com.rubecula.darwin.domain.genetics
Class Locus_Random

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.genetics.Locus_
          com.rubecula.darwin.domain.genetics.Locus_Random

All Implemented Interfaces:

Locus, Progenitor, SexLinked, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Locus_Sex, Locus_Triversian, Locus_TS

public abstract class Locus_Random
extends Locus_

Lifespan: permanent. Default implementation of Locus which uses a random number source to pick alleles during seeding.

Author:

Robin Hillyard

Field Summary

protected Randomizer

_random

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

LOG

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

ID_SEX

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

Locus_Random(java.lang.String identifier, org.apache.commons.math.random.RandomGenerator random)

Method Summary

java.lang.String	add(Allele allele, int frequency) This is used only when a mutation occurs.
protected void	onChange() This method is invoked whenever the set of alleles or their frequencies changes
java.lang.String	pickAllele() Randomly choose a particular allele from the possible alleles at this locus.
void	setAlleles(java.util.Map<? extends Allele,java.lang.Integer> map) Preferred method of setting up the allele/frequency map (rather than using add()).

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

addAllele, equals, getAllele, getAlleleMap, getAlleles, getAlleleValues, getChromosome, getFrequencies, getIdentifier, getKey, getParent, getPolygenic, hashCode, isLegal, isSexLinked, makeGene, putAllele, setParent, setPolygenic, size

Methods inherited from class net.sf.tostring0.AToString

toString, toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

Field Detail

_random

protected final Randomizer _random

Constructor Detail

Locus_Random

public Locus_Random(java.lang.String identifier,
                    org.apache.commons.math.random.RandomGenerator random)

Parameters:

identifier -

random -

Method Detail

add

public java.lang.String add(Allele allele,
                            int frequency)

This is used only when a mutation occurs. Normally the legal alleles at the start of an evolution are set using setAlleles(Map).

Parameters:

allele - An allele which can possibly appear at this locus.

frequency - The relative frequency with which this allele appears at this locus in the gene pool. This is used when seeding a population.

Returns:

the result of invoking Locus_.putAllele(Allele, int) with allele and frequency as the parameters. TODO eliminating this and using putAllele directly.

See Also:

Locus.add(com.rubecula.darwin.domain.helper.Allele, int)

pickAllele

public java.lang.String pickAllele()

Randomly choose a particular allele from the possible alleles at this locus.

Returns:

the key to the allele. XXX this should probably be combined with the Seed stuff.

See Also:

Locus.pickAllele()

setAlleles

public void setAlleles(java.util.Map<? extends Allele,java.lang.Integer> map)

Description copied from class: Locus_

Preferred method of setting up the allele/frequency map (rather than using add()).

Overrides:

setAlleles in class Locus_

See Also:

Locus_.setAlleles(Map)

onChange

protected void onChange()

Description copied from class: Locus_

This method is invoked whenever the set of alleles or their frequencies changes

Overrides:

onChange in class Locus_