Uses of Interface
org.encog.ml.ea.genome.Genome

Packages that use Genome
org.encog.ml.ea.codec   
org.encog.ml.ea.genome   
org.encog.ml.ea.opp   
org.encog.ml.ea.population   
org.encog.ml.ea.rules   
org.encog.ml.ea.score   
org.encog.ml.ea.score.adjust   
org.encog.ml.ea.score.parallel   
org.encog.ml.ea.sort   
org.encog.ml.ea.species   
org.encog.ml.ea.train   
org.encog.ml.ea.train.basic   
org.encog.ml.genetic   
org.encog.ml.genetic.crossover   
org.encog.ml.genetic.genome   
org.encog.ml.genetic.mutate   
org.encog.ml.prg   
org.encog.ml.prg.opp   
org.encog.ml.prg.species   
org.encog.ml.prg.train   
org.encog.ml.prg.train.rewrite   
org.encog.neural.hyperneat   
org.encog.neural.neat   
org.encog.neural.neat.training   
org.encog.neural.neat.training.opp   
org.encog.neural.neat.training.species   
 

Uses of Genome in org.encog.ml.ea.codec
 

Methods in org.encog.ml.ea.codec that return Genome
 Genome GenomeAsPhenomeCODEC.encode(MLMethod phenotype)
          Attempt to build a genome from a phenome.
 Genome GeneticCODEC.encode(MLMethod phenotype)
          Attempt to build a genome from a phenome.
 

Methods in org.encog.ml.ea.codec with parameters of type Genome
 MLMethod GenomeAsPhenomeCODEC.decode(Genome genome)
          Decode the specified genome into a phenome.
 MLMethod GeneticCODEC.decode(Genome genome)
          Decode the specified genome into a phenome.
 

Uses of Genome in org.encog.ml.ea.genome
 

Classes in org.encog.ml.ea.genome that implement Genome
 class BasicGenome
          A basic abstract genome.
 

Methods in org.encog.ml.ea.genome that return Genome
 Genome GenomeFactory.factor()
           
 Genome GenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Methods in org.encog.ml.ea.genome with parameters of type Genome
 void Genome.copy(Genome source)
          Copy from the specified genome into this one.
 Genome GenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Uses of Genome in org.encog.ml.ea.opp
 

Methods in org.encog.ml.ea.opp with parameters of type Genome
 void EvolutionaryOperator.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void EvolutionaryOperator.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void CompoundOperator.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void CompoundOperator.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 

Uses of Genome in org.encog.ml.ea.population
 

Methods in org.encog.ml.ea.population that return Genome
 Genome PopulationGenerator.generate(Random rnd)
          Generate a random genome.
 Genome BasicPopulation.getBestGenome()
          
 Genome Population.getBestGenome()
           
 

Methods in org.encog.ml.ea.population that return types with arguments of type Genome
 List<Genome> BasicPopulation.flatten()
          Flatten the species into a single list of genomes.
 List<Genome> Population.flatten()
          Flatten the species into a single list of genomes.
 

Methods in org.encog.ml.ea.population with parameters of type Genome
 void BasicPopulation.setBestGenome(Genome genome)
          Set the best genome.
 void Population.setBestGenome(Genome bestGenome)
          Set the best genome.
 

Uses of Genome in org.encog.ml.ea.rules
 

Methods in org.encog.ml.ea.rules with parameters of type Genome
 boolean RuleHolder.isValid(Genome genome)
          Determine if the specified genome is valid according to the constraint rules.
 boolean ConstraintRule.isValid(Genome genome)
          Is this genome valid?
 boolean BasicRuleHolder.isValid(Genome genome)
          Determine if the specified genome is valid according to the constraint rules.
 void RuleHolder.rewrite(Genome genome)
          Rewrite the specified genome.
 boolean RewriteRule.rewrite(Genome genome)
          Rewrite the specified genome.
 void BasicRuleHolder.rewrite(Genome prg)
          Rewrite the specified genome.
 

Uses of Genome in org.encog.ml.ea.score
 

Methods in org.encog.ml.ea.score with parameters of type Genome
 double AdjustScore.calculateAdjustment(Genome genome)
          Calculate the score adjustment.
 

Uses of Genome in org.encog.ml.ea.score.adjust
 

Methods in org.encog.ml.ea.score.adjust with parameters of type Genome
 double ComplexityAdjustedScore.calculateAdjustment(Genome genome)
          Calculate the score adjustment.
 

Uses of Genome in org.encog.ml.ea.score.parallel
 

Constructors in org.encog.ml.ea.score.parallel with parameters of type Genome
ParallelScoreTask(Genome genome, ParallelScore theOwner)
          Construct the parallel task.
 

