All Classes

AbstractCheckpointable AcceptEqualOrBetter AcceptEqualOrBetterTest AcceptImprovement AcceptImprovementTest AcceptableSecondBrokenEdge AcceptableSecondVertex Accepter Accepter AccepterTest AccessWindow AccessWindowTest AccessWindowWeight AccessWindowsList AddDirectedEdge AddDirectedVertex AddEdge AddVertex AllTests Allele AlleleSetup AlleleTemplate AlleleTemplateTest AlleleTest AmericanWireGauge AmericanWireGaugeTest And AntiTournament AntiTournamentLocal AntiTournamentLocalTest AntiTournamentTest AssumedParameters AssumedParametersTest Atom Atom.ExtendedTypeKey AtomTest AtomicSpecies AvailabilityTimeline AvailabilityTimelineTest AvailableNode AvailableNodeTest apsp Benzene Bodies BodiesTest Body Bond BottomSubBreeder Breeder Breeder Breeder Breeder Breeder BreederElitist BreederSteadyState BreederSteadyState2 BreederWithTeachers Brick3d Brick3dTest Brick3dWithSegments Brick3dWithSegmentsTest BrokenEdge BrokenGraph CandidatePopulation CandidateReporter ChangeFunctionByGeneration ChangeFunctionByGenerationTest ChangingWeightsObject ChangingWeightsObjectTest Checkpointer ChildMaker ChildMaker ChildMaker ChildMakerChain ChildMakerDownFractionComparatorTest ChildMakerEvolvingProvider ChildMakerEvolvingProvider2 ChildMakerEvolvingProvider2Test ChildMakerEvolvingProviderTest ChildMakerProvider ChildMakerProviderRandom ChildMakerProviderRandomMutations ChildMakerProviderTest ChildMakerProviderWeighted ChildMakerRandomCreator ChildMakerTest ChooseForDeath ChooseParents Chromosome ChromosomeArrayCrossover ChromosomeCrossover ChromosomeDistanceFitness ChromosomeIndividual ChromosomeIntervalCrossover ChromosomeIntervalCrossoverTest ChromosomeMutation ChromosomeMutationTest ChromosomeParameterValues ChromosomeParameters ChromosomePopulation ChromosomeReporter ChromosomeXoverWithMutation ChromosomeXoverWithMutationTest CircularIntQueue ComparativeStatistics ComparativeStatisticsTest Compatible Constants Constants CoreUtility CoreUtilityTest CrossTrackSlew CrossTrackSlewTest Crossover CrossoverAdewaya CrossoverAdewayaTest CrossoverInterval CrossoverIntervalTest CrossoverOnePoint CrossoverOnePointEach CrossoverOnePointEachTest CrossoverOnePointTest CrossoverPickOne CrossoverPickOneTest CrossoverTest CrossoverTwoPoints CrossoverTwoPointsEach CrossoverTwoPointsEachTest CrossoverTwoPointsTest CyclesSimilarity compareTechniquesMain DataTable DeJongFitnessFunctions DeJongFitnessFunctionsTest Debug Debug Debug DescendingWeightsComparator DescendingWeightsComparatorTest DirectedEdge DirectedGraph DirectedVertex DissimilarEdgeCompatibleWithVertices Distribution DoubleInterval DoubleIntervalTest DoublesList DoublesListTest DutyCycleConstraint DutyCycleConstraintTest EOSModel EOSModelTest EOSschedulingEvolvable EOSschedulingEvolvableTest EOSschedulingIndividual EOSschedulingParameters EOSschedulingPopulation EOSschedulingReporter EarliestFirstPlacer EarliestFirstPlacerTest EarliestFromChosenWindowPlacer EarliestFromRandomWindowPlacer EasyFile Edge EdgeIterator Element Error Evolvable EvolvableDouble EvolvableDoubleList EvolvableDoubleListTest EvolvableDoubleTest EvolvableTest ExperimentMain