Serialized Form

  • Package ec

    • Class ec.Breeder

      class Breeder extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • sequentialBreeding
          boolean sequentialBreeding
          The flag to let the coevolutionary system know that we're doing sequential breeding. You shouldn't play with this flag unless you're SimpleBreeder -- keep it at false otherwise.

    • Class ec.BreedingPipeline

      class BreedingPipeline extends BreedingSource implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • likelihood
          double likelihood
        • mybase
          Parameter mybase
          My parameter base -- I keep it around so I can print some messages that are useful with it (not deep cloned)
        • sources
          BreedingSource[] sources
          Array of sources feeding the pipeline

    • Class ec.BreedingSource

      class BreedingSource extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • probability
          double probability
          The probability that this BreedingSource will be chosen to breed over other BreedingSources. This may or may not be used, depending on what the caller to this BreedingSource is. It also might be modified by external sources owning this object, for their own purposes. A BreedingSource should not use it for any purpose of its own, nor modify it except when setting it up.

          The most common modification is to normalize it with some other set of probabilities, then set all of them up in increasing summation; this allows the use of the fast static BreedingSource-picking utility method, BreedingSource.pickRandom(...). In order to use this method, for example, if four breeding source probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.

    • Class ec.Evaluator

      class Evaluator extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.EvolutionState

      class EvolutionState extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • breeder
          Breeder breeder
          The population breeder, a singleton object. You should only access this in a read-only fashion.
        • breedthreads
          int breedthreads
          The requested number of threads to be used in breeding, excepting perhaps a "parent" thread which gathers the other threads. If breedthreads = 1, then the system should not be multithreaded during breeding. Don't modify this during a run.
        • checkpoint
          boolean checkpoint
          Should we checkpoint at all?
        • checkpointDirectory
          File checkpointDirectory
          The requested directory where checkpoints should be located. This must be a directory, not a file. You probably shouldn't modify this during a run.
        • checkpointModulo
          int checkpointModulo
          The requested number of generations that should pass before we write out a checkpoint file.
        • checkpointPrefix
          String checkpointPrefix
          The requested prefix to start checkpoint filenames, not including a following period. You probably shouldn't modify this during a run.
        • data
          HashMap[] data
          An array of HashMaps, indexed by the thread number you were given (or, if you're not in a multithreaded area, use 0). This allows you to store per-thread specialized information (typically keyed with a string).
        • evalthreads
          int evalthreads
          The requested number of threads to be used in evaluation, excepting perhaps a "parent" thread which gathers the other threads. If evalthreads = 1, then the system should not be multithreaded during evaluation. Don't modify this during a run.
        • evaluations
          int evaluations
          The current number of evaluations which have transpired so far in the run. This is only updated on a generational boundary.
        • evaluator
          Evaluator evaluator
          The population evaluator, a singleton object. You should only access this in a read-only fashion.
        • exchanger
          Exchanger exchanger
          The population exchanger, a singleton object. You should only access this in a read-only fashion.
        • finisher
          Finisher finisher
          The population finisher, a singleton object. You should only access this in a read-only fashion.
        • generation
          int generation
          The current generation of the population in the run. For non-generational approaches, this probably should represent some kind of incrementing value, perhaps the number of individuals evaluated so far. You probably shouldn't modify this.
        • initializer
          Initializer initializer
          The population initializer, a singleton object. You should only access this in a read-only fashion.
        • innovationNumber
          long innovationNumber
          Global birthday tracker number for genes in representations such as NEAT. Accessed and modified during run time
        • job
          Object[] job
          Current job iteration variables, set by Evolve. The default version simply sets this to a single Object[1] containing the current job iteration number as an Integer (for a single job, it's 0). You probably should not modify this inside an evolutionary run.
        • lock
          Object[] lock
        • numEvaluations
          long numEvaluations
          The number of evaluations the evolutionary computation system will run until it ends (up to the next generation boundary), or UNDEFINED
        • numGenerations
          int numGenerations
          The number of generations the evolutionary computation system will run until it ends, or UNDEFINED
        • output
          Output output
          The output and logging facility (threadsafe). Keep in mind that output in Java is expensive.
        • parameters
          ParameterDatabase parameters
          The parameter database (threadsafe). Parameter objects are also threadsafe. Nonetheless, you should generally try to treat this database as read-only.
        • population
          Population population
          The current population. This is not a singleton object, and may be replaced after every generation in a generational approach. You should only access this in a read-only fashion.
        • quitOnRunComplete
          boolean quitOnRunComplete
          Whether or not the system should prematurely quit when Evaluator returns true for runComplete(...) (that is, when the system found an ideal individual.
        • random
          MersenneTwisterFast[] random
          An array of random number generators, indexed by the thread number you were given (or, if you're not in a multithreaded area, use 0). These generators are not threadsafe in and of themselves, but if you only use the random number generator assigned to your thread, as was intended, then you get random numbers in a threadsafe way. These generators must each have a different seed, of course.
        • randomSeedOffset
          int randomSeedOffset
          An amount to add to each random number generator seed to "offset" it -- often this is simply the job number. If you are using more random number generators internally than the ones initially created for you in the EvolutionState, you might want to create them with the seed value of seedParameter+randomSeedOffset. At present the only such class creating additional generators is ec.eval.MasterProblem.
        • runtimeArguments
          String[] runtimeArguments
          The original runtime arguments passed to the Java process. You probably should not modify this inside an evolutionary run.
        • statistics
          Statistics statistics
          The population statistics, a singleton object. You should generally only access this in a read-only fashion.

    • Class ec.Exchanger

      class Exchanger extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.Finisher

      class Finisher extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.Fitness

      class Fitness extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • context
          Individual[] context
          Auxiliary variable, used by coevolutionary processes, to store the individuals involved in producing this given Fitness value. By default context=null and stays that way. Note that individuals stored here may possibly not themselves have Fitness values to avoid circularity when cloning.
        • trials
          ArrayList trials
          Auxiliary variable, used by coevolutionary processes, to compute the number of trials used to compute this Fitness value. By default trials=null and stays that way. If you set this variable, all of the elements of the ArrayList must be immutable -- once they're set they never change internally.

    • Class ec.Individual

      class Individual extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • evaluated
          boolean evaluated
          Has the individual been evaluated and its fitness determined yet?
        • fitness
          Fitness fitness
          The fitness of the Individual.
        • species
          Species species
          The species of the Individual.

    • Class ec.Initializer

      class Initializer extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.Population

      class Population extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.Problem

      class Problem extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.SelectionMethod

      class SelectionMethod extends BreedingSource implements Serializable
      serialVersionUID:
      1L

    • Class ec.Species

      class Species extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • f_prototype
          Fitness f_prototype
          The prototypical fitness for individuals of this species.
        • i_prototype
          Individual i_prototype
          The prototypical individual for this species.
        • pipe_prototype
          BreedingSource pipe_prototype
          The prototypical breeding pipeline for this species.

    • Class ec.Statistics

      class Statistics extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • children
          Statistics[] children
        • silentFile
          boolean silentFile
        • silentPrint
          boolean silentPrint

    • Class ec.Subpopulation

      class Subpopulation extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • extraBehavior
          int extraBehavior
          What is our fill behavior beyond files?
        • file
          Parameter file
        • individuals
          ArrayList<Individual> individuals
          The subpopulation's individuals.
        • initialSize
          int initialSize
          initial expected size of the subpopulation
        • loadInds
          boolean loadInds
        • numDuplicateRetries
          int numDuplicateRetries
          Do we allow duplicates?
        • species
          Species species
          The species for individuals in this subpopulation.
        • warned
          boolean warned
          Prints an entire subpopulation in a form readable by humans, with a verbosity of Output.V_NO_GENERAL.

