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

- Packages that use Genome
  Package | Description
  --- | ---
  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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Class and Description
    --- | ---
    `class` | `BasicGenome` A basic abstract genome.

    Methods in org.encog.ml.ea.genome that return Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Constructor and Description
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `Genome` | Species.`getLeader()`
    `Genome` | BasicSpecies.`getLeader()`

    Methods in org.encog.ml.ea.species that return types with arguments of type Genome
    Modifier and Type | Method and Description
    --- | ---
    `List<Genome>` | Species.`getMembers()`
    `List<Genome>` | BasicSpecies.`getMembers()`

    Methods in org.encog.ml.ea.species with parameters of type Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Constructor and Description
    `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
    Modifier and Type | Method and Description
    --- | ---
    `Genome` | EvolutionaryAlgorithm.`getBestGenome()`

    Methods in org.encog.ml.ea.train with parameters of type Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `Genome` | BasicEA.`getBestGenome()`
    `Genome` | BasicEA.`getOldBestGenome()`

    Methods in org.encog.ml.ea.train.basic with parameters of type Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Class and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Interface and Description
    --- | ---
    `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
    Modifier and Type | Class and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Class and Description
    --- | ---
    `class` | `EncogProgram` Holds an Encog Programming Language (EPL) program.

    Methods in org.encog.ml.prg that return Genome
    Modifier and Type | Method and Description
    --- | ---
    `Genome` | PrgCODEC.`encode(MLMethod phenotype)` Attempt to build a genome from a phenome.

    Methods in org.encog.ml.prg with parameters of type Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Class and Description
    --- | ---
    `class` | `HyperNEATGenome` A HyperNEAT genome.

    Methods in org.encog.neural.hyperneat that return Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Class and Description
    --- | ---
    `class` | `NEATGenome` Implements a NEAT genome.

    Methods in org.encog.neural.neat.training with parameters of type Genome
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `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
    Modifier and Type | Method and Description
    --- | ---
    `double` | OriginalNEATSpeciation.`getCompatibilityScore(Genome gen1, Genome gen2)` Determine how compatible two genomes are.

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