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| Packages that use com.rubecula.darwin.domain.helper | |
|---|---|
| com.rubecula.darwin.domain.environment | |
| com.rubecula.darwin.domain.fitness | Math |
| com.rubecula.darwin.domain.genetics | Genetics |
| com.rubecula.darwin.domain.helper | Darwin |
| com.rubecula.darwin.domain.world | Darwin |
| com.rubecula.darwin.evolution | |
| com.rubecula.darwin.examples.pepperedmoth | Peppered Moth Example |
| com.rubecula.darwin.examples.travelingsalesman | Traveling Salesman Example |
| com.rubecula.darwin.foundation | |
| com.rubecula.darwin.visualization | Display Package |
| com.rubecula.darwin.visualization.swing | Display Package |
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.domain.environment | |
|---|---|
| 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. |
|
| Attribute_
Abstract class representing a named attribute, and is the base class for Variant_, Allele_ and EcoFactor_. |
|
| CacheSignature
Interface to define the notion of a cache key signature. |
|
| Census
|
|
| Censusible
This interface defines the census operation. |
|
| Colony
This super-interface of Population addresses the more basic aspects
of an Evolvable, Visualizable and Countable group. |
|
| DarwinException
This application-independent exception class is used to track runtime exceptions which may occur in the Darwin classes. |
|
| EcoFactor
Defines the methods supported by the EcoFactor interface. |
|
| 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 |
|
| Fit
Defines the aspect of an object which measures its fitness with respect to an environment. |
|
| FitnessEngine
Registry for fitness functions for Taxon (Evolutionary Computation) Systems. |
|
| Gene
Defines the operations and properties of a Gene. |
|
| Locus
Defines a Locus at which one of several Alleles may appear. |
|
| 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. |
|
| 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. |
|
| SexLinked
|
|
| Sink
Interface to capture the essence of place where output can go, a sink in the engineering sense of sources and sinks. |
|
| 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. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.domain.fitness | |
|---|---|
| CacheSignature
Interface to define the notion of a cache key signature. |
|
| EcoFactor
Defines the methods supported by the EcoFactor interface. |
|
| Environment
Defines the concept of an Environment, modeled as a map of EcoFactor
objects. |
|
| Fitness
Type representing a pair whose mutual fitness can be estimated. |
|
| FitnessCache
This cache maintains a set of fitness values indexed by Signature/FitnessEngine pair. |
|
| FitnessEngine
Registry for fitness functions for Taxon (Evolutionary Computation) Systems. |
|
| FitnessFunction
|
|
| Phenotype
Defines the methods supported by instances of Phenotype interface. |
|
| Realm
Interface which defines the concept of the "model" which is undergoing evolution. |
|
| Trait
A Trait is the phenotypic analog to a (genotypic) Gene. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.domain.genetics | |
|---|---|
| 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. |
|
| Attribute_
Abstract class representing a named attribute, and is the base class for Variant_, Allele_ and EcoFactor_. |
|
| Basic
|
|
| 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. |
|
| EitherOr
|
|
| 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. |
|
| Fecundity
Defines methods to determine how fecund will be a particular mating in a population, i.e. |
|
| Gene
Defines the operations and properties of a Gene. |
|
| 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. |
|
| GeneticsException
|
|
| 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. |
|
| Locus
Defines a Locus at which one of several Alleles may appear. |
|
| Mating
Defines the mating of a pair of organisms, one male, one female. |
|
| Meiosis
Defines how alleles are chosen during Meiosis. |
|
| 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. |
|
| 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. |
|
| Progenitor
This marker interface represents the "parent" of a Locus. |
|
| Replicator
|
|
| SexLinked
|
|
| Sexual
Defines the one method which must be supported by sex-based objects, viz. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.domain.helper | |
|---|---|
| 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. |
|
| Attribute_
Abstract class representing a named attribute, and is the base class for Variant_, Allele_ and EcoFactor_. |
|
| Basic
|
|
| 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_
Abstract base class for implementing a Cache. |
|
| Cache_MBean
|
|
| CacheSignature
Interface to define the notion of a cache key signature. |
|
| Census
|
|
| Census_
|
|
| Census_Sink
Base implementation the SinkCensus interface. |
|
| 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. |
|
| 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. |
|
| FitnessCache
This cache maintains a set of fitness values indexed by Signature/FitnessEngine pair. |
|
| FitnessEngine
Registry for fitness functions for Taxon (Evolutionary Computation) Systems. |
|
| Gene
Defines the operations and properties of a Gene. |
|
| GenerationListener
Defines a callback method for invocation whenever a Evolution runs. |
|
| GenerationListener_
|
|
| 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. |
|
| GeneticsException
|
|
| 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. |
|
| PhenotypeCache
This cache maintains a set of Phenotypes indexed by Basic/Identifiable pair. |
|
| 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. |
|
| Realm
Interface which defines the concept of the "model" which is undergoing evolution. |
|
| Registry
|
|
| Replicator
|
|
| SexLinked
|
|
| Sink
Interface to capture the essence of place where output can go, a sink in the engineering sense of sources and sinks. |
|
| Sink_
|
|
| 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. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.domain.world | |
