$ A B C D E F G H I K L M N O P Q R S T U V _

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EcoFactor - Interface in com.rubecula.darwin.core

Defines the methods supported by the EcoFactor interface.

EcoFactor_Abstract - Class in com.rubecula.darwin.core

Abstract class providing base functionality for implementers of EcoFactor.

EcoFactor_Abstract(Object, Object) - Constructor for class com.rubecula.darwin.core.EcoFactor_Abstract

Protected constructor.

EcoFactor_Default - Class in com.rubecula.darwin.core

This default implementer of EcoFactor represents an environmental factor with a double value.

EcoFactor_Default(String, double) - Constructor for class com.rubecula.darwin.core.EcoFactor_Default

Construct an EcoFactor_Default from an identifier string and a value.

EcoFactor_Default(double) - Constructor for class com.rubecula.darwin.core.EcoFactor_Default

Construct an EcoFactor_Default with the identifier "default ecofactor" and with a specific value.

EcoFactor_TS - Class in com.rubecula.darwin.examples.travelingsalesman

EcoFactor_TS(List<Client>) - Constructor for class com.rubecula.darwin.examples.travelingsalesman.EcoFactor_TS

Construct an eco factor for the traveling salesman problem.

enumerateCollection(Census, PrintWriter) - Method in interface com.rubecula.darwin.core.CensusibleCollection

Method to cycle through every object "owned" by this object, and apply the individual census taker method to it.

enumerateCollection(Census, PrintWriter) - Method in class com.rubecula.darwin.core.Population_Abstract

Method to enumerate this population for census purposes.

enumerateIndividual(Object, PrintWriter) - Method in interface com.rubecula.darwin.core.Census

Output census information about the individual specified.

enumerateIndividual(Object, PrintWriter) - Method in class com.rubecula.darwin.core.Census_Abstract

enumerateIndividual(Object, PrintWriter) - Method in class com.rubecula.darwin.examples.pepperedmoth.Census_WingColor

enumerateIndividual(Object, PrintWriter) - Method in class com.rubecula.darwin.examples.travelingsalesman.Census_TS

Environment - Interface in com.rubecula.darwin.core

Defines the concept of an Environment, modeled as a map of EcoFactor objects.

Environment_Abstract - Class in com.rubecula.darwin.core

Abstract class defining base methods which implement Environment interface.

Environment_Abstract() - Constructor for class com.rubecula.darwin.core.Environment_Abstract

Construct an empty unidentified environment (no eco factors).

Environment_Abstract(String) - Constructor for class com.rubecula.darwin.core.Environment_Abstract

Construct an empty identified environment (no eco factors).

Environment_Default - Class in com.rubecula.darwin.core

This class provides a default implementation of the Environment interface.

Environment_Default() - Constructor for class com.rubecula.darwin.core.Environment_Default

Environment_Default(int) - Constructor for class com.rubecula.darwin.core.Environment_Default

Environment_Default(EcoFactor) - Constructor for class com.rubecula.darwin.core.Environment_Default

Environment_PepperedMoth - Class in com.rubecula.darwin.examples.pepperedmoth

This class provides an implementation of the Environment interface for the peppered moth example.

Environment_PepperedMoth(double, String) - Constructor for class com.rubecula.darwin.examples.pepperedmoth.Environment_PepperedMoth

environmentChanged() - Method in class com.rubecula.darwin.core.Environment_Abstract

This method should be called whenever the environment has changed.

environmentChanged(Environment) - Method in interface com.rubecula.darwin.core.EnvironmentListener

This method is called on a environment listener to notify it that the environment p has changed.

EnvironmentListener - Interface in com.rubecula.darwin.core

Defines the mechanism for notifying interested objects about changes in an environment.

equals(Object) - Method in class com.rubecula.darwin.core.Allele_Abstract

equals(Object) - Method in class com.rubecula.darwin.core.Organism_Abstract

equals(Object) - Method in class com.rubecula.darwin.core.Trait_Abstract

equals(Object) - Method in class com.rubecula.darwin.examples.travelingsalesman.Phenotype_TS

equals(Object) - Method in class com.rubecula.darwin.visualization.Individual_Abstract

This is purely for debugging/logging purposes.

evaluateFitness(Phenome, Environment) - Method in interface com.rubecula.darwin.core.Fit

This method evaluates the fitness of this in the context of the environment and with reference to the phenome.

evaluateFitness(Phenome, Environment) - Method in class com.rubecula.darwin.core.Organism_Abstract

FIXME This appears to recurse via phenotype.evaluateFitness()

evaluateFitness(Phenome, Environment) - Method in class com.rubecula.darwin.core.Phenotype_Abstract

This implementation of evaluateFitness is relatively obvious: for each trait in this phenotype, and for every factor in the environment, calculate the fitness and weight and add these to total fitness and total weight.

evaluateFitness(Phenome, Environment) - Method in class com.rubecula.darwin.examples.travelingsalesman.Phenotype_TS

EvaluationExpression - Interface in com.rubecula.darwin.expressions

Defines the methods to get and set an (evaluation) expression.

