com.rubecula.darwin.core
Class Genome_Abstract

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

All Implemented Interfaces:

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

Direct Known Subclasses:

Genome_Diploid, Genome_Haploid

public abstract class Genome_Abstract
extends AuditableVector
implements Genome

Abstract class implementing base methods for the Genome interface.

Author:

Robin Hillyard TODO define this class using generics so that only Locus objects can be added/retrieved.

See Also:

Serialized Form

Field Summary

protected static org.apache.commons.logging.Log

log The logger for this class.

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

protected	Genome_Abstract(String identifier, int ode, Meiosis meioter, Expression expresser, Factory factory) Constructor for a new Genome_Abstract instance.
protected	Genome_Abstract(String identifier, int ode, Meiosis meioter, Mutator mutator, Expression expresser, Factory factory) Constructor for a new Genome_Abstract instance.

Method Summary

void	add(int index, Locus locus) Method to add a Locus at the specified index.
void	add(int arg0, Object arg1)
boolean	add(Locus locus) Method to add a Locus at the end of this Genome.
Expression	getExpresser() The implementer of Expression which an application has specified.
Factory	getFactory()
Locus	getLocus(int index)
Meiosis	getMeioter()
Mutator	getMutator()
int	getOde() Method to return the genetic form for this genome.

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

Field Detail

log

protected static final org.apache.commons.logging.Log log

The logger for this class.

Constructor Detail

Genome_Abstract

protected Genome_Abstract(String identifier,
                          int ode,
                          Meiosis meioter,
                          Expression expresser,
                          Factory factory)

Constructor for a new Genome_Abstract instance. This type of Genome undergoes no mutations.

Parameters:

identifier - the identifier for this Genome.

ode - the ode (haploid/diploid/etc).

meioter - the 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_Abstract

protected Genome_Abstract(String identifier,
                          int ode,
                          Meiosis meioter,
                          Mutator mutator,
                          Expression expresser,
                          Factory factory)

Constructor for a new Genome_Abstract instance.

Parameters:

identifier - the identifier for this Genome.

ode - the ode (haploid/diploid/etc).

meioter - the implementer of Meiosis.

mutator - the implementer of Mutator which will be applied to all new genotypes.

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

factory - the implementer of Factory.

Method Detail

add

public void add(int index,
                Locus locus)

Description copied from interface: Genome

Method to add a Locus at the specified index.

Specified by:

add in interface Genome

Parameters:

index - the index at which the new object will appear.

locus - a locus to be inserted into this Genome.

See Also:

List.add(int, java.lang.Object)

add

public void add(int arg0,
                Object arg1)

Specified by:

add in interface List

Overrides:

add in class Vector

add

public boolean add(Locus locus)

Method to add a Locus at the end of this Genome.

Specified by:

add in interface Genome

Parameters:

locus - a locus to be inserted into this Genome.

Returns:

true, always.

See Also:

add(int, Locus)

getExpresser

public Expression getExpresser()

Description copied from interface: Genome

The implementer of Expression which an application has specified.

Specified by:

getExpresser in interface Genome

Returns:

the implementer of Expression for this Genome.

getFactory

public Factory getFactory()

Specified by:

getFactory in interface Genome

Returns:

the factory

getLocus

public Locus getLocus(int index)

Specified by:

getLocus in interface Genome

Returns:

the locus defined by index (0..N)

getMeioter

public Meiosis getMeioter()

Specified by:

getMeioter in interface Genome

Returns:

the application-specified implementer of Meiosis

getMutator

public Mutator getMutator()

Specified by:

getMutator in interface Genome

Returns:

the mutator

getOde

public int getOde()

Description copied from interface: Genome

Method to return the genetic form for this genome.

Specified by:

getOde in interface Genome

Returns:

the "oidity" which will normally be either Genome.HAPLOID, i.e. simple or Genome.DIPLOID, i.e. double.