  • Package ec.breed

  • Package ec.coevolve

  • Package ec.de

  • Package ec.display

  • Package ec.display.chart

  • Package ec.display.portrayal

  • Package ec.eda.amalgam

    • Class ec.eda.amalgam.AMALGAMBreeder

      class AMALGAMBreeder extends Breeder implements Serializable

    • Class ec.eda.amalgam.AMALGAMSpecies

      class AMALGAMSpecies extends FloatVectorSpecies implements Serializable

      • Serialized Fields

        • aggCovarMatrix
          org.ejml.data.DenseMatrix64F aggCovarMatrix
        • alphaAMS
          double alphaAMS
        • choleskyLower
          org.ejml.data.DenseMatrix64F choleskyLower
        • constraintViolations
          IdentityHashMap<Individual,Integer> constraintViolations
        • covarMatrix
          org.ejml.data.DenseMatrix64F covarMatrix
        • deltaAMS
          double deltaAMS
        • distributionMultiplier
          double distributionMultiplier
        • distributionMultiplierDecrease
          double distributionMultiplierDecrease
        • distributionMultiplierIncrease
          double distributionMultiplierIncrease
        • etaP
          double etaP
        • etaS
          double etaS
        • firstGeneration
          boolean firstGeneration
        • fitnessVarianceTolerance
          double fitnessVarianceTolerance
        • genCovarMatrix
          org.ejml.data.DenseMatrix64F genCovarMatrix
        • maximumNoImprovementStretch
          int maximumNoImprovementStretch
        • mean
          org.ejml.data.DenseMatrix64F mean
          The mean of the distribution.
        • meanShift
          org.ejml.data.DenseMatrix64F meanShift
        • noImprovementStretch
          int noImprovementStretch
        • prevMean
          org.ejml.data.DenseMatrix64F prevMean
        • stDevRatioThresh
          double stDevRatioThresh
        • tau
          double tau
        • temp
          org.ejml.data.DenseMatrix64F temp
        • temp2
          org.ejml.data.DenseMatrix64F temp2
        • temp3
          org.ejml.data.DenseMatrix64F temp3
        • tempMatrix
          org.ejml.data.DenseMatrix64F tempMatrix
        • useAltTermination
          boolean useAltTermination
        • userAlphaAMS
          double userAlphaAMS
        • userEtaP
          double userEtaP
        • userEtaS
          double userEtaS
        • xAvgImp
          org.ejml.data.DenseMatrix64F xAvgImp

  • Package ec.eda.cmaes

    • Class ec.eda.cmaes.CMAESBreeder

      class CMAESBreeder extends Breeder implements Serializable

    • Class ec.eda.cmaes.CMAESInitializer

      class CMAESInitializer extends SimpleInitializer implements Serializable
      serialVersionUID:
      1L

    • Class ec.eda.cmaes.CMAESSpecies

      class CMAESSpecies extends FloatVectorSpecies implements Serializable

      • Serialized Fields

        • altGeneratorTries
          int altGeneratorTries
          How many times should we try to generate a valid individual before we give up and use the useAltGenerator approach?
        • b
          org.ejml.simple.SimpleMatrix b
          The "B" matrix, eigendecomposed from the "C" covariance matrix of the distribution.
        • bd
          org.ejml.data.DenseMatrix64F bd
          b x d
        • c
          org.ejml.simple.SimpleMatrix c
          The "C" covariance matrix of the distribution.
        • c1
          double c1
          The c_1 rank-1 update learning rate. If not specified in the parameters, by default c1 = 2 / ((n + 1.3) * (n + 1.3) + mueff) where n is the genome size.
        • cc
          double cc
          The c_c rank-one evolution path cumulation parameter. If not specified in the parameters, by default cc = (4 + mueff / n) / (n + 4 + 2 * mueff/n) where n is the genome size.
        • chiN
          double chiN
          An estimate of the expected size of the standard multivariate gaussian N(0,I). This is chiN = Math.sqrt(n)*(1.0-1.0/(4.0*n)+1.0/(21.0*n*n))
        • cmu
          double cmu
          The c_{\mu} rank-mu update learning rate. If not specified in the parameters, by default cmu = Math.min(1-c1, 2 * (mueff - 2 + 1/mueff) / ((n+2)*(n+2) + mueff)) where n is the genome size.
        • cs
          double cs
          The c_{\sigma} mutation rate evolution path learning rate. If not specified in the parameters, by default cs = (mueff + 2) / (n + mueff + 5) where n is the genome size.
        • d
          org.ejml.simple.SimpleMatrix d
          The "C" matrix, eigendecomposed from the "C" covariance matrix of the distribution.
        • damps
          double damps
          The d_{\sigma} dampening for the mutation rate update. If not specified in the parameters, by default damps = cs + 2 * Math.max(1, Math.sqrt((mueff - 1) / (n + 1))) - 1 otherwise known as damps = 1 + 2 * Math.max(0, Math.sqrt((mueff - 1) / (n + 1)) - 1) + cs where n is the genome size.
        • invsqrtC
          org.ejml.simple.SimpleMatrix invsqrtC
          C^{-1/2}. This is equal to B x D^{-1} x B^T
        • lambda
          int lambda
          The individuals generated from the distribution. If not specified in the parameters, by default lambda = 4+(int)Math.floor(3*Math.log(n));
        • lastEigenDecompositionGeneration
          int lastEigenDecompositionGeneration
          The most recent generation where an eigendecomposition on C was performed into B and D
        • mu
          int mu
          The truncated individuals used to update the distribution. If not specified in the parameters, by default mu = (int)Math.floor(lambda/2.0);
        • mueff
          double mueff
          The "mu_{eff}" constant in CMA-ES. This is set to 1.0 / the sum of the squares of each of the weights[...]
        • pc
          org.ejml.simple.SimpleMatrix pc
          The p_c evolution path vector.
        • ps
          org.ejml.simple.SimpleMatrix ps
          The p_{\sigma} evolution path vector.
        • sbd
          org.ejml.data.DenseMatrix64F sbd
          bd x sigma
        • sigma
          double sigma
          The "sigma" scaling factor for the covariance matrix.
        • useAltGenerator
          boolean useAltGenerator
          If, after trying altGeneratorTries to build an indiviual, we are still building one which violates min/max gene constraints, should we instead fill those violated genes with uniformly-selected values between the min and max?
        • useAltTermination
          boolean useAltTermination
          Should we terminate when the eigenvalues get too small? If we don't, they might go negative and the eigendecomposition will fail.
        • weights
          double[] weights
          The ranked fitness weights for the mu individuals. If not specified in the parameters, by default weights[i] = ln((lambda + 1) / 2i). Then all the weights are normalized so that they sum to 1.
        • xmean
          org.ejml.simple.SimpleMatrix xmean
          The mean of the distribution.

  • Package ec.eda.dovs

    • Class ec.eda.dovs.DOVSBreeder

      class DOVSBreeder extends Breeder implements Serializable

    • Class ec.eda.dovs.DOVSEvaluator

      class DOVSEvaluator extends SimpleEvaluator implements Serializable

    • Class ec.eda.dovs.DOVSFitness

      class DOVSFitness extends SimpleFitness implements Serializable

      • Serialized Fields

        • mean
          double mean
          Mean fitness value of the current individual.
        • numOfObservations
          int numOfObservations
          Number of evaluation have been performed on this individual.
        • sum
          double sum
          Sum of the all the fitness value with all the evaluation.
        • sumSquared
          double sumSquared
          Sum of the all the squared fitness value with all the evaluation.
        • variance
          double variance
          Variance of the fitness value of the current individual.

    • Class ec.eda.dovs.DOVSInitializer

      class DOVSInitializer extends SimpleInitializer implements Serializable
      serialVersionUID:
      1L

    • Class ec.eda.dovs.DOVSSpecies

      class DOVSSpecies extends IntegerVectorSpecies implements Serializable

      • Serialized Fields

        • A
          ArrayList<double[]> A
          Constraint coefficients
        • activeSolutions
          ArrayList<Individual> activeSolutions
          activeSolutions contains all the samples that is on the boundary of the most promising area.
        • b
          double[] b
          Constratin coefficients
        • corners
          ArrayList<CornerMap> corners
          CornerMaps for the all the visisted individuals. This record the key-value pair for each individuals, where key is the coordinates and value is individual itself.
        • Ek
          ArrayList<Individual> Ek
          This is the Ek in original paper, where is the collection all the individuals evaluated in generation k.
        • initialReps
          int initialReps
          Base value of number evaluation for each individual.
        • numOfTotalSamples
          long numOfTotalSamples
          This is for future using.
        • optimalIndex
          int optimalIndex
          This integer indicate the index of optimal individual in the visited array.
        • repetition
          int repetition
          This value will be updated at each generation to determine how many evaluation is needed for one individual. It make use of the initialReps.
        • stochastic
          boolean stochastic
          Is the problem a stochastic problem.
        • visited
          ArrayList<Individual> visited
          This list contains all the sample we have visited during current algorithm run.
        • visitedIndexMap
          HashMap<Individual,Integer> visitedIndexMap
          Given a individual, return the index of this individual in ArrayList visited
        • warmUp
          int warmUp
          warm up period for RMD sampling.

