Package com.rubecula.darwin.domain.world

Darwin

See:
Description

Interface Summary

Asexual	Defines operations on asexual organisms.
Attraction	This interface enables sexual selection.
HasMean
Managed	Interface to define the operations on a Population where after stabilizing on a best (fittest) solution, we update the environment, kill off the colonies other than the one containing the best organism, create daughter colonies, each of which has a differently modified environment based on the original environment.
Viability

Class Summary

Attraction_	Base class for Attraction.
Attraction_Uniform	Lifespan: permanent.
Best_Organism	This class keeps track of the best organism, where best is defined as having the greatest fitness.
Census_Darwinian	Class to provide a default implementation of Census_Sink TODO do we really need this class? No it is obsolete!
Census_Detail	Implementation of SinkCensus specifically which tries to do sensible things for general types of phenotypes and genotypes.
Colony_
Colony_Mayrian	Default implementation of a Colony.
Environment_Muirian	Lifespan: permanent.
Expresser_Mendelian	Lifespan: permanent.
Expresser_Sex	Lifespan: permanent.
Frequency	Well, sometimes Java is simply bizarre.
FrequencyMap<T>	Class to implement a frequency map.
Function_Choosy	This class implements the Choosy.getMinimumDesirability(double) function and allows dynamic varying of the specific formula, by emplying an Evaluator.
Function_Desirable	Concrete implementation of Desirable which extends Function_ and implements HasExpressions (thus it can be updated graphically at runtime).
Genomic_Asexual	Lifespan: permanent.
Genomic_Sexual	Lifespan: permanent.
Lek	Lifespan: temporary Concrete class to model a collection of breeding males from which a female may choose a mate.
Mate	Class to model a potential (male) mate.
MateChoice_	Abstract class defining the base methods of MateChoice.
MateChoice_Evaluator
MateChoice_Wrightian	Default implementation of MateChoice.
Messages
MortalityStats
NumericFrequencyMap	This is a FrequencyMap where the keys each have an intrinsic value, yielded by invoking Number.doubleValue().
Organism_	Abstract class defining the base methods and fields of an implementation of Organism interface.
Organism_Asexual	This concrete class represents an individual organism within a Taxon .
Organism_Sexual	This concrete class represents an individual organism within a Taxon .
OrganismCensusContext
OrganismFactory	Factory Class to create Organism objects.
Population_	Abstract class defining the base methods and fields for an instance of the Population interface.
Population_Malthusian	This concrete class is the default implementation of Population.
Population_Managed	This abstract class is designed to be a base class for populations whose evolution is "managed".
QuantifiableFrequencyMap	This is a FrequencyMap where the keys each have an intrinsic value, yielded by invoking Quantifiable.doubleValue().
Realm_Wallacian	Standard implementation of Realm.
Registry_
Registry_None	This is the default concrete implementation of Registry and, as the name suggests, it does nothing at all.
Taxon_	Abstract class implementing Taxon interface.
Taxon_Darwinian	Lifespan: permanent.
TraitFrequencyMap	Note that the objects that go into this frequency map may be variable and therefore we call Trait.getKey() to determine how to uniquely identify the trait for purposes of the frequency map.
Viability_
VisualizableListener_Census	Implementation of VisualizableListener which knows how to take a census of the (changed) population.

Package com.rubecula.darwin.domain.world Description

Darwin

Contents:

• Copyright Notice
• Overview
• Darwin Philosophy
• Programming Conventions
• Class Structure
• Links

Copyright Notice

Darwin Framework Project.
Copyright (C) 2003, 2007, 2009 Rubecula Software.
This library is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

CVS Version: $Revision: 1.5 $

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World Package Overview

Here's an update of the registration text:

This project provides a set of framework classes for the development of Evolutionary Computation applications in Java. Such applications, which might be classed as genetic algorithms, genetic programming, etc., enable problems, typically complex and non-analytical, to be solved by successively evaluating a population of possible solutions and breeding from the better-fitting solutions to generate a new population. The code is platform-independent. It is my intention to make this project a resource which can be used and or contributed to by anyone working in the field. As such it is designed to be extremely general in its class structure, with a well-defined separation between method (framework) code and application code.

