JavaGenes, NASA Ames. Written largely by Al Globus
A B C D E F G H I K L M N O P Q R S T U V W X Y Z _

A

A_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
AbstractCheckpointable - class gov.nasa.javaGenes.core.AbstractCheckpointable.
Classes which wish to be Checkpointable can use this as a superclass which will do some standard implementations of the Checkpointable interface.
AbstractCheckpointable() - Constructor for class gov.nasa.javaGenes.core.AbstractCheckpointable
 
AcceptEqualOrBetter - class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetter.
 
AcceptEqualOrBetter() - Constructor for class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetter
 
AcceptEqualOrBetterTest - class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetterTest.
 
AcceptEqualOrBetterTest(String) - Constructor for class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetterTest
 
AcceptImprovement - class gov.nasa.javaGenes.hillClimbing.AcceptImprovement.
 
AcceptImprovement() - Constructor for class gov.nasa.javaGenes.hillClimbing.AcceptImprovement
 
AcceptImprovementTest - class gov.nasa.javaGenes.hillClimbing.AcceptImprovementTest.
 
AcceptImprovementTest(String) - Constructor for class gov.nasa.javaGenes.hillClimbing.AcceptImprovementTest
 
AcceptableSecondBrokenEdge - class gov.nasa.javaGenes.graph.AcceptableSecondBrokenEdge.
The execute() method will determine whether a BrokenEdge may be merged with the BrokenEdge argument to the constructor.
AcceptableSecondBrokenEdge(BrokenEdge, boolean) - Constructor for class gov.nasa.javaGenes.graph.AcceptableSecondBrokenEdge
 
AcceptableSecondVertex - class gov.nasa.javaGenes.graph.AcceptableSecondVertex.
Used to find a vertex to make an edge to.
AcceptableSecondVertex(Vertex) - Constructor for class gov.nasa.javaGenes.graph.AcceptableSecondVertex
 
Accepter - class gov.nasa.javaGenes.hillClimbing.Accepter.
 
Accepter() - Constructor for class gov.nasa.javaGenes.hillClimbing.Accepter
 
Accepter - class gov.nasa.javaGenes.simulatedAnnealing.Accepter.
 
Accepter(double, double, int) - Constructor for class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
Accepter(double, double, int, int) - Constructor for class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
AccepterTest - class gov.nasa.javaGenes.simulatedAnnealing.AccepterTest.
 
AccepterTest(String) - Constructor for class gov.nasa.javaGenes.simulatedAnnealing.AccepterTest
 
AccessWindow - class gov.nasa.javaGenes.EOSscheduling.AccessWindow.
 
AccessWindow() - Constructor for class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
AccessWindow(int, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
AccessWindow(int, int, Sensor) - Constructor for class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
AccessWindowTest - class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest.
 
AccessWindowTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
AccessWindowWeight - class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowWeight.
 
AccessWindowWeight() - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowWeight
 
AccessWindowWeight(TaskWeight, AccessWindow) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowWeight
assumes the associated sensor is cross track slewable.
AccessWindowsList - class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowsList.
 
AccessWindowsList() - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowsList
 
AddDirectedEdge - class gov.nasa.javaGenes.graph.AddDirectedEdge.
Mutation operator to add a DirectedEdge between two DirectedVertex in a DirectedGraph.
AddDirectedEdge(VertexAndEdgeProvider) - Constructor for class gov.nasa.javaGenes.graph.AddDirectedEdge
 
AddDirectedVertex - class gov.nasa.javaGenes.graph.AddDirectedVertex.
Mutation operator to add a DirectedVertex by a DirectedEdge to a random vertex in a DirectedGraph.
AddDirectedVertex(VertexAndEdgeProvider) - Constructor for class gov.nasa.javaGenes.graph.AddDirectedVertex
 
AddEdge - class gov.nasa.javaGenes.graph.AddEdge.
Mutation operator to add an Edge between two Vertex in a Graph.
AddEdge(VertexAndEdgeProvider) - Constructor for class gov.nasa.javaGenes.graph.AddEdge
 
AddVertex - class gov.nasa.javaGenes.graph.AddVertex.
Mutation operator to add a Vertex by an Edge to a random vertex in a Graph.
AddVertex(VertexAndEdgeProvider) - Constructor for class gov.nasa.javaGenes.graph.AddVertex
 
AllTests - class gov.nasa.alsUtility.AllTests.
 
AllTests() - Constructor for class gov.nasa.alsUtility.AllTests
 
Allele - class gov.nasa.javaGenes.forceFields.Allele.
Used to control a single double value in a chromosome.
Allele(DoubleInterval) - Constructor for class gov.nasa.javaGenes.forceFields.Allele
 
Allele(double, double) - Constructor for class gov.nasa.javaGenes.forceFields.Allele
 
Allele(String, DoubleInterval) - Constructor for class gov.nasa.javaGenes.forceFields.Allele
 
AlleleSetup - class gov.nasa.javaGenes.forceFields.AlleleSetup.
 
AlleleSetup() - Constructor for class gov.nasa.javaGenes.forceFields.AlleleSetup
 
AlleleTemplate - class gov.nasa.javaGenes.forceFields.AlleleTemplate.
a two-dimensional array of alleles.
AlleleTemplate(int[]) - Constructor for class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
AlleleTemplate(int) - Constructor for class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
AlleleTemplateTest - class gov.nasa.javaGenes.forceFields.AlleleTemplateTest.
 
AlleleTemplateTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.AlleleTemplateTest
 
AlleleTest - class gov.nasa.javaGenes.forceFields.AlleleTest.
 
AlleleTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.AlleleTest
 
AmericanWireGauge - class gov.nasa.alsUtility.AmericanWireGauge.
 
AmericanWireGauge() - Constructor for class gov.nasa.alsUtility.AmericanWireGauge
 
AmericanWireGaugeTest - class gov.nasa.alsUtility.AmericanWireGaugeTest.
 
AmericanWireGaugeTest(String) - Constructor for class gov.nasa.alsUtility.AmericanWireGaugeTest
 
And - class gov.nasa.alsUtility.And.
logical and
And(Predicate, Predicate) - Constructor for class gov.nasa.alsUtility.And
arguments are the predicates we want the logical and of
AntiTournament - class gov.nasa.javaGenes.core.AntiTournament.
assumes that the tournament size is usually quite a bit smaller than the index interval from which the indices are chosen
AntiTournament(int) - Constructor for class gov.nasa.javaGenes.core.AntiTournament
 
AntiTournamentLocal - class gov.nasa.javaGenes.core.AntiTournamentLocal.
 
AntiTournamentLocal(int, int) - Constructor for class gov.nasa.javaGenes.core.AntiTournamentLocal
 
AntiTournamentLocalTest - class gov.nasa.javaGenes.core.AntiTournamentLocalTest.
 
AntiTournamentLocalTest(String) - Constructor for class gov.nasa.javaGenes.core.AntiTournamentLocalTest
 
AntiTournamentTest - class gov.nasa.javaGenes.core.AntiTournamentTest.
 
AntiTournamentTest(String) - Constructor for class gov.nasa.javaGenes.core.AntiTournamentTest
 
Apsp(int[][]) - Static method in class gov.nasa.javaGenes.graph.apsp
apsp - Floyd Warshall algorithm for computing All-Pairs Shortest Paths.
AssumedParameters - class gov.nasa.javaGenes.forceFields.AssumedParameters.
 
AssumedParameters(String) - Constructor for class gov.nasa.javaGenes.forceFields.AssumedParameters
 
AssumedParametersTest - class gov.nasa.javaGenes.forceFields.AssumedParametersTest.
 
AssumedParametersTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.AssumedParametersTest
 
Atom - class gov.nasa.javaGenes.chemistry.Atom.
Represent a chemical atom.
Atom(int) - Constructor for class gov.nasa.javaGenes.chemistry.Atom
 
Atom(Element) - Constructor for class gov.nasa.javaGenes.chemistry.Atom
 
Atom(String) - Constructor for class gov.nasa.javaGenes.chemistry.Atom
 
Atom(Atom) - Constructor for class gov.nasa.javaGenes.chemistry.Atom
 
Atom.ExtendedTypeKey - class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey.
Represents the extended type of this atom for use as a hashtable key.
Atom.ExtendedTypeKey() - Constructor for class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
Atom.ExtendedTypeKey(Atom) - Constructor for class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
AtomTest - class gov.nasa.javaGenes.chemistry.AtomTest.
 
AtomTest(String) - Constructor for class gov.nasa.javaGenes.chemistry.AtomTest
 
AtomicSpecies - class gov.nasa.javaGenes.forceFields.AtomicSpecies.
For a multibody atomic potential, this class is used to indicate what atomic element a body has.
AtomicSpecies(Atom) - Constructor for class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
AtomicSpecies(Element) - Constructor for class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
AtomicSpecies(String) - Constructor for class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
AtomicSpecies(String, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
AtomicSpecies(String, double) - Constructor for class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
AvailabilityTimeline - class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline.
when using duty cycle constraints, all task durations must fill the window to schedule.
AvailabilityTimeline() - Constructor for class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
AvailabilityTimeline(Horizon, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
AvailabilityTimelineTest - class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest.
RESTRICTION: the dutyCylce constraint assumes that the task duration is equal to the access window -- i.e, there is no point in trying to move the task around in time.
AvailabilityTimelineTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
AvailableIndex - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
AvailableNode - class gov.nasa.javaGenes.EOSscheduling.AvailableNode.
 
AvailableNode() - Constructor for class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
AvailableNodeTest - class gov.nasa.javaGenes.EOSscheduling.AvailableNodeTest.
 
AvailableNodeTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.AvailableNodeTest
 
a - Variable in class gov.nasa.javaGenes.forceFields.AssumedParametersTest
 
a1_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
a2_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
a_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
accept(Fitness, Fitness) - Method in class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetter
 
accept(Fitness, Fitness) - Method in class gov.nasa.javaGenes.hillClimbing.AcceptImprovement
 
accept(Fitness, Fitness) - Method in class gov.nasa.javaGenes.hillClimbing.Accepter
 
accept(Fitness, Fitness) - Method in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
acceptPromotion(Individual, Population) - Method in class gov.nasa.javaGenes.core.HFC.BottomSubBreeder
 
acceptPromotion(Individual, Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
acceptRandomIndividualFitnessThreshold - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
accepter - Variable in class gov.nasa.javaGenes.hillClimbing.Breeder
 
acceptsOutput - Variable in class gov.nasa.javaGenes.graph.DirectedGraph.SecondVertex
 
accessWindow - Variable in class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowWeight
 
accessWindowWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
accessWindows - Variable in class gov.nasa.javaGenes.EOSscheduling.Task
 
accessWindowsArray - Variable in class gov.nasa.javaGenes.EOSscheduling.Task
 
accessWindowsList - Variable in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
accuracyOfLineSearch - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
add(Object) - Method in class gov.nasa.alsUtility.GrowOnlyArray
 
add(Object) - Method in class gov.nasa.alsUtility.KeyCounter
add to key's count
add(Object, int) - Method in class gov.nasa.alsUtility.KeyCounter
 
add(Object, BigInteger) - Method in class gov.nasa.alsUtility.KeyCounter
 
add(double[]) - Method in class gov.nasa.alsUtility.MinMaxes
 
add(float) - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
add(int) - Method in class gov.nasa.alsUtility.ReinitializableInt
 
add(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
add(Vector3d, Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
add(int) - Method in class gov.nasa.alsUtility.integer
 
add(Molecule) - Method in class gov.nasa.javaGenes.chemistry.Molecules
molecules will be keep in the order added.
add(int, FitnessFunction) - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
add(ChildMaker) - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
add a ChildMaker to the list
add(ChildMaker) - Method in class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
 
add(double, ChildMaker) - Method in class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
 
add(ChangingWeightsObject) - Method in class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
 
add(double, FitnessFunction) - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
add(FitnessFunction) - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
add(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessMultiObjective
 
add(ChangingWeightsObject) - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
add(double, FitnessFunction) - Method in class gov.nasa.javaGenes.core.Weighted0to1
 
add(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
add(MultiBodiesForOneEnergy, double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
add(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
add(MultiBody) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
add(SecondBody) - Method in class gov.nasa.javaGenes.forceFields.OneBody
 
add(Bodies[]) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
add a set of multi-bodies to create one test case
add(Bodies[][]) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
create multiple test cases (the first dimension of array bodies)
add(Vector) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
add a set of bodies to create one test case
add(ThirdBody) - Method in class gov.nasa.javaGenes.forceFields.SecondBody
 
add(String, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber.ChromosomeParametersData
 
add(BrokenEdge) - Method in class gov.nasa.javaGenes.graph.BrokenGraph
 
add(Edge) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
not implemented
add(Graph) - Method in class gov.nasa.javaGenes.graph.Graph
add actual (not copies) vertices and edges of g to this.
add(Edge) - Method in class gov.nasa.javaGenes.graph.Graph
 
add(Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
 
add(Edge) - Method in class gov.nasa.javaGenes.graph.Trail
add a new edge to the trail and update ends[1]
add(Edge) - Method in class gov.nasa.javaGenes.graph.Vertex
 
add(Vertex) - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
add v to the vertices to be provided
add(Edge) - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
add e to the edges to be provided
add(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
add(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
addAccessWindow(AccessWindow) - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
addAll(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
addArray(int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
addArray(int) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
addChildMakers(ChildMaker, Individual[]) - Method in class gov.nasa.javaGenes.core.Evolvable
 
addData(double[]) - Method in class gov.nasa.alsUtility.WeightedStatistics
 
addData(double[], double[]) - Method in class gov.nasa.alsUtility.WeightedStatistics
 
addDatum(double) - Method in class gov.nasa.alsUtility.RootMeanSquares
 
addDatum(double) - Method in class gov.nasa.alsUtility.Sample
add datum d to the sample
addDatum(double) - Method in class gov.nasa.alsUtility.WeightedStatistics
add datum d to the sample
addDatum(double, double) - Method in class gov.nasa.alsUtility.WeightedStatistics
 
addDouble(EvolvableDouble) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
addDoubleValue(double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
addEnergy(double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
addFFF(int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
addIndex(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
addIndexTest(String, int[], int[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.IndicesTest
 
addInputEdge(DirectedEdge) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
addKeyCounter(KeyCounter) - Method in class gov.nasa.alsUtility.KeyCounter
 
addMutator(ChildMaker, double) - Method in class gov.nasa.javaGenes.core.ChildMakerChain
mutator must take one parent only
addNoEvolution(String, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber.ChromosomeParametersData
 
addOutputEdge(DirectedEdge) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
addPlacer(Placer) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
addPointingRequirement(PointingRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
addPointingRequirement(AccessWindow, int, String[]) - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
addPostfix(String[], String) - Method in class gov.nasa.javaGenes.core.Reporter
 
addSatellite(Satellite) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
addSensor(Sensor) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
addSensor(Sensor) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
addSlewMotor(SlewMotor) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
addSpecialThreeBody(String, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
addTask(Task) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
addThreeBody(String, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
addThreeBody(String, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
addToArraySizes(int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
addToEnergies(double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
addToHigh(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
addToInitial(float) - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
addToInitial(int) - Method in class gov.nasa.alsUtility.ReinitializableInt
 
addToLow(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
addTwoBody(String, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
addTwoBody(String, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
addVector(Vector) - Method in class gov.nasa.alsUtility.ExtendedVector
addElement the elements in Vector v
afterCheckpoint() - Method in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
afterCheckpoint() - Method in class gov.nasa.javaGenes.core.Run
 
afterNextGeneration() - Method in class gov.nasa.javaGenes.core.Run
 
allTakeImages - Variable in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
alleleSetup - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.AssumedParametersTest
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossoverTest
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ChromosomePopulation
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutationTest
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ImmigrantTest
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.ImmigrantsTest
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
alleles - Variable in class gov.nasa.javaGenes.forceFields.Tersoff
 
alpha_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
althyp1 - Static variable in class gov.nasa.alsUtility.ComparativeStatistics
 
angle(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
angle - Variable in class gov.nasa.javaGenes.forceFields.ThirdBody
the angle between the lines joining the second and third bodies and the first body
angleInDegrees - Variable in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
 
angleInterval - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
antiTournamentGetIndex(Population) - Method in class gov.nasa.javaGenes.core.Breeder
returns index of tournament loser
anyUnAvailableNodeTooLong(AvailableNode, int, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
append(Vector) - Method in class gov.nasa.alsUtility.ExtendedVector
 
appendToFile(Molecule, String) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
 
apsp - class gov.nasa.javaGenes.graph.apsp.
All-pairs-shortest-path algorithm and supporting functions for graphs.
apsp() - Constructor for class gov.nasa.javaGenes.graph.apsp
 
areAccessWindowsInEarliestFirstOrder() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
areDifferent(int[]) - Static method in class gov.nasa.alsUtility.Utility
 
areDifferent(int[], int) - Static method in class gov.nasa.alsUtility.Utility
 
areDifferent(Object[]) - Static method in class gov.nasa.alsUtility.Utility
 
areDifferent(Object[], boolean) - Static method in class gov.nasa.alsUtility.Utility
 
areIndividualsInFitnessRange(Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
areValidIndices(int[]) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
areYouPreparingToDie() - Static method in class gov.nasa.javaGenes.core.Checkpointer
Called by an external agency.
areYouPreparingToDieLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
areYouReadyToDie() - Static method in class gov.nasa.javaGenes.core.Checkpointer
Called by an external agency.
areYouReadyToDieLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
array - Variable in class gov.nasa.alsUtility.GrowOnlyArray
 
arrayCreated() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
arraySum(int[]) - Static method in class gov.nasa.alsUtility.Utility
 
arrayToTabSeparated(String[]) - Static method in class gov.nasa.alsUtility.Utility
 
arrayToTabSeparated(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
asDouble() - Method in class gov.nasa.javaGenes.core.Fitness
 
asDouble() - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
asDouble() - Method in class gov.nasa.javaGenes.core.StudentFitness
 
assertCorrect() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskList
does nothing.
assertEqual(int, int) - Static method in class gov.nasa.alsUtility.Error
 
assertFalse(boolean) - Static method in class gov.nasa.alsUtility.Error
 
assertFalse(boolean, String) - Static method in class gov.nasa.alsUtility.Error
 
assertFalse(String, boolean) - Static method in class gov.nasa.alsUtility.Error
 
assertIndividualsInFitnessRange(Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
assertIsValid() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
assertIsValid() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
assertIsValid() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
assertIsValid() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
assertIsValid() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
assertLegal() - Method in class gov.nasa.alsUtility.IntegerInterval
 
assertNearlyEqual(double, double) - Static method in class gov.nasa.alsUtility.Error
uses a slightly larger epsilon that Utility.nearlyEqual so EOSscheduling.HBSS.contention tests smoother
assertNearlyEqual(double, double, double) - Static method in class gov.nasa.alsUtility.Error
 
assertNotNull(Object) - Static method in class gov.nasa.alsUtility.Error
 
assertOk() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
assertStatusValid(Population) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
fail is anything wrong.
assertTrue(boolean) - Static method in class gov.nasa.alsUtility.Error
 
assertTrue(boolean, String) - Static method in class gov.nasa.alsUtility.Error
 
assertTrue(String, boolean) - Static method in class gov.nasa.alsUtility.Error
 
assertTrue(boolean) - Static method in class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
assignmentString - Static variable in class gov.nasa.alsUtility.PropertiesList
 
assignmentString() - Static method in class gov.nasa.alsUtility.PropertiesList
 
assumed - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
atEnd() - Method in class gov.nasa.javaGenes.core.Run
 
atom - Static variable in class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
atomicNumber - Variable in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
availableTimeline - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
averageFitness() - Method in class gov.nasa.javaGenes.core.Population
 
azimuth - Variable in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 

B

BAD_FITNESS - Static variable in class gov.nasa.javaGenes.core.Fitness
 
BAD_VALUE - Variable in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
BCCLatticConstant - Static variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
B_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
BarnesHutTheta - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
Benzene - class gov.nasa.javaGenes.chemistry.Benzene.
A benzene molecule.
Benzene() - Constructor for class gov.nasa.javaGenes.chemistry.Benzene
 
BetaI(double, double, double) - Static method in class gov.nasa.alsUtility.ComparativeStatistics
 
Betacf(double, double, double) - Static method in class gov.nasa.alsUtility.ComparativeStatistics
 
Bodies - class gov.nasa.javaGenes.forceFields.Bodies.
Holds a set of bodies for a multibody potential to find the energy of
Bodies() - Constructor for class gov.nasa.javaGenes.forceFields.Bodies
 
Bodies(Molecule) - Constructor for class gov.nasa.javaGenes.forceFields.Bodies
 
BodiesTest - class gov.nasa.javaGenes.forceFields.BodiesTest.
 
BodiesTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.BodiesTest
 
Body - class gov.nasa.javaGenes.forceFields.Body.
This is used as a superclass by OneBody, TwoBody, and ThreeBody
Body(Species) - Constructor for class gov.nasa.javaGenes.forceFields.Body
 
Bond - class gov.nasa.javaGenes.chemistry.Bond.
Represent a chemical bond.
Bond() - Constructor for class gov.nasa.javaGenes.chemistry.Bond
create a single bond
Bond(int) - Constructor for class gov.nasa.javaGenes.chemistry.Bond
create a bond.
Bond(Atom, Atom, int) - Constructor for class gov.nasa.javaGenes.chemistry.Bond
Create a bond between the two atoms.
BottomSubBreeder - class gov.nasa.javaGenes.core.HFC.BottomSubBreeder.
 
BottomSubBreeder(ChildMakerProvider, FitnessFunction) - Constructor for class gov.nasa.javaGenes.core.HFC.BottomSubBreeder
 
BottomSubBreeder(ChildMakerProvider, FitnessFunction, boolean) - Constructor for class gov.nasa.javaGenes.core.HFC.BottomSubBreeder
 
Breeder - class gov.nasa.javaGenes.EOSscheduling.HBSS.Breeder.
 
Breeder(Parameters) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.Breeder
 
Breeder(Parameters, Accepter, RestartPolicy) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.Breeder
 
Breeder - class gov.nasa.javaGenes.core.Breeder.
Used to breed a population.
Breeder(Parameters) - Constructor for class gov.nasa.javaGenes.core.Breeder
The argument contains many parameters including those necessary for breeding
Breeder - class gov.nasa.javaGenes.core.HFC.Breeder.
 
Breeder(Parameters, RandomEvolvableProducer) - Constructor for class gov.nasa.javaGenes.core.HFC.Breeder
 
Breeder - class gov.nasa.javaGenes.hillClimbing.Breeder.
Population size must be 2.
Breeder(Parameters, Accepter, RestartPolicy, ChildMaker) - Constructor for class gov.nasa.javaGenes.hillClimbing.Breeder
 
Breeder - class gov.nasa.javaGenes.simulatedAnnealing.Breeder.
implements simulated annealing.
Breeder(Parameters, Accepter) - Constructor for class gov.nasa.javaGenes.simulatedAnnealing.Breeder
 
BreederElitist - class gov.nasa.javaGenes.core.BreederElitist.
Implement elitist breeding.
BreederElitist(Parameters, int) - Constructor for class gov.nasa.javaGenes.core.BreederElitist
 
BreederSteadyState - class gov.nasa.javaGenes.core.BreederSteadyState.
implements steady state breeding
BreederSteadyState(Parameters) - Constructor for class gov.nasa.javaGenes.core.BreederSteadyState
 
BreederSteadyState2 - class gov.nasa.javaGenes.core.BreederSteadyState2.
 
BreederSteadyState2(Parameters) - Constructor for class gov.nasa.javaGenes.core.BreederSteadyState2
 
BreederSteadyState2(Parameters, ChooseParents, ChooseForDeath) - Constructor for class gov.nasa.javaGenes.core.BreederSteadyState2
 
BreederWithTeachers - class gov.nasa.javaGenes.core.BreederWithTeachers.
 
BreederWithTeachers(Parameters, int, int, ChildMakerProvider) - Constructor for class gov.nasa.javaGenes.core.BreederWithTeachers
 
Brick3d - class gov.nasa.alsUtility.Brick3d.
 
Brick3d(Brick3d) - Constructor for class gov.nasa.alsUtility.Brick3d
 
Brick3d(Vector3d, Vector3d) - Constructor for class gov.nasa.alsUtility.Brick3d
 
Brick3d(double, double, double, double, double, double) - Constructor for class gov.nasa.alsUtility.Brick3d
 
Brick3d(DoubleInterval, DoubleInterval, DoubleInterval) - Constructor for class gov.nasa.alsUtility.Brick3d
 
Brick3dTest - class gov.nasa.alsUtility.Brick3dTest.
 
Brick3dTest(String) - Constructor for class gov.nasa.alsUtility.Brick3dTest
 
Brick3dWithSegments - class gov.nasa.alsUtility.Brick3dWithSegments.
 
Brick3dWithSegments(Brick3d, int[]) - Constructor for class gov.nasa.alsUtility.Brick3dWithSegments
NOTE: the segments are created here and never updated, even if you change the brick
Brick3dWithSegmentsTest - class gov.nasa.alsUtility.Brick3dWithSegmentsTest.
 
Brick3dWithSegmentsTest(String) - Constructor for class gov.nasa.alsUtility.Brick3dWithSegmentsTest
 
BrokenEdge - class gov.nasa.javaGenes.graph.BrokenEdge.
When an edge is cut during crossover, this class is used to remember the cut edge and the vertex it is associated with.
BrokenEdge() - Constructor for class gov.nasa.javaGenes.graph.BrokenEdge
 
BrokenEdge(Edge, Vertex) - Constructor for class gov.nasa.javaGenes.graph.BrokenEdge
 
BrokenGraph - class gov.nasa.javaGenes.graph.BrokenGraph.
Two of these classes are used to represent the sub-graphs produced when ripping a graph in half during crossover.
BrokenGraph(Class) - Constructor for class gov.nasa.javaGenes.graph.BrokenGraph
 
backLargerThanForward - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
backSameAsForward - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
backSmallerThanForward - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
badMoves - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
basicSetup() - Static method in class gov.nasa.alsUtility.VRMLUtility
 
beforeCheckpoint() - Method in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
beforeCheckpoint() - Method in class gov.nasa.javaGenes.core.Run
 
beforeNextGeneration() - Method in class gov.nasa.javaGenes.core.Run
 
beginScheduling() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
beginScheduling(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
best(ChildMaker, ChildMaker) - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider
 
bestDouble() - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
bestDouble() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
bestEvolvablesFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
bestFitness() - Method in class gov.nasa.javaGenes.core.Population
 
bestFitnessAllowed - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
bestIndividual() - Method in class gov.nasa.javaGenes.core.Population
 
bestIndividualIndex(Individual[]) - Static method in class gov.nasa.javaGenes.core.Individual
 
bestIndividualIndex() - Method in class gov.nasa.javaGenes.core.Population
 
beta_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
between - Variable in class gov.nasa.alsUtility.LogComparisons
 
bodies - Variable in class gov.nasa.javaGenes.forceFields.PotentialEnergyTestCase
 
bondCounts - Variable in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
bondLengthFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
bondLengthInterval - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
bondValenceSum() - Method in class gov.nasa.javaGenes.chemistry.Atom
What portion of the valence is used by existing bonds?
border - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
bottom - Variable in class gov.nasa.alsUtility.DoubleInterval
the lowest value in the interval
bottom - Variable in class gov.nasa.alsUtility.IntegerInterval
 
breed(Population) - Method in class gov.nasa.javaGenes.core.Breeder
execute the breeding.
breed(Population, int) - Method in class gov.nasa.javaGenes.core.Breeder
 
breed(Population, int) - Method in class gov.nasa.javaGenes.core.BreederElitist
 
breed(Population) - Method in class gov.nasa.javaGenes.core.BreederElitist
 
breed(Population, int) - Method in class gov.nasa.javaGenes.core.BreederSteadyState
 
breed(Population, int) - Method in class gov.nasa.javaGenes.core.BreederSteadyState2
 
breed(Population, int) - Method in class gov.nasa.javaGenes.core.BreederWithTeachers
 
breed(Population, int) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
breed(Population, int) - Method in class gov.nasa.javaGenes.hillClimbing.Breeder
 
breedOnce(Population) - Method in class gov.nasa.javaGenes.core.BreederSteadyState2
 
breedOnce(Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
breeder - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
breeder - Variable in class gov.nasa.javaGenes.core.Parameters
 
breederReportFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
buffer - Variable in class gov.nasa.alsUtility.CircularIntQueue
 
buffer(Object) - Method in class gov.nasa.alsUtility.Saver
add object to the buffer for later saving

C

CANNOT_DO_ANALYSIS - Static variable in class gov.nasa.alsUtility.ComparativeStatistics
 
CTabToAdjM(int[][], int) - Static method in class gov.nasa.javaGenes.graph.apsp
CTabToAdjM - Converts a connection table (CT) into an adjcency matrix.
C_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
CandidatePopulation - class gov.nasa.javaGenes.core.CandidatePopulation.
 
CandidatePopulation() - Constructor for class gov.nasa.javaGenes.core.CandidatePopulation
 
CandidateReporter - class gov.nasa.javaGenes.core.CandidateReporter.
 
CandidateReporter() - Constructor for class gov.nasa.javaGenes.core.CandidateReporter
 
ChangeFunctionByGeneration - class gov.nasa.javaGenes.core.ChangeFunctionByGeneration.
 
ChangeFunctionByGeneration() - Constructor for class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
ChangeFunctionByGenerationTest - class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest.
 
ChangeFunctionByGenerationTest(String) - Constructor for class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest
 
ChangingWeightsObject - class gov.nasa.javaGenes.core.ChangingWeightsObject.
returns weights for an object.
ChangingWeightsObject(Object) - Constructor for class gov.nasa.javaGenes.core.ChangingWeightsObject
 
ChangingWeightsObject(Object, double, double) - Constructor for class gov.nasa.javaGenes.core.ChangingWeightsObject
 
ChangingWeightsObject(Object, double, double, double) - Constructor for class gov.nasa.javaGenes.core.ChangingWeightsObject
 
ChangingWeightsObjectTest - class gov.nasa.javaGenes.core.ChangingWeightsObjectTest.
 
ChangingWeightsObjectTest(String) - Constructor for class gov.nasa.javaGenes.core.ChangingWeightsObjectTest
 
Checkpointer - class gov.nasa.javaGenes.core.Checkpointer.
Runs a Checkpointable job.
ChildMaker - class gov.nasa.javaGenes.EOSscheduling.HBSS.ChildMaker.
NOTE: it doesn't really matter what childmaker is used because the HBSS algorithm will rearrange the permutation to reflect the order tasks were chosen by the TaskList (a RouletteWheel of one sort or another
ChildMaker() - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.ChildMaker
 
ChildMaker - class gov.nasa.javaGenes.core.ChildMaker.
This is the superclass for all transmission operators.
ChildMaker() - Constructor for class gov.nasa.javaGenes.core.ChildMaker
 
ChildMaker - class gov.nasa.javaGenes.evolvableDoubleList.ChildMaker.
 
ChildMaker() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMaker
 
ChildMaker(Selector) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMaker
 
ChildMakerChain - class gov.nasa.javaGenes.core.ChildMakerChain.
probabalistically mutates the children of a ChildMaker.
ChildMakerChain(ChildMaker) - Constructor for class gov.nasa.javaGenes.core.ChildMakerChain
 
ChildMakerChain.ChainElement - class gov.nasa.javaGenes.core.ChildMakerChain.ChainElement.
 
ChildMakerChain.ChainElement(ChildMaker, double) - Constructor for class gov.nasa.javaGenes.core.ChildMakerChain.ChainElement
 
ChildMakerDownFractionComparatorTest - class gov.nasa.javaGenes.core.ChildMakerDownFractionComparatorTest.
 
ChildMakerDownFractionComparatorTest(String) - Constructor for class gov.nasa.javaGenes.core.ChildMakerDownFractionComparatorTest
 
ChildMakerEvolvingProvider - class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider.
 
ChildMakerEvolvingProvider() - Constructor for class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider
 
ChildMakerEvolvingProvider2 - class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2.
starts with a set of random ChildMakers.
ChildMakerEvolvingProvider2(int, int, int, double, ChildMakerRandomCreator) - Constructor for class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
ChildMakerEvolvingProvider2Test - class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2Test.
 
ChildMakerEvolvingProvider2Test(String) - Constructor for class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2Test
 
ChildMakerEvolvingProviderTest - class gov.nasa.javaGenes.core.ChildMakerEvolvingProviderTest.
 
ChildMakerEvolvingProviderTest(String) - Constructor for class gov.nasa.javaGenes.core.ChildMakerEvolvingProviderTest
 
ChildMakerProvider - class gov.nasa.javaGenes.core.ChildMakerProvider.
This class keeps a list of ChildMaker.
ChildMakerProvider() - Constructor for class gov.nasa.javaGenes.core.ChildMakerProvider
 
ChildMakerProviderRandom - class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom.
 
ChildMakerProviderRandom() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
ChildMakerProviderRandom(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
for fixed length representations with no modulo/offset
ChildMakerProviderRandom(int, int, int, boolean, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
for fixed length representations
ChildMakerProviderRandom(int, int, int, boolean, boolean, int[], int[], int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
ChildMakerProviderRandomMutations - class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations.
for fixed length representations
ChildMakerProviderRandomMutations(int, int, double, double) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations
 
ChildMakerProviderTest - class gov.nasa.javaGenes.core.ChildMakerProviderTest.
 
ChildMakerProviderTest(String) - Constructor for class gov.nasa.javaGenes.core.ChildMakerProviderTest
 
ChildMakerProviderWeighted - class gov.nasa.javaGenes.core.ChildMakerProviderWeighted.
 
ChildMakerProviderWeighted() - Constructor for class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
 
ChildMakerRandomCreator - interface gov.nasa.javaGenes.core.ChildMakerRandomCreator.
 
ChildMakerTest - class gov.nasa.javaGenes.core.ChildMakerTest.
 
ChildMakerTest(String) - Constructor for class gov.nasa.javaGenes.core.ChildMakerTest
 
ChooseForDeath - interface gov.nasa.javaGenes.core.ChooseForDeath.
 
ChooseParents - interface gov.nasa.javaGenes.core.ChooseParents.
 
Chromosome - class gov.nasa.javaGenes.forceFields.Chromosome.
Implement the representation of a two-dimensional array of double.
Chromosome(AlleleTemplate) - Constructor for class gov.nasa.javaGenes.forceFields.Chromosome
Sets the array sizes to that of alleles.
Chromosome(Chromosome) - Constructor for class gov.nasa.javaGenes.forceFields.Chromosome
Creates a raise with the same structure as c, but does not copy the values
Chromosome(TokenizeInput) - Constructor for class gov.nasa.javaGenes.forceFields.Chromosome
Creates a new chromosome from within a checkpoint file
ChromosomeArrayCrossover - class gov.nasa.javaGenes.forceFields.ChromosomeArrayCrossover.
 
ChromosomeArrayCrossover() - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeArrayCrossover
 
ChromosomeCrossover - class gov.nasa.javaGenes.forceFields.ChromosomeCrossover.
Implements a uniform crossover operator where the value of each double in the child has an equal probability of coming from the father or the mother
ChromosomeCrossover() - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeCrossover
 
ChromosomeDistanceFitness - class gov.nasa.javaGenes.forceFields.ChromosomeDistanceFitness.
fitness is the distance from a target chromosome.
ChromosomeDistanceFitness(Chromosome) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeDistanceFitness
 
ChromosomeIndividual - class gov.nasa.javaGenes.forceFields.ChromosomeIndividual.
 
ChromosomeIndividual(Evolvable, FitnessFunction) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeIndividual
Sets the evolvable to e and calculates the fitness using FitnessFunction f.
ChromosomeIndividual(TokenizeInput) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeIndividual
restore from a checkpoint
ChromosomeIntervalCrossover - class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover.
Implements a form of crossover were each allele in the child is a function of a random number and values in the mother and father.
ChromosomeIntervalCrossover(AlleleTemplate) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
ChromosomeIntervalCrossoverTest - class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossoverTest.
 
ChromosomeIntervalCrossoverTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossoverTest
 
ChromosomeMutation - class gov.nasa.javaGenes.forceFields.ChromosomeMutation.
Mutates some fraction of the alleles with a random number chosen from a Gaussian distribution
ChromosomeMutation() - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
ChromosomeMutation(AlleleTemplate) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
ChromosomeMutation(AlleleTemplate, double) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
ChromosomeMutation(AlleleTemplate, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
ChromosomeMutationTest - class gov.nasa.javaGenes.forceFields.ChromosomeMutationTest.
 
ChromosomeMutationTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeMutationTest
 
ChromosomeParameterValues - class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues.
 
ChromosomeParameterValues(String) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
ChromosomeParameterValues(FieldRecordText) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
ChromosomeParameters - class gov.nasa.javaGenes.forceFields.ChromosomeParameters.
 
ChromosomeParameters() - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeParameters
Sets up all parameters
ChromosomePopulation - class gov.nasa.javaGenes.forceFields.ChromosomePopulation.
 
ChromosomePopulation(ChromosomeParameters) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomePopulation
Generate a random population
ChromosomePopulation(int, AlleleTemplate, FitnessFunction) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomePopulation
 
ChromosomePopulation(TokenizeInput) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomePopulation
checkpoint
ChromosomePopulation(int) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomePopulation
create an empty population with int size members
ChromosomeReporter - class gov.nasa.javaGenes.forceFields.ChromosomeReporter.
 
ChromosomeReporter(Parameters) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeReporter
 
ChromosomeReporter(Parameters, TokenizeInput) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeReporter
 
ChromosomeXoverWithMutation - class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation.
 
ChromosomeXoverWithMutation(AlleleTemplate, double, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation
 
ChromosomeXoverWithMutationTest - class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutationTest.
 
ChromosomeXoverWithMutationTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutationTest
 
CircularIntQueue - class gov.nasa.alsUtility.CircularIntQueue.
 
CircularIntQueue(int) - Constructor for class gov.nasa.alsUtility.CircularIntQueue
 
ComparativeStatistics - class gov.nasa.alsUtility.ComparativeStatistics.
Implements comparative statistics measures on Sample objects.
ComparativeStatistics() - Constructor for class gov.nasa.alsUtility.ComparativeStatistics
 
ComparativeStatisticsTest - class gov.nasa.alsUtility.ComparativeStatisticsTest.
 
ComparativeStatisticsTest(String) - Constructor for class gov.nasa.alsUtility.ComparativeStatisticsTest
 
Compatible - interface gov.nasa.alsUtility.Compatible.
for objects to decide if they are compatible with each other.
Constants - class gov.nasa.alsUtility.Constants.
 
Constants() - Constructor for class gov.nasa.alsUtility.Constants
 
Constants - class gov.nasa.javaGenes.chemistry.Constants.
 
Constants() - Constructor for class gov.nasa.javaGenes.chemistry.Constants
 
CoreUtility - class gov.nasa.javaGenes.core.utility.CoreUtility.
 
CoreUtility() - Constructor for class gov.nasa.javaGenes.core.utility.CoreUtility
 
CoreUtilityTest - class gov.nasa.javaGenes.core.utility.CoreUtilityTest.
 
CoreUtilityTest(String) - Constructor for class gov.nasa.javaGenes.core.utility.CoreUtilityTest
 
CrossTrackSlew - class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew.
 
CrossTrackSlew(double) - Constructor for class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
 
CrossTrackSlew(PointingRequirement) - Constructor for class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
 
CrossTrackSlewTest - class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlewTest.
 
CrossTrackSlewTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlewTest
 
Crossover - class gov.nasa.javaGenes.evolvableDoubleList.Crossover.
contains useful stuff for one and two point crossover classes
Crossover(NeighboringPairsSelector) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
CrossoverAdewaya - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya.
Implementation of Adewaya's MIT Master's Thesis "New Methods in Genetic Search with Real-Valued Chromosomes" 1996.
CrossoverAdewaya() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
CrossoverAdewaya(Selector) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
CrossoverAdewaya(Selector, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
CrossoverAdewayaTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest.
 
CrossoverAdewayaTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest
 
CrossoverInterval - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval.
 
CrossoverInterval(Selector, double) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval
 
CrossoverIntervalTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverIntervalTest.
 
CrossoverIntervalTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverIntervalTest
 
CrossoverOnePoint - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint.
 
CrossoverOnePoint() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint
 
CrossoverOnePoint(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint
 
CrossoverOnePoint(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint
 
CrossoverOnePoint(SelectOneNeighboringPair) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint
 
CrossoverOnePointEach - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach.
 
CrossoverOnePointEach() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
CrossoverOnePointEach(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
CrossoverOnePointEach(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
CrossoverOnePointEach(SelectOneNeighboringPair) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
CrossoverOnePointEachTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEachTest.
 
CrossoverOnePointEachTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEachTest
 
CrossoverOnePointTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointTest.
 
CrossoverOnePointTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointTest
 
CrossoverPickOne - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne.
 
CrossoverPickOne() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne
 
CrossoverPickOne(Selector) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne
 
CrossoverPickOneTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOneTest.
 
CrossoverPickOneTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOneTest
 
CrossoverTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTest.
 
CrossoverTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTest
 
CrossoverTwoPoints - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints.
 
CrossoverTwoPoints() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
 
CrossoverTwoPoints(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
 
CrossoverTwoPoints(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
 
CrossoverTwoPoints(SelectTwoNeighboringPairs) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
 
CrossoverTwoPointsEach - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach.
 
CrossoverTwoPointsEach() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
CrossoverTwoPointsEach(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
CrossoverTwoPointsEach(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
CrossoverTwoPointsEach(SelectTwoNeighboringPairs) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
CrossoverTwoPointsEachTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEachTest.
 
CrossoverTwoPointsEachTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEachTest
 
CrossoverTwoPointsTest - class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsTest.
 
CrossoverTwoPointsTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsTest
 
CyclesSimilarity - class gov.nasa.javaGenes.graph.CyclesSimilarity.
fitness function that compares the number of cycles in an individual with the number of cycles in a target using the Tanimoto coefficient.
CyclesSimilarity(Graph) - Constructor for class gov.nasa.javaGenes.graph.CyclesSimilarity
 
calculate() - Method in class gov.nasa.alsUtility.Sample
calculate (if necessary) and cache all statistics
calculate(double, double) - Static method in class gov.nasa.alsUtility.Tanimoto
 
calculateCrossTrackSlew(PointingRequirement) - Static method in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
When the azimuth is far from normal to the satellite track this gives somewhat inaccurate.
calculateDelta(double, double) - Method in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
calculateDelta(double, double) - Method in class gov.nasa.javaGenes.forceFields.MMEFreferenceTanimoto
 
calculateDistance(double, double) - Method in class gov.nasa.javaGenes.forceFields.ForceFitnessTanimoto
 
calculateDistance(double, double) - Method in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
calculateDistance(double, double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
calculateDistance(double, double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessRatio
 
calculateDistance(double, double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessTanimotoDistance
 
calculateDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
calculateEnergy(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
calculateEnergy(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
calculateForce(double, double, double, double, double, double, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
calculateOutputMeasures(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
calculateOutputMeasures(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
calculateOutputMeasures(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
calculateTranslations(Vector3d, Vector3d, double, double, int) - Static method in class gov.nasa.alsUtility.Vector3d
 
calculateTwoBodyEnergy(double, double, double, double, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
calculateWeight(double) - Method in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
callsAtThisTemperature - Variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
callsPerStaticTemperature - Variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
callsPerTermperatureChange - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
canAcceptEdge() - Method in class gov.nasa.javaGenes.chemistry.Atom
Will adding another bond exceed valence?
canAcceptEdge(Edge) - Method in class gov.nasa.javaGenes.chemistry.Atom
Will attaching to this bond exceed valence?
canAcceptEdge() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
canAcceptEdge(Edge) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
if an error to call this
canAcceptEdge() - Method in class gov.nasa.javaGenes.graph.Vertex
 
canAcceptEdge(Edge) - Method in class gov.nasa.javaGenes.graph.Vertex
 
canAcceptEdgesOf(Vertex) - Method in class gov.nasa.javaGenes.chemistry.Atom
can all of the edges of v be connected to this?
canAcceptEdgesOf(Vertex) - Method in class gov.nasa.javaGenes.graph.Vertex
 
canAcceptInputEdge() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
canAcceptOutputEdge() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
canAcceptVerticesOf(Edge) - Method in class gov.nasa.javaGenes.chemistry.Bond
can the atoms of the argument be connected by this bond (e)?
canAcceptVerticesOf(Edge) - Method in class gov.nasa.javaGenes.graph.Edge
 
canMate(Graph) - Method in class gov.nasa.javaGenes.graph.Graph
can I perform crossover with graph?
canModel(MultiBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
cancelDeath() - Static method in class gov.nasa.javaGenes.core.Checkpointer
Called by an external agency.
cancelDeathLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
cell - Variable in class gov.nasa.javaGenes.chemistry.UnitCell
 
center - Variable in class gov.nasa.alsUtility.RandomGaussianDistribution
center of the Gaussian distribution
chain - Variable in class gov.nasa.javaGenes.core.ChildMakerChain
 
changed() - Method in class gov.nasa.javaGenes.graph.Graph
Must be called when the graph changes.
check(Predicate) - Method in class gov.nasa.alsUtility.ExtendedVector
 
check(Predicate, int) - Method in class gov.nasa.alsUtility.ExtendedVector
 
check() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
checkEndNode(AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
checkLastResults(int, int, int, int) - Method in class gov.nasa.javaGenes.core.ChildMaker
 
checkOnTimes(int[]) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
checkResults(int, int, int, int) - Method in class gov.nasa.alsUtility.LogComparisons
for testing only
checkResults(int, int, int, int) - Method in class gov.nasa.javaGenes.core.ChildMaker
for testing only
checkpoint() - Static method in class gov.nasa.javaGenes.core.Checkpointer
called by a Checkpointable.
checkpoint(String) - Static method in class gov.nasa.javaGenes.core.Checkpointer
called by a Checkpointable.
checkpoint() - Method in class gov.nasa.javaGenes.core.Run
 
checkpointASAP - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
checkpointLocal(String) - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
checkpointLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
checkpointTimer - Variable in class gov.nasa.javaGenes.core.Run
 
checkpointTimesFile - Variable in class gov.nasa.javaGenes.core.Run
 
checkpointWhenPossible() - Static method in class gov.nasa.javaGenes.core.Checkpointer
Called by an external agency.
checkpointWhenPossibleLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
checkpointer - Variable in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
checkpointer - Variable in class gov.nasa.javaGenes.core.PeriodicCheckpoints
 
childMakerCreator - Variable in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
childMakerFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
childMakerProvider - Variable in class gov.nasa.javaGenes.core.Breeder
 
childMakerProvider - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
childMakerProvider - Variable in class gov.nasa.javaGenes.core.Parameters
 
childMakerReport(int, String, boolean) - Method in class gov.nasa.javaGenes.core.Reporter
 
childMakerSoFarFilenameBase - Static variable in class gov.nasa.javaGenes.core.Reporter
 
childMakers - Variable in class gov.nasa.javaGenes.core.ChildMakerProvider
 
childMakersForBestEvolvableFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
childMakersUsed - Variable in class gov.nasa.javaGenes.core.Evolvable
 
children - Variable in class gov.nasa.javaGenes.core.BreederElitist
 
chooseBest(Individual, Individual) - Method in class gov.nasa.javaGenes.core.Breeder
 
chooseWorst(Individual, Individual) - Method in class gov.nasa.javaGenes.core.Breeder
 
chromosome - Variable in class gov.nasa.javaGenes.forceFields.Chromosome
 
chromosome - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
chromosome - Variable in class gov.nasa.javaGenes.forceFields.Tersoff
 
clear() - Method in class gov.nasa.alsUtility.LogComparisons
 
clearLast() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
cliff - Variable in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
clone() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
deep copy the permutation, but set up as if never scheduled
clone() - Method in class gov.nasa.javaGenes.forceFields.Chromosome
deep copy
clone() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
copy the MultiBodiesForOneEnergy and make copies molecule and the multiBodies
clone() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
 
clone() - Method in class gov.nasa.javaGenes.graph.BrokenGraph
make a copy of the brokenEdges vector, make new BrokenEdges, ?old but don't make copies of the edges themselves?.
clone() - Method in class gov.nasa.javaGenes.graph.DirectedGraph
copy the graph and make copies of all edges and vertices
clone() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
restore from checkpoint file
clone() - Method in class gov.nasa.javaGenes.graph.Edge
 
clone() - Method in class gov.nasa.javaGenes.graph.Graph
copy the graph and make copies of all edges and vertices
clone() - Method in class gov.nasa.javaGenes.graph.Trail
keeps original edges and vertices
clone() - Method in class gov.nasa.javaGenes.graph.Vertex
don't make copies of the edges
clone() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
deep copy
close() - Method in class gov.nasa.alsUtility.EasyFile
 
close() - Method in class gov.nasa.alsUtility.FieldRecordText
 
close() - Method in class gov.nasa.alsUtility.LogFile
 
close() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
close() - Method in class gov.nasa.javaGenes.core.TokenizeOutput
 
closestLineSegmentPoints(Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.MathUtility
 
commonVertex(Edge) - Method in class gov.nasa.javaGenes.graph.Edge
 
comparator - Variable in class gov.nasa.javaGenes.core.RouletteWheel
 
compare(Object, Object) - Method in class gov.nasa.javaGenes.core.DescendingWeightsComparator
 
compareTechniquesMain - class gov.nasa.javaGenes.main.compareTechniquesMain.
 
compareTechniquesMain() - Constructor for class gov.nasa.javaGenes.main.compareTechniquesMain
 
concatenate(String[], String[]) - Static method in class gov.nasa.alsUtility.Utility
 
conflevel1 - Static variable in class gov.nasa.alsUtility.ComparativeStatistics
 
considerOnlyHigherFitness - Variable in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
containsBadNumbers(double[]) - Static method in class gov.nasa.alsUtility.Utility
does d contain any numbers that aren't normal?
containsData() - Method in class gov.nasa.alsUtility.EasyFile
 
containsData() - Method in class gov.nasa.alsUtility.LogFile
 
convertAllGroundStationAccessWindowsToSSRdump() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
convertBack(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
copy() - Method in class gov.nasa.alsUtility.ExtendedVector
 
copy() - Method in class gov.nasa.alsUtility.IntegerInterval
 
copy(double[][][]) - Static method in class gov.nasa.alsUtility.Utility
 
copy(double[][]) - Static method in class gov.nasa.alsUtility.Utility
 
copy(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
copy(int[]) - Static method in class gov.nasa.alsUtility.Utility
 
copy(String[]) - Static method in class gov.nasa.alsUtility.Utility
 
copy(boolean[]) - Static method in class gov.nasa.alsUtility.Utility
 
copy() - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
copy() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
copy() - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
copy() - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
copy() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
copy() - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
copyForEvolution() - Method in class gov.nasa.javaGenes.core.Evolvable
should be implemented by all subclasses, but isn't for all of the older code.
copyForEvolution() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
copyForEvolution(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
copyForEvolutionTest(String, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
copyIndex(PermutationEvolvable, int, PermutationEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.PositionCrossover
 
copyIndex(PermutationEvolvable, int, PermutationEvolvable, int) - Method in class gov.nasa.javaGenes.permutation.PermutationChildMaker
 
couldBeScheduledWith(AccessWindow) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
test for sensor, slewing and time compatibility.
count - Variable in class gov.nasa.alsUtility.RootMeanSquares
 
count - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
count - Variable in class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildren
 
countOfNonNormalNumbers - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
countParts(Iterator, Hashtable) - Method in class gov.nasa.javaGenes.core.Population
 
create() - Method in interface gov.nasa.javaGenes.core.ChildMakerRandomCreator
 
create() - Method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
create() - Method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations
 
createAlleleTemplate(FitnessFunction) - Static method in class gov.nasa.javaGenes.core.BreederWithTeachers
return each interval is from best to worst possible fitness for each objective
createAlleleTemplate(Population) - Static method in class gov.nasa.javaGenes.core.BreederWithTeachers
return based on the population given.
createArrays() - Method in class gov.nasa.javaGenes.forceFields.Bodies
Must be called before this is handed to a potential.
createArrays(Vector) - Static method in class gov.nasa.javaGenes.forceFields.Bodies
converts a vector of bodies into an array of bodies and has all of the bodies convert the internal vectors into arrays for fast access
createArrays() - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
createArrays() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
createArrays() - Method in class gov.nasa.javaGenes.forceFields.OneBody
moves the TwoBody(s) from any ExtendedVector to an array for fast access
createArrays() - Method in class gov.nasa.javaGenes.forceFields.SecondBody
moves the ThreeBody(s) from the vector to the array
createDifferenceChromosome(Chromosome) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
createFreshTimelines() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
createRandomIndividual(int, Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
createRandomIndividual(int, int, Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
createSchedule(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
 
createSchedule(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
createSchedule(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
this must always be called by subclasses before calculating fitness
createSegmentCoordinates(DoubleInterval, int) - Method in class gov.nasa.alsUtility.Brick3dWithSegments
 
createSubBreeders(int, ChildMakerProvider, FitnessFunction, boolean) - Static method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
cross(Vector3d, Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
crossover(EvolvableDoubleList, EvolvableDoubleList, EvolvableDoubleList, int[], int[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
crossover(EvolvableDoubleList, EvolvableDoubleList, EvolvableDoubleList, int[], int[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint
 
crossover(EvolvableDoubleList, EvolvableDoubleList, EvolvableDoubleList, int[], int[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
insertInto (the first parent) chooses the elements between the indices to replace, takeFrom (the second parent) insertInto.
crossover(Graph, Graph) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
Mate
crossover(PermutationEvolvable, PermutationEvolvable, boolean[]) - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
crossoverIntervalRange - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
cumulative - Variable in class gov.nasa.javaGenes.core.ChildMaker
 
currentCheckpointer - Static variable in class gov.nasa.javaGenes.core.Checkpointer
 
currentSize - Variable in class gov.nasa.alsUtility.GrowOnlyArray
 
currentSize() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
currentTemperature - Variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
currentWeights - Variable in class gov.nasa.javaGenes.weightNetwork.WeightList
 
currentlyContains(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
cutOffDistance(int, int) - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
cutoff - Variable in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
cutoff(double, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
cutoffInterval - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
cutoffs - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
cyclesInterval - Variable in class gov.nasa.javaGenes.graph.GraphParameters
an interval to choose a random number of Graph cycles from.

D

DEFAULT_GROWBY - Static variable in class gov.nasa.alsUtility.GrowOnlyArray
 
DEFAULT_INITIAL_SIZE - Static variable in class gov.nasa.alsUtility.GrowOnlyArray
 
DEFAULT_MAXIMUM_TRIES - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
DELTA_REDUCE - Static variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
DataTable - class gov.nasa.alsUtility.DataTable.
handles named Vectors of double data.
DataTable() - Constructor for class gov.nasa.alsUtility.DataTable
 
DeJongFitnessFunctions - class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions.
The well know De Jong fitness functions.
DeJongFitnessFunctions(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
DeJongFitnessFunctionsTest - class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest.
 
DeJongFitnessFunctionsTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest
 
Debug - class gov.nasa.javaGenes.EOSscheduling.Debug.
 
Debug() - Constructor for class gov.nasa.javaGenes.EOSscheduling.Debug
 
Debug - class gov.nasa.javaGenes.core.Debug.
 
Debug() - Constructor for class gov.nasa.javaGenes.core.Debug
 
Debug - class gov.nasa.javaGenes.permutation.Debug.
 
Debug() - Constructor for class gov.nasa.javaGenes.permutation.Debug
 
DescendingWeightsComparator - class gov.nasa.javaGenes.core.DescendingWeightsComparator.
 
DescendingWeightsComparator() - Constructor for class gov.nasa.javaGenes.core.DescendingWeightsComparator
 
DescendingWeightsComparatorTest - class gov.nasa.javaGenes.core.DescendingWeightsComparatorTest.
 
DescendingWeightsComparatorTest(String) - Constructor for class gov.nasa.javaGenes.core.DescendingWeightsComparatorTest
 
DiamondLatticConstant - Static variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
DirectedEdge - class gov.nasa.javaGenes.graph.DirectedEdge.
 
DirectedEdge() - Constructor for class gov.nasa.javaGenes.graph.DirectedEdge
 
DirectedGraph - class gov.nasa.javaGenes.graph.DirectedGraph.
 
DirectedGraph() - Constructor for class gov.nasa.javaGenes.graph.DirectedGraph
 
DirectedGraph.SecondVertex - class gov.nasa.javaGenes.graph.DirectedGraph.SecondVertex.
this predicate decides if a vertex is acceptable as a second vertex when adding an edge during graph construction
DirectedGraph.SecondVertex(DirectedVertex) - Constructor for class gov.nasa.javaGenes.graph.DirectedGraph.SecondVertex
 
DirectedVertex - class gov.nasa.javaGenes.graph.DirectedVertex.
 
DirectedVertex() - Constructor for class gov.nasa.javaGenes.graph.DirectedVertex
 
DissimilarEdgeCompatibleWithVertices - class gov.nasa.javaGenes.graph.DissimilarEdgeCompatibleWithVertices.
 
DissimilarEdgeCompatibleWithVertices(Edge) - Constructor for class gov.nasa.javaGenes.graph.DissimilarEdgeCompatibleWithVertices
 
Distribution - class gov.nasa.alsUtility.Distribution.
abstract class for a distribution of double numbers.
Distribution() - Constructor for class gov.nasa.alsUtility.Distribution
 
DoubleInterval - class gov.nasa.alsUtility.DoubleInterval.
implements an interval between two double values
DoubleInterval() - Constructor for class gov.nasa.alsUtility.DoubleInterval
create an interval 0 to 1
DoubleInterval(double, double) - Constructor for class gov.nasa.alsUtility.DoubleInterval
create an interval with between x and y.
DoubleInterval(double, boolean, double, boolean) - Constructor for class gov.nasa.alsUtility.DoubleInterval
 
DoubleInterval(DoubleInterval) - Constructor for class gov.nasa.alsUtility.DoubleInterval
 
DoubleInterval(Vector) - Constructor for class gov.nasa.alsUtility.DoubleInterval
 
DoubleInterval(double[]) - Constructor for class gov.nasa.alsUtility.DoubleInterval
 
DoubleIntervalTest - class gov.nasa.alsUtility.DoubleIntervalTest.
 
DoubleIntervalTest(String) - Constructor for class gov.nasa.alsUtility.DoubleIntervalTest
 
DoublesList - class gov.nasa.alsUtility.DoublesList.
 
DoublesList(String) - Constructor for class gov.nasa.alsUtility.DoublesList
 
DoublesListTest - class gov.nasa.alsUtility.DoublesListTest.
 