    • Class ec.eda.dovs.HyperboxSpecies

      class HyperboxSpecies extends DOVSSpecies implements Serializable

      • Serialized Fields

        • boxA
          ArrayList<double[]> boxA
          boxA and boxB contain the current constraint hyperbox.
        • boxB
          ArrayList<Double> boxB
          boxA and boxB contain the current constraint hyperbox.

  • Package ec.eda.pbil

  • Package ec.es

  • Package ec.eval

    • Class ec.eval.MasterProblem

      class MasterProblem extends Problem implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ec.eval.MetaProblem

      class MetaProblem extends Problem implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • base
          Parameter base
          The parameter base from which the MetaProblem was loaded.
        • bestUnderlyingIndividual
          Individual[] bestUnderlyingIndividual
          The best underlying individual array, one per subpopulation. We retain the best underlying individual here rather than storing it in (say) the associated fitness because fitnesses are *averaged* over trials, so we wouldn't be able to keep track of the *max* fitness and associated individual that way. So we do it here.
        • currentDatabase
          ParameterDatabase currentDatabase
          This points to the database presently used by the underlying (base-level) evolutionary computation system. It is a cloned and modified version of p_database.
        • domain
          Object[] domain
          A list of domain information, one per parameter in the genome.
        • lock
          Object lock
          Acquire this lock before accessing bestUnderlyingIndividual
        • p_database
          ParameterDatabase p_database
          A prototypical parameter database for the underlying (base-level) evolutionary computation system. This is never directly used, just cloned.
        • reevaluateIndividuals
          boolean reevaluateIndividuals
          Whether to reevaluate individuals if and when they appear for evaluation in the future.
        • runs
          int runs
          The number of base-level evolutionary runs to perform to evaluate an individual.
        • setRandom
          boolean setRandom

  • Package ec.evolve

  • Package ec.exchange

    • Class ec.exchange.InterPopulationExchange

      class InterPopulationExchange extends Exchanger implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • base
          Parameter base
          My parameter base -- I need to keep this in order to help the server reinitialize contacts
        • chatty
          boolean chatty
        • exchangeInformation
          ec.exchange.InterPopulationExchange.IPEInformation[] exchangeInformation
        • immigrants
          Individual[][] immigrants
        • nImmigrants
          int[] nImmigrants
        • nrSources
          int nrSources

    • Class ec.exchange.IslandExchange

      class IslandExchange extends Exchanger implements Serializable
      serialVersionUID:
      1L

      • Serialization Methods

      • Serialized Fields

        • alreadyReadGoodBye
          boolean alreadyReadGoodBye
        • base
          Parameter base
          My parameter base -- I need to keep this in order to help the server reinitialize contacts
        • chatty
          boolean chatty
          Our chattiness
        • clientPort
          int clientPort
          The port of the client mailbox
        • compressedCommunication
          boolean compressedCommunication
          whether the communication is compressed or not
        • fromServer
          DataInputStream fromServer
        • iAmServer
          boolean iAmServer
          whether the server should be running on the current island or not
        • immigrantsSelectionMethod
          SelectionMethod immigrantsSelectionMethod
          the selection method for immigrants
        • indsToDieSelectionMethod
          SelectionMethod indsToDieSelectionMethod
          the selection method for individuals to be replaced by immigrants
        • mailbox
          ec.exchange.IslandExchangeMailbox mailbox
        • mailboxThread
          Thread mailboxThread
        • message
          String message
        • modulo
          int modulo
          how often to send individuals
        • number_of_destination_islands
          int number_of_destination_islands
        • offset
          int offset
          after how many generations to start sending individuals
        • outgoingIds
          String[] outgoingIds
        • outSockets
          Socket[] outSockets
        • outWriters
          DataOutputStream[] outWriters
        • ownId
          String ownId
          the id of the current island
        • running
          boolean[] running
        • serverAddress
          String serverAddress
          The address of the server
        • serverPort
          int serverPort
          The port of the server
        • serverSocket
          Socket serverSocket
        • serverThread
          Thread serverThread
          The thread of the server (is different than null only for the island with the server)
        • size
          int size
          how many individuals to send each time
        • synchronous
          boolean synchronous
          synchronous or asynchronous communication
        • toServer
          DataOutputStream toServer

  • Package ec.gp

    • Class ec.gp.ADF

      class ADF extends GPNode implements Serializable

      • Serialized Fields

        • associatedTree
          int associatedTree
          The ADF's associated tree
        • name
          String name
          The "function name" of the ADF, to distinguish it from other GP functions you might provide.

    • Class ec.gp.ADFArgument

      class ADFArgument extends GPNode implements Serializable

      • Serialized Fields

        • argument
          int argument
        • name
          String name
          The "function name" of the ADFArgument, to distinguish it from other GP functions you might provide.

    • Class ec.gp.ADFContext

      class ADFContext extends Object implements Serializable

      • Serialized Fields

        • adf
          ADF adf
          The ADF/ADM node proper
        • arguments
          GPData[] arguments
          An array of GPData nodes (none of the null, when it's used) holding an ADF's arguments' return results

    • Class ec.gp.ADFStack

      class ADFStack extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ec.gp.ADM

      class ADM extends ADF implements Serializable

    • Class ec.gp.ERC

      class ERC extends GPNode implements Serializable

    • Class ec.gp.GPAtomicType

      class GPAtomicType extends GPType implements Serializable

    • Class ec.gp.GPBreedingPipeline

      class GPBreedingPipeline extends BreedingPipeline implements Serializable

    • Class ec.gp.GPData

      class GPData extends Object implements Serializable

    • Class ec.gp.GPFunctionSet

      class GPFunctionSet extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialization Methods

      • Serialized Fields

        • name
          String name
          Name of the GPFunctionSet
        • nodes
          GPNode[][] nodes
          The nodes that our GPTree can use: nodes[type][thenodes].
        • nodes_h
          Hashtable nodes_h
          The nodes that our GPTree can use: arrays of nodes hashed by type.
        • nodesByArity
          GPNode[][][] nodesByArity
          Nodes == a given arity, that is: nodesByArity[type][arity][thenodes]
        • nodesByName
          Hashtable nodesByName
          The nodes that our GPTree can use, hashed by name().
        • nonterminals
          GPNode[][] nonterminals
          The nonterminals our GPTree can use: nonterminals[type][thenodes].
        • nonterminals_h
          Hashtable nonterminals_h
          The nonterminals our GPTree can use: arrays of nonterminals hashed by type.
        • nonterminalsOverArity
          GPNode[][][] nonterminalsOverArity
          Nonterminals >= a given arity, that is: nonterminalsOverArity[type][arity][thenodes] -- this will be O(n^2). Obviously, the number of nonterminals at arity slot 0 is all the nonterminals of that type.
        • nonterminalsUnderArity
          GPNode[][][] nonterminalsUnderArity
          Nonterminals invalid input: '<'= a given arity, that is: nonterminalsUnderArity[type][arity][thenodes] -- this will be O(n^2). Obviously, the number of nonterminals at arity slot 0 is 0.
        • terminals
          GPNode[][] terminals
          The terminals our GPTree can use: terminals[type][thenodes].
        • terminals_h
          Hashtable terminals_h
          The terminals our GPTree can use: arrays of terminals hashed by type.