ExtendedTreeSet ExtendedTreeSetTest ExtendedTypeSimilarity ExtendedVector ExtendedVectorTest FieldRecordText FieldRecordTextTest FindMinimumInTsdFile FirstClusterLowestEnergyFitnessFunction FirstClusterLowestEnergyFitnessFunctionTest Fitness FitnessBad FitnessDouble FitnessFunction FitnessFunctionBadSize FitnessFunctionBadSizeTest FitnessFunctionFixed FitnessFunctionMultiObjective FitnessFunctionMultiObjectiveToOne FitnessFunctionRandom FitnessFunctionWorstFitness FitnessFunctionWorstFitnessManyTries FitnessFunctionWorstFitnessManyTriesTest FitnessFunctionWorstFitnessTest FitnessMultiObjective FitnessMultiObjectiveTest ForceFitnessRMS ForceFitnessRMSTest ForceFitnessTanimoto FunctionalForm GetLengthsAndAngles Graph Graph.TrailKey GraphElement GraphGenerator GraphIndividual GraphLayout GraphParameters GraphPopulation GraphTest GrowOnlyArray GrowOnlyArrayTest HasInputEdgeFrom HasOutputEdgesTo Horizon HorizonTest IO IOTest Immigrant ImmigrantTest Immigrants ImmigrantsTest IncrementIterator IndexIterator Indices IndicesTest Individual IntegerInterval IntegerIntervalTest IsEqual IsInstanceOf IsMarked Iterator integer KeyCounter KeyCounterTest LatticeConstantEnergies LogComparisons LogComparisonsTest LogFile LowestToHighestEnergyFitness LowestToHighestEnergyFitnessTest LowestToHighestEnergyGradualFitness LowestToHighestEnergyGradualFitnessTest MMEFreferenceRMS MMEFreferenceRMSTest MMEFreferenceTanimoto Main Main MakeDimer MakeDimerPair MakeSeeds MakeSiFMolecules MakeThreeBodyXyz MakeTrimer ManyMoleculesEnergyFitness ManyMoleculesEnergyFitnessRatio ManyMoleculesEnergyFitnessTanimotoDistance ManyMultiBodiesForOneEnergy ManySamples Mark MarkIsSet MathUtility MathUtilityTest Matrix3d MiddleSubBreeder MinMaxes MinMaxesTest MinimizeSlewingFitness Molecule MoleculeIndividual MoleculeLayout MoleculeMain MoleculeParameters MoleculePopulation MoleculeTest MoleculeTwoVertexCrossover Molecules MultiBodiesForOneEnergy MultiBodiesForOneEnergyTest MultiBody MultiStageFitnessFunction MultiStageFitnessFunctionTest MutateEdge MutateVertex Mutation3Parents Mutation3parents Mutation3parentsTest MutationDelete MutationDeleteTest MutationFixedStdDev MutationFixedStdDevTest MutationInsert MutationInsertTest molFormat NeighboringPairsSelector Node NodeArrayTest NodeFactory NodeTest Not NotFoundException NumberOfTakeImagesFitness ObjectCache ObjectCacheTest ObjectCompatible ObjectEquals OneBody Or OrderMutation Parameters Parameters Parameters2tsd ParametersAndLog2tsd ParametersSerializationTest ParsimonyFitness PeriodicCheckpoints PermutationChildMaker PermutationEvolvable PermutationIndividual PermutationKCutMutation PermutationKCutMutationTest PermutationOrderMutation PermutationOrderMutationTest PermutationParameters PermutationPopulation PermutationPositionCrossover PermutationPositionCrossoverTest PermutationTestFitness PhenotypeChanger PhenotypeChangerDummy Placer PointingRequirement PointingRequirementTest Population PopulationTest PositionCrossover Potential PotentialEnergyFitness PotentialEnergyTestCase Predicate PrintTabSeparatedData Procedure ProductFitnessFunction ProductFitnessFunctionTest