com.rubecula.darwin.domain.fitness
Class Fitness_Hamiltonian

java.lang.Object
  com.rubecula.darwin.domain.fitness.Fitness_
      com.rubecula.darwin.domain.fitness.Fitness_Hamiltonian

All Implemented Interfaces:

Fitness, com.rubecula.jexpression.EvalExpression

public final class Fitness_Hamiltonian
extends Fitness_

This is a standard implementation of Fitness well suited to configuration via XML and dependency injection. It is however very basic and is not normally used where a fitness function is complex, for example in the peppered moth application. In order for this implementation to work properly, the weights must be set by calling the method putWeighting(String, EcoFactor) with the appropriate pair of values: a String which corresponds to the key (identifier) of a phenotypic character; and an EcoFactor against which traits of the character will be measured for fitness.
This concrete class is named in honor of W. D. Hamilton, although I don't claim that the specifics of the class's behavior have anything to do with inclusive fitness.

Author:

Robin Hillyard

Field Summary

Fields inherited from class com.rubecula.darwin.domain.fitness.Fitness_

LOG

Constructor Summary

Fitness_Hamiltonian()

Fitness_Hamiltonian(FitnessFunction fitnessFunction, FunctionListener functionListener)

Method Summary

protected double	bandwidth(java.lang.String key) Concrete sub-classes must implement this method to indicate how sharp the fitness curve should be with respect to the possible values of the variate.
double	getFitness(Trait trait, EcoFactor factor)
int	getWeight(java.lang.String character, EcoFactor factor)
EcoFactor	putWeighting(java.lang.String character, EcoFactor factor)
void	setBandwidth(double bandwidth)

Methods inherited from class com.rubecula.darwin.domain.fitness.Fitness_

calculateFitness, compare, equals, getEnvironmentFactor, getExpression, getExpressionTerms, getFitnessFunction, getTolerance, hashCode, resetAdjustment, resetEnvironmentFactor, scaleFactor, scaleTrait, setTolerance, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Fitness_Hamiltonian

public Fitness_Hamiltonian()

Fitness_Hamiltonian

public Fitness_Hamiltonian(FitnessFunction fitnessFunction,
                           FunctionListener functionListener)

Parameters:

fitnessFunction -

functionListener -

Method Detail

getFitness

public double getFitness(Trait trait,
                         EcoFactor factor)
                  throws FitnessException

Returns:

the fitness between 0 (unfit) and 1 (perfect fit).

Throws:

FitnessException

See Also:

Fitness.getFitness(com.rubecula.darwin.domain.helper.Trait, com.rubecula.darwin.domain.helper.EcoFactor)

getWeight

public int getWeight(java.lang.String character,
                     EcoFactor factor)

Parameters:

character - the identifier (or key) of the phenotypic character whose traits/variants will be measured for fitness against the given factor.

Returns:

the relative weighting for this fitness (0: not a significant fitness match)

See Also:

Fitness.getWeight(String, com.rubecula.darwin.domain.helper.EcoFactor)

putWeighting

public EcoFactor putWeighting(java.lang.String character,
                              EcoFactor factor)

Parameters:

character - the key (identifier) for the character whose traits will be measured for fitness against factor.

factor -

Returns:

the previous value corresponding to this key.

See Also:

HashMap.put(java.lang.Object, java.lang.Object)

setBandwidth

public void setBandwidth(double bandwidth)

Parameters:

bandwidth - the bandwidth to set

bandwidth

protected double bandwidth(java.lang.String key)

Description copied from class: Fitness_

Concrete sub-classes must implement this method to indicate how sharp the fitness curve should be with respect to the possible values of the variate.

Specified by:

bandwidth in class Fitness_

Parameters:

key - the key which determines which bandwidth to get (trait or ecofactor).

Returns:

the value of bandwidth.

See Also:

Fitness_.bandwidth(java.lang.String)