Package ec.neat

Class NEATGene

java.lang.Object
ec.vector.Gene
ec.neat.NEATGene
All Implemented Interfaces:
Prototype, Setup, Serializable, Cloneable
public class NEATGene extends Gene
NEATGene is the combination of class Gene and class Link in original code. It is used to represent a single connection between two nodes (NEATNode) of a neural network, and extends the abstract Gene class to make use of its read/write utilities.
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    boolean
    enable
    Is the link this gene represent is enable in network activation.
    boolean
    frozen
    Is this gene frozen, a frozen gene's weight cannot get mutated in breeding procedure.
    NEATNode
    inNode
    The actual in node this gene connect to.
    int
    inNodeId
    The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.
    int
    innovationNumber
    The innovation number of this link.
    boolean
    isRecurrent
    Is the link this gene represent a recurrent link.
    double
    mutationNumber
    The mutation number of this gene, Used to see how much mutation has changed.
    NEATNode
    outNode
    The actual out node this gene connect to.
    int
    outNodeId
    The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.
    static final String
    P_GENE
     
    boolean
    timeDelay
    Time delay of the link, used in network activation.
    double
    weight
    The weight of link this gene is represent.

  • Constructor Summary

    Constructors
    Constructor
    Description
    NEATGene()
     

  • 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.
    boolean
    equals(Object o)
    Unlike the standard form for Java, this function should return true if this gene is "genetically identical" to the other gene.
    int
    hashCode()
    "Placeholder" method for generating a hashcode.
    String
    printGeneToString()
    This method is used to output a gene that is same as the format in start genome file.
    String
    printGeneToStringForHumans()
    Prints the gene to a string in a human-readable fashion.
    void
    readGeneFromString(String string, EvolutionState state)
    This method is used to read a gene in start genome from file.
    void
    reset(double w, int iNodeId, int oNodeId, boolean recur, int innov, double mutNum)
    Reset the gene with given parameters.
    void
    reset(EvolutionState state, int thread)
    The reset method randomly reinitializes the gene.
    void
    setup(EvolutionState state, Parameter base)
    The setup method initializes a "meaningless" gene that does not specify any connection.
    String
    toString()
    This method convert the gene in to human readable format.

    Methods inherited from class ec.vector.Gene

    mutate, printGene, printGene, printGeneForHumans, readGene, readGene, writeGene

    Methods inherited from class java.lang.Object

    finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • P_GENE

      public static final String P_GENE
      See Also:

    • weight

      public double weight
      The weight of link this gene is represent.

    • inNode

      public NEATNode inNode
      The actual in node this gene connect to.

    • outNode

      public NEATNode outNode
      The actual out node this gene connect to.

    • inNodeId

      public int inNodeId
      The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.

    • outNodeId

      public int outNodeId
      The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.

    • isRecurrent

      public boolean isRecurrent
      Is the link this gene represent a recurrent link.

    • timeDelay

      public boolean timeDelay
      Time delay of the link, used in network activation.

    • innovationNumber

      public int innovationNumber
      The innovation number of this link.

    • mutationNumber

      public double mutationNumber
      The mutation number of this gene, Used to see how much mutation has changed.

    • enable

      public boolean enable
      Is the link this gene represent is enable in network activation.

    • frozen

      public boolean frozen
      Is this gene frozen, a frozen gene's weight cannot get mutated in breeding procedure.

  • Constructor Details

    • NEATGene

      public NEATGene()

  • Method Details

    • setup

      public void setup(EvolutionState state, Parameter base)
      The setup method initializes a "meaningless" gene that does not specify any connection.
      Specified by:
      setup in interface Prototype
      Specified by:
      setup in interface Setup
      Overrides:
      setup in class Gene

    • 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(...).
      Specified by:
      defaultBase in interface Prototype
      Overrides:
      defaultBase in class Gene

    • reset

      public void reset(EvolutionState state, int thread)
      Description copied from class: Gene
      The reset method randomly reinitializes the gene.
      Specified by:
      reset in class Gene

    • reset

      public void reset(double w, int iNodeId, int oNodeId, boolean recur, int innov, double mutNum)
      Reset the gene with given parameters.

    • 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 Gene

    • printGeneToStringForHumans

      public String printGeneToStringForHumans()
      Description copied from class: Gene
      Prints the gene to a string in a human-readable fashion. The default simply calls toString().
      Overrides:
      printGeneToStringForHumans in class Gene

    • toString

      public String toString()
      This method convert the gene in to human readable format. It can be useful in debugging.
      Overrides:
      toString in class Object

    • printGeneToString

      public String printGeneToString()
      This method is used to output a gene that is same as the format in start genome file.
      Overrides:
      printGeneToString in class Gene

    • readGeneFromString

      public void readGeneFromString(String string, EvolutionState state)
      This method is used to read a gene in start genome from file. Example : i1|i4|d0|0.0|Fi1|d0|0.0|T have these parts : i1 i4 d0|0.0 F i1 d0|0.0 T which are: inNode outNode weight isRecurrent innovationNumber mutationNumber enable
      Overrides:
      readGeneFromString in class Gene

    • hashCode

      public int hashCode()
      "Placeholder" method for generating a hashcode. The algorithm is stolen from GPIndividual and modified a bit to use NEATGene's variables. It is by no means "good" and is subject for improvement.
      Specified by:
      hashCode in class Gene

    • equals

      public boolean equals(Object o)
      Description copied from class: Gene
      Unlike the standard form for Java, this function should return true if this gene is "genetically identical" to the other gene.
      Specified by:
      equals in class Gene