Uses of Interface
com.rubecula.darwin.domain.helper.Locus

Packages that use Locus

com.rubecula.darwin.domain.environment
com.rubecula.darwin.domain.genetics	Genetics
com.rubecula.darwin.domain.helper	Darwin
com.rubecula.darwin.domain.world	Darwin
com.rubecula.darwin.examples.pepperedmoth	Peppered Moth Example
com.rubecula.darwin.examples.travelingsalesman	Traveling Salesman Example

Uses of Locus in com.rubecula.darwin.domain.environment

Methods in com.rubecula.darwin.domain.environment with parameters of type Locus

java.lang.String	Expresser_.getComplement(Locus locus, java.lang.String allele) This implementation of getComplement first checks to make sure that the locus is binary (i.e.
boolean	Expresser_.isComplementary(Locus locus, java.lang.String allele1, java.lang.String allele2) XXX Be careful -- this needs to be overridden for any meaningful result.

Uses of Locus in com.rubecula.darwin.domain.genetics

Classes in com.rubecula.darwin.domain.genetics that implement Locus

class	Locus_ Abstract class defining the base methods and fields for an implementer of Locus.
class	Locus_Random Lifespan: permanent.
class	Locus_Sex Lifespan: permanent.
class	Locus_Triversian Lifespan: permanent.

Fields in com.rubecula.darwin.domain.genetics with type parameters of type Locus

protected java.util.Map<Locus,Expresser>

Genomic_.expressers

Methods in com.rubecula.darwin.domain.genetics that return Locus

Locus	Gene_.getLocus()
Locus	Allele_.getLocus() Return the value of Allele_.locus.
Locus	Genomic_.getLocus(int n) method to step through each chromosome and get the nth locus relative to this genom object.
Locus	Chromosome_.getLocus(int index)
Locus	Locus_.getPolygenic()
Locus	Chromosome_Sex.getSexLocus()
protected Locus	Chromosome_.remove(int index) Actually remove a locus, even if it is the sex locus (unless this method is overridden by Chromosome_Sex.

Methods in com.rubecula.darwin.domain.genetics that return types with arguments of type Locus

java.util.Map<Locus,Expresser>	Genomic_.getExpressers() This is a bean property (not part of an interface).
java.util.Collection<Locus>	Chromosome_.getLoci()

Methods in com.rubecula.darwin.domain.genetics with parameters of type Locus

protected void	Chromosome_.add(int index, Locus locus)
protected boolean	Chromosome_.add(Locus o)
void	Chromosome_.addLocus(int index, Locus locus) add locus and set the locus to point to this Chromosome as its owner.
boolean	Chromosome_.addLocus(Locus locus) Method to add a Locus at the end of this Genomic.
Expresser	Genomic_.getExpresser(Locus locus) Get the expresser for the specific locus.
static Gene	GeneFactory.makeDiploid(Locus locus, java.lang.String allele1, java.lang.String allele2) Construct a new Gene_Diploid with the given allele indexes
static Gene	GeneFactory.makeGene(java.lang.Class<? extends Gene> clazz, Locus locus, java.lang.Object... parameters) TEST
static Gene	GeneFactory.makeHaploid(Locus locus, java.lang.String allele)
Expresser	Genomic_.putExpresser(Locus locus, Expresser expresser) Register an expresser.
void	Gene_.setLocus(Locus locus)
void	Allele_.setLocus(Locus locus) Set the value of the locus for this Allele.
void	Locus_.setPolygenic(Locus locus) Bean method to set the next locus in a chain of polygenic loci.

Method parameters in com.rubecula.darwin.domain.genetics with type arguments of type Locus

protected boolean	Chromosome_.addAll(java.util.Collection<? extends Locus> loci)
void	Genomic_.setExpressers(java.util.Map<Locus,Expresser> expressers) Used by dependency injection: sets the expresser map.
void	Chromosome_.setLoci(java.util.Collection<Locus> loci) This is now the preferred method to set the loci.

Uses of Locus in com.rubecula.darwin.domain.helper

Methods in com.rubecula.darwin.domain.helper that return Locus

Locus	Gene.getLocus()
Locus	Allele.getLocus()
Locus	Genomic.getLocus(int n)
Locus	Chromosome.getLocus(int index)
Locus	Locus.getPolygenic()

Methods in com.rubecula.darwin.domain.helper that return types with arguments of type Locus

java.util.Collection<Locus>

Chromosome.getLoci() Getter/setter typically used by reflection.

Methods in com.rubecula.darwin.domain.helper with parameters of type Locus

void	Chromosome.addLocus(int index, Locus locus) Method to add a Locus at the specified index.
boolean	Chromosome.addLocus(Locus locus) Method to add a Locus at the end of this Genomic.
java.lang.String	Expresser.getComplement(Locus locus, java.lang.String allele) Get the complementary allele key, such that Expresser.isComplementary(Locus, String, String) will be true.
Expresser	Genomic.getExpresser(Locus locus)
boolean	Expresser.isComplementary(Locus locus, java.lang.String allele1, java.lang.String allele2)
Expresser	Genomic.putExpresser(Locus locus, Expresser expresser) Method to register an implementer of Expresser for a specific Locus.
void	Gene.setLocus(Locus locus) Set the locus for this gene.
void	Allele.setLocus(Locus locus)

Method parameters in com.rubecula.darwin.domain.helper with type arguments of type Locus

void	Chromosome.setLoci(java.util.Collection<Locus> loci) This is now the preferred method to set the loci.

Uses of Locus in com.rubecula.darwin.domain.world

Methods in com.rubecula.darwin.domain.world that return Locus

Locus

Genomic_Sexual.getLocusSex() XXX consider reducing scope for this.

Methods in com.rubecula.darwin.domain.world that return types with arguments of type Locus

java.util.Collection<Locus>

Genomic_Asexual.getLoci()

Methods in com.rubecula.darwin.domain.world with parameters of type Locus

void	Genomic_Asexual.addLocus(int index, Locus locus) TEST
boolean	Genomic_Asexual.addLocus(Locus locus)

Method parameters in com.rubecula.darwin.domain.world with type arguments of type Locus

void	Genomic_Sexual.setExpressers(java.util.Map<Locus,Expresser> expressers) Reset the expresser map, but include the sex chromosome expresser.
void	Genomic_Asexual.setLoci(java.util.Collection<Locus> loci)

Uses of Locus in com.rubecula.darwin.examples.pepperedmoth

Methods in com.rubecula.darwin.examples.pepperedmoth with parameters of type Locus

static Allele

Mutator_PepperedMoth.makeAllele(Locus locus, boolean which) TODO consider copying from the existing set of alleles rather than creating new instances.

Uses of Locus in com.rubecula.darwin.examples.travelingsalesman

Classes in com.rubecula.darwin.examples.travelingsalesman that implement Locus

class

Locus_TS

Methods in com.rubecula.darwin.examples.travelingsalesman with parameters of type Locus

java.lang.String	Expresser_TS.getComplement(Locus locus, java.lang.String allele) In this implementation, if the locus is a swap, then we simply return the allele passed in because two identical swaps are complementary.
boolean	Expresser_TS.isComplementary(Locus locus, java.lang.String allele1, java.lang.String allele2) In this implementation of isComplementary, there are two situations: swap or rotate.