    • Class ec.gp.GPIndividual

      class GPIndividual extends Individual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ec.gp.GPInitializer

      class GPInitializer extends SimpleInitializer implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • functionSetRepository
          Hashtable functionSetRepository
        • nodeConstraintRepository
          Hashtable nodeConstraintRepository
        • nodeConstraints
          GPNodeConstraints[] nodeConstraints
        • numAtomicTypes
          int numAtomicTypes
        • numNodeConstraints
          byte numNodeConstraints
        • numSetTypes
          int numSetTypes
        • numTreeConstraints
          byte numTreeConstraints
        • treeConstraintRepository
          Hashtable treeConstraintRepository
        • treeConstraints
          GPTreeConstraints[] treeConstraints
        • typeRepository
          Hashtable typeRepository
          TODO Comment these members. TODO Make clients of these members more efficient by reducing unnecessary casting.
        • types
          GPType[] types

    • Class ec.gp.GPNode

      class GPNode extends Object implements Serializable

      • Serialized Fields

        • argposition
          byte argposition
          The argument position of the child in its parent. This is a byte to save space (GPNode is the critical object space-wise) -- besides, how often do you have 256 children? You can change this to a short or int easily if you absolutely need to. It's possible to eliminate even this and have the child find itself in its parent, but that's an O(children[]) operation, and probably not inlinable, so I figure a byte is okay.
        • children
          GPNode[] children
        • constraints
          byte constraints
          The GPNode's constraints. This is a byte to save space -- how often do you have 256 different GPNodeConstraints? Well, I guess it's not infeasible. You can increase this to an int without much trouble. You typically shouldn't access the constraints through this variable -- use the constraints(state) method instead.
        • parent
          GPNodeParent parent
          The GPNode's parent. 4 bytes. :-( But it really helps simplify breeding.

    • Class ec.gp.GPNodeBuilder

      class GPNodeBuilder extends Object implements Serializable

      • Serialized Fields

        • maxSize
          int maxSize
          the minium possible size -- if unused, it's 0
        • minSize
          int minSize
        • sizeDistribution
          double[] sizeDistribution
          the maximum possible size -- if unused, it's 0

    • Class ec.gp.GPNodeConstraints

      class GPNodeConstraints extends Object implements Serializable

      • Serialized Fields

        • childtypes
          GPType[] childtypes
          The children types for a GPNode
        • constraintNumber
          byte constraintNumber
          The byte value of the constraints -- we can only have 256 of them
        • name
          String name
          The name of the GPNodeConstraints object -- this is NOT the name of the GPNode
        • probabilityOfSelection
          double probabilityOfSelection
          Probability of selection -- an auxillary measure mostly used by PTC1/PTC2 right now
        • returntype
          GPType returntype
          The return type for a GPNode
        • zeroChildren
          GPNode[] zeroChildren
          A little memory optimization: if GPNodes have no children, they are welcome to use share this zero-sized array as their children array.

    • Class ec.gp.GPNodeGatherer

      class GPNodeGatherer extends Object implements Serializable

      • Serialized Fields

    • Class ec.gp.GPProblem

      class GPProblem extends Problem implements Serializable

      • Serialized Fields

        • input
          GPData input
          The GPProblem's GPData
        • stack
          ADFStack stack
          The GPProblem's stack

    • Class ec.gp.GPSetType

      class GPSetType extends GPType implements Serializable

      • Serialized Fields

        • types_h
          Hashtable types_h
          The hashtable of types in the set
        • types_packed
          int[] types_packed
          A packed, sorted array of atomic types in the set
        • types_sparse
          boolean[] types_sparse
          A sparse array of atomic types in the set

    • Class ec.gp.GPSpecies

      class GPSpecies extends Species implements Serializable

    • Class ec.gp.GPTree

      class GPTree extends Object implements Serializable

      • Serialized Fields

        • child
          GPNode child
          the root GPNode in the GPTree
        • constraints
          byte constraints
          constraints on the GPTree -- don't access the constraints through this variable -- use the constraints() method instead, which will give the actual constraints object.
        • owner
          GPIndividual owner
          the owner of the GPTree
        • printStyle
          int printStyle
          The print style of the GPTree.
        • printTerminalsAsVariablesInC
          boolean printTerminalsAsVariablesInC
          When using c to print for humans, do we print terminals as variables? (as opposed to zero-argument functions)?
        • printTwoArgumentNonterminalsAsOperatorsInC
          boolean printTwoArgumentNonterminalsAsOperatorsInC
          When using c to print for humans, do we print two-argument nonterminals in operator form "a op b"? (as opposed to functions "op(a, b)")?

    • Class ec.gp.GPTreeConstraints

      class GPTreeConstraints extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • constraintNumber
          byte constraintNumber
          The byte value of the constraints -- we can only have 256 of them
        • functionset
          GPFunctionSet functionset
          The function set for nodes in the tree
        • init
          GPNodeBuilder init
          The builder for the tree
        • name
          String name
        • treetype
          GPType treetype
          The type of the root of the tree

    • Class ec.gp.GPType

      class GPType extends Object implements Serializable

      • Serialized Fields

        • name
          String name
          The name of the type
        • type
          int type
          The preassigned integer value for the type

  • Package ec.gp.breed

    • Class ec.gp.breed.InternalCrossoverPipeline

      class InternalCrossoverPipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • maxDepth
          int maxDepth
          The deepest tree the pipeline is allowed to form. Single terminal trees are depth 1.
        • nodeselect0
          GPNodeSelector nodeselect0
          How the pipeline chooses the first subtree
        • nodeselect1
          GPNodeSelector nodeselect1
          How the pipeline chooses the second subtree
        • numTries
          int numTries
          How many times the pipeline attempts to pick nodes until it gives up.
        • tree1
          int tree1
          Is the first tree fixed? If not, this is -1
        • tree2
          int tree2
          Is the second tree fixed? If not, this is -1

    • Class ec.gp.breed.MutateAllNodesPipeline

      class MutateAllNodesPipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • nodeselect
          GPNodeSelector nodeselect
          How the pipeline chooses a subtree to mutate
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.MutateDemotePipeline

      class MutateDemotePipeline extends GPBreedingPipeline implements Serializable

      • Serialized Fields

        • demotableNode
          GPNode demotableNode
        • maxDepth
          int maxDepth
          The maximum depth of a mutated tree
        • numTries
          int numTries
          The number of times the pipeline tries to build a valid mutated tree before it gives up and just passes on the original
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.MutateERCPipeline

      class MutateERCPipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • nodeselect
          GPNodeSelector nodeselect
          How the pipeline chooses a subtree to mutate
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.MutateOneNodePipeline

      class MutateOneNodePipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • nodeselect
          GPNodeSelector nodeselect
          How the pipeline chooses a subtree to mutate
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.MutatePromotePipeline

      class MutatePromotePipeline extends GPBreedingPipeline implements Serializable

      • Serialized Fields

        • numTries
          int numTries
          The number of times the pipeline tries to build a valid mutated tree before it gives up and just passes on the original
        • promotableNode
          GPNode promotableNode
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.MutateSwapPipeline

      class MutateSwapPipeline extends GPBreedingPipeline implements Serializable

      • Serialized Fields

        • numTries
          int numTries
          The number of times the pipeline tries to build a valid mutated tree before it gives up and just passes on the original
        • swappableNode
          GPNode swappableNode
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.RehangPipeline

      class RehangPipeline extends GPBreedingPipeline implements Serializable

      • Serialized Fields

        • numTries
          int numTries
          The number of times the pipeline tries to find a tree with a nonterminal before giving up and just copying the individual.
        • rehangableNode
          GPNode rehangableNode
        • tree
          int tree
          Is our tree fixed? If not, this is -1

    • Class ec.gp.breed.SizeFairCrossoverPipeline

      class SizeFairCrossoverPipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • homologous
          boolean homologous
        • maxDepth
          int maxDepth
          The deepest tree the pipeline is allowed to form. Single terminal trees are depth 1.
        • nodeselect1
          GPNodeSelector nodeselect1
          How the pipeline selects a node from individual 1
        • nodeselect2
          GPNodeSelector nodeselect2
          How the pipeline selects a node from individual 2
        • numTries
          int numTries
          How many times the pipeline attempts to pick nodes until it gives up.
        • parents
          ArrayList<Individual> parents
          Temporary holding place for parents
        • tossSecondParent
          boolean tossSecondParent
          Should the pipeline discard the second parent after crossing over?
        • tree1
          int tree1
          Is the first tree fixed? If not, this is -1
        • tree2
          int tree2
          Is the second tree fixed? If not, this is -1

  • Package ec.gp.build

    • Class ec.gp.build.PTC1

      class PTC1 extends GPNodeBuilder implements Serializable

      • Serialized Fields

        • expectedSize
          int expectedSize
          The default expected tree size for PTC1
        • maxDepth
          int maxDepth
          The largest maximum tree depth PTC1 can specify -- should be big.

