RealChromosome (JEvolution)

java.lang.Object
- evSOLve.JEvolution.chromosomes.Chromosome
- - evSOLve.JEvolution.chromosomes.RealChromosome

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable
```
public class RealChromosome
extends Chromosome
```
See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`EACH` Object parameters are mutated with a strategy parameter (sigma) for each object parameter.
`protected double`	`high` The largest real number for initialization.
`protected double`	`low` The lowest real number for initialization.
`static int`	`NONE` Object parameters are mutated with a constant mutation rate.
`protected java.util.List<java.lang.Double>`	`objectBases` The genetic information carrier for the object parameters.
`static int`	`SINGLE` Object parameters are mutated with a single strategy parameter (sigma).
`protected int`	`strategy` The type of self-adaptation strategy.
`protected java.util.List<java.lang.Double>`	`strategyBases` The genetic information carrier for the strategy parameters.
`protected double`	`tau` The second parameter for mutation of strategy parameters.
`protected double`	`tauPrime` The first parameter for mutation of strategy parameters.

Fields inherited from class evSOLve.JEvolution.chromosomes.Chromosome
BIASED, crossoverPoints, crossoverRate, LAPLACE, length, mutationRate, soupType

Constructor Summary

Constructors
Constructor and Description
`RealChromosome()` Creates a default chromosome.
`RealChromosome(Element c)` Creates a RealChromosome via XML.
`RealChromosome(int length)` Constructs a chromosome of given length and default values for 'low' (0.0) and 'high' (1.0), and 'mutationRate' (0.05).

Method Summary

Methods
Modifier and Type	Method and Description
`java.lang.Object`	`clone()` A proper clone, cloning the bases deeply by creating new objects.
`void`	`doCrossover(Chromosome father)` Discrete recombination of two random parents.
`void`	`doMutation()` Mutate by adding normal noise with constant, single, or specific standard deviation (strategy parameters).
`boolean`	`equals(java.lang.Object o)` An efficient check for equality.
`void`	`fromString(java.lang.String b)` Create bases from String.
`java.lang.Object`	`getBases()` Return the genetic code for object parameters.
`double`	`getHigh()` Gives upper bound of initial real values.
`double`	`getLow()` Gives lower bound of initial real values.
`int`	`getStrategy()` Gives strategy type.
`java.lang.Object`	`getStrategyBases()` Return the genetic code for strategy parameters.
`int`	`hashCode()` An efficient hash code.
`void`	`mixSoup()` Initial creation of the alleles.
`void`	`setHigh(double high)` Changes upper bound of initial real values.
`void`	`setLow(double low)` Changes lower bound of initial real values.
`void`	`setStrategy(int strategy)` Changes number of strategy parameters.
`java.lang.String`	`toString()` Convert chromosome (object parameters) to string.
`Element`	`toXml(Element parent)` Saves the current state to XML.

Methods inherited from class evSOLve.JEvolution.chromosomes.Chromosome
create, getCrossoverPoints, getCrossoverRate, getLength, getMutationRate, getSoupType, setCrossoverPoints, setCrossoverRate, setLength, setMutationRate, setSoupType

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - NONE
```
public static final int NONE
```
    Object parameters are mutated with a constant mutation rate.
    
    See Also:
    Constant Field Values
  - SINGLE
```
public static final int SINGLE
```
    Object parameters are mutated with a single strategy parameter (sigma).
    
    See Also:
    Constant Field Values
  - EACH
```
public static final int EACH
```
    Object parameters are mutated with a strategy parameter (sigma) for each object parameter.
    
    See Also:
    Constant Field Values
  - objectBases
```
protected java.util.List<java.lang.Double> objectBases
```
    The genetic information carrier for the object parameters.
  - strategy
```
protected int strategy
```
    The type of self-adaptation strategy.
  - strategyBases
```
protected java.util.List<java.lang.Double> strategyBases
```
    The genetic information carrier for the strategy parameters.
  - low
```
protected double low
```
    The lowest real number for initialization.
  - high
```
protected double high
```
    The largest real number for initialization.
  - tauPrime
```
protected double tauPrime
```
    The first parameter for mutation of strategy parameters.
  - tau
```
protected double tau
```
    The second parameter for mutation of strategy parameters.
- Constructor Detail
  - RealChromosome
```
public RealChromosome()
```
    Creates a default chromosome.
  - RealChromosome
```
public RealChromosome(int length)
```
    Constructs a chromosome of given length and default values for 'low' (0.0) and 'high' (1.0), and 'mutationRate' (0.05).
    
    Parameters:
    length - the number of bases
  - RealChromosome
```
public RealChromosome(Element c)
```
    Creates a RealChromosome via XML.
    
    Parameters:
    c - an XML Chromosome element
- Method Detail
  - clone
```
public java.lang.Object clone()
```
    A proper clone, cloning the bases deeply by creating new objects.
    