|---|---|
| Allele
Models the concept of an Allele, that is to say a specific instance of a Genes which "compete" for presence at a Locus |
|
| CacheSignature
Interface to define the notion of a cache key signature. |
|
| Census
|
|
| Census_Sink
Base implementation the SinkCensus interface. |
|
| 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. |
|
| 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. |
|
| Fecundity
Defines methods to determine how fecund will be a particular mating in a population, i.e. |
|
| FitnessCache
This cache maintains a set of fitness values indexed by Signature/FitnessEngine pair. |
|
| FitnessEngine
Registry for fitness functions for Taxon (Evolutionary Computation) Systems. |
|
| Gene
Defines the operations and properties of a Gene. |
|
| Genetic
Interface with defines a "genetic" object, i.e. |
|
| GeneticsException
|
|
| Genome
Defines the genetic information contained in an Organism belonging to
a Taxon. |
|
| Genomic
Defines the genetic information contained in a Taxon. |
|
| 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. |
|
| PhenotypeCache
This cache maintains a set of Phenotypes indexed by Basic/Identifiable pair. |
|
| 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. |
|
| Realm
Interface which defines the concept of the "model" which is undergoing evolution. |
|
| Realm_
Base implementation of Realm. |
|
| 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. |
|
| Sink_
|
|
| 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. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.evolution | |
|---|---|
| GenerationListener
Defines a callback method for invocation whenever a Evolution runs. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.examples.pepperedmoth | |
|---|---|
| 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. |
|
| Attribute_
Abstract class representing a named attribute, and is the base class for Variant_, Allele_ and EcoFactor_. |
|
| CacheSignature
Interface to define the notion of a cache key signature. |
|
| Census
|
|
| Census_Sink
Base implementation the SinkCensus interface. |
|
| Censusible
This interface defines the census operation. |
|
| 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. |
|
| 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. |
|
| Fitness
Type representing a pair whose mutual fitness can be estimated. |
|
| FitnessEngine
Registry for fitness functions for Taxon (Evolutionary Computation) Systems. |
|
| GenerationListener
Defines a callback method for invocation whenever a Evolution runs. |
|
| Locus
Defines a Locus at which one of several Alleles may appear. |
|
| MateChoice
Defines methods to determine how mates are chosen. |
|
| Mutator
Defines the methods for gene and genome mutators. |
|
| Organism
Defines methods on an individual organism within a Taxon. |
|
| 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
|
|
| Sink
Interface to capture the essence of place where output can go, a sink in the engineering sense of sources and sinks. |
|
| Sink_
|
|
| SinkCensus
This application interface is used to define how an individual object should be processed for a census. |
|
| Trait
A Trait is the phenotypic analog to a (genotypic) Gene. |
|
| Variant
Defines the methods support by instances of the Variant interface. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.examples.travelingsalesman | |
|---|---|
| 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. |
|
| Attribute_
Abstract class representing a named attribute, and is the base class for Variant_, Allele_ and EcoFactor_. |
|
| Basic
|
|
| CacheSignature
Interface to define the notion of a cache key signature. |
|
| Census
|
|
| Census_Sink
Base implementation the SinkCensus interface. |
|
| Censusible
This interface defines the census operation. |
|
| 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. |
|
| 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 |
|
| 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. |
|
| Gene
Defines the operations and properties of a Gene. |
|
| Genetic
Interface with defines a "genetic" object, i.e. |
|
| Genome
Defines the genetic information contained in an Organism belonging to
a Taxon. |
|
| Locus
Defines a Locus at which one of several Alleles may appear. |
|
| 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. |
|
| Organism
Defines methods on an individual organism within a Taxon. |
|
| Pharacter
This interface represents the concept of a Phenotypic Character. |
|
| Phenotype
Defines the methods supported by instances of Phenotype interface. |
|
| 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. |
|
| Realm
Interface which defines the concept of the "model" which is undergoing evolution. |
|
| Registry
|
|
| SexLinked
|
|
| Sink
Interface to capture the essence of place where output can go, a sink in the engineering sense of sources and sinks. |
|
| Sink_
|
|
| SinkCensus
This application interface is used to define how an individual object should be processed for a census. |
|
| Trait
A Trait is the phenotypic analog to a (genotypic) Gene. |
|
| TraitMap
Defines the operations on a read-only collection of Trait instances. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.foundation | |
|---|---|
| Censusible
This interface defines the census operation. |
|
| Realm
Interface which defines the concept of the "model" which is undergoing evolution. |
|
| Sink
Interface to capture the essence of place where output can go, a sink in the engineering sense of sources and sinks. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.visualization | |
|---|---|
| EnvironmentListener
Defines the mechanism for notifying interested objects about changes in an environment. |
|
| Classes in com.rubecula.darwin.domain.helper used by com.rubecula.darwin.visualization.swing | |
|---|---|
| GenerationListener
Defines a callback method for invocation whenever a Evolution runs. |
|
|
||||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||