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

Packages that use Genome

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 Genome in com.rubecula.darwin.domain.genetics

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

class	Genome_ This abstract class provides base definitions for implementers of Genome, the genetic information contained in an Organism belonging to a Taxon.
class	Genome_Linear Lifespan: transient.

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

Genome	Genomic_.createGamete(Genes genes) XXX This is very similar to the way SeedGenome works.
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)
Genome	Genome_.fertilize(Genes other) Method to fuse this haploid genome with other genome into a new diploid genome.
Genome	Nuclear_.getGenome() XXX
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 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(Genome gameteX, Genes gameteY)
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.
Genome	Mutator_.mutate(Genome genome) By default, the copy of the genome is returned, such that the individual genes have been processed using the Mutator_.mutate(Allele) method.
Genome	Genomic_.mutate(Genome genome) Non-mutating method to mutate this Genome and return a mutated copy.
Genome	Genome_.mutate(Mutator mutator)

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

static Nuclear	NuclearFactory.makeClone(Genome genome, java.lang.String colonyId)
static Nuclear	NuclearFactory.makeNuclear(java.lang.Class<? extends Nuclear> clazz, Genome genome, java.lang.String popId)
static Genome	GenomeFactory.makeZygote(Genome gameteX, Genes gameteY)
static Nuclear	NuclearFactory.makeZygote(Genome genome, java.lang.String colonyId)
Genome	Mutator_.mutate(Genome genome) By default, the copy of the genome is returned, such that the individual genes have been processed using the Mutator_.mutate(Allele) method.
Genome	Genomic_.mutate(Genome genome) Non-mutating method to mutate this Genome and return a mutated copy.
void	Mutator_.normalize(Genome genome, Genome reference)
void	Genomic_.normalize(Genome genome, Genome reference) Normalize the given genome with respect to the reference genome.
boolean	Mutator_.simplify(Genome genome) Do nothing.
boolean	Genomic_.simplify(Genome genome) Repeatedly invoke the simplify method of the mutator on the genome until there are no further changes.

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

static Genome

GenomeFactory.makeGenome(java.lang.Class<? extends Genome> clazz, Genomic genomic, java.lang.Object... parameters) TEST

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

Nuclear_(Genome genome, java.lang.String populationTag)
Protected Primary Constructor

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

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

Genome	Replicator.createGamete(Genes genes) Method to create a "gamete", a single (haploid) set of genes, for example an X or Y chromosome in the human genome.
Genome	Meiosis.doMeiosis(Genomic genomic, Genes genes, Chromosome chromosome) This method determines which alleles will be chosen for a complete chromosome.
Genome	Genome.fertilize(Genes other) Method to fuse this haploid genome with other genome into a new diploid genome.
Genome	Genetic.getGenome()
Genome	Mutator.mutate(Genome genome) Method to take a genome and mutate it.
Genome	Genomic.mutate(Genome genome) Non-mutating method to mutate this Genome and return a mutated copy.
Genome	Genome.mutate(Mutator mutator) Method to mutate a Genome using a particular mutator.

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

Genome	Mutator.mutate(Genome genome) Method to take a genome and mutate it.
Genome	Genomic.mutate(Genome genome) Non-mutating method to mutate this Genome and return a mutated copy.
void	Mutator.normalize(Genome genome, Genome reference) Normalize the given genome with respect to the reference genome.
void	Genomic.normalize(Genome genome, Genome reference) Normalize the given genome with respect to the reference genome.
void	Organism.normalizeGenome(Genome referenceGenome, java.util.Map<java.lang.String,Genome> cache, Environment environment)
boolean	Mutator.simplify(Genome genome) Simplify the genome, typically by removing any non-functional groups of genes.
boolean	Genomic.simplify(Genome genome)

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

void	Organism.normalizeGenome(Genome referenceGenome, java.util.Map<java.lang.String,Genome> cache, Environment environment)

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

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

Genome

Organism_.getGenome()

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

static Organism	Organism_Asexual.makeProgeny(java.lang.String identifier, Colony colony, Genome genome)
void	Organism_.normalizeGenome(Genome referenceGenome, java.util.Map<java.lang.String,Genome> cache, Environment environment) TODO consider adding this to the Organism interface.

Method parameters in com.rubecula.darwin.domain.world with type arguments of type Genome

void	Organism_.normalizeGenome(Genome referenceGenome, java.util.Map<java.lang.String,Genome> cache, Environment environment) TODO consider adding this to the Organism interface.

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

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

Genome

Mutator_TS.mutate(Genome genome) Mutate the given genome.

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

Genome	Mutator_TS.mutate(Genome genome) Mutate the given genome.
boolean	Mutator_TS.simplify(Genome genome) Iterate through the genome, removing pairs of complementary genes.