com.rubecula.darwin.domain.world
Class Organism_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.world.Organism_

All Implemented Interfaces:

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

Direct Known Subclasses:

Organism_Asexual, Organism_Sexual

public abstract class Organism_
extends net.sf.tostring0.AToString
implements Organism, java.lang.Cloneable

Abstract class defining the base methods and fields of an implementation of Organism interface. TODO this is a huge type file. Consider splitting up.

Author:

Robin Hillyard

Field Summary

protected java.lang.String	_identifier An identifier for this organism.
protected Nuclear	_nuclear The cell (in effect the nuclear DNA) to which this organism conforms.
protected static org.apache.commons.logging.Log	LOG The logger for this class.

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

Constructor Summary

protected

Organism_(java.lang.String identifier, Colony colony, Nuclear nuclear) Construct a new organism with the following attributes:

Method Summary

void	age() Age this organism by one year.
boolean	censusMe(Census census, java.lang.Object context) There are two paths through this method: 1) if context is an instance of OrganismCensusContext, then we call doCensusInContext(OrganismCensusContext) and consider ourselves done (no need for going deeper through children); 2) otherwise, we output information about this Organism and return true (OK not yet done -- need to iterate through children).
java.lang.Object	clone()
int	compareTo(Valuable o)
boolean	equals(java.lang.Object obj)
int	getAge()
java.util.Collection<? extends Censusible>	getCensusibleChildren() Method to return a list of censusible children of this object.
Colony	getColony() Method to determine to which population this organism currently belongs.
java.lang.Number	getFitness(FitnessEngine fitnessEngine)
Genome	getGenome()
java.lang.String	getIdentifier()
protected Mortality	getMortality() Get the mortality for this mortal object (from the system of the colony to which this organism belongs).
Nuclear	getNuclear()
Phenotype	getPhenotype() Get the phenotype by expressing the genome in the context of the colony.
java.lang.Number	getValue() Get the fitness for this Organism, either from the cache for the fitness engine, or by calculation.
Visualizable	getVisualizable() TEST
int	hashCode()
boolean	isMortal(double fitness) TODO calculate fitness within this method rather than have it passed in.
boolean	isNew() TEST
boolean	isViable()
boolean	isVisible() TEST
void	normalizeGenome(Genome referenceGenome, java.util.Map<java.lang.String,Genome> cache, Environment environment) TODO consider adding this to the Organism interface.
void	onEnvironmentChange(Environment env) flush the fitness cache completely.
void	setColony(Colony colony) Reset the owning colony of this organism.
boolean	setViability(Viability viability)
void	setViable(boolean viable)

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.Organism

createMate, createPairBond, getAsexualProgeny

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

Field Detail

LOG

protected static final org.apache.commons.logging.Log LOG

The logger for this class.

_nuclear

protected final Nuclear _nuclear

The cell (in effect the nuclear DNA) to which this organism conforms.

_identifier

protected final java.lang.String _identifier

An identifier for this organism.

Constructor Detail

Organism_

protected Organism_(java.lang.String identifier,
                    Colony colony,
                    Nuclear nuclear)

Construct a new organism with the following attributes:

Parameters:

identifier - a string by which to identify this organism (may be null).

colony - the Population to which this specific organism belongs

nuclear - the Genome to which this organism (and all its relatives) adheres.

Method Detail

age

public void age()

Age this organism by one year.

Specified by:

age in interface Mortal

See Also:

Mortal.age()

censusMe

public boolean censusMe(Census census,
                        java.lang.Object context)

There are two paths through this method: 1) if context is an instance of OrganismCensusContext, then we call doCensusInContext(OrganismCensusContext) and consider ourselves done (no need for going deeper through children); 2) otherwise, we output information about this Organism and return true (OK not yet done -- need to iterate through children).

Specified by:

censusMe in interface Censusible

Parameters:

census - the census object which will present the results of taking this census

context - an arbitrary object which can be used by the census object to provide appropriate context for this object.

Returns:

true if we should continue censusing this object at deeper levels. If the result is false, then we do not call Censusible.getCensusibleChildren().

See Also:

Censusible.censusMe(Census, java.lang.Object)

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

See Also:

Object.clone()

compareTo

public int compareTo(Valuable o)

Specified by:

compareTo in interface java.lang.Comparable<Valuable>

See Also:

Comparable.compareTo(java.lang.Object)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

getAge

public int getAge()

Specified by:

getAge in interface Mortal

Returns:

the current age of this organism

See Also:

Mortal.getAge()

getCensusibleChildren

public java.util.Collection<? extends Censusible> getCensusibleChildren()

Description copied from interface: Censusible

Method to return a list of censusible children of this object.