PropertiesList PropertiesListTest Purine PutPotentialEnergiesAndForces Pyridine Quat4d RandomChild RandomDistribution RandomEvolvableDoubleListProducer RandomEvolvableProducer RandomGaussianDistribution RandomNumber RandomNumberTest ReinitializableFloat ReinitializableFloatTest ReinitializableFloatWithFactor ReinitializableFloatWithFactorTest ReinitializableInt ReinitializableIntTest Reporter RestartAfterNChildrenWithoutAcceptance RestartAfterNChildrenWithoutAcceptanceTest RestartAfterNChildrenWithoutImprovement RestartAfterNChildrenWithoutImprovementTest RestartEveryNChildren RestartEveryNChildrenTest RestartNever RestartPolicy RootMeanSquares RootMeanSquaresTest RouletteWheel RouletteWheel RouletteWheelChooseLowWeight RouletteWheelChooseLowWeightTest RouletteWheelTest RouletteWheelTest Run Run RunChromosome RunMolecule RunPermutation randomizeManyMolecules randomizeXYZ runEOSscheduling SSRNode SSRNodeTest SSRTimeline SSRTimelineNone SSRTimelineTest STKAccessFile STKAccessFileTest Sample SampleTest Satellite Saver Scheduler Scheduler SchedulerTest SchedulingData SchedulingFitnessFunction SecondBody SelectAll SelectAllTest SelectByProbability SelectByProbabilityTest SelectChunk SelectChunkTest SelectFixedIndices SelectFixedIndicesTest SelectFixedNumber SelectFixedNumberTest SelectModulo SelectModuloTest SelectOne SelectOneNeighboringPair SelectOneNeighboringPairTest SelectOneTest SelectTwoNeighboringPairs SelectTwoNeighboringPairsTest Selector Sensor SensorTest SensorType SetMark SlewMotor SlewMotorNone SlewMotorTest SlewNode SlewNone SlewRequirement SlewTimeline SlewTimelineNone SlewTimelineTest Slewable SmallSlewsFitness Species Species2IndexMap SqueakyWheelPlacedTSM SqueakyWheelPlacedTSMTest SqueakyWheelShiftForward SqueakyWheelShiftForwardTest SqueakyWheelTournamentSwapMutation SqueakyWheelTournamentSwapMutationTest SteadyStateDiscreteBreeder SteadyStateDiscreteBreederTest StillingerWeber StillingerWeberEnergies StillingerWeberPartialSiF StillingerWeberPrintEnergiesAndForces StillingerWeberSi StillingerWeberSiF StillingerWeberSiFTest StillingerWeberSiTest StillingerWeberTest StudentFitness StudentFitnessFunction StudentTeacherTest SubBreeder TakeImage Tanimoto Task TaskAndAccessWindowGenerator TaskAndAccessWindowGeneratorTest TaskList TaskPlacementData TaskPriorityFitness TaskTest TaskWeight TaskWeightTest TeacherFitnessFunction TeacherPopulation Tersoff TersoffTest TestFitnessFunction1 ThirdBody ThreeBody ThreeBodyTest TimeInterval Timeline TimelineTest Timer TokenizeInput TokenizeOutput TopSubBreeder Tournament TournamentLocal TournamentLocalTest TournamentTest Trail TwoBody TwoBodyTest TwoVertexGraphCrossover UnitCell UnitCellNone UnitCellTest UpdateAndPropagatable UpdateAndPropagateList Utility UtilityTest VRMLUtility VecMathTest Vector3d Vector3dTest VectorIterator Vertex VertexAcceptsEdge VertexAcceptsInputEdge VertexAcceptsOutputEdge VertexAndEdgeProvider VertexAndTrailIterator VertexIterator VertexPairsDistanceSimilarity VertexTest Weight WeightList WeightListTest Weighted0to1 WeightedStatistics WeightedStatisticsTest WeightedSumFitness WeightedSumFitnessTest xyzFormat