com.rubecula.darwin.core
Class Genome_Haploid

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_Haploid

All Implemented Interfaces:

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

public class Genome_Haploid
extends Genome_Abstract

Concrete implementation of Genome representing the possible genetic information contained in a Darwinian system. A Genome_Haploid may contain any number of gene Loci. A Genome_Haploid 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: 1.2 $

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_Haploid(String identifier, Expression expresser, Factory factory)
Constructor for a new Genome_Diploid instance using the default meiosis implementation.

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

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

Genome_Haploid(String identifier, Mutator mutator, Expression expresser)
Deprecated.

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_Haploid

public Genome_Haploid(String identifier,
                      Expression expresser,
                      Factory factory)

Constructor for a new Genome_Diploid instance using the default meiosis implementation.

Parameters:

identifier - the identifier for this Genome.

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

factory - the implementer of Factory. TODO this is OK I think since we don't need meioter for haploid

Genome_Haploid

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

Constructor for a new Genome_Haploid instance using the given meiosis implementation.

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_Haploid

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

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

Parameters:

identifier -

meioter -

mutator -

expresser -

factory - the implementer of Factory.

Genome_Haploid

public Genome_Haploid(String identifier,
                      Mutator mutator,
                      Expression expresser)

Deprecated.

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

Parameters:

identifier -

mutator -

expresser -