DoublesListTest(String) - Constructor for class gov.nasa.alsUtility.DoublesListTest
 
DutyCycleConstraint - class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint.
Implements constraints of the form: resource must be Available for no more than onTime in any totalTime period.
DutyCycleConstraint(Horizon, int, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
holds data for a constraint where something must be off for at least inOffTime in every period of inTotalTime
DutyCycleConstraintTest - class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest.
RESTRICTION: the dutyCylce constraint assumes that the task duration is equal to the access window -- i.e, there is no point in trying to move the task around in time.
DutyCycleConstraintTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
data - Variable in class gov.nasa.alsUtility.Sample
 
data - Variable in class gov.nasa.alsUtility.Saver
 
date() - Static method in class gov.nasa.alsUtility.Utility
 
date2seconds(Date) - Static method in class gov.nasa.alsUtility.Utility
 
datum(int) - Method in class gov.nasa.alsUtility.Sample
 
deJongNumber - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
deathRow - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
debug - Static variable in class gov.nasa.javaGenes.EOSscheduling.Debug
 
debug - Static variable in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
debug - Static variable in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
debug - Static variable in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
debug - Static variable in class gov.nasa.javaGenes.core.Breeder
 
debug - Static variable in class gov.nasa.javaGenes.core.Debug
 
debug - Static variable in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
debug - Static variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
debug - Static variable in class gov.nasa.javaGenes.permutation.Debug
 
debugFilename - Static variable in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
debugPrint(String) - Static method in class gov.nasa.alsUtility.Utility
 
debugPrintln(String) - Static method in class gov.nasa.alsUtility.Utility
 
deepCopyBrokenGraph() - Method in class gov.nasa.javaGenes.graph.BrokenGraph
make a copy of the brokenEdges vector, make new BrokenEdges, but don't make copies of the edges themselves.
deepCopyChromosome() - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
deepCopyDirectedGraph() - Method in class gov.nasa.javaGenes.graph.DirectedGraph
copy the graph and make copies of all edges and vertices
deepCopyGraph() - Method in class gov.nasa.javaGenes.graph.Graph
copy the graph and make copies of all edges and vertices
deepCopyMultiBodiesForOneEnergy() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
copy the graph and make copies of all edges and vertices
deepCopyPermutationEvolvable() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
deepCopyPermutationEvolvable() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
defaultCrossoverIntervalRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
defaultMutationStandardDeviationRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
defaultSelectionProbabilityRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
defaultStart() - Static method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
defaultWeightRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
degrees2radians(double) - Static method in class gov.nasa.alsUtility.Utility
 
delete(Edge) - Method in class gov.nasa.javaGenes.graph.Graph
Removes Edge e from graph, removes the vertices from e, and removes e from its vertices.
deleteFile(String) - Static method in class gov.nasa.alsUtility.Utility
 
deleteNodeAndNextNode(Node) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
deletePointingData() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
deleteSizes - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
delta_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
dimerForcePropertyName - Static variable in class gov.nasa.javaGenes.chemistry.Molecule
 
directoryName - Variable in class gov.nasa.alsUtility.Saver
directory to save data in
directoryNames - Static variable in class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
dissimilarEdgeCompatibleWithVertices(Edge) - Method in class gov.nasa.javaGenes.chemistry.Bond
 
dissimilarEdgeCompatibleWithVertices(Edge) - Method in class gov.nasa.javaGenes.graph.Edge
 
distance(Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.MathUtility
 
distance(double, double) - Static method in class gov.nasa.alsUtility.Tanimoto
 
distance(KeyCounter, KeyCounter) - Static method in class gov.nasa.alsUtility.Tanimoto
 
distanceBetweenLineSegments(Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.MathUtility
 
distanceColumn - Static variable in class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
distanceColumnHeading - Static variable in class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
distanceFrom(double) - Method in class gov.nasa.alsUtility.DoubleInterval
how far outside of the interval is value?
distanceFrom(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
distanceFrom(Evolvable) - Method in class gov.nasa.javaGenes.core.Evolvable
Subclasses will almost always override this.
distanceFrom(Evolvable) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
distanceFrom(Evolvable) - Method in class gov.nasa.javaGenes.graph.Graph
 
distanceFrom(Evolvable) - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
distanceTo(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
distanceToSquared(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
divideBy(int) - Method in class gov.nasa.alsUtility.integer
 
divideHowManyBy(double) - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
doPerAtomEnergies - Variable in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
doPerAtomEnergies - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
doesConnect(Vertex) - Method in class gov.nasa.javaGenes.graph.Edge
 
done(Population) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingReporter
 
done(Population) - Method in class gov.nasa.javaGenes.core.Reporter
Call when the run is finished.
done(Population) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeReporter
 
doneFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
doneWithTimelines() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
dontCheckpoint() - Static method in class gov.nasa.javaGenes.core.Checkpointer
Called by an external agency.
dontCheckpointLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
dontEvolve() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
dot(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
doubleArraySum(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
doubleSize - Static variable in class gov.nasa.javaGenes.chemistry.molFormat
 
doubleValue(Vector, int) - Static method in class gov.nasa.alsUtility.Utility
 
doubleValue(Object) - Static method in class gov.nasa.alsUtility.Utility
 
down - Variable in class gov.nasa.alsUtility.LogComparisons
 
downFractionComparator - Variable in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
duration - Variable in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
duration - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
duration - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
duration - Variable in class gov.nasa.javaGenes.EOSscheduling.Task
 
durationInEndBucket(int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
durationInStartBucket(int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
dutyCycle - Variable in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
dutyCycleMask - Variable in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 

E

END_TOKEN - Static variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
EOSModel - class gov.nasa.javaGenes.EOSscheduling.EOSModel.
 
EOSModel() - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
EOSModel(Horizon) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
EOSModelTest - class gov.nasa.javaGenes.EOSscheduling.EOSModelTest.
 
EOSModelTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSModelTest
 
EOSschedulingEvolvable - class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable.
 
EOSschedulingEvolvable(int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
EOSschedulingEvolvable(int, String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
EOSschedulingEvolvableTest - class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvableTest.
 
EOSschedulingEvolvableTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvableTest
 
EOSschedulingIndividual - class gov.nasa.javaGenes.EOSscheduling.EOSschedulingIndividual.
 
EOSschedulingIndividual(Evolvable, FitnessFunction) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingIndividual
Sets the evolvable to e and calculates the fitness using FitnessFunction f.
EOSschedulingIndividual() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingIndividual
 
EOSschedulingParameters - class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters.
 
EOSschedulingParameters() - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
Sets up all parameters
EOSschedulingParameters(int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
EOSschedulingPopulation - class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation.
 
EOSschedulingPopulation(EOSschedulingParameters) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation
 
EOSschedulingPopulation(int, int, FitnessFunction) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation
 
EOSschedulingPopulation(int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation
create an empty population with int size members
EOSschedulingReporter - class gov.nasa.javaGenes.EOSscheduling.EOSschedulingReporter.
 
EOSschedulingReporter(Parameters) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EOSschedulingReporter
 
EarliestFirstPlacer - class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer.
puts tasks in available AccessWindow that starts earliest.
EarliestFirstPlacer() - Constructor for class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
EarliestFirstPlacerTest - class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest.
 
EarliestFirstPlacerTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
EarliestFromChosenWindowPlacer - class gov.nasa.javaGenes.EOSscheduling.EarliestFromChosenWindowPlacer.
 
EarliestFromChosenWindowPlacer() - Constructor for class gov.nasa.javaGenes.EOSscheduling.EarliestFromChosenWindowPlacer
 
EarliestFromRandomWindowPlacer - class gov.nasa.javaGenes.EOSscheduling.EarliestFromRandomWindowPlacer.
 
EarliestFromRandomWindowPlacer() - Constructor for class gov.nasa.javaGenes.EOSscheduling.EarliestFromRandomWindowPlacer
 
EasyFile - class gov.nasa.alsUtility.EasyFile.
create a file and add text to it from time to time
EasyFile(String) - Constructor for class gov.nasa.alsUtility.EasyFile
 
Edge - class gov.nasa.javaGenes.graph.Edge.
Edges in Graphs.
Edge() - Constructor for class gov.nasa.javaGenes.graph.Edge
 
EdgeIterator - class gov.nasa.javaGenes.graph.EdgeIterator.
serves as an iterator for a vector of Edge objects
EdgeIterator(Vector) - Constructor for class gov.nasa.javaGenes.graph.EdgeIterator
 
Element - class gov.nasa.javaGenes.chemistry.Element.
represents elements in the periodic table.
Element() - Constructor for class gov.nasa.javaGenes.chemistry.Element
 
Element(int) - Constructor for class gov.nasa.javaGenes.chemistry.Element
 
EnergiesFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeReporter
 
Error - class gov.nasa.alsUtility.Error.
handle errors and hand out warnings.
Error() - Constructor for class gov.nasa.alsUtility.Error
 
Evolvable - class gov.nasa.javaGenes.core.Evolvable.
objects that can evolve in a genetic software system.
Evolvable() - Constructor for class gov.nasa.javaGenes.core.Evolvable
for testing only
EvolvableDouble - class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble.
keeps its internal value between 0 and 1.
EvolvableDouble() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
EvolvableDouble(double) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
EvolvableDoubleList - class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList.
 
EvolvableDoubleList() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
EvolvableDoubleList(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
EvolvableDoubleList(int, double) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
used for testing
EvolvableDoubleList(double[]) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
EvolvableDoubleList(double[], double) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
used for testing
EvolvableDoubleListTest - class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest.
 
EvolvableDoubleListTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
EvolvableDoubleTest - class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest.
 
EvolvableDoubleTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest
 
EvolvableTest - class gov.nasa.javaGenes.core.EvolvableTest.
 
EvolvableTest(String) - Constructor for class gov.nasa.javaGenes.core.EvolvableTest
 
ExperimentMain - class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.ExperimentMain.
 
ExperimentMain() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.ExperimentMain
 
ExtendedTreeSet - class gov.nasa.alsUtility.ExtendedTreeSet.
 
ExtendedTreeSet() - Constructor for class gov.nasa.alsUtility.ExtendedTreeSet
 
ExtendedTreeSetTest - class gov.nasa.alsUtility.ExtendedTreeSetTest.
 
ExtendedTreeSetTest(String) - Constructor for class gov.nasa.alsUtility.ExtendedTreeSetTest
 
ExtendedTypeSimilarity - class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity.
a fitness function consisting of the Tanimoto distance to a target.
ExtendedTypeSimilarity(Graph) - Constructor for class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity
 
ExtendedVector - class gov.nasa.alsUtility.ExtendedVector.
Extends the capabilities of Vector.
ExtendedVector() - Constructor for class gov.nasa.alsUtility.ExtendedVector
 
ExtendedVector(int[]) - Constructor for class gov.nasa.alsUtility.ExtendedVector
add Integer objects corresponding to array
ExtendedVector(Object[]) - Constructor for class gov.nasa.alsUtility.ExtendedVector
 
ExtendedVector(Enumeration) - Constructor for class gov.nasa.alsUtility.ExtendedVector
create an ExtendedVector with the elements from Enumeration e
ExtendedVectorTest - class gov.nasa.alsUtility.ExtendedVectorTest.
 
ExtendedVectorTest(String) - Constructor for class gov.nasa.alsUtility.ExtendedVectorTest
 
edge - Variable in class gov.nasa.javaGenes.graph.BrokenEdge
 
edge - Variable in class gov.nasa.javaGenes.graph.DissimilarEdgeCompatibleWithVertices
 
edge() - Method in class gov.nasa.javaGenes.graph.EdgeIterator
 
edge - Variable in class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider
 
edge - Variable in class gov.nasa.javaGenes.graph.VertexAcceptsEdge
the edge to be accepted
edgeLength - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
edges - Variable in class gov.nasa.javaGenes.graph.Graph
 
edges - Variable in class gov.nasa.javaGenes.graph.Trail
 
edges - Variable in class gov.nasa.javaGenes.graph.Vertex
 
edges - Variable in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
the edges to be provided
element - Variable in class gov.nasa.javaGenes.chemistry.Atom
 
element - Variable in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
elements - Variable in class gov.nasa.javaGenes.forceFields.Tersoff
 
elevation - Variable in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
end - Variable in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
end - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
end1 - Variable in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
end2 - Variable in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
endDate - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
endJavaEpoch - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
endScheduling() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
endScheduling(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
endTimeOK(SlewNode, int, SlewRequirement, Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
ends - Variable in class gov.nasa.javaGenes.graph.Trail
 
energies - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
energiesToExamineBestIndividual - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
energy - Variable in class gov.nasa.javaGenes.forceFields.PotentialEnergyTestCase
the ideal energies for bodies
energyPropertyName - Static variable in class gov.nasa.javaGenes.chemistry.Molecule
 
energyRangeDivideBy - Variable in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
energyUnitErgPerAtom - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
energyUnitKcalPerMol - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
equalIncrements(int) - Method in class gov.nasa.alsUtility.DoubleInterval
 
equalIncrements(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
equals(Object) - Method in class gov.nasa.alsUtility.IntegerInterval
 
equals(int[], int[]) - Static method in class gov.nasa.alsUtility.Utility
 
equals(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
equals(Object) - Method in class gov.nasa.alsUtility.integer
 
equals(SensorType) - Method in class gov.nasa.javaGenes.EOSscheduling.SensorType
 
equals(Object) - Method in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
equals(Element) - Method in class gov.nasa.javaGenes.chemistry.Element
 
equals() - Method in class gov.nasa.javaGenes.core.FitnessBad
 
equals(FitnessDouble) - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
equals(Object) - Method in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
equals(Object) - Method in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
equals(int[]) - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
used for testing
equalsExtremes(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
equivalent(PointingRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
equivalent(SlewRequirement, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
equivalent(SlewRequirement, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.Slewable
 
eval - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.MinimizeSlewingFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.NumberOfTakeImagesFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SmallSlewsFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPriorityFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.FitnessFunctionBadSize
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.FitnessFunctionFixed
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.FitnessFunctionRandom
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
evaluateFitness(FitnessFunction) - Method in class gov.nasa.javaGenes.core.Individual
evaluate the fitness
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.MultiStageFitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.ParsimonyFitness
 
evaluateFitness(FitnessFunction) - Method in class gov.nasa.javaGenes.core.Population
Calculate the fitness of all individuals in the population.
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.ProductFitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.StudentFitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.TeacherFitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.Weighted0to1
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.core.WeightedSumFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.evolvableDoubleList.TestFitnessFunction1
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeDistanceFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.graph.CyclesSimilarity
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity
 
evaluateFitness(Evolvable) - Method in class gov.nasa.javaGenes.permutation.PermutationTestFitness
 
evaluationFunction - Variable in class gov.nasa.javaGenes.core.Parameters
 
everContains(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
evolutionScaleFactor - Variable in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
evolvable - Variable in class gov.nasa.javaGenes.core.Individual
 
evolvableSize() - Method in class gov.nasa.javaGenes.core.Individual
 
evolvableSize - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations
 
evolvableSize - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
evolve() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
evolveSiOnly() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
evolve_c2d2betaN_Only() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
excessiveTimeBetweenCheckpointOKs - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
execute(Object) - Method in class gov.nasa.alsUtility.And
 
execute(Object) - Method in class gov.nasa.alsUtility.IsEqual
 
execute(Object) - Method in class gov.nasa.alsUtility.IsInstanceOf
 
execute(Object) - Method in class gov.nasa.alsUtility.IsMarked
 
execute(Object) - Method in class gov.nasa.alsUtility.MarkIsSet
 
execute(Object) - Method in class gov.nasa.alsUtility.Not
 
execute(Object) - Method in class gov.nasa.alsUtility.ObjectCompatible
 
execute(Object) - Method in class gov.nasa.alsUtility.ObjectEquals
 
execute(Object) - Method in class gov.nasa.alsUtility.Or
 
execute(Object) - Method in interface gov.nasa.alsUtility.Predicate
executes this predicate on object
execute(Object) - Method in interface gov.nasa.alsUtility.Procedure
execute the procedure on object
execute(Object) - Method in class gov.nasa.alsUtility.SetMark
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.AcceptableSecondBrokenEdge
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.AcceptableSecondVertex
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.DirectedGraph.SecondVertex
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.DissimilarEdgeCompatibleWithVertices
calls edge.dissimilarEdgeCompatibleWithVertices((Edge)object);
execute(Object) - Method in class gov.nasa.javaGenes.graph.HasInputEdgeFrom
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.HasOutputEdgesTo
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.VertexAcceptsEdge
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.VertexAcceptsInputEdge
 
execute(Object) - Method in class gov.nasa.javaGenes.graph.VertexAcceptsOutputEdge
 
executeOnAll(Procedure) - Method in class gov.nasa.alsUtility.ExtendedVector
execute Procedure p on all elements
executeOnEdges(Procedure) - Method in class gov.nasa.javaGenes.graph.Graph
 
executeOnVertices(Procedure) - Method in class gov.nasa.javaGenes.graph.Graph
Execute Procedure p on all vertices
expand(double) - Method in class gov.nasa.alsUtility.DoubleInterval
change the interval of this by a factor keeping the center of the interval the same.
expand(int) - Method in class gov.nasa.alsUtility.IntegerInterval
change the interval of this by a factor keeping the center of the interval the same.
expandByAddition(double) - Method in class gov.nasa.alsUtility.Brick3d
 
expandByAddition(double) - Method in class gov.nasa.alsUtility.Brick3dWithSegments
 
expandByAddition(double) - Method in class gov.nasa.alsUtility.DoubleInterval
 
expandIntervalsBy - Variable in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval
 
expandToInclude(Vector3d) - Method in class gov.nasa.alsUtility.Brick3d
 
exponentInterval - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
extendFromFirstParentIndex - Variable in class gov.nasa.javaGenes.core.TournamentLocal
 
extendFromFirstParentIndices - Variable in class gov.nasa.javaGenes.core.AntiTournamentLocal
 
extendIfNecessary(double) - Method in class gov.nasa.alsUtility.DoubleInterval
 
extendedTypeCache - Variable in class gov.nasa.javaGenes.graph.Vertex
 
extension() - Static method in class gov.nasa.alsUtility.VRMLUtility
 
extension - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
interval crossover fraction of distance between
extensionWithDot() - Static method in class gov.nasa.alsUtility.VRMLUtility
 

F

FACTOR_REDUCE - Static variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
FCCLatticConstant - Static variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
FieldRecordText - class gov.nasa.alsUtility.FieldRecordText.
 
FieldRecordText(String) - Constructor for class gov.nasa.alsUtility.FieldRecordText
 
FieldRecordText(String, String) - Constructor for class gov.nasa.alsUtility.FieldRecordText
 
FieldRecordTextTest - class gov.nasa.alsUtility.FieldRecordTextTest.
 
FieldRecordTextTest(String) - Constructor for class gov.nasa.alsUtility.FieldRecordTextTest
 
FindMinimumInTsdFile - class gov.nasa.javaGenes.main.FindMinimumInTsdFile.
 
FindMinimumInTsdFile() - Constructor for class gov.nasa.javaGenes.main.FindMinimumInTsdFile
 
FirstClusterLowestEnergyFitnessFunction - class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction.
 
FirstClusterLowestEnergyFitnessFunction() - Constructor for class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
FirstClusterLowestEnergyFitnessFunction(Potential, ManyMultiBodiesForOneEnergy, double) - Constructor for class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
FirstClusterLowestEnergyFitnessFunctionTest - class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunctionTest.
 
FirstClusterLowestEnergyFitnessFunctionTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunctionTest
 
Fitness - class gov.nasa.javaGenes.core.Fitness.
 
Fitness() - Constructor for class gov.nasa.javaGenes.core.Fitness
 
FitnessBad - class gov.nasa.javaGenes.core.FitnessBad.
 
FitnessBad() - Constructor for class gov.nasa.javaGenes.core.FitnessBad
 
FitnessDouble - class gov.nasa.javaGenes.core.FitnessDouble.
lower values are fitter
FitnessDouble(double) - Constructor for class gov.nasa.javaGenes.core.FitnessDouble
 
FitnessFunction - class gov.nasa.javaGenes.core.FitnessFunction.
fitness function for Evolvables.
FitnessFunction() - Constructor for class gov.nasa.javaGenes.core.FitnessFunction
 
FitnessFunctionBadSize - class gov.nasa.javaGenes.core.FitnessFunctionBadSize.
 
FitnessFunctionBadSize(IntegerInterval) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionBadSize
 
FitnessFunctionBadSizeTest - class gov.nasa.javaGenes.core.FitnessFunctionBadSizeTest.
 
FitnessFunctionBadSizeTest(String) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionBadSizeTest
 
FitnessFunctionFixed - class gov.nasa.javaGenes.core.FitnessFunctionFixed.
 
FitnessFunctionFixed(double) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionFixed
 
FitnessFunctionMultiObjective - class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective.
 
FitnessFunctionMultiObjective() - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
FitnessFunctionMultiObjectiveToOne - class gov.nasa.javaGenes.core.FitnessFunctionMultiObjectiveToOne.
 
FitnessFunctionMultiObjectiveToOne() - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionMultiObjectiveToOne
 
FitnessFunctionRandom - class gov.nasa.javaGenes.core.FitnessFunctionRandom.
 
