ec

Class BreedingPipeline

java.lang.Object

ec.BreedingSource

ec.BreedingPipeline

All Implemented Interfaces:

Prototype, Setup, SteadyStateBSourceForm, RandomChoiceChooserD, Serializable, Cloneable

Direct Known Subclasses:

BufferedBreedingPipeline, CheckingPipeline, ForceBreedingPipeline, GeneDuplicationPipeline, GenerationSwitchPipeline, GETruncationPipeline, GPBreedingPipeline, InitializationPipeline, ListCrossoverPipeline, MultiBreedingPipeline, MultipleVectorCrossoverPipeline, OurMutatorPipeline, ReproductionPipeline, RuleCrossoverPipeline, RuleMutationPipeline, VectorCrossoverPipeline, VectorMutationPipeline

public abstract class BreedingPipeline
extends BreedingSource
implements SteadyStateBSourceForm

A BreedingPipeline is a BreedingSource which provides "fresh" individuals which can be used to fill a new population. BreedingPipelines might include Crossover pipelines, various Mutation pipelines, etc. This abstract class provides some default versions of various methods to simplify matters for you. It also contains an array of breeding sources for your convenience. You don't have to use them of course, but this means you have to customize the default methods below to make sure they get distributed to your special sources. Note that these sources may contain references to the same object -- they're not necessarily distinct. This is to provide both some simple DAG features and also to conserve space.

A BreedingPipeline implements SteadyStateBSourceForm, meaning that it receives the individualReplaced(...) and sourcesAreProperForm(...) messages. however by default it doesn't do anything with these except distribute them to its sources. You might override these to do something more interesting.

Parameters

base.num-sources int >= 1	(User-specified number of sources to the pipeline. Some pipelines have hard-coded numbers of sources; others indicate (with the java constant DYNAMIC_SOURCES) that the number of sources is determined by this user parameter instead.)
base.source.n classname, inherits and != BreedingSource, or the value same	(Source n for this BreedingPipeline. If the value is set to same, then this source is the exact same source object as base.source.n-1, and further parameters for this object will be ignored and treated as the same as those for n-1. same is not valid for base.source.0)

Parameter bases

base.source.n

Source n

Version:

1.0

Author:

Sean Luke

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	DYNAMIC_SOURCES Indicates that the number of sources is variable and determined by the user in the parameter file.
double	likelihood
Parameter	mybase My parameter base -- I keep it around so I can print some messages that are useful with it (not deep cloned)
static String	P_LIKELIHOOD Indicates the probability that the Breeding Pipeline will perform its mutative action instead of just doing reproduction.
static String	P_NUMSOURCES Standard parameter for number of sources (only used if numSources returns DYNAMIC_SOURCES
static String	P_SOURCE Standard parameter for individual-selectors associated with a BreedingPipeline
BreedingSource[]	sources Array of sources feeding the pipeline
static String	V_SAME Indicates that a source is the exact same source as the previous source.

Fields inherited from class ec.BreedingSource

NO_PROBABILITY, P_PROB, probability

Constructor Summary

Constructors

Constructor and Description
BreedingPipeline()

Method Summary

Methods

Modifier and Type	Method and Description
Object	clone() Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.
void	finishProducing(EvolutionState state, int subpopulation, int thread) Called after produce(...), usually once a generation, or maybe only once if you're doing steady-state evolution (at the end of the run).
void	individualReplaced(SteadyStateEvolutionState state, int subpopulation, int thread, int individual) Called whenever an individual has been replaced by another in the population.
int	maxChildProduction() Returns the maximum among the typicalIndsProduced() for any children -- a function that's useful internally, not very useful for you to call externally.
int	minChildProduction() Returns the minimum among the typicalIndsProduced() for any children -- a function that's useful internally, not very useful for you to call externally.
abstract int	numSources() Returns the number of sources to this pipeline.
void	preparePipeline(Object hook) A hook which should be passed to all your subsidiary breeding sources.
void	prepareToProduce(EvolutionState state, int subpopulation, int thread) Called before produce(...), usually once a generation, or maybe only once if you're doing steady-state evolution, to let the breeding source "warm up" prior to producing.
boolean	produces(EvolutionState state, Population newpop, int subpopulation, int thread) Returns true if this BreedingSource, when attached to the given subpopulation, will produce individuals of the subpopulation's species.
int	reproduce(int n, int start, int subpopulation, Individual[] inds, EvolutionState state, int thread, boolean produceChildrenFromSource) Performs direct cloning of n individuals.
void	setup(EvolutionState state, Parameter base) Sets up the BreedingPipeline.
void	sourcesAreProperForm(SteadyStateEvolutionState state) Issue an error (not a fatal -- we guarantee that callers of this method will also call exitIfErrors) if any of your sources, or their sources, etc., are not of SteadyStateBSourceForm.
int	typicalIndsProduced() Returns the "typical" number of individuals produced -- by default this is the minimum typical number of individuals produced by any children sources of the pipeline.