Specified by:

getCensusibleChildren in interface Censusible

Returns:

either null or an ArrayList of censusible objects.

See Also:

Censusible.getCensusibleChildren()

getColony

public Colony getColony()

Description copied from interface: Organism

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

Specified by:

getColony in interface Organism

Returns:

the value of field colony.

See Also:

Organism.getColony()

getFitness

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

Specified by:

getFitness in interface Organism

Parameters:

fitnessEngine -

Returns:

the fitness of this Organism in its Environment.

Throws:

FitnessException

See Also:

Organism.getFitness(com.rubecula.darwin.domain.helper.FitnessEngine)

getGenome

public Genome getGenome()

Specified by:

getGenome in interface Genetic

Returns:

the genome for this genetic object.

See Also:

Genetic.getGenome()

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

See Also:

Identifiable.getIdentifier()

getNuclear

public Nuclear getNuclear()

Specified by:

getNuclear in interface Organism

Returns:

the nuclear object underlying this organism

getPhenotype

public Phenotype getPhenotype()

Get the phenotype by expressing the genome in the context of the colony.

Specified by:

getPhenotype in interface Organism

Returns:

the phenotype for this organism.

See Also:

Organism.getPhenotype()

getValue

public java.lang.Number getValue()
                          throws ValueException

Get the fitness for this Organism, either from the cache for the fitness engine, or by calculation. The higher the value, the fitter is the organism.

Specified by:

getValue in interface Valuable

Returns:

the fitness of this Organism by invoking getFitness(FitnessEngine) and passing it the fitness engine for the phenome for the system for the colony.

Throws:

ValueException

See Also:

Valuable.getValue()

getVisualizable

public Visualizable getVisualizable()

TEST

Specified by:

getVisualizable in interface Individual

Returns:

the Visualizable object of which this Individual is a member.

See Also:

Individual.getVisualizable()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

isMortal

public boolean isMortal(double fitness)

TODO calculate fitness within this method rather than have it passed in.

Specified by:

isMortal in interface Organism

Parameters:

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

Returns:

true if the organism's number is up (i.e. to be eliminated).

isNew

public boolean isNew()

TEST

Specified by:

isNew in interface Individual

Returns:

true if this individual has not yet been visualized.

See Also:

Individual.isNew()

isViable

public boolean isViable()

Specified by:

isViable in interface Mortal

Returns:

true if this organism is part of a population model (generally this is true, except temporarily when an organism is first born or newly dead)

See Also:

Mortal.isViable()

isVisible

public boolean isVisible()

TEST

Specified by:

isVisible in interface Individual

Returns:

true if this individual should be visualized.

See Also:

Individual.isVisible()

normalizeGenome

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

TODO consider adding this to the Organism interface.

Specified by:

normalizeGenome in interface Organism

Parameters:

referenceGenome - the genome to which this Organism's genome will be normalized

cache - map of bases -> genome pairs

environment - the environment to which this Organism belongs.

onEnvironmentChange

public void onEnvironmentChange(Environment env)

flush the fitness cache completely. Note that is is not sufficient to flush just the value for the genome because some genomes may have been lost from the gene pool, but not flushed from the cache, thus they would never get flushed and cause the wrong fitness values to be picked up later when an identical genome comes along which, because of the environment change, would have a different fitness value. TODO find a way to flush all only once on an environment change and then in this method we could then revert to simple flushing the cache for the genome, provided that we remove values from cache when they no longer exist in the gene pool.

Specified by:

onEnvironmentChange in interface EnvironmentListener

Parameters:

env - the environment which has changed.

See Also:

EnvironmentListener.onEnvironmentChange(com.rubecula.darwin.domain.helper.Environment)

setColony

public void setColony(Colony colony)

Reset the owning colony of this organism. This is only ever done

Specified by:

setColony in interface Organism

Parameters:

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

See Also:

Organism.setColony(Colony)

setViability

public boolean setViability(Viability viability)
                     throws FitnessException

Specified by:

setViability in interface Organism

Parameters:

viability - the determinant of viability for this Organism

Returns:

true if setViable(boolean) was invoked on this Organism.

Throws:

FitnessException

setViable

public void setViable(boolean viable)

Specified by:

setViable in interface Mortal

Parameters:

viable - if false, then we (temporarily) mark this organism as not being part of a population model.

See Also:

Mortal.setViable(boolean)

getMortality

protected Mortality getMortality()

Get the mortality for this mortal object (from the system of the colony to which this organism belongs).

Returns:

the mortality of the system of the colony.