FitnessFunctionRandom(DoubleInterval) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionRandom
 
FitnessFunctionWorstFitness - class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness.
this fitness function will run another fitness function N times on variations of the Evolvable.
FitnessFunctionWorstFitness(FitnessFunction, PhenotypeChanger) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
FitnessFunctionWorstFitnessManyTries - class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries.
this fitness function will run another fitness function N times on variations of the Evolvable.
FitnessFunctionWorstFitnessManyTries(int, Fitness, FitnessFunction, PhenotypeChanger) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries
 
FitnessFunctionWorstFitnessManyTriesTest - class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTriesTest.
 
FitnessFunctionWorstFitnessManyTriesTest(String) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTriesTest
 
FitnessFunctionWorstFitnessTest - class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessTest.
 
FitnessFunctionWorstFitnessTest(String) - Constructor for class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessTest
 
FitnessMultiObjective - class gov.nasa.javaGenes.core.FitnessMultiObjective.
 
FitnessMultiObjective(FitnessFunctionMultiObjective) - Constructor for class gov.nasa.javaGenes.core.FitnessMultiObjective
 
FitnessMultiObjectiveTest - class gov.nasa.javaGenes.core.FitnessMultiObjectiveTest.
 
FitnessMultiObjectiveTest(String) - Constructor for class gov.nasa.javaGenes.core.FitnessMultiObjectiveTest
 
ForceFitnessRMS - class gov.nasa.javaGenes.forceFields.ForceFitnessRMS.
 
ForceFitnessRMS(Potential, double, String) - Constructor for class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
ForceFitnessRMSTest - class gov.nasa.javaGenes.forceFields.ForceFitnessRMSTest.
 
ForceFitnessRMSTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ForceFitnessRMSTest
 
ForceFitnessTanimoto - class gov.nasa.javaGenes.forceFields.ForceFitnessTanimoto.
 
ForceFitnessTanimoto(Potential, double, String) - Constructor for class gov.nasa.javaGenes.forceFields.ForceFitnessTanimoto
 
FunctionalForm - class gov.nasa.javaGenes.forceFields.FunctionalForm.
 
FunctionalForm() - Constructor for class gov.nasa.javaGenes.forceFields.FunctionalForm
 
factor - Variable in class gov.nasa.alsUtility.ReinitializableFloatWithFactor
 
factor - Variable in class gov.nasa.javaGenes.core.ParsimonyFitness
 
factorInterval - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
factoryRandom(DoubleInterval) - Static method in class gov.nasa.alsUtility.Vector3d
 
farWallFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
fastFitCheck(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
used for a quick screening check.
fastFits(AvailabilityTimeline, AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
if a period of 'duration' length starting at startTime became UnAvailable, would the timeline be consistant with the dutycycle constraint?
fatal(String) - Static method in class gov.nasa.alsUtility.Error
 
fatal(Exception) - Static method in class gov.nasa.alsUtility.Error
 
file - Variable in class gov.nasa.alsUtility.EasyFile
 
file - Variable in class gov.nasa.alsUtility.LogFile
 
file - Variable in class gov.nasa.javaGenes.core.TokenizeOutput
 
file2StringArray(String) - Static method in class gov.nasa.alsUtility.Utility
 
fileDirectory - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
fileSeparator() - Static method in class gov.nasa.alsUtility.Utility
 
filename - Variable in class gov.nasa.alsUtility.EasyFile
 
filename - Variable in class gov.nasa.alsUtility.LogFile
 
filename - Static variable in class gov.nasa.javaGenes.core.Checkpointer
 
filename - Variable in class gov.nasa.javaGenes.core.TokenizeInput
 
filename - Variable in class gov.nasa.javaGenes.core.TokenizeOutput
 
filename - Variable in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
filename - Variable in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
filename - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
fillEntropy(ManySamples, Hashtable, int, String) - Method in class gov.nasa.javaGenes.core.Population
 
fillRandomly(IntegerInterval, int[]) - Static method in class gov.nasa.alsUtility.RandomNumber
fill results with random numbers in integer i inclusive.
fillSamples(ManySamples) - Method in class gov.nasa.javaGenes.core.Population
Add Sample objects to ManySamples samples that summarize the population.
fillSamples(ManySamples) - Method in class gov.nasa.javaGenes.forceFields.ChromosomePopulation
Add Sample objects to ManySamples samples that summarize the population.
fillSamples(ManySamples) - Method in class gov.nasa.javaGenes.graph.GraphPopulation
Add Sample objects to ManySamples samples that summarize the population.
finalize() - Method in class gov.nasa.alsUtility.EasyFile
close the file if necessary
finalize() - Method in class gov.nasa.alsUtility.LogFile
close the file if necessary
finalize() - Method in class gov.nasa.javaGenes.core.TokenizeInput
close the file if necessary
finalize() - Method in class gov.nasa.javaGenes.core.TokenizeOutput
close the file if necessary
findAll(Predicate) - Method in class gov.nasa.alsUtility.ExtendedVector
 
findEarliest(int, int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
findEarliest(int, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
findEarliest(int, int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
SSRuse is modelled as instantaneous.
findEarliest(int, int, double) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
This will happen a lot and must be very fast.
findEarliest(int, int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
findEarliest(int, int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
findEarliest(int, int, int, SlewRequirement, Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
This will happen a lot and must be very fast.
findEarliest(int, int, int, SlewRequirement, Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
findEarliest(int, int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
findObject(double) - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
first - Variable in class gov.nasa.javaGenes.graph.AcceptableSecondBrokenEdge
 
fitness - Variable in class gov.nasa.javaGenes.core.FitnessDouble
 
fitness - Variable in class gov.nasa.javaGenes.core.FitnessMultiObjective
 
fitness - Variable in class gov.nasa.javaGenes.core.Individual
 
fitnessEachGenerationFilename - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingReporter
 
fitnessFunction - Variable in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
fitnessFunction - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
fitnessFunction - Variable in class gov.nasa.javaGenes.core.Parameters
 
fitnessFunctions - Variable in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
fitnessFunctions - Variable in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
fitnessFunctions - Variable in class gov.nasa.javaGenes.core.Weighted0to1
 
fitnessMeanAndStdDevString(Population) - Method in class gov.nasa.javaGenes.core.Reporter
 
fits(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
fits(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
fits(AvailabilityTimeline) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
fits(AvailabilityTimeline, AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
fits(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
fits(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
fits(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
fits(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
fits(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
fitsDutyCycles() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
fitsDutyCycles(AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
is this time and duration compatible with the duty cylce constraint (if any).
fitterThan(Fitness) - Method in class gov.nasa.javaGenes.core.Fitness
 
fitterThan(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessBad
 
fitterThan(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
fitterThan(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessMultiObjective
 
fitterThan(Individual) - Method in class gov.nasa.javaGenes.core.Individual
 
fitterThan(Fitness) - Method in class gov.nasa.javaGenes.core.StudentFitness
 
fittestTextFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
fixDouble(double) - Static method in class gov.nasa.alsUtility.Utility
convert a double to something that is a specific number.
fixedLength - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
flourineThreeBodyParametersIncrement - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
flush() - Method in class gov.nasa.alsUtility.EasyFile
 
flush() - Method in class gov.nasa.alsUtility.LogFile
 
forEvolution - Variable in class gov.nasa.javaGenes.core.ChildMaker
 
forceColumn - Static variable in class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
forceColumnHeading - Static variable in class gov.nasa.javaGenes.forceFields.ForceFitnessRMS
 
forceFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
forceInsideAlleleLimits(Allele, double, double) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
formSetup() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
formSetup() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberPartialSiF
 
formSetup() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSi
 
formSetup() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
foundPerfection - Variable in class gov.nasa.javaGenes.core.Run
 
foxholes - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
frequency - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
average fraction of the alleles to be used.
frequencyOfASCIIPopulations - Variable in class gov.nasa.javaGenes.core.Parameters
 
ftest(Sample, Sample) - Static method in class gov.nasa.alsUtility.ComparativeStatistics
implements and f-test between two Samples
fullDistance - Variable in class gov.nasa.javaGenes.chemistry.UnitCell
 
function - Variable in class gov.nasa.javaGenes.core.FitnessMultiObjective
 

G

G - Static variable in class gov.nasa.alsUtility.Constants
 
GROW_BY - Static variable in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
 
Gammln(double) - Static method in class gov.nasa.alsUtility.ComparativeStatistics
 
GetLengthsAndAngles - class gov.nasa.javaGenes.forceFields.GetLengthsAndAngles.
 
GetLengthsAndAngles() - Constructor for class gov.nasa.javaGenes.forceFields.GetLengthsAndAngles
 
Graph - class gov.nasa.javaGenes.graph.Graph.
A information theoretic graph, in other words, a set of vertices and a set of edges.
Graph() - Constructor for class gov.nasa.javaGenes.graph.Graph
 
Graph(VertexAndEdgeProvider, int, int) - Constructor for class gov.nasa.javaGenes.graph.Graph
Generates a random graph.
Graph.TrailKey - class gov.nasa.javaGenes.graph.Graph.TrailKey.
An object that efficiently represents a path for use in as a key Hashtables and KeyCounters.
Graph.TrailKey() - Constructor for class gov.nasa.javaGenes.graph.Graph.TrailKey
 
Graph.TrailKey(Object, Object, int) - Constructor for class gov.nasa.javaGenes.graph.Graph.TrailKey
 
GraphElement - class gov.nasa.javaGenes.graph.GraphElement.
Superclass for parts of a graph.
GraphElement() - Constructor for class gov.nasa.javaGenes.graph.GraphElement
 
GraphGenerator - class gov.nasa.javaGenes.graph.GraphGenerator.
 
GraphGenerator(GraphParameters) - Constructor for class gov.nasa.javaGenes.graph.GraphGenerator
 
GraphIndividual - class gov.nasa.javaGenes.graph.GraphIndividual.
Represents a genetic software graph individual.
GraphIndividual(Evolvable, FitnessFunction) - Constructor for class gov.nasa.javaGenes.graph.GraphIndividual
Sets the evolvable to Graph e and calculates the fitness using FitnessFunction f.
GraphLayout - class gov.nasa.javaGenes.graph.GraphLayout.
this class is an interface to the jiggle package that does graph layout for viewing.
GraphLayout() - Constructor for class gov.nasa.javaGenes.graph.GraphLayout
 
GraphLayout.CoordinateProvider - class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider.
 
GraphLayout.CoordinateProvider(double, double) - Constructor for class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider
 
GraphParameters - class gov.nasa.javaGenes.graph.GraphParameters.
Parameters and setup for genetic graph runs.
GraphParameters() - Constructor for class gov.nasa.javaGenes.graph.GraphParameters
 
GraphPopulation - class gov.nasa.javaGenes.graph.GraphPopulation.
Represents a population of evolvable Graph objects
GraphPopulation(GraphParameters) - Constructor for class gov.nasa.javaGenes.graph.GraphPopulation
Generate a random population
GraphPopulation(int) - Constructor for class gov.nasa.javaGenes.graph.GraphPopulation
create an empty population with int size members
GraphTest - class gov.nasa.javaGenes.graph.GraphTest.
 
GraphTest(String) - Constructor for class gov.nasa.javaGenes.graph.GraphTest
 
GrowOnlyArray - class gov.nasa.alsUtility.GrowOnlyArray.
growing list of objects that will never need the garbage collector (for speed)
GrowOnlyArray() - Constructor for class gov.nasa.alsUtility.GrowOnlyArray
 
GrowOnlyArray(int, int) - Constructor for class gov.nasa.alsUtility.GrowOnlyArray
 
GrowOnlyArrayTest - class gov.nasa.alsUtility.GrowOnlyArrayTest.
 
GrowOnlyArrayTest(String) - Constructor for class gov.nasa.alsUtility.GrowOnlyArrayTest
 
gamma_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
gauss() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
generate(boolean, Sensor, STKAccessFile) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
generateGroundStationAccessWindows(STKAccessFile) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
must be called before setSSR
generateTakeImages(EOSModel, int, Sensor, int, STKAccessFile) - Static method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
generateTakeImages(EOSModel, int, Sensor, STKAccessFile) - Static method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
for tasks with no SSR use.
generateTakeImages(EOSModel, int, Sensor[], int, STKAccessFile[]) - Static method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
The sensors and csvFiles arrays are parallel with the accesses for each sensor in the corresponding file.
generation - Variable in class gov.nasa.javaGenes.core.Population
 
generation - Variable in class gov.nasa.javaGenes.core.Run
 
generationIsComplete() - Method in class gov.nasa.javaGenes.core.Breeder
 
generationJustStarting() - Method in class gov.nasa.javaGenes.core.Breeder
 
generationNotComplete(int) - Method in class gov.nasa.javaGenes.core.Breeder
 
generationTimer - Variable in class gov.nasa.javaGenes.core.Run
 
get(int) - Method in class gov.nasa.alsUtility.Distribution
 
get(int) - Method in class gov.nasa.alsUtility.DoubleInterval
 
get(int) - Method in class gov.nasa.alsUtility.DoublesList
 
get(int) - Method in class gov.nasa.alsUtility.GrowOnlyArray
 
get(int) - Method in class gov.nasa.alsUtility.RandomDistribution
 
get(int) - Method in class gov.nasa.alsUtility.RandomGaussianDistribution
 
get(int) - Method in class gov.nasa.javaGenes.chemistry.Molecules
 
get() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider
 
get() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
get() - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
get(int) - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
get(int) - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
get(int) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
get(int) - Method in class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider
 
getAW(TaskWeight, int) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
getAccessWindow() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowWeight
 
getAccessWindow(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
getAccessWindowList() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
getAccessWindows() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
getAllAtoms(String) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getAllTakeImages() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
getAllele(int, int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
getAllele(String) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
getAlleles() - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getAlleles() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getAlleles() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
getAndClearLastTabSeparatedResults() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
getAngle(Vertex, Vertex, Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
getAngle(Vertex, Vertex, Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
getAngle() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
getAngleBetween(Vertex, Vertex) - Method in class gov.nasa.javaGenes.graph.Vertex
 
getArray(int) - Method in class gov.nasa.javaGenes.core.TeacherPopulation
do not modify return value
getArray() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
getArray(int) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
getArrayOfAllValues() - Method in class gov.nasa.alsUtility.IntegerInterval
 
getAtom(int) - Method in class gov.nasa.javaGenes.chemistry.Bond
 
getAtom(int) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getAtom(String) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getAtomicNumber() - Method in class gov.nasa.javaGenes.chemistry.Atom
 
getAtomicNumber() - Method in class gov.nasa.javaGenes.chemistry.Element
 
getAtomicWeight() - Method in class gov.nasa.javaGenes.chemistry.Element
 
getAvailabilityTimeline() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getAvailableNodeAtOrAfter(int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
getAzimuth() - Method in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
getBadNumberCount() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getBestFitnessAllowed() - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
getBetween() - Method in class gov.nasa.alsUtility.LogComparisons
 
getBetweenFraction(int) - Method in class gov.nasa.alsUtility.LogComparisons
 
getBetweenFranction() - Method in class gov.nasa.alsUtility.LogComparisons
 
getBodiesNames() - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
getBodiesNames() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
getBond(int) - Method in class gov.nasa.javaGenes.chemistry.Atom
Return the i'th bond
getBondTypeIntegerCode() - Method in class gov.nasa.javaGenes.chemistry.Bond
Return a value to be used as an array index (starting at 0).
getBoolean() - Static method in class gov.nasa.alsUtility.RandomNumber
flip a virtual coin
getBoolean() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
getBottomCornerPoint() - Method in class gov.nasa.alsUtility.Brick3d
 
getBrokenEdges() - Method in class gov.nasa.javaGenes.graph.BrokenGraph
 
getBufferedReader(String) - Static method in class gov.nasa.alsUtility.IO
 
getCapacityArray() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
for test and debug
getChemicalSymbol(BufferedReader) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
 
getChildMaker(int) - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
getChildMaker(int) - Method in class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
return a ChildMaker based on a weighted roulette wheel.
getChildMakersUsed() - Method in class gov.nasa.javaGenes.core.Evolvable
 
getChosenIndex(Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getChosenIndex(IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getChosenIndices(int, Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getChosenIndices(int, IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getChosenIndices(int[], int, IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getChromosome() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIndividual
 
getChromosome() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getChromosome() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
getChromosomeArraySizes() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getChromosomeArraySizes() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSi
 
getChromosomeParameters(String[]) - Method in class gov.nasa.javaGenes.forceFields.RunChromosome
 
getClass(String) - Static method in class gov.nasa.alsUtility.Utility
 
getComment() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getConnectedSubgraph(Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
Walks the graph starting at Vertex v adding copies of all edges and vertices to the new graph.
getConnectionTable() - Method in class gov.nasa.javaGenes.graph.Graph
 
getCount(Object) - Method in class gov.nasa.alsUtility.KeyCounter
 
getCurrent() - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
getCurrent() - Method in class gov.nasa.alsUtility.ReinitializableFloatWithFactor
 
getCurrent() - Method in class gov.nasa.alsUtility.ReinitializableInt
 
getCurrentLineNumber() - Method in class gov.nasa.alsUtility.FieldRecordText
 
getCurrentLineNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
getCurrentTemperature() - Method in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
getCurrentWeightSumFromCalculation() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getCutoff() - Method in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
getCutoff(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getCutoff(ThreeBody) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getCutoff(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getCutoff(ThreeBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getCutoffTerm(double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getData(String) - Method in class gov.nasa.alsUtility.DataTable
get the data associated with a name.
getDataNames() - Method in class gov.nasa.alsUtility.ManySamples
 
getDatum(int) - Method in class gov.nasa.alsUtility.Sample
 
getDeathRowIndex(int[], Population) - Method in class gov.nasa.javaGenes.core.AntiTournament
 
getDeathRowIndex(int[], IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.AntiTournament
 
getDeathRowIndex(int[], IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.AntiTournamentLocal
 
getDeathRowIndex(int[], Population) - Method in interface gov.nasa.javaGenes.core.ChooseForDeath
 
getDeathRowIndex(int[], IntegerInterval, Population) - Method in interface gov.nasa.javaGenes.core.ChooseForDeath
 
getDifference(Potential) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyTestCase
 
getDimerForce() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getDirectedEdge() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
 
getDirectedEdge(int) - Method in class gov.nasa.javaGenes.graph.DirectedGraph
 
getDirectedEdge() - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getDirectedEdge(Predicate) - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getDirectedVertex() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
 
getDirectedVertex(int) - Method in class gov.nasa.javaGenes.graph.DirectedGraph
 
getDirectedVertex() - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getDirectedVertex(Predicate) - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getDistance(Vertex, Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
getDistance(Vertex, Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
getDistanceTo(Vertex) - Method in class gov.nasa.javaGenes.graph.Vertex
 
getDouble() - Static method in class gov.nasa.alsUtility.RandomNumber
 
getDouble(double) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getDouble(DoubleInterval) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getDouble(BufferedReader) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
 
getDouble() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
getDouble(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
getDoubleInterval(int) - Method in class gov.nasa.alsUtility.MinMaxes
do not modify return value
getDoubleModulo(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
getDoubleValue(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
getDoubleValueModulo(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
getDown() - Method in class gov.nasa.alsUtility.LogComparisons
 
getDownFraction(int) - Method in class gov.nasa.alsUtility.LogComparisons
 
getDownFranction() - Method in class gov.nasa.alsUtility.LogComparisons
 
getDummySize(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
getDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
getDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
getDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
getDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.TimeInterval
 
getDurationOf(String, String) - Static method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
getEOSschedulingParameters(String[]) - Method in class gov.nasa.javaGenes.EOSscheduling.runEOSscheduling
 
getEarliestStartTimeInNode(SlewNode, int, SlewRequirement, Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
getEdge(int) - Method in class gov.nasa.javaGenes.graph.Graph
 
getEdge(int) - Method in class gov.nasa.javaGenes.graph.Vertex
 
getEdge() - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getEdge(Predicate) - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getEdgeIterator() - Method in class gov.nasa.javaGenes.graph.Graph
 
