	Chromosome.getGenomic()

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

Genome	Meiosis.doMeiosis(Genomic genomic, Genes genes, Chromosome chromosome) This method determines which alleles will be chosen for a complete chromosome.
void	Chromosome.setGenomic(Genomic genomic)

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

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

class	Genomic_Asexual Lifespan: permanent.
class	Genomic_Sexual Lifespan: permanent.

Fields in com.rubecula.darwin.domain.world declared as Genomic

protected Genomic

Taxon_._genomic The Genomic of this Taxon (fixed).

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

Genomic	Taxon_.getGenomic() XXX
Genomic	Genomic_Asexual.getGenomic()

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

Organism	Organism_Asexual.reproduce(java.lang.String identifier, Genomic genomic)
Organism	Asexual.reproduce(java.lang.String identifier, Genomic genomic) Method to perform asexual reproduction.
void	Genomic_Asexual.setGenomic(Genomic genomic) TEST

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

Taxon_(java.lang.String identifier, Realm realm, Genomic genomic, Phenome phenome, Census censusTaker, Mortality mortality, MateChoice chooser, Fecundity fecundity)
Constructor to create a Taxon with no populations.

Taxon_Darwinian(java.lang.String identifier, Realm realm, Genomic genomic, Phenome phenome, Census censusTaker, double infantMortality, MateChoice chooser, Fecundity fecundity, org.apache.commons.math.random.RandomGenerator random)
Constructor to create a Taxon with no populations, and with the default mortality implementer.

Taxon_Darwinian(java.lang.String identifier, Realm realm, Genomic genomic, Phenome phenome, Census censusTaker, Mortality mortality, MateChoice chooser, Fecundity fecundity)
Constructor to create a Taxon with no populations.