com.rubecula.darwin.domain.helper
Interface Taxon

All Superinterfaces:

Censusible, Evolvable, Generational, HasPhenotypeCache, net.sf.tostring0.Identifiable, Registry, Terminal, Theological

All Known Implementing Classes:

Taxon_, Taxon_Darwinian

public interface Taxon
extends Evolvable, Registry, HasPhenotypeCache, Censusible

Defines the methods supported by a unit of evolutionary computation (Taxon). Try not to get too hung up on the name "Taxon": a rose by any other name... Indeed, "unit", "system", "species", "clade", "phylogenetic entity", etc. would all be reasonable names for this type family. Essentially a Taxon is an evolvable object which "owns" a collection of Organisms which all share the same Genomic and Phenome, in other words what we commonly refer to as a species. If you want to model the interaction of two such species, for example predator and prey, then you need to have more than one taxon in your Evolution. The chief properties (fixed unless otherwise specified) of a taxon are:

realm

the implementer of Realm (i.e. the "model") to which the taxon belongs;

populations

a (variable) set of Population instances but TODO populations should belong to the realm, not the taxon;

fecundity

the implementer of the Fecundity interface,

which defines how well organisms of the taxon reproduce;

genomic

the implementer of the Genomic interface, which defines the genomic organization for all organisms of the taxon;

phenome

the implementer of the Phenome interface,

which defines the phenome for all organisms of the taxon;

mortality

the implementer of the Mortality interface, which defines how likely organisms of the taxon are to die;

chooser

the implementer of the MateChoice interface, which defines how organisms of the taxon choose a mate;

population listeners

a (variable) set of implementers of the VisualizableListener interface, each of which will be notified via its callback method when the population changes (typically at the end of each generation)

census taker

the implementer of the Census interface, which defines how census operations are performed on the organisms.

Version:

$Revision: 1.2 $

Author:

Robin Hillyard

Method Summary

int	addPopulation(Population population) Mutating method to add a population to the system.
void	addVisualizableListener(VisualizableListener listener) Mutating method to add, for each of this system's populations, a listener, i.e.
void	doCensus() Method to enumerate this population for census purposes.
Census	getCensusTaker()
MateChoice	getChooser()
Fecundity	getFecundity()
Genomic	getGenomic()
Mortality	getMortality()
Phenome	getPhenome() Method to get the phenome for this system, i.e.
java.lang.Object	getProperty(java.lang.Object key)
Realm	getRealm()
int	getSeedPopulation()
java.util.Collection<VisualizableListener>	getVisualizableListeners() Getter/setter typically called by reflection.
boolean	isLastGeneration()
void	setPopulations(java.util.Collection<Population> populations)
java.lang.Object	setProperty(java.lang.String key, java.lang.Object value) Method to set an arbitrary property for this system.
void	setVisualizableListeners(java.util.Collection<VisualizableListener> listeners) Getter/setter typically called by reflection.

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

getGeneration, getResult

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

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

nextGeneration

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

cullMembers, seedMembers

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

isFinished

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

registerBirths, registerDeaths, registerMarriages

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

getPhenotypeCache

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

censusMe, getCensusibleChildren

Method Detail

addPopulation

int addPopulation(Population population)

Mutating method to add a population to the system.

Parameters:

population - an implementer of Population.

Returns:

true if the population was added successfully.

addVisualizableListener

void addVisualizableListener(VisualizableListener listener)

Mutating method to add, for each of this system's populations, a listener, i.e. an implementer of VisualizableListener.

Parameters:

listener - the listener of population change events.

doCensus

void doCensus()
              throws java.io.IOException

Method to enumerate this population for census purposes.

Throws:

java.io.IOException

getCensusTaker

Census getCensusTaker()

Returns:

the application-specific implementer of Census.

getChooser

MateChoice getChooser()

Returns:

the application-specific implementer of MateChoice.

getFecundity

Fecundity getFecundity()

Returns:

the application-specific implementer of Fecundity.

getGenomic

Genomic getGenomic()

Returns:

the Genomic for this Taxon System.

getMortality

Mortality getMortality()

Returns:

the application-specific implementer of Mortality.

getPhenome

Phenome getPhenome()

Method to get the phenome for this system, i.e. the implementer of Phenome.

Returns:

value of (private) field _Phenome.

getProperty

java.lang.Object getProperty(java.lang.Object key)

Parameters:

key -

Returns:

the property for the key.

getRealm

Realm getRealm()

Returns:

the realm to which this system belongs

getSeedPopulation

int getSeedPopulation()

Returns:

the seed population

getVisualizableListeners

java.util.Collection<VisualizableListener> getVisualizableListeners()

Getter/setter typically called by reflection.

Returns:

the population listeners as a collection.

isLastGeneration

boolean isLastGeneration()

Returns:

true if this is the last generation we will process

setPopulations

void setPopulations(java.util.Collection<Population> populations)

Parameters:

populations - Getter/setter typically called by reflection.

setProperty

java.lang.Object setProperty(java.lang.String key,
                             java.lang.Object value)

Method to set an arbitrary property for this system.

Parameters:

key -

value -

Returns:

the previous value of the property for this key, if any.

setVisualizableListeners

void setVisualizableListeners(java.util.Collection<VisualizableListener> listeners)

Getter/setter typically called by reflection.

Parameters:

listeners -