com.rubecula.darwin.domain.helper
Interface Organism

All Superinterfaces:

Censusible, java.lang.Comparable<Valuable>, ComparableValue, EnvironmentListener, Genetic, net.sf.tostring0.Identifiable, Individual, net.sf.tostring0.IToString, Mortal, Valuable

All Known Implementing Classes:

Organism_, Organism_Asexual, Organism_Sexual, Organism_TS

public interface Organism
extends Mortal, Genetic, net.sf.tostring0.IToString, EnvironmentListener, Censusible, ComparableValue

Defines methods on an individual organism within a Taxon. An Organism exhibits the following properties:

genome

the (possibly) unique genome for the individual, (from which may be derived a Phenotype in the context of a Genomic);

age

the age of the individual (a count of the number of times the method Mortal.age() has been called on it);

phenotype

the phenotype of this individual (not necessarily a fixed property - may be derived on the fly)

;

colony

the colony to which this organism belongs;

Version:

$Revision: 1.20 $

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

Method Summary

Mate	createMate(MateChoice chooser, Organism female) Create a Mate object based on this (male) organism and its desirability to the given female.
Mating	createPairBond(MateChoice chooser, Lek lek, Lek alternativeLek)
java.util.Collection<Organism>	getAsexualProgeny(int howMany)
Colony	getColony() Method to determine to which population this organism currently belongs.
java.lang.Number	getFitness(FitnessEngine fitnessEngine)
Nuclear	getNuclear()
Phenotype	getPhenotype()
boolean	isMortal(double fitness) TODO consider change the name and sense of the result so that the method returns true if it stays alive.
void	normalizeGenome(Genome referenceGenome, java.util.Map<java.lang.String,Genome> cache, Environment environment)
void	setColony(Colony colony) Mutating method to change the current population for this organism, as a result of migration.
boolean	setViability(Viability viability)

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

age, getAge, isViable, setViable

Methods inherited from interface com.rubecula.darwin.foundation.Individual

getVisualizable, isNew, isVisible

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

getGenome

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

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

onEnvironmentChange

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

censusMe, getCensusibleChildren

Methods inherited from interface com.rubecula.darwin.foundation.Valuable

getValue

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

Methods inherited from interface java.lang.Comparable

compareTo

Method Detail

createMate

Mate createMate(MateChoice chooser,
                Organism female)

Create a Mate object based on this (male) organism and its desirability to the given female.

Parameters:

chooser - the object which will calculate the desirability of this organism to the given female.

female - the organism looking for a mate.

Returns:

if organism is male, then a newly constructed Mate based on the organism and that organism's desirability as a mate; otherwise null.

createPairBond

Mating createPairBond(MateChoice chooser,
                      Lek lek,
                      Lek alternativeLek)

Parameters:

chooser -

lek - the breeding males from which we will choose a mate

alternativeLek - may be null

Returns:

a new Mating object which is a pair bond between this organism (assuming it's a female) and a male from the population specified.

getAsexualProgeny

java.util.Collection<Organism> getAsexualProgeny(int howMany)

Parameters:

howMany - the number of progeny to be born.

Returns:

a collection of progeny from the given organism.

getColony

Colony getColony()

Method to determine to which population this organism currently belongs. Getter/setter typically called by reflection.

Returns:

the population to which this organism belongs.

getFitness

java.lang.Number getFitness(FitnessEngine fitnessEngine)
                            throws FitnessException

Parameters:

fitnessEngine -

Returns:

the fitness of this organism in its environment

Throws:

FitnessException

getNuclear

Nuclear getNuclear()

Returns:

the cellular object underlying this organism

getPhenotype

Phenotype getPhenotype()

Returns:

the phenotype for this organism.

isMortal

boolean isMortal(double fitness)

TODO consider change the name and sense of the result so that the method returns true if it stays alive.

Parameters:

fitness - the fitness of the organism whose mortality we are discovering

Returns:

true if the organism's number is up

normalizeGenome

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

Parameters:

referenceGenome -

cache -

environment -

setColony

void setColony(Colony colony)

Mutating method to change the current population for this organism, as a result of migration. If this is called programatically, the call should be followed by invoking EnvironmentListener.onEnvironmentChange(Environment), although that isn't necessary when "killing" an organism. Getter/setter typically called by reflection.

Parameters:

colony - the new population to which this organism now belongs.

setViability

boolean setViability(Viability viability)
                     throws FitnessException

Parameters:

viability - XXX

Returns:

true if this Organism's viability has been reset.

Throws:

FitnessException