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

Packages that use Allele

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 Allele in com.rubecula.darwin.domain.environment

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

java.lang.Object

ExpresserFunction.express(Allele allele) Express the given allele in a non-Mendelian manner.

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

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

class	Allele_ This abstract provides base operations for implementations of Allele, which are specific, competing genes which may appear at a Locus.
class	Allele_Binary Abstract type of allele which has two values, based on a boolean.
class	Allele_Dominance Lifespan: permanent.
class	Allele_Sex Unlike Allele_Dominance, which uses upper and lower case to denote dominance, the two different alleles of the Allele_Sex type are "Y" and "X" for male and female, respectively.

Fields in com.rubecula.darwin.domain.genetics declared as Allele

static Allele	Allele_Sex.X Allele_Sex(false)
static Allele	Allele_Sex.Y Allele_Sex(true)

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

Allele	Gene_.getAllele(int index)
Allele	Locus_.getAllele(java.lang.String key)
static Allele	AlleleFactory.makeAllele(java.lang.Class<? extends Allele> clazz, java.lang.Object key, java.lang.Object value) TEST
static Allele	AlleleFactory.makeDominanceAllele(java.lang.String identifier, boolean dominant) Construct a new Allele_Dominance with the given allele indexes TEST
static Allele	AlleleFactory.makeSexAllele(boolean male)
Allele	Mutator_Random.mutate(Allele allele)
Allele	Mutator_.mutate(Allele allele) By default, the allele is returned unchanged.

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

java.util.Map<java.lang.String,Allele>	Locus_.getAlleleMap()
java.util.Map<Allele,java.lang.Integer>	Locus_.getAlleles() TODO reduce to default scope.
java.util.Collection<Allele>	Locus_.getAlleleValues()

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

java.lang.String	Locus_Random.add(Allele allele, int frequency) This is used only when a mutation occurs.
java.lang.String	Locus_.addAllele(Allele allele) Incrementally add the given allele to this Locus.
protected static void	Mutator_.addToLocusIfUnknown(Allele allele)
java.lang.String	Locus_.getKey(Allele allele)
Allele	Mutator_Random.mutate(Allele allele)
Allele	Mutator_.mutate(Allele allele) By default, the allele is returned unchanged.
java.lang.String	Locus_.putAllele(Allele allele, int frequency)

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

void	Genotype_.doCensus(FrequencyMap<Allele> alleleFrequencies)
static Allele	AlleleFactory.makeAllele(java.lang.Class<? extends Allele> clazz, java.lang.Object key, java.lang.Object value) TEST
void	Locus_Random.setAlleles(java.util.Map<? extends Allele,java.lang.Integer> map)
void	Locus_.setAlleles(java.util.Map<? extends Allele,java.lang.Integer> map) Preferred method of setting up the allele/frequency map (rather than using add()).

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

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

Allele	Gene.getAllele(int index) Accessor method to return the indexth allele for this gene.
Allele	Locus.getAllele(java.lang.String key)
Allele	Mutator.mutate(Allele allele) Method to take an allele and mutate it.

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

java.util.Map<java.lang.String,Allele>	Locus.getAlleleMap()
java.util.Collection<Allele>	Locus.getAlleleValues()

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

java.lang.String	Locus.add(Allele allele, int frequency) Method to add an allele to this locus.
java.lang.String	Locus.addAllele(Allele allele) Method to add an allele to this locus.
java.lang.String	Locus.getKey(Allele allele)
Allele	Mutator.mutate(Allele allele) Method to take an allele and mutate it.

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

void	Genotype.doCensus(FrequencyMap<Allele> alleleFrequencies)

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

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

FrequencyMap<Allele>

OrganismCensusContext.getAlleleFrequencies()

Constructor parameters in com.rubecula.darwin.domain.world with type arguments of type Allele

OrganismCensusContext(Pharacter character, FrequencyMap<Allele> alleleFrequencies, NumericFrequencyMap ageFrequencies, FrequencyMap<java.lang.String> sexFrequencies, FrequencyMap<Trait> traitFrequencies)

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

Methods in com.rubecula.darwin.examples.pepperedmoth that return Allele

static Allele	Mutator_PepperedMoth.makeAllele(Locus locus, boolean which) TODO consider copying from the existing set of alleles rather than creating new instances.
Allele	Mutator_PepperedMoth.mutate(Allele allele) If we get index 1 from the randomizer, we flip the type of allele.

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

Allele

Mutator_PepperedMoth.mutate(Allele allele) If we get index 1 from the randomizer, we flip the type of allele.

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

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

class

Allele_Number This class is at the heart of the solution to the traveling salesman problem.

Methods in com.rubecula.darwin.examples.travelingsalesman that return Allele

static Allele	Allele_Number.makeNumberAllele(java.lang.String type, int value)
Allele	Mutator_TS.mutate(Allele allele)

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

Allele

Mutator_TS.mutate(Allele allele)