ec.vector

Class Gene

    • Constructor Detail

      • Gene

        public Gene()

    • Method Detail

      • setup

        public void setup(EvolutionState state,
         Parameter base)
        Description copied from interface: Prototype
        Sets up the object by reading it from the parameters stored in state, built off of the parameter base base. If an ancestor implements this method, be sure to call super.setup(state,base); before you do anything else.

        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.

        Specified by:
        setup in interface Prototype
        Specified by:
        setup in interface Setup

      • 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

      • 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 Object

      • hashCode

        public abstract int hashCode()
        Generates a hash code for this gene -- the rule for this is that the hash code must be the same for two genes that are equal to each other genetically.
        Overrides:
        hashCode in class Object

      • equals

        public abstract boolean equals(Object other)
        Unlike the standard form for Java, this function should return true if this gene is "genetically identical" to the other gene.
        Overrides:
        equals in class Object

      • reset

        public abstract void reset(EvolutionState state,
         int thread)
        The reset method randomly reinitializes the gene.

      • mutate

        public void mutate(EvolutionState state,
          int thread)
        Mutate the gene. The default form just resets the gene.

      • printGeneForHumans

        public void printGeneForHumans(EvolutionState state,
                      int verbosity,
                      int log)
        Nice printing. The default form simply calls printGeneToStringForHumans and prints the result, but you might want to override this.

      • printGeneToStringForHumans

        public String printGeneToStringForHumans()
        Prints the gene to a string in a human-readable fashion. The default simply calls toString().

      • printGeneToString

        public String printGeneToString()
        Prints the gene to a string in a fashion readable by readGeneFromString and parseable by readGene(state, reader). Override this. The default form returns toString().

      • readGeneFromString

        public void readGeneFromString(String string,
                      EvolutionState state)
        Reads a gene from a string, which may contain a final '\n'. Override this method. The default form generates an error.

      • printGene

        public void printGene(EvolutionState state,
             int verbosity,
             int log)
        Prints the gene in a way that can be read by readGene(). The default form simply calls printGeneToString(). Override this gene to do custom writing to the log, or just override printGeneToString(...), which is probably easier to do.

      • printGene

        public void printGene(EvolutionState state,
             PrintWriter writer)
        Prints the gene in a way that can be read by readGene(). The default form simply calls printGeneToString(state). Override this gene to do custom writing, or just override printGeneToString(...), which is probably easier to do.

      • readGene

        public void readGene(EvolutionState state,
            LineNumberReader reader)
              throws IOException
        Reads a gene printed by printGene(...). The default form simply reads a line into a string, and then calls readGeneFromString() on that line. Override this gene to do custom reading, or just override readGeneFromString(...), which is probably easier to do.
        Throws:
        IOException

Copyright © 2014 Evolutionary Computation Laboratory at George Mason University. All rights reserved.