com.rubecula.darwin.domain.helper
Interface Genome

All Superinterfaces:

Basic, CacheSignature, Censusible, java.util.Collection<Gene>, Genes, Genotype, net.sf.tostring0.Identifiable, java.lang.Iterable<Gene>, net.sf.tostring0.IToString, java.util.List<Gene>, Ploidy

All Known Implementing Classes:

Genome_, Genome_Linear

public interface Genome
extends Genotype

Defines the genetic information contained in an Organism belonging to a Taxon. A Genome may contain any number of instances of Gene , though in practice the number is determined by the Genomic which defines this Genome. The structure of Genome is approximately parallel to that of Genomic.

TODO consider restructuring a Genome such that is contains one or two Genotypes (according to the Ploidy) and that each Genotype is a (haploid) collection of Genes with a single allele each. This would clarify the concept of a Genotype. It would also mean a lot of work.

Author:

Robin Hillyard

Field Summary

Fields inherited from interface net.sf.tostring0.IToString

ANGBR_OPEN, ANGBRA_CLSE, BRA_CLSE, BRA_OPEN, BRCE_OPEN, BRCS_CLSE, COLON, LIST_SEPARATOR, MAX_ELEMENTS_DEFAULT, S_MT, S_PERCENT, SEPARATOR, SPACE

Fields inherited from interface com.rubecula.darwin.domain.helper.Ploidy

DIPLOID, HAPLOID

Method Summary

void	environmentChanged(Visualizable colony) Flush the cached phenotype for this genome/colony combination.
Phenotype	express(Colony colony) Express the genes of this Genome in the context of population and return the result as a Phenotype.
Genome	fertilize(Genes other) Method to fuse this haploid genome with other genome into a new diploid genome.
Gene	getGene(java.lang.String id)
Genomic	getGenomic()
boolean	getSex()
Genes	invert()
Genome	mutate(Mutator mutator) Method to mutate a Genome using a particular mutator.

Methods inherited from interface com.rubecula.darwin.domain.helper.Genotype

addGene, addGene, addGenes, doCensus

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

Methods inherited from interface com.rubecula.darwin.domain.helper.Ploidy

getPloidy

Methods inherited from interface com.rubecula.darwin.domain.helper.Genes

getGene

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from interface com.rubecula.darwin.domain.helper.Basic

getBases

Methods inherited from interface com.rubecula.darwin.domain.helper.CacheSignature

getSignature

Methods inherited from interface com.rubecula.darwin.domain.helper.Censusible

censusMe, getCensusibleChildren

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

Method Detail

environmentChanged

void environmentChanged(Visualizable colony)

Flush the cached phenotype for this genome/colony combination. This must be called for any significant population change in the colony, or change to the colony's environment. A significant change is one that would result in a different phenotype being returned. TODO consider implementing VisualizableListener instead, but the semantics are slightly different in that we want to note changes to populations and/or environments.

Parameters:

colony -

express

Phenotype express(Colony colony)

Express the genes of this Genome in the context of population and return the result as a Phenotype.

Parameters:

colony - the population this genome belongs to, often ignored.

Returns:

a Phenotype corresponding to the expressed genes of this Genome, in the context of population.

fertilize

Genome fertilize(Genes other)

Method to fuse this haploid genome with other genome into a new diploid genome. In theory, at least, there is no implied ordering of the two gametes. The resulting genome should express as a phenotype regardless of the ordering of the arguments x and y. At meiosis, the ordering of the parents x, y is semi-significant - but the effect should be masked by the seeding of the random number generator for a mating. This and the other gamete must conform to the same Genomic, otherwise, no fertilization can take place. TODO in theory, we could allow this and two other Genes parameters to combine into a triploid result.

Parameters:

other - the gamete to be fused with this gamete

Returns:

the resulting genome.

getGene

Gene getGene(java.lang.String id)

Parameters:

id -

Returns:

the Gene whose locus has the identifier id

getGenomic

Genomic getGenomic()

Returns:

the genomic to which this genome conforms.

getSex

boolean getSex()
               throws GeneticsException

Returns:

the sex of this genome.

Throws:

GeneticsException

invert

Genes invert()

Returns:

a set of genes which is complementary to this genome.

mutate

Genome mutate(Mutator mutator)

Method to mutate a Genome using a particular mutator. Implementers of this method should normally return a copy of this Genome, rather than simply a reference (although if the mutator is the identity mutator, it is acceptable to return a reference to the original).

Parameters:

mutator - the mutator

Returns:

possibly mutated copy of this (or possibly a reference to the unmutated original).