    • Class ec.gp.build.PTC2

      class PTC2 extends GPNodeBuilder implements Serializable

      • Serialized Fields

        • dequeue_argpos
          int dequeue_argpos
        • dequeue_depth
          int dequeue_depth
        • dequeue_node
          GPNode dequeue_node
        • maxDepth
          int maxDepth
          The largest maximum tree depth GROW can specify -- should be big.
        • s_argpos
          int[] s_argpos
        • s_depth
          int[] s_depth
        • s_node
          GPNode[] s_node
        • s_size
          int s_size

    • Class ec.gp.build.PTCFunctionSet

      class PTCFunctionSet extends GPFunctionSet implements Serializable

      • Serialized Fields

        • p_y
          double[][] p_y
          cache of nonterminal selection probabilities -- dense array [size-1][type]. If any items are null, they're not in the dense cache.
        • q_ny
          double[][] q_ny
          nonterminal probabilities[type][thenodes], in organized form
        • q_ty
          double[][] q_ty
          terminal probabilities[type][thenodes], in organized form

    • Class ec.gp.build.RandomBranch

      class RandomBranch extends GPNodeBuilder implements Serializable

    • Class ec.gp.build.RandTree

      class RandTree extends GPNodeBuilder implements Serializable

      • Serialized Fields

        • arities
          int[] arities
        • aritySetupDone
          boolean aritySetupDone
        • permutations
          LinkedList permutations

    • Class ec.gp.build.Uniform

      class Uniform extends GPNodeBuilder implements Serializable

      • Serialized Fields

        • _functionsets
          Hashtable _functionsets
        • _truesizes
          BigInteger[][][] _truesizes
        • CHILD_D
          double[][][][][] CHILD_D
        • funcnodes
          Hashtable funcnodes
        • functionsets
          GPFunctionSet[] functionsets
        • maxarity
          int maxarity
        • maxtreesize
          int maxtreesize
        • NUMCHILDPERMUTATIONS
          BigInteger[][][][][] NUMCHILDPERMUTATIONS
        • numfuncnodes
          int numfuncnodes
        • NUMTREESOFTYPE
          BigInteger[][][] NUMTREESOFTYPE
        • NUMTREESROOTEDBYNODE
          BigInteger[][][] NUMTREESROOTEDBYNODE
        • ROOT_D
          ec.gp.build.UniformGPNodeStorage[][][][] ROOT_D
        • ROOT_D_ZERO
          boolean[][][] ROOT_D_ZERO
        • truesizes
          double[][][] truesizes
        • useTrueDistribution
          boolean useTrueDistribution

  • Package ec.gp.ge

  • Package ec.gp.koza

    • Class ec.gp.koza.CrossoverPipeline

      class CrossoverPipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • maxDepth
          int maxDepth
          The deepest tree the pipeline is allowed to form. Single terminal trees are depth 1.
        • maxSize
          int maxSize
          The largest tree (measured as a nodecount) the pipeline is allowed to form.
        • nodeselect1
          GPNodeSelector nodeselect1
          How the pipeline selects a node from individual 1
        • nodeselect2
          GPNodeSelector nodeselect2
          How the pipeline selects a node from individual 2
        • numTries
          int numTries
          How many times the pipeline attempts to pick nodes until it gives up.
        • parents
          ArrayList<Individual> parents
          Temporary holding place for parents
        • tossSecondParent
          boolean tossSecondParent
          Should the pipeline discard the second parent after crossing over?
        • tree1
          int tree1
          Is the first tree fixed? If not, this is -1
        • tree2
          int tree2
          Is the second tree fixed? If not, this is -1

    • Class ec.gp.koza.FullBuilder

      class FullBuilder extends KozaBuilder implements Serializable

    • Class ec.gp.koza.GrowBuilder

      class GrowBuilder extends KozaBuilder implements Serializable

    • Class ec.gp.koza.HalfBuilder

      class HalfBuilder extends KozaBuilder implements Serializable

      • Serialized Fields

        • pickGrowProbability
          double pickGrowProbability
          The likelihood of using GROW over FULL.

    • Class ec.gp.koza.KozaBuilder

      class KozaBuilder extends GPNodeBuilder implements Serializable

      • Serialized Fields

        • maxDepth
          int maxDepth
          The largest maximum tree depth RAMPED HALF-AND-HALF can specify.
        • minDepth
          int minDepth
          The smallest maximum tree depth RAMPED HALF-AND-HALF can specify.

    • Class ec.gp.koza.KozaFitness

      class KozaFitness extends Fitness implements Serializable

      • Serialized Fields

        • hits
          int hits
          This auxillary measure is used in some problems for additional information. It's a traditional feature of Koza-style GP, and so although I think it's not very useful, I'll leave it in anyway.
        • standardizedFitness
          double standardizedFitness
          This ranges from 0 (best) to infinity (worst). I define it here as equivalent to the standardized fitness.

    • Class ec.gp.koza.KozaNodeSelector

      class KozaNodeSelector extends Object implements Serializable

      • Serialized Fields

        • nodes
          int nodes
          The number of nodes in the tree, -1 if unknown.
        • nonterminalProbability
          double nonterminalProbability
          The probability a nonterminal must be chosen.
        • nonterminals
          int nonterminals
          The number of nonterminals in the tree, -1 if unknown.
        • rootProbability
          double rootProbability
          The probability the root must be chosen
        • terminalProbability
          double terminalProbability
          The probability a terminal must be chosen
        • terminals
          int terminals
          The number of terminals in the tree, -1 if unknown.

    • Class ec.gp.koza.KozaShortStatistics

      class KozaShortStatistics extends SimpleShortStatistics implements Serializable

      • Serialized Fields

        • doDepth
          boolean doDepth
        • totalDepthSoFarTree
          long[][] totalDepthSoFarTree
        • totalDepthThisGenTree
          long[][] totalDepthThisGenTree
        • totalSizeSoFarTree
          long[][] totalSizeSoFarTree
        • totalSizeThisGenTree
          long[][] totalSizeThisGenTree

    • Class ec.gp.koza.MutationPipeline

      class MutationPipeline extends GPBreedingPipeline implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • builder
          GPNodeBuilder builder
          How the pipeline builds a new subtree
        • equalSize
          boolean equalSize
          Do we try to replace the subtree with another of the same size?
        • maxDepth
          int maxDepth
          The maximum depth of a mutated tree
        • maxSize
          int maxSize
          The largest tree (measured as a nodecount) the pipeline is allowed to form.
        • nodeselect
          GPNodeSelector nodeselect
          How the pipeline chooses a subtree to mutate
        • numTries
          int numTries
          The number of times the pipeline tries to build a valid mutated tree before it gives up and just passes on the original
        • tree
          int tree
          Is our tree fixed? If not, this is -1

  • Package ec.gp.push

  • Package ec.multiobjective

    • Class ec.multiobjective.HypervolumeStatistics

      class HypervolumeStatistics extends SimpleStatistics implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • referencePoint
          double[] referencePoint

    • Class ec.multiobjective.MultiObjectiveFitness

      class MultiObjectiveFitness extends Fitness implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • maximize
          boolean[] maximize
          Maximization. Shared.
        • maxObjective
          double[] maxObjective
          Desired maximum fitness values. By default these are 1.0. Shared.
        • minObjective
          double[] minObjective
          Desired minimum fitness values. By default these are 0.0. Shared.
        • objectives
          double[] objectives
          The various fitnesses.

    • Class ec.multiobjective.MultiObjectiveStatistics

      class MultiObjectiveStatistics extends SimpleStatistics implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • doHypervolume
          boolean doHypervolume
        • frontLog
          int frontLog
          The pareto front log
        • referencePoint
          double[] referencePoint
        • silentFront
          boolean silentFront
        • warned
          boolean warned
          Logs the best individual of the generation.

  • Package ec.multiobjective.nsga2

  • Package ec.multiobjective.spea2

  • Package ec.neat

    • Class ec.neat.NEATBreeder

      class NEATBreeder extends Breeder implements Serializable

    • Class ec.neat.NEATGene

      class NEATGene extends Gene implements Serializable

      • Serialized Fields

        • enable
          boolean enable
          Is the link this gene represent is enable in network activation.
        • frozen
          boolean frozen
          Is this gene frozen, a frozen gene's weight cannot get mutated in breeding procedure.
        • inNode
          NEATNode inNode
          The actual in node this gene connect to.
        • inNodeId
          int inNodeId
          The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.
        • innovationNumber
          int innovationNumber
          The innovation number of this link.
        • isRecurrent
          boolean isRecurrent
          Is the link this gene represent a recurrent link.
        • mutationNumber
          double mutationNumber
          The mutation number of this gene, Used to see how much mutation has changed.
        • outNode
          NEATNode outNode
          The actual out node this gene connect to.
        • outNodeId
          int outNodeId
          The id of the in node, this is useful in reading a gene from file, we will use this id to find the actual node after we finish reading the genome file.
        • timeDelay
          boolean timeDelay
          Time delay of the link, used in network activation.
        • weight
          double weight
          The weight of link this gene is represent.