Methods inherited from class ec.BreedingSource

getProbability, pickRandom, produce, setProbability, setupProbabilities

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ec.Prototype

defaultBase

Field Detail

V_SAME

public static final String V_SAME

Indicates that a source is the exact same source as the previous source.

See Also:

Constant Field Values

P_LIKELIHOOD

public static final String P_LIKELIHOOD

Indicates the probability that the Breeding Pipeline will perform its mutative action instead of just doing reproduction.

See Also:

Constant Field Values

DYNAMIC_SOURCES

public static final int DYNAMIC_SOURCES

Indicates that the number of sources is variable and determined by the user in the parameter file.

See Also:

Constant Field Values

P_NUMSOURCES

public static final String P_NUMSOURCES

Standard parameter for number of sources (only used if numSources returns DYNAMIC_SOURCES

See Also:

Constant Field Values

P_SOURCE

public static final String P_SOURCE

Standard parameter for individual-selectors associated with a BreedingPipeline

See Also:

Constant Field Values

mybase

public Parameter mybase

My parameter base -- I keep it around so I can print some messages that are useful with it (not deep cloned)

likelihood

public double likelihood

sources

public BreedingSource[] sources

Array of sources feeding the pipeline

Constructor Detail

BreedingPipeline

public BreedingPipeline()

Method Detail

numSources

public abstract int numSources()

Returns the number of sources to this pipeline. Called during BreedingPipeline's setup. Be sure to return a value > 0, or DYNAMIC_SOURCES which indicates that setup should check the parameter file for the parameter "num-sources" to make its determination.

minChildProduction

public int minChildProduction()

Returns the minimum among the typicalIndsProduced() for any children -- a function that's useful internally, not very useful for you to call externally.

maxChildProduction

public int maxChildProduction()

Returns the maximum among the typicalIndsProduced() for any children -- a function that's useful internally, not very useful for you to call externally.

typicalIndsProduced

public int typicalIndsProduced()

Returns the "typical" number of individuals produced -- by default this is the minimum typical number of individuals produced by any children sources of the pipeline. If you'd prefer something different, override this method.

Specified by:

typicalIndsProduced in class BreedingSource

setup

public void setup(EvolutionState state,
         Parameter base)

Description copied from class: BreedingSource

Sets up the BreedingPipeline. You can use state.output.error here because the top-level caller promises to call exitIfErrors() after calling setup. Note that probability might get modified again by an external source if it doesn't normalize right.

The most common modification is to normalize it with some other set of probabilities, then set all of them up in increasing summation; this allows the use of the fast static BreedingSource-picking utility method, BreedingSource.pickRandom(...). In order to use this method, for example, if four breeding source probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.

Specified by:

setup in interface Prototype

Specified by:

setup in interface Setup

Overrides:

setup in class BreedingSource

See Also:

Prototype.setup(EvolutionState,Parameter)

clone

public Object clone()

Description copied from interface: Prototype

Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.

Typically this should be a full "deep" clone. However, you may share certain elements with other objects rather than clone hem, depending on the situation:

• If you hold objects which are shared with other instances, don't clone them.
• If you hold objects which must be unique, clone them.
• If you hold objects which were given to you as a gesture of kindness, and aren't owned by you, you probably shouldn't clone them.
• DON'T attempt to clone: Singletons, Cliques, or Groups.
• Arrays are not cloned automatically; you may need to clone an array if you're not sharing it with other instances. Arrays have the nice feature of being copyable by calling clone() on them.

