com.rubecula.darwin.core
Class Genome_Diploid

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.Vector
              com.rubecula.util.AuditableVector
                  com.rubecula.darwin.core.Genome_Abstract
                      com.rubecula.darwin.core.Genome_Diploid

All Implemented Interfaces:

Genome, Auditable, Identifiable, Serializable, Cloneable, Iterable, Collection, List, RandomAccess

public class Genome_Diploid
extends Genome_Abstract

Concrete implementation of Genome representing the possible genetic information contained in a Darwinian system. A Genome_Diploid may contain any number of gene Loci. A Genome_Diploid is essentially a template for a Genotype. Both structures are approximately parallel.
Note that there is currently no division of Loci into Chromosomes. TODO Is that reasonable?

Version:

$Revision: 1.1 $

Author:

Robin Hillyard

See Also:

Serialized Form

Field Summary

Fields inherited from class com.rubecula.darwin.core.Genome_Abstract

log

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Fields inherited from interface com.rubecula.darwin.core.Genome

DIPLOID, HAPLOID

Constructor Summary

Genome_Diploid(String identifier, Meiosis meioter, Expression expresser, Factory factory)
Constructor for a new Genome_Diploid instance using the given meiosis implementaion.

Genome_Diploid(String identifier, Meiosis meioter, Mutator mutator, Expression expresser, Factory factory)
Constructor for a new Genome_Diploid instance using the given meiosis implementation and the given mutator implementation.

Method Summary

Methods inherited from class com.rubecula.darwin.core.Genome_Abstract

add, add, add, getExpresser, getFactory, getLocus, getMeioter, getMutator, getOde

Methods inherited from class com.rubecula.util.AuditableVector

audit, audit, audit, getIdentifier

Methods inherited from class java.util.Vector

add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.rubecula.darwin.core.Genome

size

Methods inherited from interface java.util.List

iterator, listIterator, listIterator

Constructor Detail

Genome_Diploid

public Genome_Diploid(String identifier,
                      Meiosis meioter,
                      Expression expresser,
                      Factory factory)

Constructor for a new Genome_Diploid instance using the given meiosis implementaion.

Parameters:

identifier - the identifier for this Genome.

meioter - an implementer of Meiosis.

expresser - an implementer of Expression. which allows any Genotype conforming to this Genome to be expressed as a Phenotype.

factory - the implementer of Factory.

Genome_Diploid

public Genome_Diploid(String identifier,
                      Meiosis meioter,
                      Mutator mutator,
                      Expression expresser,
                      Factory factory)

Constructor for a new Genome_Diploid instance using the given meiosis implementation and the given mutator implementation.

Parameters:

identifier -

meioter -

mutator -

expresser -

factory - the implementer of Factory.