Package com.rubecula.darwin.domain.helper

Darwin

See:
Description

Interface Summary

Allele	Models the concept of an Allele, that is to say a specific instance of a Genes which "compete" for presence at a Locus
Attribute	Defines the methods supported by Attribute objects.
Basic
Beans
Cache	This defines a general caching mechanism where the cache is made up of entries of the form: key -> value, for example when some significant amount of calculation is required to generate value and we therefore prefer to look it up to see if it's already been calculated.
Cache_MBean
CacheSignature	Interface to define the notion of a cache key signature.
Census
Censusible	This interface defines the census operation.
Chromosome	Defines part of a Genomic.
Colony	This super-interface of Population addresses the more basic aspects of an Evolvable, Visualizable and Countable group.
EcoFactor	Defines the methods supported by the EcoFactor interface.
EitherOr
Environment	Defines the concept of an Environment, modeled as a map of EcoFactor objects.
EnvironmentListener	Defines the mechanism for notifying interested objects about changes in an environment.
ExPhen	Type to represent an "extended phenotype" that is to say a variant of an EcoFactor which has been modified by an organism whose Genome is expressed as the ExPhen.
Expresser	Defines the operations supported by an "expresser", that is an object that can take a Gene (or Genome) and express that gene(s) in the context of an environment.
Expression	Generic marker interface for Traits and ExtPhen
Fecundity	Defines methods to determine how fecund will be a particular mating in a population, i.e.
Fit	Defines the aspect of an object which measures its fitness with respect to an environment.
Fitness	Type representing a pair whose mutual fitness can be estimated.
FitnessEngine	Registry for fitness functions for Taxon (Evolutionary Computation) Systems.
FitnessFunction
Gene	Defines the operations and properties of a Gene.
GenerationListener	Defines a callback method for invocation whenever a Evolution runs.
Genes	This interface represents the read-only aspects of (possibly a subset of) a Genome, although the Ploidy is not included here.
Genetic	Interface with defines a "genetic" object, i.e.
Genome	Defines the genetic information contained in an Organism belonging to a Taxon.
Genomic	Defines the genetic information contained in a Taxon.
Genotype	A Genotype is a (diploid or haploid) set of genes which can be manipulated.
HasPhenotypeCache
Insular	This defines the concept of separation, as of the separation of a colony from other colonies.
Locus	Defines a Locus at which one of several Alleles may appear.
MateChoice	Defines methods to determine how mates are chosen.
Mating	Defines the mating of a pair of organisms, one male, one female.
Meiosis	Defines how alleles are chosen during Meiosis.
Mortal	Interface to define the operations supported by a "mortal" object, i.e.
Mortality	Defines how mortality is calculated for individual objects (organisms) in Taxons.
Mutator	Defines the methods for gene and genome mutators.
Nuclear	Defines operations supported by a Nuclear object.
Organism	Defines methods on an individual organism within a Taxon.
Pharacter	This interface represents the concept of a Phenotypic Character.
Phenome	Defines the methods for implementations of the Phenome interface.
Phenotype	Defines the methods supported by instances of Phenotype interface.
Ploidy	This interface defines the concept of "ploidy", that is to say whether a genetic object is diploid or haploid, i.e.
Population	Defines the properties (methods) which characterize a population in an Evolutionary Computation.
PopulationExposed	MBean interface for Population.
Progenitor	This marker interface represents the "parent" of a Locus.
Quantifiable	This interface is in lieu of a Java interface to do the same thing.
Realm	Interface which defines the concept of the "model" which is undergoing evolution.
Registry
Replicator
SexLinked
Sexual	Defines the one method which must be supported by sex-based objects, viz.
Sink	Interface to capture the essence of place where output can go, a sink in the engineering sense of sources and sinks.
SinkCensus	This application interface is used to define how an individual object should be processed for a census.
Taxon	Defines the methods supported by a unit of evolutionary computation (Taxon).
Trait	A Trait is the phenotypic analog to a (genotypic) Gene.
TraitMap	Defines the operations on a read-only collection of Trait instances.
Variant	Defines the methods support by instances of the Variant interface.

Class Summary

Attribute_	Abstract class representing a named attribute, and is the base class for Variant_, Allele_ and EcoFactor_.
Attribute_Standard	Default implementation of Attribute.
Cache_<K extends Identifiable,V>	Abstract base class for implementing a Cache.
Census_
Census_Log
Census_Sink	Base implementation the SinkCensus interface.
Census_Standard	Class to provide a default implementation of Census_Sink
FitnessCache	This cache maintains a set of fitness values indexed by Signature/FitnessEngine pair.
FitnessCacheKey	This class is used to form the key for the FitnessCache
GenerationListener_
GenerationListener_Standard
LogFactoryNoOp	This class is necessary to allow the system to run as a (remote) Applet.
PhenotypeCache	This cache maintains a set of Phenotypes indexed by Basic/Identifiable pair.
PhenotypeCacheKey	This class is used to form the key for the PhenotypeCache
Realm_	Base implementation of Realm.
Sink_
Sink_Bucket	This is the bit bucket.
Sink_Log

Exception Summary

DarwinException	This application-independent exception class is used to track runtime exceptions which may occur in the Darwin classes.
GeneticsException

Package com.rubecula.darwin.domain.helper 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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Helper 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 helper 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