Package org.biojavax.ga.util

Class GATools

java.lang.Object

org.biojavax.ga.util.GATools

public final class GATools
extends Object

Utility methods for the GA library

Since:

1.5

Version:

1.0

Author:

Mark Schreiber

Constructor Summary

Constructors

Constructor	Description
GATools()

Method Summary

Modifier and Type	Method	Description
static SymbolList	createBinary(String binarySequence)	Creates a SymbolList in the GABinary Alphabet
static FiniteAlphabet	getBinaryAlphabet()	Gets a Reference to the FlyWeight GA_Binary Alphabet.
static AtomicSymbol	one()
static OrderNDistribution	standardMutationDistribution(FiniteAlphabet a)	Makes a mutation Distribution where the probability of a Symbol being mutated to itself is zero and the probability of it being changed to any other Symbol in the Alphabet a is 1.0 / (a.size() - 1.0)
static OrderNDistribution	uniformMutationDistribution(FiniteAlphabet a)	Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).
static AtomicSymbol	zero()

Methods inherited from class java.lang.Object

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

Constructor Detail

GATools

public GATools()

Method Detail

getBinaryAlphabet

public static FiniteAlphabet getBinaryAlphabet()

Gets a Reference to the FlyWeight GA_Binary Alphabet. It contains the Symbols one and zero.

Returns:

the finite, flyweight Binary Alphabet

one

public static AtomicSymbol one()

Returns:

the GA_Binary symbol "one"

createBinary

public static SymbolList createBinary(String binarySequence)
                               throws IllegalSymbolException

Creates a SymbolList in the GABinary Alphabet

Parameters:

binarySequence - a String like "01010000101010101" with no white space

Returns:

a SymbolList parsed from binarySequence

Throws:

IllegalSymbolException - if a character other than 1 or 0 is found.

zero

public static AtomicSymbol zero()

Returns:

the GA_Binary symbol "zero"

uniformMutationDistribution

public static OrderNDistribution uniformMutationDistribution(FiniteAlphabet a)
                                                      throws IllegalAlphabetException

Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).

Parameters:

a - the zero order Alphabet which will be multiplied into the 1st order alphabet

Returns:

the "1st order" distribution

Throws:

IllegalAlphabetException - if the Distribution cannot be constructed from a.

standardMutationDistribution

public static OrderNDistribution standardMutationDistribution(FiniteAlphabet a)
                                                       throws IllegalAlphabetException

Makes a mutation Distribution where the probability of a Symbol being mutated to itself is zero and the probability of it being changed to any other Symbol in the Alphabet a is 1.0 / (a.size() - 1.0)

Parameters:

a - the FiniteAlphabet which mutations are sampled from.

Returns:

A Distribution suitable for use in a MutationFunction

Throws:

IllegalAlphabetException - if the Distribution cannot be made over the FiniteAlphabet