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java.lang.Object | +--ec.Species
Species is a prototype which defines the features for a set of individuals in the population. Typically, individuals may breed if they belong to the same species (but it's not a hard-and-fast rule). Each Subpopulation has one Species object which defines the species for individuals in that Subpopulation.
Species are generally responsible for creating individuals, through their newIndividual(...) method. This method usually clones its prototypical individual and makes some additional modifications to the clone, then returns it.
Species also holds a prototypical breeding pipeline meant to breed this individual. To breed individuals of this species, clone the pipeline and use the clone.
Parameters
base.ind classname, inherits and != ec.Individual |
(the class for the prototypical individual for the species) |
base.numpipes int >= 1 |
(total number of breeding pipelines for the species) |
base.pipe classname, inherits and != ec.BreedingPipeline |
(the class for the prototypical Breeding Pipeline) |
Parameter bases
base.ind | i_prototype (the prototypical individual) |
base.pipe | pipe_prototype (breeding pipeline prototype) |
Field Summary | |
Individual |
i_prototype
The prototypical individual for this species. |
static java.lang.String |
P_INDIVIDUAL
|
static java.lang.String |
P_PIPE
|
BreedingPipeline |
pipe_prototype
|
Constructor Summary | |
Species()
|
Method Summary | |
abstract Individual |
newIndividual(EvolutionState state,
Subpopulation _population,
Fitness _fitness)
override this to provide a brand-new individual to fill in a population. |
abstract Individual |
newIndividual(EvolutionState state,
Subpopulation _population,
Fitness _fitness,
int thread,
java.io.LineNumberReader reader)
override this to provide an individual read from a file; the individual will appear as it was written by printIndividual(...). |
java.lang.Object |
protoClone()
Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context. |
java.lang.Object |
protoCloneSimple()
This should be implemented in a the top-level Prototype ONLY; in fact, it should probably be declared final. |
void |
setup(EvolutionState state,
Parameter base)
Sets up the object by reading it from the parameters stored in state, built off of the parameter base base. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Field Detail |
public static final java.lang.String P_INDIVIDUAL
public static final java.lang.String P_PIPE
public Individual i_prototype
public BreedingPipeline pipe_prototype
Constructor Detail |
public Species()
Method Detail |
public java.lang.Object protoClone() throws java.lang.CloneNotSupportedException
The question here is whether or not this means to perform a "deep" or "light" ("shallow") clone, or something in-between. You may need to deep-clone parts of your object rather than simply copying their references, depending on the situation:
Implementations.
public Object protoClone() throws CloneNotSupportedException
{
return super.clone();
}
public Object protoClone() throws CloneNotSupportedException
{
myobj = (MyObject) (super.clone());
// put your deep-cloning code here...
// ...you should use protoClone and not
// protoCloneSimple to clone subordinate objects...
return myobj;
}
public Object protoClone() throws CloneNotSupportedException
{
MyObject myobj = (MyObject)(super.protoClone());
// put your deep-cloning code here...
// ...you should use protoClone and not
// protoCloneSimple to clone subordinate objects...
return myobj;
}
If you know that your superclasses will never change their protoClone() implementations, you might try inlining them in your overridden protoClone() method. But this is dangerous (though it yields a small net increase).
In general, you want to keep your deep cloning to an absolute minimum, so that you don't have to call protoClone() but one time.
The approach taken here is the fastest that I am aware of while still permitting objects to be specified at runtime from a parameter file. It would be faster to use the "new" operator; but that would require hard-coding that we can't do. Although using java.lang.Object.clone() entails an extra layer that deals with stripping away the "protected" keyword and also wrapping the exception handling (which is a BIG hit, about three times as slow as using "new"), it's still MUCH faster than using java.lang.Class.newInstance(), and also much faster than rolling our own Clone() method.
public final java.lang.Object protoCloneSimple()
public final Object protoCloneSimple()
{
try { return protoClone(); }
catch (CloneNotSupportedException e)
{ throw new InternalError(); } // never happens
}
public abstract Individual newIndividual(EvolutionState state, Subpopulation _population, Fitness _fitness) throws java.lang.CloneNotSupportedException
public abstract Individual newIndividual(EvolutionState state, Subpopulation _population, Fitness _fitness, int thread, java.io.LineNumberReader reader) throws java.io.IOException, java.lang.CloneNotSupportedException
public void setup(EvolutionState state, Parameter base)
For prototypes, setup(...) is typically called once for the prototype instance; cloned instances do not receive the setup(...) call. setup(...) may be called more than once; the only guarantee is that it will get called at least once on an instance or some "parent" object from which it was ultimately cloned.
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