    • Class ec.neat.NEATIndividual

      class NEATIndividual extends GeneVectorIndividual implements Serializable

      • Serialized Fields

        • adjustedFitness
          double adjustedFitness
          Fitness after the adjustment.
        • champion
          boolean champion
          Marks the subspecies champion, which is the individual who has the highest fitness with the subspecies.
        • eliminate
          boolean eliminate
          Marker for destruction of inferior individual.
        • expectedOffspring
          double expectedOffspring
          Number of children this individual may have for next generation.
        • generation
          int generation
          Tells which generation this individual is from.
        • highFit
          double highFit
          debug variable, highest fitness of champion
        • nodes
          ArrayList<NEATNode> nodes
          All the node of this individual. Nodes are arranged so that the first part of the nodes are SENSOR nodes.
        • popChampion
          boolean popChampion
          Marks the best individual in current generation of the population.
        • popChampionChild
          boolean popChampionChild
          Marks the duplicate child of a champion (for tracking purposes).
        • subspecies
          NEATSubspecies subspecies
          The individual's subpecies
        • superChampionOffspring
          int superChampionOffspring
          Number of reserved offspring for a population leader. This is used for delta coding.
        • timeAlive
          int timeAlive
          When playing in real-time allows knowing the maturity of an individual

    • Class ec.neat.NEATInitializer

      class NEATInitializer extends SimpleInitializer implements Serializable
      serialVersionUID:
      1L

    • Class ec.neat.NEATInnovation

      class NEATInnovation extends Object implements Serializable

      • Serialized Fields

        • inNodeId
          int inNodeId
          Two nodes specify where the link innovation took place : this is the input node.
        • innovationNum1
          int innovationNum1
          The number assigned to the innovation.
        • innovationNum2
          int innovationNum2
          If this is a new node innovation,then there are 2 innovations (links) added for the new node.
        • innovationType
          int innovationType
          Either NEWNODE (0) or NEWLINK (1).
        • newNodeId
          int newNodeId
          If a new node was created, this is its node id.
        • newWeight
          double newWeight
          If a link is added, this is its weight.
        • oldInnovationNum
          int oldInnovationNum
          If a new node was created, this is the innovation number of the gene's link it is being stuck inside.
        • outNodeId
          int outNodeId
          Two nodes specify where the link innovation took place : this is the output node.
        • recurFlag
          boolean recurFlag
          Is the link innovation a recurrent link.

    • Class ec.neat.NEATNetwork

      class NEATNetwork extends Object implements Serializable

    • Class ec.neat.NEATNode

      class NEATNode extends Object implements Serializable

      • Serialized Fields

        • activation
          double activation
          The total activation entering the node.
        • activationCount
          int activationCount
          Keeps track of which activation the node is currently in.
        • activeFlag
          boolean activeFlag
          To make sure outputs are active.
        • activeSum
          double activeSum
          The incoming activity before being processed.
        • frozen
          boolean frozen
          When it's true, the node cannot be mutated.
        • functionType
          NEATNode.FunctionType functionType
          The activation function, use sigmoid for default, but can use some other choice, like ReLU.
        • geneticNodeLabel
          NEATNode.NodePlace geneticNodeLabel
          Distinguish the input node, hidden or output node.
        • incomingGenes
          ArrayList<NEATGene> incomingGenes
          A list of incoming links, it is used to get activation status of the nodes on the other ends.
        • innerLevel
          int innerLevel
          The depth of current node in current network, this field is used in counting max depth in a network.
        • isTraversed
          boolean isTraversed
          Indicate if this node has been traversed in max depth counting.
        • lastActivation
          double lastActivation
          Holds the previous step's activation for recurrence.
        • nodeId
          int nodeId
          Node id for this node.
        • override
          boolean override
          Indicates if the value of current node has been override by method other than network's activation.
        • overrideValue
          double overrideValue
          Contains the activation value that will override this node's activation.
        • previousLastActivation
          double previousLastActivation
          Holds the activation BEFORE the previous step's This is necessary for a special recurrent case when the inNode of a recurrent link is one time step ahead of the outNode. The innode then needs to send from TWO time steps ago.
        • type
          NEATNode.NodeType type
          Distinguish the Sensor node or other neuron node.

    • Class ec.neat.NEATSpecies

      class NEATSpecies extends GeneVectorSpecies implements Serializable

      • Serialized Fields

        • addNodeMaxGenomeLength
          int addNodeMaxGenomeLength
          Beyond this genome length, mutateAddNode does a pure random split rather than a bias.
        • ageSignificance
          double ageSignificance
          How much does age matter?
        • babiesStolen
          int babiesStolen
          The number of babies to siphen off to the champions.
        • base
          Parameter base
        • compatThreshold
          double compatThreshold
          Compatible threshold to determine if two individual are compatible.
        • currInnovNum
          int currInnovNum
          Current innovation number that is available.
        • currNodeId
          int currNodeId
          Current node id that is available.
        • disjointCoeff
          double disjointCoeff
          Coefficient for disjoint gene in compatibility computation.
        • dropoffAge
          int dropoffAge
          Age where Species starts to be penalized.
        • excessCoeff
          double excessCoeff
          Coefficient for excess genes in compatibility computation.
        • highestFitness
          double highestFitness
          Used for delta coding, stagnation detector.
        • highestLastChanged
          int highestLastChanged
          Used for delta coding, If too high, leads to delta coding.
        • innoLock
          Object innoLock
        • innovationPrototype
          NEATInnovation innovationPrototype
          The prototypical innovation for individuals in this species.
        • innovations
          HashMap<NEATInnovation,NEATInnovation> innovations
          A Hashmap for easy tracking the innovation within species.
        • interspeciesMateRate
          double interspeciesMateRate
          Probability of doing interspecies crossover.
        • mateMultipointAvgProb
          double mateMultipointAvgProb
          Probability of doing multipoint crossover with averaging two genes.
        • mateMultipointProb
          double mateMultipointProb
          Probability of doing multipoint crossover.
        • mateOnlyProb
          double mateOnlyProb
          Probability of mating without mutation.
        • mateSinglepointProb
          double mateSinglepointProb
          Probability of doing single point crossover (not in used in this implementation, always set to 0).
        • maxNetworkDepth
          int maxNetworkDepth
          how deep a node can be in the network, measured by number of parents
        • mutateAddLinkProb
          double mutateAddLinkProb
          Probability of doing add-link mutation.
        • mutateAddNodeProb
          double mutateAddNodeProb
          Probability of doing add-node mutation.
        • mutateGeneReenableProb
          double mutateGeneReenableProb
          Probability of reenable a disabled gene.
        • mutateLinkWeightsProb
          double mutateLinkWeightsProb
          Probability of doing link weight mutate.
        • mutateOnlyProb
          double mutateOnlyProb
          Probility of a non-mating reproduction.
        • mutateToggleEnableProb
          double mutateToggleEnableProb
          Probability of changing the enable status of gene.
        • mutDiffCoeff
          double mutDiffCoeff
          Coefficient for mutational difference genes in compatibility computation.
        • networkPrototype
          NEATNetwork networkPrototype
          The prototypical network.
        • newLinkTries
          int newLinkTries
          Number of tries mutateAddLink will attempt to find an open link.
        • newNodeTries
          int newNodeTries
          Number of tries mutateAddNode will attempt to build a new node.
        • nodePrototype
          NEATNode nodePrototype
          The prototypical node for individuals in this species.
        • recurOnlyProb
          double recurOnlyProb
          Probability of forcing selection of ONLY links that are naturally recurrent.
        • subspecies
          ArrayList<NEATSubspecies> subspecies
          A list of the all the subspecies.
        • subspeciesPrototype
          NEATSubspecies subspeciesPrototype
          The prototypical subspecies for individuals in this species.
        • survivalThreshold
          double survivalThreshold
          Percent of ave fitness for survival.
        • weightMutationPower
          double weightMutationPower
          The Mutation power of the link's weights.