Uses of Genome in org.encog.ml.ea.sort
 

Methods in org.encog.ml.ea.sort with parameters of type Genome
 int SortGenomesForSpecies.compare(Genome g1, Genome g2)
          
 int MaximizeScoreComp.compare(Genome p1, Genome p2)
          
 int MinimizeScoreComp.compare(Genome p1, Genome p2)
          
 int MaximizeAdjustedScoreComp.compare(Genome p1, Genome p2)
          
 int MinimizeAdjustedScoreComp.compare(Genome p1, Genome p2)
          
 boolean MaximizeScoreComp.isBetterThan(Genome prg, Genome betterThan)
          Determine if one genome is better than the other genome.
 boolean GenomeComparator.isBetterThan(Genome genome1, Genome genome2)
          Determine if one genome is better than the other genome.
 boolean MinimizeScoreComp.isBetterThan(Genome prg, Genome betterThan)
          Determine if one genome is better than the other genome.
 boolean MaximizeAdjustedScoreComp.isBetterThan(Genome prg, Genome betterThan)
          Determine if one genome is better than the other genome.
 boolean MinimizeAdjustedScoreComp.isBetterThan(Genome prg, Genome betterThan)
          Determine if one genome is better than the other genome.
 

Uses of Genome in org.encog.ml.ea.species
 

Methods in org.encog.ml.ea.species that return Genome
 Genome Species.getLeader()
           
 Genome BasicSpecies.getLeader()
          
 

Methods in org.encog.ml.ea.species that return types with arguments of type Genome
 List<Genome> Species.getMembers()
           
 List<Genome> BasicSpecies.getMembers()
          
 

Methods in org.encog.ml.ea.species with parameters of type Genome
 void Species.add(Genome genome)
          Add a genome to this species.
 void BasicSpecies.add(Genome genome)
          Add a genome to this species.
 void ThresholdSpeciation.addSpeciesMember(Species species, Genome genome)
          Add a genome.
abstract  double ThresholdSpeciation.getCompatibilityScore(Genome genome1, Genome genome2)
          Determine how compatible two genomes are.
 void Species.setLeader(Genome theLeader)
          Set the leader of this species.
 void BasicSpecies.setLeader(Genome theLeader)
          Set the leader of this species.
 

Method parameters in org.encog.ml.ea.species with type arguments of type Genome
 void Speciation.performSpeciation(List<Genome> genomeList)
          Perform the speciation.
 void SingleSpeciation.performSpeciation(List<Genome> genomeList)
          Perform the speciation.
 void ThresholdSpeciation.performSpeciation(List<Genome> genomeList)
          Perform the speciation.
 

Constructors in org.encog.ml.ea.species with parameters of type Genome
BasicSpecies(Population thePopulation, Genome theFirst)
          Construct a species.
 

Uses of Genome in org.encog.ml.ea.train
 

Methods in org.encog.ml.ea.train that return Genome
 Genome EvolutionaryAlgorithm.getBestGenome()
           
 

Methods in org.encog.ml.ea.train with parameters of type Genome
 void EvolutionaryAlgorithm.calculateScore(Genome g)
          Calculate the score for a genome.
 

Uses of Genome in org.encog.ml.ea.train.basic
 

Methods in org.encog.ml.ea.train.basic that return Genome
 Genome BasicEA.getBestGenome()
           
 Genome BasicEA.getOldBestGenome()
           
 

Methods in org.encog.ml.ea.train.basic with parameters of type Genome
 boolean BasicEA.addChild(Genome genome)
          Add a child to the next iteration.
 void BasicEA.calculateScore(Genome g)
          Calculate the score for a genome.
static void BasicEA.calculateScoreAdjustment(Genome genome, List<AdjustScore> adjusters)
          Calculate the score adjustment, based on adjusters.
 

Uses of Genome in org.encog.ml.genetic
 

Classes in org.encog.ml.genetic that implement Genome
 class MLMethodGenome
          Implements a genome that allows a feedforward neural network to be trained using a genetic algorithm.
 

Methods in org.encog.ml.genetic that return Genome
 Genome MLEncodableCODEC.encode(MLMethod phenotype)
          Attempt to build a genome from a phenome.
 Genome MLMethodGenomeFactory.factor()
          
 Genome MLMethodGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Methods in org.encog.ml.genetic with parameters of type Genome
 MLMethod MLEncodableCODEC.decode(Genome genome)
          Decode the specified genome into a phenome.
 Genome MLMethodGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Uses of Genome in org.encog.ml.genetic.crossover
 

Methods in org.encog.ml.genetic.crossover with parameters of type Genome
 void Splice.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void Splice.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void SpliceNoRepeat.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void SpliceNoRepeat.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 

Uses of Genome in org.encog.ml.genetic.genome
 

Subinterfaces of Genome in org.encog.ml.genetic.genome
 interface ArrayGenome
          An array genome represents an array of "something", this allows array operators such as crossover and mutate to work on the genome.
 

Classes in org.encog.ml.genetic.genome that implement Genome
 class DoubleArrayGenome
          A genome made up of continuous doubles.
 class IntegerArrayGenome
          A genome that is an array of discrete integer values.
 

