Chromosome (JEvolution)

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

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

BitChromosome, IntChromosome, RealChromosome, TreeChromosome
```
public abstract class Chromosome
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable
```
See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`BIASED`
`protected int`	`crossoverPoints` The number of crossover sites (default = 2).
`protected double`	`crossoverRate` The crossover rate (default = 0.6).
`static int`	`LAPLACE` Initial mode of creation of Chromosome.
`protected int`	`length` The default length of the Chromosome.
`protected double`	`mutationRate` The mutation rate (default = 0.1).
`protected int`	`soupType` Method of generation of start population (default = LAPLACE).

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`Chromosome(Element c)` Creates a Chromosome via XML.
`protected`	`Chromosome(int length)` Constructs a chromosome of given length.

Method Summary

Methods
Modifier and Type	Method and Description
`java.lang.Object`	`clone()` The Chromosome's clone, which has to be done properly, i.e., all objects representing the chromosome should be replicated exactly.
`static Chromosome`	`create(Element element)` Creates the chromosome designated by an XML element by calling the XML constructor.
`abstract void`	`doCrossover(Chromosome mate)` Crossover.
`abstract void`	`doMutation()` Mutation of Chromosome.
`abstract boolean`	`equals(java.lang.Object o)` This is very important for usage of the fitness repository.
`abstract void`	`fromString(java.lang.String representation)` Constructs the Chromosome from its string representation.
`abstract java.lang.Object`	`getBases()` Returns the genetic information carrier of the Chromosome.
`int`	`getCrossoverPoints()` Access crossover points.
`double`	`getCrossoverRate()` Access crossover rate.
`int`	`getLength()` Return length of the Chromosome.
`double`	`getMutationRate()` Access mutation rate.
`int`	`getSoupType()` Access soup type.
`abstract int`	`hashCode()` The Chromosome's hash code.
`abstract void`	`mixSoup()` Generate initial chromosomes.
`void`	`setCrossoverPoints(int crossoverPoints)` Change crossover points.
`void`	`setCrossoverRate(double crossoverRate)` Change crossover rate.
`void`	`setLength(int length)` Change Chromosome length.
`void`	`setMutationRate(double mutationRate)` Change mutation rate.
`void`	`setSoupType(int soupType)` Change soup type.
`abstract java.lang.String`	`toString()` Returns bases of the Chromosome as String.
`Element`	`toXml(Element parent)` Saves the current state to XML.

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

- Field Detail
  - length
```
protected int length
```
    The default length of the Chromosome.
  - mutationRate
```
protected double mutationRate
```
    The mutation rate (default = 0.1).
  - crossoverRate
```
protected double crossoverRate
```
    The crossover rate (default = 0.6).
  - crossoverPoints
```
protected int crossoverPoints
```
    The number of crossover sites (default = 2).
  - LAPLACE
```
public static final int LAPLACE
```
    Initial mode of creation of Chromosome. With LAPLACE all 1s (and 0s) have a probability of 0.5. With BIASED for each chromosome a random probability is drawn, which determines the probability of a 1.
    
    See Also:
    Constant Field Values
  - BIASED
```
public static final int BIASED
```
    See Also:
    Constant Field Values
  - soupType
```
protected int soupType
```
    Method of generation of start population (default = LAPLACE).
- Constructor Detail
  - Chromosome
```
protected Chromosome(int length)
```
    Constructs a chromosome of given length.
    
    Parameters:
    length - the number of bases
  - Chromosome
```
protected Chromosome(Element c)
```
    Creates a Chromosome via XML.
    
    Parameters:
    c - an XML Chromosome element
- Method Detail
  - clone
```
public java.lang.Object clone()
```
    The Chromosome's clone, which has to be done properly, i.e., all objects representing the chromosome should be replicated exactly. Specifically, the bases of the Chromosome must be cloned.
    
    Overrides:
    
    clone in class java.lang.Object
  - equals
```
public abstract boolean equals(java.lang.Object o)
```
    This is very important for usage of the fitness repository. This method of a specific Chromosome should be as efficient as possible, e.g., if the bases of the Chromosome are implemented as BitSet, then the corresponding equals() method of BitSet should be called. For other Chromosomes it might be beneficial, if a specific, efficient equals() is implemented. Of course, you could also use the inherited equals(), but it will affect performance of the fitness repository, maybe even to the point that it is not used at all.
    
