Hierarchy For All Packages

Package Hierarchies:

org.jaga.definitions, org.jaga.exampleApplications, org.jaga.exampleApplications.proteinLocation, org.jaga.fitnessEvaluation.largerNumbers, org.jaga.fitnessEvaluation.multiplexer, org.jaga.fitnessEvaluation.proteinLocation, org.jaga.hooks, org.jaga.individualRepresentation.booleanFormulas, org.jaga.individualRepresentation.greycodedNumbers, org.jaga.individualRepresentation.proteinLocation, org.jaga.masterAlgorithm, org.jaga.reproduction, org.jaga.reproduction.booleanFormulas, org.jaga.reproduction.booleanFormulas.nodes, org.jaga.reproduction.greycodedNumbers, org.jaga.reproduction.proteinLocation, org.jaga.selection, org.jaga.util

Class Hierarchy

• class java.lang.Object
  • class org.jaga.selection.AbsoluteFitness (implements org.jaga.definitions.Fitness)
    • class org.jaga.selection.ClassifierFitness
  • class org.jaga.selection.AbsoluteFitnessIndividualComparator (implements java.util.Comparator)
  • class org.jaga.individualRepresentation.proteinLocation.AminoAcidFactory
  • class org.jaga.individualRepresentation.proteinLocation.AminoAcidPropertyFactory
  • class org.jaga.hooks.AnalysisHook.Entry
  • class org.jaga.util.BitString
  • class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTree (implements org.jaga.definitions.Individual)
  • class org.jaga.individualRepresentation.booleanFormulas.BooleanFormulaTreeFactory (implements org.jaga.definitions.IndividualsFactory)
  • class org.jaga.reproduction.booleanFormulas.nodes.BooleanFormulaTreeNode
    • class org.jaga.reproduction.booleanFormulas.nodes.ConstantNode
      • class org.jaga.reproduction.booleanFormulas.nodes.FalseNode
      • class org.jaga.reproduction.booleanFormulas.nodes.TrueNode
    • class org.jaga.reproduction.booleanFormulas.nodes.OperatorNode
      • class org.jaga.reproduction.booleanFormulas.nodes.BinaryOperatorNode
        • class org.jaga.reproduction.booleanFormulas.nodes.ANDNode
        • class org.jaga.reproduction.booleanFormulas.nodes.EQUIVNode
        • class org.jaga.reproduction.booleanFormulas.nodes.IMPLNode
        • class org.jaga.reproduction.booleanFormulas.nodes.NANDNode
        • class org.jaga.reproduction.booleanFormulas.nodes.NORNode
        • class org.jaga.reproduction.booleanFormulas.nodes.ORNode
        • class org.jaga.reproduction.booleanFormulas.nodes.XORNode
      • class org.jaga.reproduction.booleanFormulas.nodes.TertiaryOperatorNode
        • class org.jaga.reproduction.booleanFormulas.nodes.IFNode
      • class org.jaga.reproduction.booleanFormulas.nodes.UnaryOperatorNode
        • class org.jaga.reproduction.booleanFormulas.nodes.NOTNode
    • class org.jaga.reproduction.booleanFormulas.nodes.TerminalNode
  • class org.jaga.reproduction.CombinedReproductionAlgorithm (implements org.jaga.definitions.ReproductionAlgorithm)
    • class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOverWithMutation
  • class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • class java.awt.Container
      • class javax.swing.JComponent (implements java.io.Serializable)
        • class javax.swing.JPanel (implements javax.accessibility.Accessible)
          • class org.jaga.hooks.AnalysisGraphPanel
      • class java.awt.Window (implements javax.accessibility.Accessible)
        • class java.awt.Frame (implements java.awt.MenuContainer)
          • class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class org.jaga.hooks.GAAnalysisFrame
  • class org.jaga.exampleApplications.proteinLocation.DataSplitter
  • class org.jaga.exampleApplications.proteinLocation.DataSplitter.Protein
  • class org.jaga.util.DefaultParameterSet (implements org.jaga.definitions.GAParameterSet)
  • class org.jaga.exampleApplications.Example1
  • class org.jaga.exampleApplications.Example1Fitness (implements org.jaga.definitions.FitnessEvaluationAlgorithm)
  • class org.jaga.exampleApplications.Example2
  • class org.jaga.exampleApplications.Example2Fitness (implements org.jaga.definitions.FitnessEvaluationAlgorithm)
  • class org.jaga.util.FittestIndividualResult (implements org.jaga.definitions.GAResult)
  • class org.jaga.fitnessEvaluation.largerNumbers.LargerDecimals (implements org.jaga.definitions.FitnessEvaluationAlgorithm)
  • class org.jaga.exampleApplications.proteinLocation.Locator
  • class org.jaga.fitnessEvaluation.multiplexer.Multiplexer
  • class org.jaga.exampleApplications.MultiplexerEvolution
  • class org.jaga.fitnessEvaluation.multiplexer.MultiplexerFitness (implements org.jaga.definitions.FitnessEvaluationAlgorithm)
  • class org.jaga.fitnessEvaluation.multiplexer.MultiplexerFitness.TestEntry