Evaluator - Interface in com.rubecula.darwin.expressions

Defines the operations to be provided by the expression evaluator.

Evaluator_JEP - Class in com.rubecula.darwin.expressions

Base methods for implementing Evaluator by employing Nathan Funk's Java Expression Parser.

Evaluator_JEP(String) - Constructor for class com.rubecula.darwin.expressions.Evaluator_JEP

Constructs an evaluator based on JEP.

Evaluator_JEP(String, boolean) - Constructor for class com.rubecula.darwin.expressions.Evaluator_JEP

Constructs an evaluator based on JEP.

EvaluatorFactory - Class in com.rubecula.darwin.expressions

Singleton class with class method to instantiate a new Evaluator

evaluatorWCSD - Static variable in class com.rubecula.darwin.examples.pepperedmoth.ApplicationDefinitions

express(Gene, Factory) - Method in interface com.rubecula.darwin.core.Expression

Method to express genetic information in physical terms.

express(Genotype, Factory) - Method in interface com.rubecula.darwin.core.Expression

Method to express genetic information in physical terms.

express(Genotype, Factory) - Method in class com.rubecula.darwin.core.Expression_Abstract

Apply Genotype_Abstract.autoExpress(Expression, Factory) to the genotype provided and return the result without further ado.

express(Gene, Factory) - Method in class com.rubecula.darwin.core.Expression_Default

This is a very simplistic expression method which relies on the values of the traits being from the same domain as the values of the alleles!

express(Genome) - Method in interface com.rubecula.darwin.core.Genotype

Method to express this genotype as a phenotype.

express(Genome) - Method in class com.rubecula.darwin.core.Genotype_Abstract

express(Gene, Factory) - Method in class com.rubecula.darwin.examples.pepperedmoth.Expression_PepperedMoth

This is a very simplistic expression method which deals with only one type of gene.

express(Gene, Factory) - Method in class com.rubecula.darwin.examples.travelingsalesman.Expression_TS

Method to express a single gene as a trait.

express(Genotype, Factory) - Method in class com.rubecula.darwin.examples.travelingsalesman.Expression_TS

This method takes the entire genome and splits it up, appropriately, into "chromosomes".

Expression - Interface in com.rubecula.darwin.core

Defines the methods to be implemented by an expresser of genes, i.e.

Expression_Abstract - Class in com.rubecula.darwin.core

Abstract class defining base implementation for Expression (of Genes).

Expression_Abstract() - Constructor for class com.rubecula.darwin.core.Expression_Abstract

Expression_Default - Class in com.rubecula.darwin.core

Default implementation of Expression.

Expression_Default() - Constructor for class com.rubecula.darwin.core.Expression_Default

Public constructor.

Expression_PepperedMoth - Class in com.rubecula.darwin.examples.pepperedmoth

Implementation of Expression specifically for the Peppered Moth example.

Expression_PepperedMoth() - Constructor for class com.rubecula.darwin.examples.pepperedmoth.Expression_PepperedMoth

Expression_TS - Class in com.rubecula.darwin.examples.travelingsalesman

Expression_TS() - Constructor for class com.rubecula.darwin.examples.travelingsalesman.Expression_TS

ExpressionEvaluator - Interface in com.rubecula.darwin.expressions

Methods to support evaluators.

ExpressionEvaluator_Abstract - Class in com.rubecula.darwin.expressions

Base methods and fields for the implementation of ExpressionEvaluator.

ExpressionEvaluator_Abstract(String, String) - Constructor for class com.rubecula.darwin.expressions.ExpressionEvaluator_Abstract

Protected constructor for an ExpressionEvaluator.

ExpressionEvaluator_Fitness - Class in com.rubecula.darwin.examples.pepperedmoth

Class which knows how to evaluate the wing-color/soot-density fitness

ExpressionEvaluator_Fitness() - Constructor for class com.rubecula.darwin.examples.pepperedmoth.ExpressionEvaluator_Fitness

Public constructor.

ExpressionEvaluator_MateChoiceDesirability - Class in com.rubecula.darwin.examples.pepperedmoth

Class which knows how to evaluate the desirability of a male mate.

ExpressionEvaluator_MateChoiceDesirability() - Constructor for class com.rubecula.darwin.examples.pepperedmoth.ExpressionEvaluator_MateChoiceDesirability

Public constructor.

ExpressionEvaluator_MateChoiceDesirabilityMinimum - Class in com.rubecula.darwin.examples.pepperedmoth

Class which knows how to evaluate the desirability of a male mate.

ExpressionEvaluator_MateChoiceDesirabilityMinimum() - Constructor for class com.rubecula.darwin.examples.pepperedmoth.ExpressionEvaluator_MateChoiceDesirabilityMinimum

Public constructor.