Methods in org.encog.ml.genetic.genome that return Genome
 Genome IntegerArrayGenomeFactory.factor()
          
 Genome DoubleArrayGenomeFactory.factor()
          
 Genome IntegerArrayGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 Genome DoubleArrayGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Methods in org.encog.ml.genetic.genome with parameters of type Genome
 void DoubleArrayGenome.copy(Genome source)
          Copy from the specified genome into this one.
 void IntegerArrayGenome.copy(Genome source)
          Copy from the specified genome into this one.
 Genome IntegerArrayGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 Genome DoubleArrayGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Uses of Genome in org.encog.ml.genetic.mutate
 

Methods in org.encog.ml.genetic.mutate with parameters of type Genome
 void MutatePerturb.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void MutatePerturb.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void MutateShuffle.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void MutateShuffle.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 

Uses of Genome in org.encog.ml.prg
 

Classes in org.encog.ml.prg that implement Genome
 class EncogProgram
          Holds an Encog Programming Language (EPL) program.
 

Methods in org.encog.ml.prg that return Genome
 Genome PrgCODEC.encode(MLMethod phenotype)
          Attempt to build a genome from a phenome.
 

Methods in org.encog.ml.prg with parameters of type Genome
 void EncogProgram.copy(Genome source)
          Copy from the specified genome into this one.
 MLMethod PrgCODEC.decode(Genome genome)
          Decode the specified genome into a phenome.
 

Uses of Genome in org.encog.ml.prg.opp
 

Methods in org.encog.ml.prg.opp with parameters of type Genome
 void SubtreeCrossover.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void SubtreeCrossover.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void ConstMutation.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void ConstMutation.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void SubtreeMutation.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void SubtreeMutation.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 

Uses of Genome in org.encog.ml.prg.species
 

Methods in org.encog.ml.prg.species with parameters of type Genome
 double PrgSpeciation.getCompatibilityScore(Genome genome1, Genome genome2)
          Determine how compatible two genomes are.
 

Uses of Genome in org.encog.ml.prg.train
 

Methods in org.encog.ml.prg.train that return Genome
 Genome PrgGenomeFactory.factor()
          
 Genome PrgGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Methods in org.encog.ml.prg.train with parameters of type Genome
 Genome PrgGenomeFactory.factor(Genome other)
          Create a clone of the other genome.
 

Uses of Genome in org.encog.ml.prg.train.rewrite
 

Methods in org.encog.ml.prg.train.rewrite with parameters of type Genome
 boolean RewriteBoolean.rewrite(Genome g)
          Rewrite the specified genome.
 boolean RewriteAlgebraic.rewrite(Genome g)
          Rewrite the specified genome.
 boolean RewriteConstants.rewrite(Genome g)
          Rewrite the specified genome.
 

Uses of Genome in org.encog.neural.hyperneat
 

Classes in org.encog.neural.hyperneat that implement Genome
 class HyperNEATGenome
          A HyperNEAT genome.
 

Methods in org.encog.neural.hyperneat that return Genome
 Genome HyperNEATCODEC.encode(MLMethod phenotype)
           
 Genome FactorHyperNEATGenome.factor(Genome other)
          Create a clone of the other genome.
 

Methods in org.encog.neural.hyperneat with parameters of type Genome
 MLMethod HyperNEATCODEC.decode(Genome genome)
          Decode the specified genome into a phenome.
 MLMethod HyperNEATCODEC.decode(NEATPopulation pop, Substrate substrate, Genome genome)
           
 Genome FactorHyperNEATGenome.factor(Genome other)
          Create a clone of the other genome.
 

Uses of Genome in org.encog.neural.neat
 

Methods in org.encog.neural.neat that return Genome
 Genome NEATCODEC.encode(MLMethod phenotype)
          This method is not currently implemented.
 Genome FactorNEATGenome.factor(Genome other)
          Create a clone of the other genome.
 

Methods in org.encog.neural.neat with parameters of type Genome
 MLMethod NEATCODEC.decode(Genome genome)
          Decode the specified genome into a phenome.
 Genome FactorNEATGenome.factor(Genome other)
          Create a clone of the other genome.
 

Uses of Genome in org.encog.neural.neat.training
 

Classes in org.encog.neural.neat.training that implement Genome
 class NEATGenome
          Implements a NEAT genome.
 

Methods in org.encog.neural.neat.training with parameters of type Genome
 void NEATGenome.copy(Genome source)
          Copy from the specified genome into this one.
 

Uses of Genome in org.encog.neural.neat.training.opp
 

Methods in org.encog.neural.neat.training.opp with parameters of type Genome
 NEATGenome NEATMutation.obtainGenome(Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Obtain the NEATGenome that we will mutate.
 NEATGenome NEATMutation.obtainGenome(Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Obtain the NEATGenome that we will mutate.
 void NEATMutateWeights.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateWeights.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateRemoveLink.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateRemoveLink.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATCrossover.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATCrossover.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateAddLink.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateAddLink.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateAddNode.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 void NEATMutateAddNode.performOperation(Random rnd, Genome[] parents, int parentIndex, Genome[] offspring, int offspringIndex)
          Perform the evolutionary operation.
 

Uses of Genome in org.encog.neural.neat.training.species
 

Methods in org.encog.neural.neat.training.species with parameters of type Genome
 double OriginalNEATSpeciation.getCompatibilityScore(Genome gen1, Genome gen2)
          Determine how compatible two genomes are.
 



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