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Darwin Philosophy

Here are some of the tenets of the philosophy behind the design and development of Darwin:

• It is object-oriented and implemented in Java.
• At a high level, it models the mechanisms found in nature, without having to be exact in every detail.
• Framework (core) classes, visualization classes, example classes, etc. are appropriately in separate packages.
• The code conforms to a set of programming conventions, including the fact that all public methods in the world package are defined by an interface.
• Documentation is an integral part of the package.
• Elegance is more important than performance.
• It is highly extensible. This extensibility is achieved through:
  • the use of Interface types to model all concepts;
  • the use of factory classes which allow developers to define their own constructors for concrete objects.
• It is open-source: comments and constructive criticism are welcomed.
• The architecture is defined such that the domain package is divided into vertical "slices": world can reference anything; genetics can reference helper.
• It is independent of commercial interests.

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Programming Conventions

• In general, each concept is modeled by the following:
  • an interface with a plain name, such as Genome;
  • an abstract class which implements the interface and whose name is concept_Abstract, for example, Genome_Abstract;
  • (usually) a default implementation class which extends the abstract class and whose name is concept_Default, for example, Genome_Default;
  • (optionally) a set of policy-specific implementation classes which extend the abstract class and whose names are of form: concept_policy, for example, Genome_Diploid;
  All references to the concept, for example types referenced in method signatures, are in terms of the concept (i.e. the interface). The abstract class is referenced only in certain restricted circumstances. The names of the concrete (implementation) classes are used only for constructors (and those are generally found only in the factory classes).
• The order of source files is generally: public class fields, public class methods, public instance methods, non-public instance fields, non-public instance methods. Some variations occur because of requirements of static initialization (some private class fields may appear first).
• Naming: class fields and methods generally begin with capital letters (exceptions when name is a Java convention such as valueOf); instance fields are of the form _Class or similar; constants (final static fields) have names beginning with "$".

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Class Structure

The following is an introduction to the major classes and interfaces of the darwin package. Use it as a starting point and/or as an adjunct to the javadoc. [NOTE: This section is far from complete - see the javadoc!] However, if there are discrepancies, then the javadoc must of course be considered definitive. Most of the classes described are found in the com.rubecula.darwin package. Some utilities, of a more general nature, are found in com.rubecula.util.

Following are descriptions of the darwin framework interfaces each having a simple concept name: Concept.

• Expression: this application interface defines how genetic information (Genes, Genomes) is "expressed" as physical information (Traits, Phenotypes).
• Gene: This application-independent class represents a particular gene at a locus of a genome. :
• Auditable which is useful for identifying items for testing purposes.

• etc.
  

Following are descriptions of the darwin classes.

• etc.
  

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Important Notes:

The package is bundled with the Jakarta Commons Logging facility, without which it will not compile. You don't need your own logger to work with JCL but a log4j configuration file is provided and, if log4j is in your classpath, it will run as expected.
However, by default, all logging is turned off (logging is directed to the NoOpLog implementation). In order to turn it on, open up LogFactory_Darwin.java (currently in the util package but needs to be moved) and comment out the return new NoOpLog(); line and uncomment the LogFactory.getLog... line.

TODO THIS IS OUTDATED. You will find a working example applet: the PepperedMoth example, in the examples package. This applet has an optional feature provided which allows you to vary the formula expressions (in the options window of the applet). Normally, you will leave this feature off (and filter out the compilation of the Evaluator_JEP class which you won't need). In order to turn this feature "on" you must do the following:

1. Procure an (open-source) license to JEP;
2. Reenable compilation of Evaluator_JEP;
3. In the config/pepperedMoth.properties file, set the expressionsEnabled property value to true.

Links:

• Darwin Home Page
• Source Forge Project Page: Darwin
• About Darwin

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Last Updated: 2007-03-01 By: Robin Hillyard