com.rubecula.darwin.examples.pepperedmoth
Class Mutator_PepperedMoth

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.genetics.Mutator_
          com.rubecula.darwin.domain.genetics.Mutator_Random
              com.rubecula.darwin.examples.pepperedmoth.Mutator_PepperedMoth

All Implemented Interfaces:

Chancy, Mutator, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

public class Mutator_PepperedMoth
extends Mutator_Random

This mutator is responsible for keeping the carbonaria allele in the population (or, conceivably, the typica allele) Every now and then, the copying of the gene goes wrong and the other allele is used instead. The frequency of errors can be set dynamically. Note that this mutator does not override the Mutator.mutate(com.rubecula.darwin.domain.helper.Genome) method so that the only type of mutation is switching alleles (no replication, deletion, etc.)

Author:

Robin Hillyard

Field Summary

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

_random

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

LOG

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

Mutator_PepperedMoth(org.apache.commons.math.random.RandomGenerator random)

Mutator_PepperedMoth(org.apache.commons.math.random.RandomGenerator random, int odds)

Method Summary

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

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

getRandom, setBands, setOdds

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

addToLocusIfUnknown, equals, getIdentifier, hashCode, isComplementary, isIdentity, mutate, normalize, 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

Constructor Detail

Mutator_PepperedMoth

public Mutator_PepperedMoth(org.apache.commons.math.random.RandomGenerator random)

Parameters:

random -

Mutator_PepperedMoth

public Mutator_PepperedMoth(org.apache.commons.math.random.RandomGenerator random,
                            int odds)

Parameters:

random -

odds -

Method Detail

makeAllele

public static Allele makeAllele(Locus locus,
                                boolean which)

TODO consider copying from the existing set of alleles rather than creating new instances.

Parameters:

locus -

which - the particular allele to make (either true for melanistic, or false for non-melanistic)

Returns:

a newly constructed allele

mutate

public Allele mutate(Allele allele)

If we get index 1 from the randomizer, we flip the type of allele.

Specified by:

mutate in interface Mutator

Overrides:

mutate in class Mutator_Random

Parameters:

allele - the original allele

Returns:

either the original allele or a mutated version of it. TODO it seems to me now that this mutation should operate on a Gene, not on an Allele, but there again we have to remember that the word "gene" is used in two different ways in common parlance.

See Also:

Mutator_.mutate(com.rubecula.darwin.domain.helper.Allele)