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## 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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