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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.

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