getEdgeIterator() - Method in class gov.nasa.javaGenes.graph.Vertex
 
getEdgesSize() - Method in class gov.nasa.javaGenes.graph.Graph
 
getElement(int) - Method in class gov.nasa.javaGenes.chemistry.Element
 
getElement(String) - Static method in class gov.nasa.javaGenes.chemistry.Element
 
getElementName() - Method in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
getElevation() - Method in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
getEnd() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getEnd() - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
getEnd() - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
getEnd() - Method in class gov.nasa.javaGenes.EOSscheduling.TimeInterval
 
getEnd() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
getEndVertex() - Method in class gov.nasa.javaGenes.graph.Trail
 
getEnergy() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getEnergy(int) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
getEnergy(int) - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
only works if a proper (xyz) molecule with an energy value is there!
getEnergy(Bodies[]) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getEnergy(Bodies[], double[]) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getEnergy(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getEnergy(MultiBody) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getEnergy(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getEnergy(MultiBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getEnergy(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getEnergy(ThreeBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getEnergy(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
getEnergy(ThreeBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
getEnergy(MultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.Tersoff
Calculate the energies for a set of multi-bodies.
getEnergyInterval() - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
getEquivalent(Graph, Edge) - Method in class gov.nasa.javaGenes.graph.Graph
 
getEquivalent(Graph, Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
 
getEvolvable() - Method in class gov.nasa.javaGenes.core.Individual
 
getEvolvable(int) - Method in class gov.nasa.javaGenes.core.Population
 
getEvolvableHeader() - Method in class gov.nasa.javaGenes.core.Population
 
getEvolvableHeader() - Method in class gov.nasa.javaGenes.forceFields.ChromosomePopulation
 
getExtendedTypeObject() - Method in class gov.nasa.javaGenes.chemistry.Atom
returns a ExtendedTypeKey (a internal class) to represent the extended type of this atom, usually as a hashtable key.
getExtendedTypeObject() - Method in class gov.nasa.javaGenes.graph.Vertex
 
getExtendedTypeString() - Method in class gov.nasa.javaGenes.chemistry.Atom
Create a string to represent the extended type of this atom.
getExtendedTypeString() - Method in class gov.nasa.javaGenes.graph.Vertex
 
getExtendedVertexTypesCounter() - Method in class gov.nasa.javaGenes.graph.Graph
 
getFilename() - Method in class gov.nasa.alsUtility.FieldRecordText
 
getFilename() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
getFilename() - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
getFilename() - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
getFilename() - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
getFirst() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getFirstIndex(PermutationEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
getFirstIndex(PermutationEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
getFirstIndex() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
getFirstIndex(PermutationEvolvable) - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
getFirstIndicesArray(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
getFirstIndicesArray(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
getFirstLineOfFile(String) - Static method in class gov.nasa.alsUtility.Utility
 
getFirstNode() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
getFirstNode() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
getFirstParentIndicesArray(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
getFirstWindow(TaskPlacementData, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
getFirstWindow(TaskPlacementData, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFromChosenWindowPlacer
 
getFirstWindow(TaskPlacementData, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFromRandomWindowPlacer
 
getFitness(int) - Method in class gov.nasa.javaGenes.core.FitnessMultiObjective
 
getFitness() - Method in class gov.nasa.javaGenes.core.Individual
 
getFitness(int) - Method in class gov.nasa.javaGenes.core.Population
 
getFitnessArray() - Method in class gov.nasa.javaGenes.core.Fitness
 
getFitnessArray() - Method in class gov.nasa.javaGenes.core.FitnessBad
 
getFitnessArray() - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
getFitnessArray() - Method in class gov.nasa.javaGenes.core.FitnessMultiObjective
 
getFitnessFunction() - Method in class gov.nasa.javaGenes.core.Breeder
 
getFitnessFunction(int) - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
getFitnessFunction() - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
getFitnessFunction() - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
getFitnessFunctionNames() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
getForce(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
getForce(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getForce(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
getFromChain(int) - Method in class gov.nasa.javaGenes.core.ChildMakerChain
 
getFunction(int) - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
getFunction(int) - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
getFunctionByIndex(int) - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
getGaussian() - Static method in class gov.nasa.alsUtility.RandomNumber
 
getGaussian(double) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getGeneration() - Method in class gov.nasa.javaGenes.core.Population
 
getGenerationIndex() - Method in class gov.nasa.javaGenes.core.Breeder
 
getGrade() - Method in class gov.nasa.javaGenes.core.StudentFitness
 
getGraph() - Method in class gov.nasa.javaGenes.graph.BrokenGraph
 
getGraph() - Method in class gov.nasa.javaGenes.graph.GraphIndividual
 
getGraphClass() - Method in class gov.nasa.javaGenes.graph.BrokenGraph
 
getGroundStationReportHeader() - Static method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getGroup() - Method in class gov.nasa.javaGenes.chemistry.Element
 
getHeader() - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
getHeaderFragment() - Method in class gov.nasa.alsUtility.LogComparisons
 
getHeaderString() - Static method in class gov.nasa.alsUtility.Sample
 
getHigh() - Method in class gov.nasa.alsUtility.Sample
 
getHorizon() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getHorizon() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
getHorizon() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
getHowMany() - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
getImmigrant(int) - Method in class gov.nasa.javaGenes.forceFields.Immigrants
 
getInVertex() - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
getIndex(int) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getIndex(int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
getIndex(Individual) - Method in class gov.nasa.javaGenes.core.Population
 
getIndex(String) - Method in class gov.nasa.javaGenes.forceFields.AlleleSetup
 
getIndex(Species) - Method in class gov.nasa.javaGenes.forceFields.Species2IndexMap
 
getIndexAt(int) - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
getIndexRange() - Method in class gov.nasa.javaGenes.core.Population
 
getIndexToKill(Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.NeighboringPairsSelector
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectAll
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
getIndices(int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndices
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumber
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectOne
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs
 
getIndices(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Selector
 
getIndices(String) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
getIndicesArray(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
getIndicesArray(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs
necessary because the pairs can overlap
getIndicesArray(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Selector
 
getIndicesArray(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Selector
 
getIndividual(int) - Method in class gov.nasa.javaGenes.core.Population
 
getInitial() - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
getInitial() - Method in class gov.nasa.alsUtility.ReinitializableFloatWithFactor
 
getInitial() - Method in class gov.nasa.alsUtility.ReinitializableInt
 
getInitialNodeForNodeArray() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
getInitialNodeForNodeArray() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
getInitialSize() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getInputEdge(int) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
getInputEdgeIterator() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
getIntCount(Object) - Method in class gov.nasa.alsUtility.KeyCounter
For testint only.
getIntFromArray(int[]) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getInteger(IntegerInterval) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getInteger(BufferedReader) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
 
getInteger() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
getIntegerTimeAt(Date) - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
getInterval(int) - Method in class gov.nasa.alsUtility.Brick3d
 
getInterval() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getInterval(String) - Method in class gov.nasa.javaGenes.forceFields.AlleleSetup
 
getLastCheckpointDate() - Static method in class gov.nasa.javaGenes.core.Checkpointer
 
getLastCheckpointDateLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
getLastGeneration(int) - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
getLastGeneration() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
getLastIndex() - Method in class gov.nasa.javaGenes.core.Population
 
getLastIndex() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
getLastLineOfFile(String) - Static method in class gov.nasa.alsUtility.Utility
 
getLastTabSeparatedResults() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
getLengthScale() - Static method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
getLengthsAndAngles() - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
getLine(BufferedReader) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
 
getLine() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
getLinearValue(double, double, double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
best <= worst
getLocationVector() - Method in class gov.nasa.javaGenes.graph.Vertex
 
getLogHeaderString() - Method in class gov.nasa.javaGenes.core.Population
 
getLogString(FitnessFunction) - Method in class gov.nasa.javaGenes.core.Population
 
getLong() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
getLow() - Method in class gov.nasa.alsUtility.Sample
 
getMark() - Method in class gov.nasa.alsUtility.Mark
 
getMax() - Method in class gov.nasa.alsUtility.WeightedStatistics
of values with non-zero weight
getMaxAbsoluteSlew() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getMaxAbsoluteSlew() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
getMaxAbsoluteSlew() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorNone
 
getMaxCurrentWeight() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getMaxSlewTimeFrom(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getMaxSlewTimeFrom(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
getMaximumBondTypes() - Static method in class gov.nasa.javaGenes.chemistry.Bond
Return the highest number that can represent a bond type (3 for triple presently)
getMean() - Method in class gov.nasa.alsUtility.Sample
 
getMean() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getMemory() - Method in class gov.nasa.javaGenes.core.Population
 
getMin() - Method in class gov.nasa.alsUtility.WeightedStatistics
of values with non-zero weight
getMinCurrentWeight() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getMinumumEvolvableSize() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete
 
getMolecule() - Method in class gov.nasa.javaGenes.chemistry.MoleculeIndividual
 
getMolecule(int) - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
getMolecule() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
getMultiBodies(int) - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
getMultiBodiesForOneEnergy(int) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
getMustRampToEnd() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
getN(int) - Method in class gov.nasa.alsUtility.LogComparisons
 
getN() - Method in class gov.nasa.alsUtility.LogComparisons
 
getN() - Method in class gov.nasa.alsUtility.Sample
 
getN() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getName() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getName() - Method in class gov.nasa.javaGenes.EOSscheduling.SensorType
 
getName() - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
getName() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getName(int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
getName(int) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
getName() - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
getNameArray() - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
getNameArray() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
getNameArray() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjectiveToOne
 
getNames() - Method in class gov.nasa.alsUtility.LogComparisons
 
getNeighboringPairsSelector() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
getNewChromosome(Chromosome) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeCrossover
 
getNewChromosome(AlleleTemplate) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
getNewChromosome(AlleleTemplate) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
getNewFitness() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
getNewFitness() - Method in class gov.nasa.javaGenes.core.StudentFitnessFunction
 
getNext() - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
getNextCrossTrackSlew() - Method in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlewTest
 
getNoEvolutionValue() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getNodeAtTime(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
getNodeTypePairsShortestTrailCounts() - Method in class gov.nasa.javaGenes.graph.Graph
 
getNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
getNumber() - Method in class gov.nasa.javaGenes.forceFields.Immigrant
 
getNumber() - Method in class gov.nasa.javaGenes.graph.Vertex
 
getNumberOfAtoms() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getNumberOfAtoms() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
getNumberOfCycles() - Method in class gov.nasa.javaGenes.graph.Graph
 
getNumberOfSSRsegments() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
getNumberOfSSRsegments() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
getNumberOfSatellites() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getNumberOfTasks() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getObject() - Method in class gov.nasa.alsUtility.ObjectCache
 
getObject() - Method in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
getObjectFromArray(Object[]) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getOnTimes(int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
getOne(Atom) - Static method in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
getOne(Object, Object, int) - Static method in class gov.nasa.javaGenes.graph.Graph.TrailKey
DANGEROUS: do not modify the objects returned!
getOneBodyArray() - Method in class gov.nasa.javaGenes.forceFields.Bodies
 
getOutVertex() - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
getOutputEdge(int) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
getOutputEdgeIterator() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
getParameter(int) - Method in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
 
getParameter(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
getParameter(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewRequirement
 
getParameterValues(String[], String) - Static method in class gov.nasa.javaGenes.core.utility.CoreUtility
 
getParameters() - Method in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
slow
getParameters() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
getParameters() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewRequirement
 
getParameters() - Method in class gov.nasa.javaGenes.core.Run
 
getParentIndices(int, Population) - Method in interface gov.nasa.javaGenes.core.ChooseParents
 
getParentIndices(int, IntegerInterval, Population) - Method in interface gov.nasa.javaGenes.core.ChooseParents
 
getParentIndices(int, Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
getParentIndices(int, Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getParentIndices(int, IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
getParentIndices(int, IntegerInterval, Population) - Method in class gov.nasa.javaGenes.core.TournamentLocal
 
getParetoFront() - Method in class gov.nasa.javaGenes.core.Population
 
getPeriod() - Method in class gov.nasa.javaGenes.chemistry.Element
 
getPermutationEvolvable() - Method in class gov.nasa.javaGenes.permutation.PermutationIndividual
 
getPrevious() - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
getPrintWriter(String) - Static method in class gov.nasa.alsUtility.IO
 
getPrintWriter(String, boolean) - Static method in class gov.nasa.alsUtility.IO
 
getPriority() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
getProbability(double) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getProperty(String) - Method in class gov.nasa.alsUtility.PropertiesList
 
getQuadraticExtremumX(double[]) - Static method in class gov.nasa.alsUtility.MathUtility
 
getQuadraticFactors(double, double, double, double, double, double) - Static method in class gov.nasa.alsUtility.MathUtility
 
getQuadraticMinimum(double[], EvolvableDoubleList[], int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
getR() - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
getRJI() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
getRJK() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
getRMS() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getRadius(int) - Static method in class gov.nasa.alsUtility.AmericanWireGauge
 
getRampArray() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
getRandomDirectedVertex(Predicate) - Method in class gov.nasa.javaGenes.graph.DirectedGraph
 
getRandomEdge() - Method in class gov.nasa.javaGenes.graph.Graph
 
getRandomEdge(Predicate) - Method in class gov.nasa.javaGenes.graph.Graph
 
getRandomEdge() - Method in class gov.nasa.javaGenes.graph.Trail
 
getRandomEdge(Predicate) - Method in class gov.nasa.javaGenes.graph.Trail
 
getRandomElement() - Method in class gov.nasa.alsUtility.ExtendedVector
 
getRandomElement(Predicate) - Method in class gov.nasa.alsUtility.ExtendedVector
return a random element that satisfies Predicate p
getRandomEvolvable() - Method in class gov.nasa.javaGenes.core.HFC.Breeder
 
getRandomEvolvable() - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
getRandomEvolvable() - Method in class gov.nasa.javaGenes.core.RandomEvolvableProducer
 
getRandomEvolvable() - Method in class gov.nasa.javaGenes.evolvableDoubleList.RandomEvolvableDoubleListProducer
 
getRandomGaussianValue(double, double) - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getRandomLogValue() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getRandomSelector(int, int, int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
getRandomSubBreeder() - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
getRandomUniqueIndices(int) - Method in class gov.nasa.alsUtility.IntegerInterval
for good performance, number must be fairly small and much smaller than intervalInclusive()
getRandomValue() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getRandomValueAbove(double) - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getRandomValueBelow(double) - Method in class gov.nasa.javaGenes.forceFields.Allele
 
getRandomVertex() - Method in class gov.nasa.javaGenes.graph.Graph
 
getRandomVertex(Predicate) - Method in class gov.nasa.javaGenes.graph.Graph
 
getRange() - Method in class gov.nasa.alsUtility.Sample
 
getRange() - Method in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
getRemainingCapacity() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRNode
 
getReportHeader() - Static method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getReportHeader() - Static method in class gov.nasa.javaGenes.EOSscheduling.Task
 
getSSRcapacity() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getSSRtime() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getSSRtimeline() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getSSRuse() - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
getSSRuse() - Method in class gov.nasa.javaGenes.EOSscheduling.TakeImage
 
getSample(String) - Method in class gov.nasa.alsUtility.ManySamples
 
getSatellite() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getSatellite(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getSatellite() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getSatellites() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getScheduledPrioritySum(EOSModel) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
getScheduledTaskCount() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
getSecondBodies() - Method in class gov.nasa.javaGenes.forceFields.OneBody
 
getSecondIndex(PermutationEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
getSecondIndex(PermutationEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
getSecondIndex(PermutationEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
getSecondIndex(PermutationEvolvable, int) - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
getSecondIndicesArray(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
getSecondIndicesArray(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
getSecondParentIndicesArray(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
getSeed() - Static method in class gov.nasa.alsUtility.RandomNumber
 
getSegmentCoordinates(int) - Method in class gov.nasa.alsUtility.Brick3dWithSegments
 
getSelector() - Method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMaker
 
getSensor() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getSensor() - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
getSensorNumber(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
getSensorNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
getSensorType() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getSensors() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getSensors() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getSensors() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
getSeparation(int, double, double) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
getSeparation(int, double, double) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
getSerialized(String) - Static method in class gov.nasa.alsUtility.Utility
 
getSerialized(URL) - Static method in class gov.nasa.alsUtility.Utility
 
getSerialized(String) - Static method in class gov.nasa.javaGenes.core.Checkpointer
 
getSideLength(int) - Method in class gov.nasa.alsUtility.Brick3d
 
getSize() - Method in class gov.nasa.alsUtility.LogComparisons
 
getSize() - Method in class gov.nasa.javaGenes.core.Evolvable
 
getSize() - Method in class gov.nasa.javaGenes.core.Population
 
getSize() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
getSize(int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
getSize(int) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
getSize() - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
getSize() - Method in class gov.nasa.javaGenes.graph.Graph
 
getSize() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
getSlew() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
getSlewArray() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
for test and debug
getSlewMotor() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getSlewMotors() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
getSlewPoint() - Method in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
 
getSlewRequirement() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getSlewRequirement(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
getSlewRequirement() - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
getSlewRequirement(PointingRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getSlewRequirement() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
getSlewTimeline() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
getSlewTimeline() - Method in class gov.nasa.javaGenes.EOSscheduling.Slewable
 
getSlewable() - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
getSmallerParent(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
getSmallest(Evolvable[]) - Static method in class gov.nasa.javaGenes.core.Evolvable
 
getSpecies2IndexMap() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
getSpeciesIndex(String) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getSpread() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getStandarPartOfLogHeaderString() - Method in class gov.nasa.javaGenes.core.Population
 
getStandardDeviation() - Method in class gov.nasa.alsUtility.Sample
 
getStart() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getStart() - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
getStart() - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
getStart() - Method in class gov.nasa.javaGenes.EOSscheduling.TimeInterval
 
getStart() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
getStartTime(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
getStartTime() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
getStartTimesArray() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
for test and debug
getStartTimesArray() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
getStartTimesArray() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
getStartVertex() - Method in class gov.nasa.javaGenes.graph.Trail
 
getString() - Method in class gov.nasa.javaGenes.core.TokenizeInput
 
getStringFromArray(String[]) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getStringKey(Vertex, Vertex, int) - Method in class gov.nasa.javaGenes.graph.Graph
Represents a path with a string.
getStringKey() - Method in class gov.nasa.javaGenes.graph.Trail
 
getStringKeys(Hashtable) - Static method in class gov.nasa.alsUtility.Utility
 
getSubBreeder(int) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
getSumOfWeights() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getSymbol() - Method in class gov.nasa.javaGenes.chemistry.Element
 
getTabSeparatedResults() - Method in class gov.nasa.alsUtility.LogComparisons
 
getTask(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getTask() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
getTaskList() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
 
getTaskPlacement(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
getTaskPrioritySum() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
getTeachers() - Method in class gov.nasa.javaGenes.core.BreederWithTeachers
 
getThirdBodies() - Method in class gov.nasa.javaGenes.forceFields.SecondBody
 
getTime() - Method in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
getTime(String[]) - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
getTime() - Method in class gov.nasa.javaGenes.core.Population
 
getTimeAtMiddle() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
getToInnerCuttof() - Method in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
getTopCornerPoint() - Method in class gov.nasa.alsUtility.Brick3d
 
getTotalNumberOfKidsProduced() - Method in class gov.nasa.javaGenes.core.Breeder
 
getTotalNumberOfKidsProduced() - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
getTotalSlewTime(Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
getTotalSlewTime() - Method in class gov.nasa.javaGenes.EOSscheduling.Slewable
 
getTotalSlewing(Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
getTrailBetween(Vertex, Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
 
getTypeString() - Method in class gov.nasa.javaGenes.graph.Edge
 
getTypeString() - Method in class gov.nasa.javaGenes.graph.Vertex
 
getUniqueIndex(int, int) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getUniqueLogValue(Individual) - Method in class gov.nasa.javaGenes.core.Population
 
getUniqueLogValueHeader() - Method in class gov.nasa.javaGenes.core.Population
 
getUnitCell() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
getUp() - Method in class gov.nasa.alsUtility.LogComparisons
 
getUpFraction(int) - Method in class gov.nasa.alsUtility.LogComparisons
 
getUpFranction() - Method in class gov.nasa.alsUtility.LogComparisons
 
getUpdateAndPropagatable(int) - Method in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
 