    • Class ec.neat.NEATSubspecies

      class NEATSubspecies extends Object implements Serializable

      • Serialized Fields

        • age
          int age
          Age of the current subspecies.
        • ageOfLastImprovement
          int ageOfLastImprovement
          Record the last time the best fitness improved within the individuals of this subspecies If this is too long ago, the subspecies will goes extinct
        • expectedOffspring
          int expectedOffspring
          Expected Offspring for next generation for this subspecies
        • individuals
          ArrayList<Individual> individuals
          The individuals within this species
        • maxFitnessEver
          double maxFitnessEver
          The max fitness the an individual in this subspecies ever achieved.
        • newGenIndividuals
          ArrayList<Individual> newGenIndividuals
          The next generation individuals within this species

  • Package ec.parsimony

  • Package ec.pso

    • Class ec.pso.Particle

      class Particle extends DoubleVectorIndividual implements Serializable

      • Serialized Fields

        • neighborhood
          int[] neighborhood
        • neighborhoodBestFitness
          Fitness neighborhoodBestFitness
        • neighborhoodBestGenome
          double[] neighborhoodBestGenome
        • personalBestFitness
          Fitness personalBestFitness
        • personalBestGenome
          double[] personalBestGenome
        • velocity
          double[] velocity

    • Class ec.pso.PSOBreeder

      class PSOBreeder extends Breeder implements Serializable

      • Serialized Fields

        • globalBest
          double[][] globalBest
        • globalBestFitness
          Fitness[] globalBestFitness
        • globalCoeff
          double globalCoeff
        • includeSelf
          boolean includeSelf
        • informantCoeff
          double informantCoeff
        • neighborhood
          int neighborhood
        • neighborhoodSize
          int neighborhoodSize
        • personalCoeff
          double personalCoeff
        • velCoeff
          double velCoeff

  • Package ec.rule

    • Class ec.rule.Rule

      class Rule extends Object implements Serializable

      • Serialized Fields

        • constraints
          byte constraints
          An index to a RuleConstraints

    • Class ec.rule.RuleConstraints

      class RuleConstraints extends Object implements Serializable

      • Serialized Fields

        • constraintNumber
          byte constraintNumber
          The byte value of the constraints -- we can only have 256 of them
        • name
          String name
          The name of the RuleConstraints object

    • Class ec.rule.RuleIndividual

      class RuleIndividual extends Individual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • rulesets
          RuleSet[] rulesets
          The individual's rulesets.

    • Class ec.rule.RuleInitializer

      class RuleInitializer extends SimpleInitializer implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • numRuleConstraints
          byte numRuleConstraints
        • numRuleSetConstraints
          byte numRuleSetConstraints
        • ruleConstraintRepository
          Hashtable ruleConstraintRepository
        • ruleConstraints
          RuleConstraints[] ruleConstraints
        • ruleSetConstraintRepository
          Hashtable ruleSetConstraintRepository
        • ruleSetConstraints
          RuleSetConstraints[] ruleSetConstraints

    • Class ec.rule.RuleSet

      class RuleSet extends Object implements Serializable

      • Serialized Fields

        • constraints
          byte constraints
          An index to a RuleSetConstraints
        • numRules
          int numRules
          How many rules are there used in the rules array
        • rules
          Rule[] rules
          The rules in the rule set

    • Class ec.rule.RuleSetConstraints

      class RuleSetConstraints extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • constraintNumber
          byte constraintNumber
          The byte value of the constraints -- we can only have 256 of them
        • maxSize
          int maxSize
        • minSize
          int minSize
        • name
          String name
          The name of the RuleSetConstraints object
        • p_add
          double p_add
        • p_del
          double p_del
        • p_randorder
          double p_randorder
        • resetMaxSize
          int resetMaxSize
        • resetMinSize
          int resetMinSize
        • rulePrototype
          Rule rulePrototype
          The prototype of the Rule that will be used in the RuleSet (the RuleSet contains only rules with the specified prototype).
        • sizeDistribution
          double[] sizeDistribution

    • Class ec.rule.RuleSpecies

      class RuleSpecies extends Species implements Serializable

  • Package ec.rule.breed

  • Package ec.select

    • Class ec.select.AnnealedSelection

      class AnnealedSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • best
          int best
        • cache
          boolean cache
        • cutdown
          double cutdown
        • t
          double t
        • temperature
          double temperature

    • Class ec.select.BestSelection

      class BestSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • bestn
          int bestn
        • bestnFrac
          double bestnFrac
        • pickWorst
          boolean pickWorst
          Do we pick the worst instead of the best?
        • probabilityOfPickingSizePlusOne
          double probabilityOfPickingSizePlusOne
          Probablity of picking the size plus one.
        • size
          int size
          Base size of the tournament; this may change.
        • sortedPop
          int[] sortedPop
          Sorted, normalized, totalized fitnesses for the population

    • Class ec.select.BoltzmannSelection

      class BoltzmannSelection extends FitProportionateSelection implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • coolingRate
          double coolingRate
          Cooling rate
        • startingTemperature
          double startingTemperature
          Starting temperature

    • Class ec.select.FirstSelection

      class FirstSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

    • Class ec.select.FitProportionateSelection

      class FitProportionateSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • fitnesses
          double[] fitnesses
          Normalized, totalized fitnesses for the population

    • Class ec.select.GreedyOverselection

      class GreedyOverselection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • gets_n_percent
          double gets_n_percent
        • sortedFitOver
          double[] sortedFitOver
        • sortedFitUnder
          double[] sortedFitUnder
        • sortedPop
          int[] sortedPop
          Sorted population -- since I *have* to use an int-sized individual (short gives me only 16K), I might as well just have pointers to the population itself. :-(
        • top_n_percent
          double top_n_percent

    • Class ec.select.LexicaseSelection

      class LexicaseSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

    • Class ec.select.MultiSelection

      class MultiSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ec.select.RandomSelection

      class RandomSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

    • Class ec.select.SigmaScalingSelection

      class SigmaScalingSelection extends FitProportionateSelection implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • fitnessFloor
          double fitnessFloor
          Floor for sigma scaled fitnesses

    • Class ec.select.SUSSelection

      class SUSSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • fitnesses
          double[] fitnesses
          The distribution of fitnesses.
        • indices
          int[] indices
          An array of pointers to individuals in the population, shuffled along with the fitnesses array.
        • lastIndex
          int lastIndex
          The index in the array of the last individual selected.
        • offset
          double offset
          The floating point value to consider for the next selected individual.
        • shuffle
          boolean shuffle
          Should we shuffle first?
        • steps
          int steps
          How many samples have been done?

    • Class ec.select.TopSelection

      class TopSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • best
          int best
        • cache
          boolean cache

    • Class ec.select.TournamentSelection

      class TournamentSelection extends SelectionMethod implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • pickWorst
          boolean pickWorst
          Do we pick the worst instead of the best?
        • probabilityOfPickingSizePlusOne
          double probabilityOfPickingSizePlusOne
          Probablity of picking the size plus one
        • size
          int size
          Base size of the tournament; this may change.

  • Package ec.simple

    • Class ec.simple.SimpleBreeder

      class SimpleBreeder extends Breeder implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • backupPopulation
          Population backupPopulation
        • clonePipelineAndPopulation
          boolean clonePipelineAndPopulation
        • elite
          int[] elite
          An array[subpop] of the number of elites to keep for that subpopulation
        • eliteFrac
          double[] eliteFrac
          An array[subpop] of the *fraction* of elites to keep for that subpopulation
        • newIndividuals
          ArrayList<Individual>[][] newIndividuals
        • pool
          ThreadPool pool
        • reevaluateElites
          boolean[] reevaluateElites

    • Class ec.simple.SimpleEvaluator

      class SimpleEvaluator extends Evaluator implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • chunkSize
          int chunkSize
        • cloneProblem
          boolean cloneProblem
        • individualCounter
          int individualCounter
        • lock
          Object[] lock
        • mergeForm
          int mergeForm
        • numTests
          int numTests
        • oldpop
          Population oldpop
        • pool
          ThreadPool pool
        • subPopCounter
          int subPopCounter

    • Class ec.simple.SimpleEvolutionState

      class SimpleEvolutionState extends EvolutionState implements Serializable
      serialVersionUID:
      1L