Implementations.

• If no ancestor of yours implements clone(), and you have no need to do clone deeply, and you are abstract, then you should not declare clone().
• If no ancestor of yours implements clone(), and you have no need to do clone deeply, and you are not abstract, then you should implement it as follows:

   public Object clone() 
       {
       try
           { 
           return super.clone();
           }
       catch ((CloneNotSupportedException e)
           { throw new InternalError(); } // never happens
       }
          

• If no ancestor of yours implements clone(), but you need to deep-clone some things, then you should implement it as follows:

   public Object clone() 
       {
       try
           { 
           MyObject myobj = (MyObject) (super.clone());
  
           // put your deep-cloning code here...
           }
       catch ((CloneNotSupportedException e)
           { throw new InternalError(); } // never happens
       return myobj;
       } 
          

• If an ancestor has implemented clone(), and you also need to deep clone some things, then you should implement it as follows:

   public Object clone() 
       { 
       MyObject myobj = (MyObject) (super.clone());
  
       // put your deep-cloning code here...
  
       return myobj;
       } 
          

Specified by:

clone in interface Prototype

Overrides:

clone in class BreedingSource

reproduce

public int reproduce(int n,
            int start,
            int subpopulation,
            Individual[] inds,
            EvolutionState state,
            int thread,
            boolean produceChildrenFromSource)

Performs direct cloning of n individuals. if produceChildrenFromSource is true, then

produces

public boolean produces(EvolutionState state,
               Population newpop,
               int subpopulation,
               int thread)

Description copied from class: BreedingSource

Returns true if this BreedingSource, when attached to the given subpopulation, will produce individuals of the subpopulation's species. SelectionMethods should additionally make sure that their Fitnesses are of a valid type, if necessary. newpop *may* be the same as state.population

Specified by:

produces in class BreedingSource

prepareToProduce

public void prepareToProduce(EvolutionState state,
                    int subpopulation,
                    int thread)

Description copied from class: BreedingSource

Called before produce(...), usually once a generation, or maybe only once if you're doing steady-state evolution, to let the breeding source "warm up" prior to producing. Individuals should be produced from old individuals in positions [start...start+length] in the subpopulation only. May be called again to reset the BreedingSource for a whole 'nuther subpopulation.

Specified by:

prepareToProduce in class BreedingSource

finishProducing

public void finishProducing(EvolutionState state,
                   int subpopulation,
                   int thread)

Description copied from class: BreedingSource

Called after produce(...), usually once a generation, or maybe only once if you're doing steady-state evolution (at the end of the run).

Specified by:

finishProducing in class BreedingSource

preparePipeline

public void preparePipeline(Object hook)

Description copied from class: BreedingSource

A hook which should be passed to all your subsidiary breeding sources. The default does this for you already, so ordinarily you don't need to change anything. If you are a BreedingPipeline and you implement your sources in a way different than using the sources[] array, be sure to override this method so that it calls preparePipeline(hook) on all of your sources.

ECJ at present does not custom-implement or call this method: it's available for you. Becuase it has custom functionality, this method might get called more than once, and by various objects as needed. If you use it, you should determine somehow how to use it to send information under the assumption that it might be sent by nested items in the pipeline; you don't want to scribble over each other's calls! Note that this method should travel *all* breeding source paths regardless of whether or not it's redundant to do so.

Overrides:

preparePipeline in class BreedingSource

individualReplaced

public void individualReplaced(SteadyStateEvolutionState state,
                      int subpopulation,
                      int thread,
                      int individual)

Description copied from interface: SteadyStateBSourceForm

Called whenever an individual has been replaced by another in the population.

Specified by:

individualReplaced in interface SteadyStateBSourceForm

sourcesAreProperForm

public void sourcesAreProperForm(SteadyStateEvolutionState state)

Description copied from interface: SteadyStateBSourceForm

Issue an error (not a fatal -- we guarantee that callers of this method will also call exitIfErrors) if any of your sources, or their sources, etc., are not of SteadyStateBSourceForm.

Specified by:

sourcesAreProperForm in interface SteadyStateBSourceForm