getValence() - Method in class gov.nasa.javaGenes.chemistry.Atom
Return the valence of this element
getValence() - Method in class gov.nasa.javaGenes.chemistry.Bond
Return the amount of valence this bond uses
getValence() - Method in class gov.nasa.javaGenes.chemistry.Element
 
getValue() - Method in class gov.nasa.alsUtility.integer
 
getValue() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
getValue(int, int) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
return the value at the indicated indices
getValue(int) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
getValue(int, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
getVariance() - Method in class gov.nasa.alsUtility.Sample
 
getVariations(Evolvable) - Method in interface gov.nasa.javaGenes.core.PhenotypeChanger
 
getVariations(Evolvable) - Method in class gov.nasa.javaGenes.core.PhenotypeChangerDummy
 
getVector3d(DoubleInterval) - Static method in class gov.nasa.alsUtility.RandomNumber
 
getVertex(int) - Method in class gov.nasa.javaGenes.graph.Edge
 
getVertex(int) - Method in class gov.nasa.javaGenes.graph.Graph
 
getVertex() - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getVertex(Predicate) - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
getVertexAndTrailIterator(Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
 
getVertexInEdgeClosestToEnd(Edge, Vertex) - Method in class gov.nasa.javaGenes.graph.Trail
 
getVertexIterator() - Method in class gov.nasa.javaGenes.graph.Graph
 
getVerticesForDivision(Graph) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
 
getVerticesSize() - Method in class gov.nasa.javaGenes.graph.Graph
 
getWavelength(double) - Static method in class gov.nasa.alsUtility.Constants
 
getWeight() - Method in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
getWeight(int) - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
getWeight() - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
getWeight(int) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getWeightList() - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
getWeightSum() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
getWeightedSum() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
getWindowNumber() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
getWorst(Evolvable[], Fitness[]) - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
getWorst(Evolvable[], Fitness[]) - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries
 
getX() - Method in class gov.nasa.alsUtility.Vector3d
 
getXyz() - Method in class gov.nasa.javaGenes.graph.Vertex
get the physical location of the vertex
getY() - Method in class gov.nasa.alsUtility.Vector3d
 
getZ() - Method in class gov.nasa.alsUtility.Vector3d
 
goodMoves - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
goodSize - Variable in class gov.nasa.javaGenes.core.FitnessFunctionBadSize
 
gov.nasa.alsUtility - package gov.nasa.alsUtility
 
gov.nasa.javaGenes.EOSscheduling - package gov.nasa.javaGenes.EOSscheduling
 
gov.nasa.javaGenes.EOSscheduling.HBSS - package gov.nasa.javaGenes.EOSscheduling.HBSS
 
gov.nasa.javaGenes.chemistry - package gov.nasa.javaGenes.chemistry
 
gov.nasa.javaGenes.core - package gov.nasa.javaGenes.core
 
gov.nasa.javaGenes.core.HFC - package gov.nasa.javaGenes.core.HFC
 
gov.nasa.javaGenes.core.utility - package gov.nasa.javaGenes.core.utility
 
gov.nasa.javaGenes.evolvableDoubleList - package gov.nasa.javaGenes.evolvableDoubleList
 
gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment - package gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment
 
gov.nasa.javaGenes.forceFields - package gov.nasa.javaGenes.forceFields
 
gov.nasa.javaGenes.graph - package gov.nasa.javaGenes.graph
 
gov.nasa.javaGenes.hillClimbing - package gov.nasa.javaGenes.hillClimbing
 
gov.nasa.javaGenes.main - package gov.nasa.javaGenes.main
 
gov.nasa.javaGenes.permutation - package gov.nasa.javaGenes.permutation
 
gov.nasa.javaGenes.simulatedAnnealing - package gov.nasa.javaGenes.simulatedAnnealing
 
gov.nasa.javaGenes.weightNetwork - package gov.nasa.javaGenes.weightNetwork
 
grid(jiggle.Graph, double) - Method in class gov.nasa.javaGenes.graph.GraphLayout
put the xy is the locations of each vertex near the points in a three-dimensional grid
grimReaper - Variable in class gov.nasa.javaGenes.core.BreederSteadyState2
 
grimReaper - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
groundStationAccessWindows - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
grow() - Method in class gov.nasa.alsUtility.GrowOnlyArray
 
growBy - Variable in class gov.nasa.alsUtility.GrowOnlyArray
 
growDirectedEdge(DirectedEdge) - Method in class gov.nasa.javaGenes.graph.DirectedGraph
add edge creating an undirected cycle
growDirectedVertex(DirectedVertex, DirectedEdge) - Method in class gov.nasa.javaGenes.graph.DirectedGraph
attached edge and acceptsOutput and attach them to a random vertex that will accept an input edge

H

HasInputEdgeFrom - class gov.nasa.javaGenes.graph.HasInputEdgeFrom.
 
HasInputEdgeFrom(DirectedVertex) - Constructor for class gov.nasa.javaGenes.graph.HasInputEdgeFrom
 
HasOutputEdgesTo - class gov.nasa.javaGenes.graph.HasOutputEdgesTo.
 
HasOutputEdgesTo(DirectedVertex) - Constructor for class gov.nasa.javaGenes.graph.HasOutputEdgesTo
 
Horizon - class gov.nasa.javaGenes.EOSscheduling.Horizon.
default timestep is seconds
Horizon() - Constructor for class gov.nasa.javaGenes.EOSscheduling.Horizon
 
Horizon(String, String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.Horizon
 
HorizonTest - class gov.nasa.javaGenes.EOSscheduling.HorizonTest.
 
HorizonTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
halfDistance - Variable in class gov.nasa.javaGenes.chemistry.UnitCell
 
hasAllAccessWindowsNow() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
hasAllele(int, int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
hasArray(String) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
hasBeenScheduled() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
hasBeenScheduledAlready - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
hasEdgeTo(Vertex) - Method in class gov.nasa.javaGenes.graph.Vertex
 
hasInputEdgeFrom(DirectedVertex) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
hasInputEdges() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
hasMore() - Method in class gov.nasa.javaGenes.forceFields.Immigrant
 
hasNormalNumbers(Vector3d) - Static method in class gov.nasa.alsUtility.Utility
 
hasOutputEdgeTo(DirectedVertex) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
hasOutputEdges() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
hasProperty(String) - Method in class gov.nasa.alsUtility.PropertiesList
 
hasThreeBody(Atom, Atom, Atom) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
hasTwoBody(Atom, Atom) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
hasUnitCell() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
hasVertexPairCloserThan(double) - Method in class gov.nasa.javaGenes.graph.Graph
 
hashCode() - Method in class gov.nasa.alsUtility.IntegerInterval
 
hashCode() - Method in class gov.nasa.alsUtility.Vector3d
 
hashCode() - Method in class gov.nasa.alsUtility.integer
 
hashCode() - Method in class gov.nasa.javaGenes.EOSscheduling.SensorType
 
hashCode() - Method in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
hashCode() - Method in class gov.nasa.javaGenes.chemistry.Element
 
hashCode() - Method in class gov.nasa.javaGenes.core.FitnessBad
 
hashCode() - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
hashCode() - Method in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
hashCode() - Method in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
header(String[]) - Method in class gov.nasa.alsUtility.LogComparisons
 
header() - Static method in class gov.nasa.alsUtility.VRMLUtility
 
headerFragment() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
headerString() - Static method in class gov.nasa.javaGenes.core.Individual
 
high() - Method in class gov.nasa.alsUtility.DoubleInterval
 
high() - Method in class gov.nasa.alsUtility.IntegerInterval
 
horizon - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
horizon - Variable in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
horizon - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
horizon - Variable in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
horizon - Variable in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
horizonIsValid() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
howMany - Variable in class gov.nasa.javaGenes.forceFields.MultiBody
 

I

INFINIT_TOKEN - Static variable in class gov.nasa.javaGenes.forceFields.Immigrants
 
INITIAL_SIZE - Static variable in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
 
IO - class gov.nasa.alsUtility.IO.
 
IO() - Constructor for class gov.nasa.alsUtility.IO
 
IOTest - class gov.nasa.alsUtility.IOTest.
 
IOTest(String) - Constructor for class gov.nasa.alsUtility.IOTest
 
Immigrant - class gov.nasa.javaGenes.forceFields.Immigrant.
 
Immigrant(FieldRecordText) - Constructor for class gov.nasa.javaGenes.forceFields.Immigrant
 
Immigrant(String) - Constructor for class gov.nasa.javaGenes.forceFields.Immigrant
 
ImmigrantTest - class gov.nasa.javaGenes.forceFields.ImmigrantTest.
 
ImmigrantTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ImmigrantTest
 
Immigrants - class gov.nasa.javaGenes.forceFields.Immigrants.
 
Immigrants(String) - Constructor for class gov.nasa.javaGenes.forceFields.Immigrants
 
Immigrants(FieldRecordText) - Constructor for class gov.nasa.javaGenes.forceFields.Immigrants
 
ImmigrantsTest - class gov.nasa.javaGenes.forceFields.ImmigrantsTest.
 
ImmigrantsTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ImmigrantsTest
 
IncrementIterator - class gov.nasa.alsUtility.IncrementIterator.
 
IncrementIterator(double, double, int) - Constructor for class gov.nasa.alsUtility.IncrementIterator
 
IndexIterator - class gov.nasa.alsUtility.IndexIterator.
 
IndexIterator() - Constructor for class gov.nasa.alsUtility.IndexIterator
 
IndexIterator(int) - Constructor for class gov.nasa.alsUtility.IndexIterator
 
Indices - class gov.nasa.javaGenes.evolvableDoubleList.Indices.
 
Indices() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.Indices
under normal conditions this constructor is used
Indices(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.Indices
for testing
IndicesTest - class gov.nasa.javaGenes.evolvableDoubleList.IndicesTest.
 
IndicesTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.IndicesTest
 
Individual - class gov.nasa.javaGenes.core.Individual.
Represents a genetic software individual.
Individual(Evolvable, FitnessFunction) - Constructor for class gov.nasa.javaGenes.core.Individual
Sets the evolvable to Evolvable e and calculates the fitness using FitnessFunction f.
Individual(TokenizeInput) - Constructor for class gov.nasa.javaGenes.core.Individual
 
Individual(Fitness) - Constructor for class gov.nasa.javaGenes.core.Individual
for testing only
IntegerInterval - class gov.nasa.alsUtility.IntegerInterval.
represent an interval from some low to some high integer
IntegerInterval() - Constructor for class gov.nasa.alsUtility.IntegerInterval
create an interval from 0 to 1
IntegerInterval(int, int) - Constructor for class gov.nasa.alsUtility.IntegerInterval
create an interval from x to y or y to x depending on which is lower
IntegerInterval(IntegerInterval) - Constructor for class gov.nasa.alsUtility.IntegerInterval
 
IntegerIntervalTest - class gov.nasa.alsUtility.IntegerIntervalTest.
 
IntegerIntervalTest(String) - Constructor for class gov.nasa.alsUtility.IntegerIntervalTest
 
IsEqual - class gov.nasa.alsUtility.IsEqual.
predicate to determine if object.Equals(another object)
IsEqual(Object) - Constructor for class gov.nasa.alsUtility.IsEqual
 
IsInstanceOf - class gov.nasa.alsUtility.IsInstanceOf.
predicate to determine if objects are isInstance() of a class
IsInstanceOf(Class) - Constructor for class gov.nasa.alsUtility.IsInstanceOf
 
IsInstanceOf(String) - Constructor for class gov.nasa.alsUtility.IsInstanceOf
 
IsMarked - class gov.nasa.alsUtility.IsMarked.
 
IsMarked(boolean) - Constructor for class gov.nasa.alsUtility.IsMarked
 
Iterator - interface gov.nasa.alsUtility.Iterator.
 
immigrant - Variable in class gov.nasa.javaGenes.forceFields.ImmigrantTest
 
immigrants - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
immigrants - Variable in class gov.nasa.javaGenes.forceFields.Immigrants
 
immigrants - Variable in class gov.nasa.javaGenes.forceFields.ImmigrantsTest
 
immigrate(ChromosomePopulation, AlleleTemplate, FitnessFunction) - Method in class gov.nasa.javaGenes.forceFields.Immigrants
 
in - Variable in class gov.nasa.alsUtility.FieldRecordText
 
includeBottom - Variable in class gov.nasa.alsUtility.DoubleInterval
does this interval include the bottom most value?
includeTop - Variable in class gov.nasa.alsUtility.DoubleInterval
does this interval include to most value?
includes(AccessWindow) - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
includes(Horizon) - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
includes(int) - Method in class gov.nasa.javaGenes.EOSscheduling.TimeInterval
 
includes(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
includes(Node) - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
is the time covered by 'node' inside this?
incompatibleSlewInMiddle(SlewRequirement, SlewNode, SlewNode, Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
increment() - Method in class gov.nasa.alsUtility.IncrementIterator
 
increment() - Method in class gov.nasa.alsUtility.IndexIterator
 
increment() - Method in class gov.nasa.alsUtility.integer
 
incrementBestFitnessAllowed(double) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
incrementHowMany() - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
index() - Method in class gov.nasa.alsUtility.IndexIterator
 
indexDifferenceSum - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
indexInPrevious(int, int[]) - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
indexOfGreatest(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
indexOfLeast(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
indexOnUnschedulable(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
used by HBSS.Scheduler to fill in tasks that contention found to be unschedulable
indexOnUnschedulableTest(int, int[]) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvableTest
 
indices - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
indices - Variable in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
indices - Variable in class gov.nasa.javaGenes.forceFields.AlleleSetup
 
indicesRange - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
indicesToSelect - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndices
 
infinitNumber - Variable in class gov.nasa.javaGenes.forceFields.Immigrant
 
initPeriodicTable() - Static method in class gov.nasa.javaGenes.chemistry.Element
 
initialChildMaker - Variable in class gov.nasa.javaGenes.core.ChildMakerChain
 
initialTemperature - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
initialValue - Variable in class gov.nasa.alsUtility.ReinitializableFloat
 
initialValue - Variable in class gov.nasa.alsUtility.ReinitializableInt
 
initialWeights - Variable in class gov.nasa.javaGenes.weightNetwork.WeightList
 
initialize() - Static method in class gov.nasa.alsUtility.RandomNumber
 
initialize() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
initialize() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
initialize() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeFactory
only call when all Nodes are no longer needed (or suffer a horrible fate)
initialize() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
initialize() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
must be called before anything else.
initializeAllTimelines() - Static method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
initializeBestFitnessAllowed(Population, double) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
initializeCSi() - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
initializeGroundStationAccess() - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
initializeIndexRange(Population) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
initializePromotionReferences() - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
initializeSubBreeders(Population, double) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
initializeWeightSum() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
initializeWeightSum() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
input - Variable in class gov.nasa.javaGenes.core.TokenizeInput
 
inputDirectory - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
inputEdges - Variable in class gov.nasa.javaGenes.graph.DirectedVertex
 
insertAfter(int, Vector) - Method in class gov.nasa.alsUtility.ExtendedVector
 
insertAfter(int, EvolvableDouble[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
insertAt(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
assumes the insertion is legal
insertAt(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
assumes the insertion is legal
insertAt(Node, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
assumes the insertion is legal
insertAt(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
insertAt(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
assumes the SSR capacity is available
insertAt(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
insertAt(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
assumes the insertion is legal
insertAt(int, int, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
assumes the insertion is legal.
insertAt(int, int, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
insertAt(int, SchedulingData) - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
insertBefore(int, Vector) - Method in class gov.nasa.alsUtility.ExtendedVector
 
insertBefore(int, EvolvableDouble[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
insertDumpAt(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
assumes SSR is completely emptied.
insertDumpAt(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
insertEarliest(int, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
This will happen a lot and must be very fast.
insertIntoTimelines(AccessWindow, Task) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
Try to insert Task into location suggested by AccessWindow starting at begining of AccessWindow.
insertSizes - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
integer - class gov.nasa.alsUtility.integer.
represent a changeable integer (Java API class Integer cannot be modified)
integer() - Constructor for class gov.nasa.alsUtility.integer
 
integer(int) - Constructor for class gov.nasa.alsUtility.integer
 
integerSize - Static variable in class gov.nasa.javaGenes.chemistry.molFormat
 
internalGeneration - Variable in class gov.nasa.javaGenes.core.BreederElitist
 
internalGenerationsPerExternalGeneration - Variable in class gov.nasa.javaGenes.core.BreederElitist
 
interplateIntoTest(String, double, double, double, double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest
 
interpolateInto(DoubleInterval) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
interpolateInto(int, DoubleInterval) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
interval() - Method in class gov.nasa.alsUtility.DoubleInterval
 
interval() - Method in class gov.nasa.alsUtility.IntegerInterval
 
interval - Variable in class gov.nasa.alsUtility.RandomDistribution
the interval from within which random numbers are produced
interval - Variable in class gov.nasa.alsUtility.RandomGaussianDistribution
the interval from within which random numbers are produced
interval - Variable in class gov.nasa.alsUtility.VecMathTest
 
interval - Variable in class gov.nasa.javaGenes.forceFields.Allele
holds the maximum and minimum values for this allele
intervalInclusive() - Method in class gov.nasa.alsUtility.IntegerInterval
 
intervals - Variable in class gov.nasa.alsUtility.Brick3d
 
intervals - Variable in class gov.nasa.alsUtility.MinMaxes
 
intervals - Variable in class gov.nasa.javaGenes.forceFields.AlleleSetup
 
isAscending(int[]) - Static method in class gov.nasa.alsUtility.Utility
 
isAvailable() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
isBetween(double) - Method in class gov.nasa.alsUtility.DoubleInterval
 
isBetween(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
isCompatible(Compatible) - Method in interface gov.nasa.alsUtility.Compatible
 
isCompatible(Compatible) - Method in class gov.nasa.javaGenes.chemistry.Bond
Is the argument a bond with the same order?
isCompatible(Individual) - Method in class gov.nasa.javaGenes.core.Individual
 
isCompatible(Compatible) - Method in class gov.nasa.javaGenes.graph.BrokenEdge
are the edges compatible for merging (the associated vertex is not considered)
isCompatible(Compatible) - Method in class gov.nasa.javaGenes.graph.Edge
 
isConnected() - Method in class gov.nasa.javaGenes.graph.Graph
 
isCurrentlyEmpty() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
isCutoffInBounds(double) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
isCutoffInBounds(double) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
isDominatedBy(Fitness) - Method in class gov.nasa.javaGenes.core.Fitness
 
isDominatedBy(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessBad
 
isDominatedBy(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
isDominatedBy(Fitness) - Method in class gov.nasa.javaGenes.core.FitnessMultiObjective
 
isDone() - Method in class gov.nasa.alsUtility.Timer
has the allocated time been used?
isDuplicate(Individual) - Method in class gov.nasa.javaGenes.core.Population
 
isDurationAvailable(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
isElement(String) - Method in class gov.nasa.javaGenes.chemistry.Atom
 
isEmpty() - Method in class gov.nasa.alsUtility.DoubleInterval
are there any numbers that fall within this interval?
isEqual(Vector) - Method in class gov.nasa.alsUtility.ExtendedVector
are the elements equals()?
isEqual(String[], String[]) - Static method in class gov.nasa.alsUtility.Utility
 
isEqual(int[], int[]) - Static method in class gov.nasa.alsUtility.Utility
 
isEqual(EvolvableDouble) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
isEqual(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
isEqual(Indices) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
isEven(int) - Static method in class gov.nasa.alsUtility.Utility
 
isExecutable() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
isIn(Atom[]) - Method in class gov.nasa.javaGenes.chemistry.Atom
 
isIn(int, int[]) - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
isInAscendingOrder() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
isInVertex(Vertex) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
isIndexLegal(int) - Method in class gov.nasa.javaGenes.core.Population
 
isInfinit() - Method in class gov.nasa.javaGenes.forceFields.Immigrant
 
isInside(Vector3d) - Method in class gov.nasa.alsUtility.Brick3d
 
isInside(Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
isInside(Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
isLastEndNode(SlewNode) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
for testing only
isLastStartNode(SlewNode) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
for testing only
isLegal() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
isLegal() - Method in class gov.nasa.javaGenes.forceFields.Allele
is there any value that can fit in the interval?
isLegal() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
 
isLegal() - Method in class gov.nasa.javaGenes.graph.Edge
 
isLegal() - Method in class gov.nasa.javaGenes.graph.Graph
 
isMarked(boolean) - Method in class gov.nasa.alsUtility.Mark
 
isNewFunction(int) - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
isNewFunction(int) - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
isNonNegative() - Method in class gov.nasa.alsUtility.IntegerInterval
 
isOdd(int) - Static method in class gov.nasa.alsUtility.Utility
 
isOutVertex(Vertex) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
isPermutation() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
isPositive() - Method in class gov.nasa.alsUtility.DoubleInterval
 
isPositive(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
isProtected(Individual) - Method in class gov.nasa.javaGenes.core.Breeder
can protect certain individuals from losing an antiTournament and being replaced
isPure(boolean[]) - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
isReasonable() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
isReasonable() - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
isRequired(BrokenEdge) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
is it essential that is broken edge be satisfied during crossover.
isSWspecial(String) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
isSame(PermutationEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
isSame(Vertex) - Method in class gov.nasa.javaGenes.chemistry.Atom
is v exactly this?
isSame(Edge) - Method in class gov.nasa.javaGenes.chemistry.Bond
is the type and valence of these bonds the same?
isSame(Individual) - Method in class gov.nasa.javaGenes.core.Individual
 
isSame(Edge) - Method in class gov.nasa.javaGenes.graph.Edge
 
isSame(Vertex) - Method in class gov.nasa.javaGenes.graph.Vertex
 
isSame(PermutationEvolvable) - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
isScheduled() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
isTaskScheduled(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
isUnAvailable() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
isValid() - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
isValid() - Method in class gov.nasa.javaGenes.core.Fitness
 
isValid() - Method in class gov.nasa.javaGenes.core.FitnessBad
 
isValid() - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
isValid(int[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
 
isValidIndex(int) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
isWithin(int) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
isWithinLimits(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
isWithinLimits(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorNone
 
isWithinLimits(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.Slewable
 
isWithinRange(double) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
iterations - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 

K

KeyCounter - class gov.nasa.alsUtility.KeyCounter.
used to count the number of several different kinds of objects.
KeyCounter() - Constructor for class gov.nasa.alsUtility.KeyCounter
 
KeyCounterTest - class gov.nasa.alsUtility.KeyCounterTest.
 