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public abstract int hashCode()
```
    The Chromosome's hash code. This is explicitely listed here, as the hashCode() method of a specific Chromosome should be as efficient as possible, e.g., if the bases of the Chromosome are implemented as BitSet, then the corresponding hashCode() method of BitSet should be called. For other Chromosomes it might be beneficial, if a specific, efficient hashCode() is implemented. Of course, you could also use the inherited hashCode(), but it will affect performance of the fitness repository, maybe even to the point that it is not used at all.
    
    Overrides:
    
    hashCode in class java.lang.Object
  - doMutation
```
public abstract void doMutation()
```
    Mutation of Chromosome. Candidate for customizable plug-in.
  - doCrossover
```
public abstract void doCrossover(Chromosome mate)
```
    Crossover. Candidate for customizable plug-in.
  - mixSoup
```
public abstract void mixSoup()
```
    Generate initial chromosomes.
  - getBases
```
public abstract java.lang.Object getBases()
```
    Returns the genetic information carrier of the Chromosome.
    
    Returns:
    the bases of the Chromosome
  - toString
```
public abstract java.lang.String toString()
```
    Returns bases of the Chromosome as String.
    
    Overrides:
    
    toString in class java.lang.Object
  - fromString
```
public abstract void fromString(java.lang.String representation)
```
    Constructs the Chromosome from its string representation.
  - getLength
```
public int getLength()
```
    Return length of the Chromosome.
    
    Returns:
    length The number of bases.
  - setLength
```
public void setLength(int length)
               throws JEvolutionException
```
    Change Chromosome length.
    
    Parameters:
    length - The number of bases.
    
    Throws:
    
    JEvolutionException - The chromosome has no length.
  - getMutationRate
```
public double getMutationRate()
```
    Access mutation rate.
    
    Returns:
    mutationRate The mutation probability.
  - setMutationRate
```
public void setMutationRate(double mutationRate)
                     throws JEvolutionException
```
    Change mutation rate.
    
    Parameters:
    mutationRate - The mutation probability.
    
    Throws:
    
    JEvolutionException - No probability value.
  - getCrossoverRate
```
public double getCrossoverRate()
```
    Access crossover rate.
    
    Returns:
    crossoverRate The crossover probability.
  - setCrossoverRate
```
public void setCrossoverRate(double crossoverRate)
                      throws JEvolutionException
```
    Change crossover rate.
    
    Parameters:
    crossoverRate - The crossover probability.
    
    Throws:
    
    JEvolutionException - No probability value.
  - getCrossoverPoints
```
public int getCrossoverPoints()
```
    Access crossover points.
    
    Returns:
    crossoverPoints The number of crossover sites.
  - setCrossoverPoints
```
public void setCrossoverPoints(int crossoverPoints)
                        throws JEvolutionException
```
    Change crossover points.
    
    Parameters:
    crossoverPoints - The number of crossover sites.
    
    Throws:
    
    JEvolutionException - Invalid number.
  - getSoupType
```
public int getSoupType()
```
    Access soup type.
    
    Returns:
    soupType How to generate initial Genotype.
  - setSoupType
```
public void setSoupType(int soupType)
```
    Change soup type.
    
    Parameters:
    soupType - How to generate initial Genotype.
  - toXml
```
public Element toXml(Element parent)
```
    Saves the current state to XML.
    
    Parameters:
    parent - the JDOM parent element
    
    Returns:
    the Chromosome element
  - create
```
public static Chromosome create(Element element)
```
    Creates the chromosome designated by an XML element by calling the XML constructor.
    
    Parameters:
    element - an XML element
    
    Returns:
    a new Chromosome (null, if problems)

Class Chromosome

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

length

mutationRate

crossoverRate

crossoverPoints

LAPLACE

BIASED

soupType

Constructor Detail

Chromosome

Chromosome

Method Detail

clone

equals

hashCode

doMutation

doCrossover

mixSoup

getBases

toString

fromString

getLength

setLength

getMutationRate

setMutationRate

getCrossoverRate

setCrossoverRate

getCrossoverPoints

setCrossoverPoints

getSoupType

setSoupType

toXml

create