com.rubecula.darwin.domain.world
Class Genomic_Asexual

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.genetics.Genomic_
          com.rubecula.darwin.domain.genetics.Genomic_Haploid
              com.rubecula.darwin.domain.world.Genomic_Asexual

All Implemented Interfaces:

Chromosome, Genomic, Ploidy, Progenitor, Replicator, SexLinked, Countable, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

public final class Genomic_Asexual
extends Genomic_Haploid
implements Chromosome

Lifespan: permanent. Concrete implementation of Genomic representing the possible genetic information contained in a Taxon. A Genomic_Asexual contains exactly one non-sex-linked chromosome, which in turn may contain any number of gene Loci. If you need a multi-chromosome haploid genome, then extend Genomic_Haploid.

Version:

$Revision: 1.12 $

Author:

Robin Hillyard

Field Summary

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

_chromosomes, expresserCommon, expressers, LOG

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

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

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

DIPLOID, HAPLOID

Constructor Summary

Genomic_Asexual(java.lang.String identifier)

Genomic_Asexual(java.lang.String identifier, org.apache.commons.math.random.RandomGenerator random, Mutator mutator)

Method Summary

void	addLocus(int index, Locus locus) TEST
boolean	addLocus(Locus locus) Method to add a Locus at the end of this Genomic.
Genomic	getGenomic()
java.lang.String	getIdentifier()
java.util.Collection<Locus>	getLoci() Getter/setter typically used by reflection.
boolean	isSexLinked()
void	setGenomic(Genomic genomic) TEST
void	setLoci(java.util.Collection<Locus> loci) This is now the preferred method to set the loci.

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

addChromosome, addChromosome, clearChromosomes, createGamete, equals, express, express, getAlphabet, getChromosome, getChromosomes, getCount, getExpresser, getExpressers, getLocus, getLocusCount, getMeiosis, getMutator, getPloidy, hashCode, mutate, normalize, putExpresser, setChromosomes, setExpresser, setExpressers, simplify

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 com.rubecula.darwin.domain.helper.Chromosome

getCount, getLocus

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

Constructor Detail

Genomic_Asexual

public Genomic_Asexual(java.lang.String identifier)

Parameters:

identifier -

Genomic_Asexual

public Genomic_Asexual(java.lang.String identifier,
                       org.apache.commons.math.random.RandomGenerator random,
                       Mutator mutator)

Parameters:

identifier -

random - random number source

mutator -

Method Detail

addLocus

public void addLocus(int index,
                     Locus locus)
              throws GeneticsException

TEST

Specified by:

addLocus in interface Chromosome

Parameters:

index - the index at which the new object will appear.

locus - a locus to be inserted into this Genomic.

Throws:

GeneticsException

See Also:

Chromosome.addLocus(int, com.rubecula.darwin.domain.helper.Locus)

addLocus

public boolean addLocus(Locus locus)
                 throws GeneticsException

Description copied from interface: Chromosome

Method to add a Locus at the end of this Genomic.

Specified by:

addLocus in interface Chromosome

Parameters:

locus - a locus to be inserted into this Genomic.

Returns:

true if the locus is added successfully.

Throws:

GeneticsException

See Also:

Chromosome.addLocus(com.rubecula.darwin.domain.helper.Locus)

getGenomic

public Genomic getGenomic()

Specified by:

getGenomic in interface Chromosome

Returns:

the Genomic to which this chromosome belongs.

See Also:

Chromosome.getGenomic()

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

Overrides:

getIdentifier in class Genomic_

Returns:

Identifiable.getIdentifier() invoked on _chromosome.

See Also:

Identifiable.getIdentifier()

getLoci

public java.util.Collection<Locus> getLoci()

Description copied from interface: Chromosome

Getter/setter typically used by reflection.

Specified by:

getLoci in interface Chromosome

Returns:

the loci as a collection of Locus objects.

See Also:

Chromosome.getLoci()

isSexLinked

public boolean isSexLinked()

Specified by:

isSexLinked in interface SexLinked

Returns:

true if this object is sex-linked, that is to say it is a sex chromosome, a locus on a sex chromosome, or a phenotypic character which derives from one/more sex-linked gene(s).

See Also:

SexLinked.isSexLinked()

setGenomic

public void setGenomic(Genomic genomic)

TEST

Specified by:

setGenomic in interface Chromosome

See Also:

Chromosome.setGenomic(com.rubecula.darwin.domain.helper.Genomic)

setLoci

public void setLoci(java.util.Collection<Locus> loci)

Description copied from interface: Chromosome

This is now the preferred method to set the loci. Any prior loci will be forgotten. Getter/setter typically used by reflection.

Specified by:

setLoci in interface Chromosome

See Also:

TEST