ec.vector
Class VectorGene

java.lang.Object
  extended by ec.vector.VectorGene
All Implemented Interfaces:
Prototype, Setup, java.io.Serializable, java.lang.Cloneable

public abstract class VectorGene
extends java.lang.Object
implements Prototype

VectorGene is an abstract superclass of objects which may be used in the genome array of GeneVectorIndividuals.

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

Default Base
vector.vect-gene

Version:
1.0
Author:
Sean Luke
See Also:
Serialized Form

Field Summary
static java.lang.String P_VECTORGENE
           
 
Constructor Summary
VectorGene()
           
 
Method Summary
 java.lang.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.
abstract  boolean equals(java.lang.Object other)
          Unlike the standard form for Java, this function should return true if this gene is "genetically identical" to the other gene.
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.
 void mutate(EvolutionState state, int thread)
          Mutate the gene.
 void printGene(EvolutionState state, int verbosity, int log)
          Prints the gene in a way that can be read by readGene().
 void printGene(EvolutionState state, java.io.PrintWriter writer)
          Deprecated. use printGeneToString instead
 void printGeneForHumans(EvolutionState state, int verbosity, int log)
          Nice printing.
 java.lang.String printGeneToString()
          Prints the gene to a string in a fashion readable by readGeneFromString and parseable by readGene(state, reader).
 java.lang.String printGeneToString(EvolutionState state)
          Deprecated. use printGeneToString() instead.
 java.lang.String printGeneToStringForHumans()
          Prints the gene to a string in a human-readable fashion.
 void readGene(EvolutionState state, java.io.DataInput dataInput)
          Override this if you need to read rules in from a binary stream
 void readGene(EvolutionState state, java.io.LineNumberReader reader)
          Reads a gene printed by printGene(...).
 void readGeneFromString(java.lang.String string, EvolutionState state)
          Reads a gene from a string, which may contain a final '\n'.
abstract  void reset(EvolutionState state, int thread)
          The reset method randomly reinitializes the gene.
 void setup(EvolutionState state, Parameter base)
          Sets up the object by reading it from the parameters stored in state, built off of the parameter base base.
 void writeGene(EvolutionState state, java.io.DataOutput dataOutput)
          Override this if you need to write rules out to a binary stream
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

P_VECTORGENE

public static final java.lang.String P_VECTORGENE
See Also:
Constant Field Values
Constructor Detail

VectorGene

public VectorGene()
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 java.lang.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 java.lang.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 java.lang.Object

equals

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


printGeneToString

public java.lang.String printGeneToString(EvolutionState state)
Deprecated. use printGeneToString() instead.

Prints the gene to a string in a fashion readable by readGeneFromString and parseable by readGene(state, reader). The default form simply calls printGeneToString().


printGeneToString

public java.lang.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(java.lang.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(state). 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,
                      java.io.PrintWriter writer)
Deprecated. use printGeneToString instead

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,
                     java.io.LineNumberReader reader)
              throws java.io.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:
java.io.IOException

writeGene

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

Throws:
java.io.IOException

readGene

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

Throws:
java.io.IOException