    • Class ec.simple.SimpleExchanger

      class SimpleExchanger extends Exchanger implements Serializable
      serialVersionUID:
      1L

    • Class ec.simple.SimpleFinisher

      class SimpleFinisher extends Finisher implements Serializable
      serialVersionUID:
      1L

    • Class ec.simple.SimpleFitness

      class SimpleFitness extends Fitness implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • fitness
          double fitness
        • isIdeal
          boolean isIdeal

    • Class ec.simple.SimpleGroupedEvaluator

      class SimpleGroupedEvaluator extends SimpleEvaluator implements Serializable
      serialVersionUID:
      1L

    • Class ec.simple.SimpleInitializer

      class SimpleInitializer extends Initializer implements Serializable
      serialVersionUID:
      1L

    • Class ec.simple.SimpleShortStatistics

      class SimpleShortStatistics extends Statistics implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • bestOfGeneration
          Individual[] bestOfGeneration
        • bestSoFar
          Individual[] bestSoFar
        • delimiter
          String delimiter
        • doHeader
          boolean doHeader
        • doSize
          boolean doSize
        • doSubpops
          boolean doSubpops
        • doTime
          boolean doTime
        • lastTime
          long lastTime
        • modulus
          int modulus
        • statisticslog
          int statisticslog
        • totalFitnessThisGen
          double[] totalFitnessThisGen
        • totalIndsSoFar
          long[] totalIndsSoFar
        • totalIndsThisGen
          long[] totalIndsThisGen
        • totalSizeSoFar
          long[] totalSizeSoFar
        • totalSizeThisGen
          long[] totalSizeThisGen

    • Class ec.simple.SimpleStatistics

      class SimpleStatistics extends Statistics implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • best_of_run
          Individual[] best_of_run
          The best individual we've found so far
        • compress
          boolean compress
          Should we compress the file?
        • doDescription
          boolean doDescription
        • doFinal
          boolean doFinal
        • doGeneration
          boolean doGeneration
        • doMessage
          boolean doMessage
        • doPerGenerationDescription
          boolean doPerGenerationDescription
        • statisticslog
          int statisticslog
          The Statistics' log
        • warned
          boolean warned
          Logs the best individual of the generation.

  • Package ec.spatial

  • Package ec.steadystate

    • Class ec.steadystate.QueueIndividual

      class QueueIndividual extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ec.steadystate.SteadyStateBreeder

      class SteadyStateBreeder extends SimpleBreeder implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • bp
          BreedingSource[] bp
          If st.firstTimeAround, this acts exactly like SimpleBreeder. Else, it only breeds one new individual per subpopulation, to place in position 0 of the subpopulation.
        • deselectors
          SelectionMethod[] deselectors
          Loaded during the first iteration of breedPopulation

    • Class ec.steadystate.SteadyStateEvaluator

      class SteadyStateEvaluator extends SimpleEvaluator implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ec.steadystate.SteadyStateEvolutionState

      class SteadyStateEvolutionState extends EvolutionState implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • emptyAtGenerationBoundary
          boolean emptyAtGenerationBoundary
          If true, the population will be emptied after each "generation," so no replacement or breeding occurrs. This is used, for example, by Ant Colony algorithms, which have no notion of breeding.
        • firstTime
          boolean firstTime
          First time calling evolve
        • generationBoundary
          boolean generationBoundary
          Did we just start a new generation?
        • generationSize
          int generationSize
          how big is a generation? Set to the size of subpopulation 0 of the initial population.
        • individualHash
          HashMap[] individualHash
          Hash table to check for duplicate individuals
        • replacementProbability
          double replacementProbability
          When a new individual arrives, with what probability should it directly replace the existing "marked for death" individual, as opposed to only replacing it if it's superior?
        • whichSubpop
          int whichSubpop
          Holds which subpopulation we are currently operating on

  • Package ec.util

  • Package ec.vector

    • Class ec.vector.BitVectorIndividual

      class BitVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          boolean[] genome

    • Class ec.vector.BitVectorSpecies

      class BitVectorSpecies extends VectorSpecies implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • mutationType
          int[] mutationType
          Mutation type, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

    • Class ec.vector.ByteVectorIndividual

      class ByteVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          byte[] genome

    • Class ec.vector.DoubleVectorIndividual

      class DoubleVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          double[] genome

    • Class ec.vector.FloatVectorIndividual

      class FloatVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          float[] genome

    • Class ec.vector.FloatVectorSpecies

      class FloatVectorSpecies extends VectorSpecies implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • gaussMutationStdev
          double[] gaussMutationStdev
          Standard deviation for Gaussian Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • maxGene
          double[] maxGene
          Max-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • minGene
          double[] minGene
          Min-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationDistributionIndex
          int[] mutationDistributionIndex
          The distribution index for Polynomial Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationIsBounded
          boolean[] mutationIsBounded
          Whether mutation is bounded to the min- and max-gene values, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationIsBoundedDefined
          boolean mutationIsBoundedDefined
          Whether the mutationIsBounded value was defined, per gene. Used internally only. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationType
          int[] mutationType
          Mutation type, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • outOfBoundsRetries
          int outOfBoundsRetries
          The number of times Polynomial Mutation or Gaussian Mutation retry for valid numbers until they get one.
        • polynomialIsAlternative
          boolean[] polynomialIsAlternative
          Whether the Polynomial Mutation method is the "alternative" method, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • polynomialIsAlternativeDefined
          boolean polynomialIsAlternativeDefined
          Whether the polymialIsAlternative value was defined, per gene. Used internally only. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • randomWalkProbability
          double[] randomWalkProbability
          The continuation probability for Integer Random Walk Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

    • Class ec.vector.Gene

      class Gene extends Object implements Serializable
      serialVersionUID:
      1L

    • Class ec.vector.GeneVectorIndividual

      class GeneVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          Gene[] genome

    • Class ec.vector.GeneVectorSpecies

      class GeneVectorSpecies extends VectorSpecies implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genePrototype
          Gene genePrototype

    • Class ec.vector.IntegerVectorIndividual

      class IntegerVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          int[] genome

    • Class ec.vector.IntegerVectorSpecies

      class IntegerVectorSpecies extends VectorSpecies implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • maxGene
          long[] maxGene
          Max-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • minGene
          long[] minGene
          Min-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationIsBounded
          boolean[] mutationIsBounded
          Whether mutation is bounded to the min- and max-gene values, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationIsBoundedDefined
          boolean mutationIsBoundedDefined
          Whether the mutationIsBounded value was defined, per gene. Used internally only. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • mutationType
          int[] mutationType
          Mutation type, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
        • randomWalkProbability
          double[] randomWalkProbability
          The continuation probability for Integer Random Walk Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

    • Class ec.vector.LongVectorIndividual

      class LongVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          long[] genome

    • Class ec.vector.ShortVectorIndividual

      class ShortVectorIndividual extends VectorIndividual implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • genome
          short[] genome

    • Class ec.vector.VectorIndividual

      class VectorIndividual extends Individual implements Serializable
      serialVersionUID:
      1L

    • Class ec.vector.VectorSpecies

      class VectorSpecies extends Species implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • chunksize
          int chunksize
          How big of chunks should we define for crossover?
        • crossoverDistributionIndex
          int crossoverDistributionIndex
          What should the SBX distribution index be?
        • crossoverProbability
          double crossoverProbability
          Probability that a gene will cross over -- ONLY used in V_ANY_POINT crossover
        • crossoverType
          int crossoverType
          What kind of crossover do we have?
        • duplicateRetries
          int[] duplicateRetries
          How often do we retry until we get a non-duplicate gene?
        • dynamicInitialSize
          boolean dynamicInitialSize
          Was the initial size determined dynamically?
        • genomeIncreaseProbability
          double genomeIncreaseProbability
          With what probability would our genome be at least 1 larger than it is now during initialization?
        • genomeResizeAlgorithm
          int genomeResizeAlgorithm
          How should we reset the genome?
        • genomeSize
          int genomeSize
          How big of a genome should we create on initialization?
        • lineDistance
          double lineDistance
          How far along the long a child can be located for line or intermediate recombination
        • maxInitialSize
          int maxInitialSize
          What's the largest legal genome?
        • minInitialSize
          int minInitialSize
          What's the smallest legal genome?
        • mutationProbability
          double[] mutationProbability
          Probability that a gene will mutate, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

  • Package ec.vector.breed