Package ec.gp.breed

# Class MutateAllNodesPipeline

java.lang.Object
ec.BreedingSource
ec.BreedingPipeline
ec.gp.GPBreedingPipeline
ec.gp.breed.MutateAllNodesPipeline

All Implemented Interfaces:
  `Prototype`, `Setup`, `SteadyStateBSourceForm`, `RandomChoiceChooserD`, `Serializable`, `Cloneable`

public class MutateAllNodesPipeline extends GPBreedingPipeline
MutateAllNodesPipeline implements the AllNodes mutation algorithm described in Kumar Chellapilla, "A Preliminary Investigation into Evolving Modular Programs without Subtree Crossover", GP98.

MutateAllNodesPipeline chooses a subtree and for each node n in that subtree, it replaces n with a randomly-picked node of the same arity and type constraints. Thus the original topological structure is the same but the nodes are different.

Typical Number of Individuals Produced Per `produce(...)` call
...as many as the source produces

Number of Sources
1

Parameters

base.`ns`.0 classname, inherits and != GPNodeSelector | (GPNodeSelector for tree)
base.`tree.0` 0 < int < (num trees in individuals), if exists | (tree chosen for mutation; if parameter doesn't exist, tree is picked at random)

Default Base
gp.breed.mutate-all-nodes

Parameter bases

base.`ns` | The GPNodeSelector selector

See Also:
  - Serialized Form

- ## Field Summary

  Fields
  Modifier and Type
  Field
  Description
  `static final String`
  `KEY_PARENTS`
  `GPNodeSelector`
  `nodeselect`
  How the pipeline chooses a subtree to mutate
  `static final int`
  `NUM_SOURCES`
  `static final String`
  `P_MUTATEALLNODES`

  ### Fields inherited from class ec.gp.GPBreedingPipeline

  `P_NODESELECTOR, P_TREE, TREE_UNFIXED`

  ### Fields inherited from class ec.BreedingPipeline

  `DYNAMIC_SOURCES, likelihood, mybase, P_LIKELIHOOD, P_NUMSOURCES, P_SOURCE, sources, V_SAME, V_STUB`

  ### Fields inherited from class ec.BreedingSource

  `NO_PROBABILITY, P_PROB, probability`

- ## Constructor Summary

  Constructors
  Constructor
  Description
  `MutateAllNodesPipeline()`

- ## Method Summary

  Modifier and Type
  Method
  Description
  `Object`
  `clone()`
  Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.
  `Parameter`
  `defaultBase()`
  Returns the default base for this prototype.
  `int`
  `numSources()`
  Returns the number of sources to this pipeline.
  `int`
  `produce(int min, int max, int subpopulation, ArrayList<Individual> inds, EvolutionState state, int thread, HashMap<String,Object> misc)`
  Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n.
  `void`
  `setup(EvolutionState state, Parameter base)`
  Sets up the BreedingPipeline.

  ### Methods inherited from class ec.gp.GPBreedingPipeline

  `produces`

  ### Methods inherited from class ec.BreedingPipeline

  `fillStubs, finishProducing, individualReplaced, maxChildProduction, minChildProduction, preparePipeline, prepareToProduce, sourcesAreProperForm, typicalIndsProduced`

  ### Methods inherited from class ec.BreedingSource

  `getProbability, pickRandom, setProbability, setupProbabilities`

  ### Methods inherited from class java.lang.Object

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

- ## Field Details

  - ### P_MUTATEALLNODES

    public static final String P_MUTATEALLNODES
    See Also:
      - Constant Field Values

  - ### NUM_SOURCES

    public static final int NUM_SOURCES
    See Also:
      - Constant Field Values

  - ### KEY_PARENTS

    public static final String KEY_PARENTS
    See Also:
      - Constant Field Values

  - ### nodeselect

    public GPNodeSelector nodeselect
    How the pipeline chooses a subtree to mutate

- ## Constructor Details

  - ### MutateAllNodesPipeline

    public MutateAllNodesPipeline()

- ## Method Details

  - ### defaultBase

    public Parameter defaultBase()
    Description copied from interface: `Prototype`
    Returns the default base for this prototype. This should generally be implemented by building off of the static base() method on the DefaultsForm object for the prototype's package. This should be callable during setup(...).

  - ### numSources

    public int numSources()
    Description copied from class: `BreedingPipeline`
    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.
    Specified by:
      `numSources` in class `BreedingPipeline`

  - ### 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 Populations, or Subpopulation.
    - 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 `BreedingPipeline`

  - ### 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 `BreedingPipeline`
    See Also:
      - `Prototype.setup(EvolutionState,Parameter)`

  - ### produce

    public int produce(int min, int max, int subpopulation, ArrayList<Individual> inds, EvolutionState state, int thread, HashMap<String,Object> misc)
    Description copied from class: `BreedingSource`
    Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n. max must be >= min, and min must be >= 1. For example, crossover might typically produce two individuals, tournament selection might typically produce a single individual, etc.
    Specified by:
      `produce` in class `BreedingSource`