com.rubecula.darwin.domain.genetics
Class Genome_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.foundation.AuditableList<Gene>
          com.rubecula.darwin.domain.genetics.Genotype_
              com.rubecula.darwin.domain.genetics.Genome_

All Implemented Interfaces:

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

Direct Known Subclasses:

Genome_Linear

public abstract class Genome_
extends Genotype_
implements Genome

This abstract class provides base definitions for implementers of Genome, the genetic information contained in an Organism belonging to a Taxon. A Genome may contain any number of Genes, 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 Genome_ extends Genotype_ and many of the uses of Genome_ could actually be narrowed to use Genotype_ instead, especially if fertilization and mutation were done at the Genotype level.

Version:

$Revision: 1.52 $

Author:

Robin Hillyard

Field Summary

Fields inherited from class com.rubecula.darwin.domain.genetics.Genotype_

_ploidy, LOG

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

Constructor Summary

protected

Genome_(Genomic genomic, int ploidy)

Method Summary

void	environmentChanged(Visualizable visualizable) Flush the cached phenotype for this genome/population combination.
boolean	equals(java.lang.Object obj) Determine equality based on the value of Genotype_.getBases().
Phenotype	express(Colony colony) Method to create a new phenotype from a collection of genes by expressing each and every gene, one at a time, using this Expresser.
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()
int	hashCode() return the hashcode of the bases.
Genes	invert() This implementation of invert() assumes that the genome is haploid.
Genome	mutate(Mutator mutator) Method to mutate a Genome using a particular mutator.

Methods inherited from class com.rubecula.darwin.domain.genetics.Genotype_

addGene, addGene, addGenes, censusMe, clone, doCensus, getBases, getCensusibleChildren, getGene, getIdentifier, getList, getPloidy, getSignature

Methods inherited from class com.rubecula.darwin.foundation.AuditableList

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

Methods inherited from class net.sf.tostring0.AToString

toString, toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

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, get, 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

Constructor Detail

Genome_

protected Genome_(Genomic genomic,
                  int ploidy)

Parameters:

genomic -

ploidy -

Method Detail

environmentChanged

public void environmentChanged(Visualizable visualizable)

Flush the cached phenotype for this genome/population combination. This must be called for any significant population change, or change to the population's environment. A significant change is one that would result in a different phenotype being returned.

Specified by:

environmentChanged in interface Genome

Parameters:

visualizable - the population which has changed.

See Also:

Genome.environmentChanged(Visualizable)

equals

public boolean equals(java.lang.Object obj)

Description copied from class: Genotype_

Determine equality based on the value of Genotype_.getBases(). Ignore the super-class.

Specified by:

equals in interface java.util.Collection<Gene>

Specified by:

equals in interface java.util.List<Gene>

Overrides:

equals in class Genotype_

See Also:

Object.equals(java.lang.Object)

express

public Phenotype express(Colony colony)

Method to create a new phenotype from a collection of genes by expressing each and every gene, one at a time, using this Expresser. This method may be overwritten by implementers of Expresser but that would be unusual. An example of why you might want to overwrite it would be to allow the expression of several genes together or to express more than one trait from any one gene. The phenotype for any particular population is cached. If the population changes in some significant way, for example a property of its environment changes, the method environmentChanged() should be called.

Specified by:

express in interface Genome

Parameters:

colony - even though generally ignored, it must be a valid population, with an environment that in turns has an environment factory.

Returns:

a Dawkinsian Phenotype filled with the expressed traits.

See Also:

Expresser.express(Colony, Gene[])

fertilize

public 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. XXX consider pulling this up into Genotype_.

Specified by:

fertilize in interface Genome

Parameters:

other - the gamete to be fused with this gamete

Returns:

the resulting genome.

getGene

public Gene getGene(java.lang.String id)

Specified by:

getGene in interface Genome

Returns:

the gene whose locus has identifier which matches id (ignoring case).

See Also:

Genome.getGene(java.lang.String)

getGenomic

public Genomic getGenomic()

Specified by:

getGenomic in interface Genome

Returns:

the genomic for this genome

getSex

public boolean getSex()
               throws GeneticsException

Specified by:

getSex in interface Genome

Returns:

the sex of this genome, expressed as a boolean (female is true if I recall).

Throws:

GeneticsException - if this Genome does not contain the sex gene, or it is improperly formed

hashCode

public int hashCode()

Description copied from class: Genotype_

return the hashcode of the bases. We ignore the super method.

Specified by:

hashCode in interface java.util.Collection<Gene>

Specified by:

hashCode in interface java.util.List<Gene>

Overrides:

hashCode in class Genotype_

See Also:

Object.hashCode()

invert

public Genes invert()

This implementation of invert() assumes that the genome is haploid. The resulting genes object is a set of genes of the same length as this genome, but result(i) = complement(gene(N-1-i)) where N is the number of genes. If you need a more complex inversion process, or for some reason, you are inverting non-haploid genomes, you will need to override this.

Specified by:

invert in interface Genome

Returns:

the inverted genome, as a Genes object.

See Also:

Genome.invert()

mutate

public Genome mutate(Mutator mutator)

Description copied from interface: Genome

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).

Specified by:

mutate in interface Genome

Parameters:

mutator - the mutator

Returns:

a distinct copy of this Genome, which may or may not be mutated.

See Also:

Genome.mutate(com.rubecula.darwin.domain.helper.Mutator)