Package ec.vector

Class Gene

java.lang.Object
ec.vector.Gene
All Implemented Interfaces:
Prototype, Setup, Serializable, Cloneable
Direct Known Subclasses:
NEATGene
public abstract class Gene extends Object implements Prototype
Gene is an abstract superclass of objects which may be used in the genome array of GeneVectorIndividuals.

In addition to serialization for checkpointing, Genes may read and write themselves to streams in three ways.

  • writeGene(...,DataOutput)/readGene(...,DataInput)   This method transmits or receives a Gene in binary. It is the most efficient approach to sending Genes over networks, etc. The default versions of writeGene/readGene throw errors. You don't need to implement them if you don't plan on using read/writeGene.
  • printGene(...,PrintWriter)/readGene(...,LineNumberReader)   This approach transmits or receives a Gene in text encoded such that the Gene is largely readable by humans but can be read back in 100% by ECJ as well. To do this, these methods will typically encode numbers using the ec.util.Code class. These methods are mostly used to write out populations to files for inspection, slight modification, then reading back in later on. readGene reads in a line, then calls readGeneFromString on that line. You are responsible for implementing readGeneFromString: the Code class is there to help you. The default version throws an error if called. printGene calls printGeneToString and printlns the resultant string. You are responsible for implementing the printGeneToString method in such a way that readGeneFromString can read back in the Gene println'd with printGeneToString. The default form of printGeneToString() simply calls toString() by default. You might override printGeneToString() to provide better information. You are not required to implement these methods, but without them you will not be able to write Genes to files in a simultaneously computer- and human-readable fashion.
  • printGeneForHumans(...,PrintWriter)   This approach prints a Gene in a fashion intended for human consumption only. printGeneForHumans calls printGeneToStringForHumans() and printlns the resultant string. The default form of this method just returns the value of toString(). You may wish to override this to provide more information instead. You should handle one of these methods properly to ensure Genes can be printed by ECJ.

Default Base
vector.gene

See Also:

  • Field Details

  • Constructor Details

    • Gene

      public Gene()

  • Method Details

    • 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 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 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

    • writeGene

      public void writeGene(EvolutionState state, DataOutput dataOutput) throws IOException
      Override this if you need to write rules out to a binary stream
      Throws:
      IOException

    • readGene

      public void readGene(EvolutionState state, DataInput dataInput) throws IOException
      Override this if you need to read rules in from a binary stream
      Throws:
      IOException