  • class org.jaga.reproduction.Mutation (implements org.jaga.definitions.ReproductionAlgorithm)
    • class org.jaga.reproduction.booleanFormulas.FunctionTreeMutation
    • class org.jaga.reproduction.proteinLocation.PolypeptidePatternElongation
    • class org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation
    • class org.jaga.reproduction.greycodedNumbers.SimpleBinaryMutation
  • class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividualSimpleFactory (implements org.jaga.definitions.IndividualsFactory)
  • class org.jaga.individualRepresentation.greycodedNumbers.NNumbersGreycodedIndivudual (implements org.jaga.individualRepresentation.greycodedNumbers.BinaryEncodedIndividual)
    • class org.jaga.individualRepresentation.greycodedNumbers.NDecimalsIndividual
  • class org.jaga.individualRepresentation.proteinLocation.PolypeptidePattern
  • class org.jaga.individualRepresentation.proteinLocation.PolypeptidePatternItem
    • class org.jaga.individualRepresentation.proteinLocation.AminoAcid
    • class org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup
    • class org.jaga.individualRepresentation.proteinLocation.AminoAcidProperty
    • class org.jaga.individualRepresentation.proteinLocation.SingleGap
  • class org.jaga.individualRepresentation.proteinLocation.Protein
  • class org.jaga.individualRepresentation.proteinLocation.ProteinGroup
  • class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifier (implements org.jaga.definitions.Individual)
  • class org.jaga.individualRepresentation.proteinLocation.ProteinLocationClassifierFactory (implements org.jaga.definitions.IndividualsFactory)
  • class org.jaga.fitnessEvaluation.proteinLocation.ProteinLocationTrainer (implements org.jaga.definitions.FitnessEvaluationAlgorithm)
  • class java.util.Random (implements java.io.Serializable)
    • class org.jaga.util.DefaultRandomGenerator (implements org.jaga.definitions.RandomGenerator)
  • class org.jaga.individualRepresentation.greycodedNumbers.RangeConstraint
  • class org.jaga.selection.RouletteWheelSelection (implements org.jaga.definitions.SelectionAlgorithm)
  • class org.jaga.util.SimpleCollectionOfIndividuals (implements org.jaga.definitions.Population)
  • class org.jaga.masterAlgorithm.SimpleGA (implements org.jaga.definitions.GeneticAlgorithm)
    • class org.jaga.masterAlgorithm.ReusableSimpleGA
      • class org.jaga.masterAlgorithm.ElitistGA
        • class org.jaga.masterAlgorithm.InitialPopulationGA
  • class org.jaga.hooks.SimpleGAHook
    • class org.jaga.hooks.AnalysisHook
    • class org.jaga.hooks.DebugHook
      • class org.jaga.hooks.BetterResultHook
    • class org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook
  • class org.jaga.exampleApplications.SimpleImplementationDemo
  • class org.jaga.individualRepresentation.proteinLocation.SimplifiedFastaFileParser (implements org.jaga.individualRepresentation.proteinLocation.ProteinFileParser)
  • class org.jaga.exampleApplications.proteinLocation.SubcellularProteinLocation
  • class org.jaga.individualRepresentation.proteinLocation.SubstitutionScoringMatrix
    • class org.jaga.individualRepresentation.proteinLocation.Blosum62
  • class java.lang.Thread (implements java.lang.Runnable)
    • class org.jaga.hooks.AnalysisFrameUpdateThread
  • class org.jaga.selection.TournamentSelection (implements org.jaga.definitions.SelectionAlgorithm)
  • class org.jaga.selection.TwoTournamentProbabalisticSelection (implements org.jaga.definitions.SelectionAlgorithm)
  • class org.jaga.exampleApplications.proteinLocation.Validator
  • class org.jaga.reproduction.XOver (implements org.jaga.definitions.ReproductionAlgorithm)
    • class org.jaga.reproduction.booleanFormulas.FunctionTreeXOver
    • class org.jaga.reproduction.proteinLocation.PolypeptidePatternXOver
    • class org.jaga.reproduction.greycodedNumbers.SimpleBinaryXOver

Interface Hierarchy

• interface org.jaga.definitions.Fitness
• interface org.jaga.definitions.FitnessEvaluationAlgorithm
• interface org.jaga.definitions.GAParameterSet
• interface org.jaga.definitions.GAResult
• interface org.jaga.definitions.GeneticAlgorithm
• interface org.jaga.definitions.Individual
  • interface org.jaga.individualRepresentation.greycodedNumbers.BinaryEncodedIndividual
• interface org.jaga.definitions.IndividualsFactory
• interface org.jaga.definitions.Population
• interface org.jaga.individualRepresentation.proteinLocation.ProteinFileParser
• interface org.jaga.definitions.RandomGenerator
• interface org.jaga.definitions.ReproductionAlgorithm
• interface org.jaga.definitions.SelectionAlgorithm