    Overrides:
    
    clone in class Chromosome
    
    Returns:
    Object the cloned RealChromosome
  - equals
```
public boolean equals(java.lang.Object o)
```
    An efficient check for equality. It only checks the bases, first, if the number of bases is equal, and then if the base values (object and strategy parameters) are the same.
    
    Specified by:
    
    equals in class Chromosome
    
    Returns:
    equal The equality of the passed object with this object.
  - hashCode
```
public int hashCode()
```
    An efficient hash code. Uses Vector.hashCode(). It just uses the object bases for hashing, however, use of the fitness repository does not seem to make any sense, as no single real chromosome will be the same as any other.
    
    Specified by:
    
    hashCode in class Chromosome
    
    Returns:
    hashCode A more or less correct hash code.
  - doMutation
```
public void doMutation()
```
    Mutate by adding normal noise with constant, single, or specific standard deviation (strategy parameters). First, the strategy parameter(s) are mutated as [sigma_i,new = sigma_i,old * exp(tau'N(0, 1) + tau N_i(0, 1))] (where N(0, 1) is the same for all i). Then the object parameters are mutated as [o_i,new = o_i,old + N(0, sigma_i,new)]. [tau = 1/sqrt(2 * sqrt(n))], [tau' = 1/sqrt(2n)], where n is the number of object parameters. If strategy is NONE, the length of the constant interval [low, high] scaled by the mutation rate is used as standard deviation.
    
    Specified by:
    
    doMutation in class Chromosome
  - doCrossover
```
public void doCrossover(Chromosome father)
```
    Discrete recombination of two random parents. Obeying the crossover rate object parameters are exchanged with p = 0.5. In GA terms this is Uniform Crossover.
    
    Specified by:
    
    doCrossover in class Chromosome
    
    Parameters:
    father - A parent Chromosome.
  - mixSoup
```
public void mixSoup()
```
    Initial creation of the alleles. Doubles for object parameters are randomly drawn from the user defined range with uniform distribution (eventually biased). The random values for the strategy parameter(s) are derived using 'mutationRate'. The mutation rate is the range of initial sigma value(s). The range is calculated as a percentage (=mutation rate) of the range high - low. The strategy parameters are then uniformly sampled from this initial range of sigma. If strategy == NONE, the mutation rate is never adapted.
    
    Specified by:
    
    mixSoup in class Chromosome
  - getLow
```
public double getLow()
```
    Gives lower bound of initial real values.
    
    Returns:
    low lower bound
  - setLow
```
public void setLow(double low)
```
    Changes lower bound of initial real values.
    
    Parameters:
    low - lower bound
  - getHigh
```
public double getHigh()
```
    Gives upper bound of initial real values.
    
    Returns:
    high upper bound
  - setHigh
```
public void setHigh(double high)
```
    Changes upper bound of initial real values.
    
    Parameters:
    high - upper bound
  - setStrategy
```
public void setStrategy(int strategy)
```
    Changes number of strategy parameters.
    
    Parameters:
    strategy - NONE, SINGLE, or EACH object parameter is controlled by a strategy base
  - getStrategy
```
public int getStrategy()
```
    Gives strategy type.
    
    Returns:
    strategy type of self-adaptation
  - getBases
```
public java.lang.Object getBases()
```
    Return the genetic code for object parameters.
    
    Specified by:
    
    getBases in class Chromosome
    
    Returns:
    bases object parameters
  - getStrategyBases
```
public java.lang.Object getStrategyBases()
```
    Return the genetic code for strategy parameters.
    
    Returns:
    bases strategy parameters
  - toString
```
public java.lang.String toString()
```
    Convert chromosome (object parameters) to string. The first base (the leftmost) has index 0.
    
    Specified by:
    
    toString in class Chromosome
  - fromString
```
public void fromString(java.lang.String b)
```
    Create bases from String. The syntax of the string must be like this: "1.3|2.4|3.5|4.34|", where the numbers are just examples, but the '|' character must be exactly at the given spots. Note that we only deal with object bases, the strategy bases are initialized using random numbers.
    
    Specified by:
    
    fromString in class Chromosome
    
    Parameters:
    b - a String describing the object bases
  - toXml
```
public Element toXml(Element parent)
```
    Saves the current state to XML.
    
    Overrides:
    
    toXml in class Chromosome
    
    Parameters:
    parent - the JDOM parent element
    
    Returns:
    the Chromosome element

Class RealChromosome

Field Summary

Fields inherited from class evSOLve.JEvolution.chromosomes.Chromosome

Constructor Summary

Method Summary

Methods inherited from class evSOLve.JEvolution.chromosomes.Chromosome

Methods inherited from class java.lang.Object

Field Detail

NONE

SINGLE

EACH

objectBases

strategy

strategyBases

low

high

tauPrime

tau

Constructor Detail

RealChromosome

RealChromosome

RealChromosome

Method Detail

clone

equals

hashCode

doMutation

doCrossover

mixSoup

getLow

setLow

getHigh

setHigh

setStrategy

getStrategy

getBases

getStrategyBases

toString

fromString

toXml