KeyCounterTest(String) - Constructor for class gov.nasa.alsUtility.KeyCounterTest
 
kidsPerGeneration - Variable in class gov.nasa.javaGenes.core.Parameters
 
killParents - Variable in class gov.nasa.javaGenes.core.HFC.BottomSubBreeder
 
killParents - Variable in class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder
 

L

LatticeConstantEnergies - class gov.nasa.javaGenes.main.LatticeConstantEnergies.
 
LatticeConstantEnergies() - Constructor for class gov.nasa.javaGenes.main.LatticeConstantEnergies
 
LogComparisons - class gov.nasa.alsUtility.LogComparisons.
 
LogComparisons(String[]) - Constructor for class gov.nasa.alsUtility.LogComparisons
 
LogComparisonsTest - class gov.nasa.alsUtility.LogComparisonsTest.
 
LogComparisonsTest(String) - Constructor for class gov.nasa.alsUtility.LogComparisonsTest
 
LogFile - class gov.nasa.alsUtility.LogFile.
create a file and add text to it from time to time
LogFile(String, boolean) - Constructor for class gov.nasa.alsUtility.LogFile
 
LogFile(String) - Constructor for class gov.nasa.alsUtility.LogFile
 
LowestToHighestEnergyFitness - class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness.
 
LowestToHighestEnergyFitness() - Constructor for class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
LowestToHighestEnergyFitness(Potential, ManyMultiBodiesForOneEnergy) - Constructor for class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
LowestToHighestEnergyFitnessTest - class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitnessTest.
 
LowestToHighestEnergyFitnessTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitnessTest
 
LowestToHighestEnergyGradualFitness - class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness.
 
LowestToHighestEnergyGradualFitness() - Constructor for class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness
for testing only
LowestToHighestEnergyGradualFitness(Potential, ManyMultiBodiesForOneEnergy) - Constructor for class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness
 
LowestToHighestEnergyGradualFitnessTest - class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitnessTest.
 
LowestToHighestEnergyGradualFitnessTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitnessTest
 
lambda_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
largestAbsoluteValue(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
last - Variable in class gov.nasa.javaGenes.core.ChildMaker
 
lastCheckpointDate - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
lastGenerations - Variable in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
lastOkToCheckpoint - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
lastStart - Variable in class gov.nasa.alsUtility.Timer
 
lastTime - Variable in class gov.nasa.javaGenes.core.PeriodicCheckpoints
 
layout - Variable in class gov.nasa.javaGenes.graph.GraphParameters
 
layout2d(Graph) - Method in class gov.nasa.javaGenes.graph.GraphLayout
provided xyz locations for every vertex in the graph in such a way that the graph looks ok in two dimensions
layoutGraph2d - Variable in class gov.nasa.javaGenes.graph.GraphParameters
 
left - Variable in class gov.nasa.alsUtility.And
 
left - Variable in class gov.nasa.alsUtility.Or
 
legalRange - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
length() - Method in class gov.nasa.alsUtility.CircularIntQueue
 
length() - Method in class gov.nasa.alsUtility.Vector3d
 
length - Variable in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
lengthTerm(double, double, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
lengthsAndAnglesFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
lessThanOrEqual(double[], double[]) - Static method in class gov.nasa.alsUtility.Utility
 
lessThanOrEqual(double, double) - Static method in class gov.nasa.alsUtility.Utility
 
limit - Variable in class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildren
 
limitTo(DoubleInterval) - Method in class gov.nasa.alsUtility.DoubleInterval
 
limitTo(double) - Method in class gov.nasa.alsUtility.DoubleInterval
 
limitTo(IntegerInterval) - Method in class gov.nasa.alsUtility.IntegerInterval
 
limitToLegalRange(double) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
limitToOriginalInterval - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
limitToOriginalInterval - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
lineSeparator() - Static method in class gov.nasa.alsUtility.Utility
 
linearPart(EvolvableDoubleList, double[], EvolvableDoubleList[], Indices) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
list - Variable in class gov.nasa.alsUtility.DoublesList
 
list - Variable in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
list2String(List) - Static method in class gov.nasa.alsUtility.Utility
 
logBestEvolvableEachGeneration - Variable in class gov.nasa.javaGenes.core.Parameters
 
logFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
low() - Method in class gov.nasa.alsUtility.DoubleInterval
 
low() - Method in class gov.nasa.alsUtility.IntegerInterval
 
lowestTaskPriority - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 

M

MAXIMUM_TRIES - Variable in class gov.nasa.javaGenes.evolvableDoubleList.Selector
 
MAX_TRIES - Static variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
MMEFreferenceRMS - class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS.
the first cluster in the ManyMultiBodiesForOneEnergy is used to calulate differences from
MMEFreferenceRMS(Potential, ManyMultiBodiesForOneEnergy, double, double, double, double, boolean) - Constructor for class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
MMEFreferenceRMS(Potential, ManyMultiBodiesForOneEnergy, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
MMEFreferenceRMS(Potential, ManyMultiBodiesForOneEnergy, boolean) - Constructor for class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
MMEFreferenceRMSTest - class gov.nasa.javaGenes.forceFields.MMEFreferenceRMSTest.
 
MMEFreferenceRMSTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.MMEFreferenceRMSTest
 
MMEFreferenceTanimoto - class gov.nasa.javaGenes.forceFields.MMEFreferenceTanimoto.
 
MMEFreferenceTanimoto(Potential, ManyMultiBodiesForOneEnergy, double, double, double, double, boolean) - Constructor for class gov.nasa.javaGenes.forceFields.MMEFreferenceTanimoto
 
MMEFreferenceTanimoto(Potential, ManyMultiBodiesForOneEnergy, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.MMEFreferenceTanimoto
 
Main - class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Main.
 
Main() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Main
 
Main - class gov.nasa.javaGenes.forceFields.Main.
 
Main() - Constructor for class gov.nasa.javaGenes.forceFields.Main
 
MakeDimer - class gov.nasa.javaGenes.forceFields.MakeDimer.
 
MakeDimer() - Constructor for class gov.nasa.javaGenes.forceFields.MakeDimer
 
MakeDimerPair - class gov.nasa.javaGenes.forceFields.MakeDimerPair.
 
MakeDimerPair() - Constructor for class gov.nasa.javaGenes.forceFields.MakeDimerPair
 
MakeSeeds - class gov.nasa.javaGenes.core.utility.MakeSeeds.
 
MakeSeeds() - Constructor for class gov.nasa.javaGenes.core.utility.MakeSeeds
 
MakeSiFMolecules - class gov.nasa.javaGenes.forceFields.MakeSiFMolecules.
requires SiF4.mol, Si2F6.mol, and Si3F8.mol to be in current directory.
MakeSiFMolecules() - Constructor for class gov.nasa.javaGenes.forceFields.MakeSiFMolecules
 
MakeThreeBodyXyz - class gov.nasa.javaGenes.forceFields.MakeThreeBodyXyz.
 
MakeThreeBodyXyz() - Constructor for class gov.nasa.javaGenes.forceFields.MakeThreeBodyXyz
 
MakeTrimer - class gov.nasa.javaGenes.forceFields.MakeTrimer.
 
MakeTrimer() - Constructor for class gov.nasa.javaGenes.forceFields.MakeTrimer
 
ManyMoleculesEnergyFitness - class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness.
 
ManyMoleculesEnergyFitness() - Constructor for class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
ManyMoleculesEnergyFitness(Potential, ManyMultiBodiesForOneEnergy, boolean) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
ManyMoleculesEnergyFitness(Potential, ManyMultiBodiesForOneEnergy) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
ManyMoleculesEnergyFitnessRatio - class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessRatio.
 
ManyMoleculesEnergyFitnessRatio(Potential, ManyMultiBodiesForOneEnergy) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessRatio
 
ManyMoleculesEnergyFitnessTanimotoDistance - class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessTanimotoDistance.
 
ManyMoleculesEnergyFitnessTanimotoDistance(Potential, ManyMultiBodiesForOneEnergy, boolean) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessTanimotoDistance
 
ManyMultiBodiesForOneEnergy - class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy.
 
ManyMultiBodiesForOneEnergy() - Constructor for class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
ManyMultiBodiesForOneEnergy(String) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
ManyMultiBodiesForOneEnergy(Potential, String) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
ManyMultiBodiesForOneEnergy(String, double) - Constructor for class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
ManySamples - class gov.nasa.alsUtility.ManySamples.
 
ManySamples() - Constructor for class gov.nasa.alsUtility.ManySamples
 
Mark - class gov.nasa.alsUtility.Mark.
implement marking.
Mark() - Constructor for class gov.nasa.alsUtility.Mark
 
MarkIsSet - class gov.nasa.alsUtility.MarkIsSet.
 
MarkIsSet(boolean) - Constructor for class gov.nasa.alsUtility.MarkIsSet
 
MathUtility - class gov.nasa.alsUtility.MathUtility.
 
MathUtility() - Constructor for class gov.nasa.alsUtility.MathUtility
 
MathUtilityTest - class gov.nasa.alsUtility.MathUtilityTest.
 
MathUtilityTest(String) - Constructor for class gov.nasa.alsUtility.MathUtilityTest
 
Matrix3d - class gov.nasa.alsUtility.Matrix3d.
meant to replace a minimal subset of javax.vecmath.Matrix3d to eliminate JavaGenes dependence on Java3d
Matrix3d() - Constructor for class gov.nasa.alsUtility.Matrix3d
 
MiddleSubBreeder - class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder.
 
MiddleSubBreeder(ChildMakerProvider, FitnessFunction) - Constructor for class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder
 
MiddleSubBreeder(ChildMakerProvider, FitnessFunction, boolean) - Constructor for class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder
 
MinMaxes - class gov.nasa.alsUtility.MinMaxes.
 
MinMaxes() - Constructor for class gov.nasa.alsUtility.MinMaxes
 
MinMaxesTest - class gov.nasa.alsUtility.MinMaxesTest.
 
MinMaxesTest(String) - Constructor for class gov.nasa.alsUtility.MinMaxesTest
 
MinimizeSlewingFitness - class gov.nasa.javaGenes.EOSscheduling.MinimizeSlewingFitness.
 
MinimizeSlewingFitness(Scheduler, EOSModel) - Constructor for class gov.nasa.javaGenes.EOSscheduling.MinimizeSlewingFitness
 
Molecule - class gov.nasa.javaGenes.chemistry.Molecule.
note: during evolution Graph objects will be created from Molecule populations.
Molecule() - Constructor for class gov.nasa.javaGenes.chemistry.Molecule
 
Molecule(VertexAndEdgeProvider, int, int) - Constructor for class gov.nasa.javaGenes.chemistry.Molecule
 
MoleculeIndividual - class gov.nasa.javaGenes.chemistry.MoleculeIndividual.
represents an individual molecule
MoleculeIndividual(Evolvable, FitnessFunction) - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeIndividual
 
MoleculeLayout - class gov.nasa.javaGenes.chemistry.MoleculeLayout.
would usually have one static method called main (it's called tasks here to get around a development environment problem).
MoleculeLayout() - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeLayout
 
MoleculeMain - class gov.nasa.javaGenes.chemistry.MoleculeMain.
 
MoleculeMain() - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeMain
 
MoleculeParameters - class gov.nasa.javaGenes.chemistry.MoleculeParameters.
 
MoleculeParameters() - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeParameters
Sets up all parameters with a default target graph.
MoleculeParameters(String) - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeParameters
Sets up all parameters with a target molecule read from a mol file.
MoleculeParameters(Molecule) - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeParameters
Sets up all parameters with target Graph target
MoleculePopulation - class gov.nasa.javaGenes.chemistry.MoleculePopulation.
 
MoleculePopulation(MoleculeParameters) - Constructor for class gov.nasa.javaGenes.chemistry.MoleculePopulation
create a random population of molecules
MoleculePopulation(int) - Constructor for class gov.nasa.javaGenes.chemistry.MoleculePopulation
create an empty population with int size members
MoleculeTest - class gov.nasa.javaGenes.chemistry.MoleculeTest.
 
MoleculeTest(String) - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeTest
 
MoleculeTwoVertexCrossover - class gov.nasa.javaGenes.chemistry.MoleculeTwoVertexCrossover.
Implement the molecule specific part of the crossover operator described in "JavaGenes: Evolving Graphs with Crossover," Al Globus, Sean Atsatt, John Lawton, Todd Wipke.
MoleculeTwoVertexCrossover() - Constructor for class gov.nasa.javaGenes.chemistry.MoleculeTwoVertexCrossover
 
Molecules - class gov.nasa.javaGenes.chemistry.Molecules.
 
Molecules() - Constructor for class gov.nasa.javaGenes.chemistry.Molecules
 
MultiBodiesForOneEnergy - class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy.
 
MultiBodiesForOneEnergy() - Constructor for class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
MultiBodiesForOneEnergy(Molecule) - Constructor for class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
MultiBodiesForOneEnergy(Molecule, Potential) - Constructor for class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
MultiBodiesForOneEnergy(Molecule, double) - Constructor for class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
MultiBodiesForOneEnergyTest - class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest.
 
MultiBodiesForOneEnergyTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
MultiBody - class gov.nasa.javaGenes.forceFields.MultiBody.
 
MultiBody(String) - Constructor for class gov.nasa.javaGenes.forceFields.MultiBody
 
MultiStageFitnessFunction - class gov.nasa.javaGenes.core.MultiStageFitnessFunction.
this fitness function will return the the first objective with a fitness value at least as great as it's weight, or the last fitness value.
MultiStageFitnessFunction() - Constructor for class gov.nasa.javaGenes.core.MultiStageFitnessFunction
 
MultiStageFitnessFunctionTest - class gov.nasa.javaGenes.core.MultiStageFitnessFunctionTest.
 
MultiStageFitnessFunctionTest(String) - Constructor for class gov.nasa.javaGenes.core.MultiStageFitnessFunctionTest
 
MutateEdge - class gov.nasa.javaGenes.graph.MutateEdge.
mutate an edge
MutateEdge(VertexAndEdgeProvider) - Constructor for class gov.nasa.javaGenes.graph.MutateEdge
 
MutateVertex - class gov.nasa.javaGenes.graph.MutateVertex.
mutate a vertex
MutateVertex(VertexAndEdgeProvider) - Constructor for class gov.nasa.javaGenes.graph.MutateVertex
 
Mutation3Parents - class gov.nasa.javaGenes.forceFields.Mutation3Parents.
Mutates all alleles with a random number chosen from a Gaussian distribution with the standard deviation taken by the difference in two of the children
Mutation3Parents(AlleleTemplate) - Constructor for class gov.nasa.javaGenes.forceFields.Mutation3Parents
 
Mutation3Parents(AlleleTemplate, double) - Constructor for class gov.nasa.javaGenes.forceFields.Mutation3Parents
 
Mutation3parents - class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parents.
Mutates selected doubles with a random number chosen from a Gaussian distribution with the standard deviation taken by the difference in two of the children
Mutation3parents(Selector) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parents
 
Mutation3parentsTest - class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parentsTest.
 
Mutation3parentsTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parentsTest
 
MutationDelete - class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete.
 
MutationDelete(Selector) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete
 
MutationDelete(Selector, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete
 
MutationDeleteTest - class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest.
 
MutationDeleteTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest
 
MutationFixedStdDev - class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDev.
 
MutationFixedStdDev(Selector, double) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDev
 
MutationFixedStdDevTest - class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDevTest.
 
MutationFixedStdDevTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDevTest
 
MutationInsert - class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert.
 
MutationInsert(int[]) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert
 
MutationInsert(Selector, int[]) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert
 
MutationInsertTest - class gov.nasa.javaGenes.evolvableDoubleList.MutationInsertTest.
 
MutationInsertTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.MutationInsertTest
 
m00 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m01 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m02 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m10 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m11 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m12 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m20 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m21 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m22 - Variable in class gov.nasa.alsUtility.Matrix3d
 
m_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
main(String[]) - Static method in class gov.nasa.javaGenes.chemistry.MoleculeMain
 
main(String[]) - Static method in class gov.nasa.javaGenes.chemistry.randomizeManyMolecules
 
main(String[]) - Static method in class gov.nasa.javaGenes.chemistry.randomizeXYZ
 
main(String[]) - Static method in class gov.nasa.javaGenes.core.Checkpointer
Will restart if a checkpoint file exists, will start if not.
main(String[]) - Static method in class gov.nasa.javaGenes.core.utility.MakeSeeds
 
main(String[]) - Static method in class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
main(String[]) - Static method in class gov.nasa.javaGenes.core.utility.ParametersAndLog2tsd
 
main(String[]) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.ExperimentMain
 
main(String[]) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Main
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.GetLengthsAndAngles
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.Main
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.MakeDimer
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.MakeDimerPair
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.MakeSiFMolecules
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.MakeThreeBodyXyz
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.MakeTrimer
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.StillingerWeberEnergies
 
main(String[]) - Static method in class gov.nasa.javaGenes.forceFields.StillingerWeberPrintEnergiesAndForces
 
main(String[]) - Static method in class gov.nasa.javaGenes.main.FindMinimumInTsdFile
 
main(String[]) - Static method in class gov.nasa.javaGenes.main.LatticeConstantEnergies
 
main(String[]) - Static method in class gov.nasa.javaGenes.main.compareTechniquesMain
 
makeArray(Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.MathUtility
 
makeArray(Species[], Distribution) - Static method in class gov.nasa.javaGenes.forceFields.SecondBody
make a set of Bodies to use in a fitness function.
makeArray(Species, Species, Species, Distribution, Distribution, Distribution, boolean) - Static method in class gov.nasa.javaGenes.forceFields.ThirdBody
create an array of Bodies to use in the fitness function
makeBond(int, int, int) - Method in class gov.nasa.javaGenes.chemistry.Molecule
make a bond between two atoms numbered starting at 1 (the way chemists count) and add the bond to the molecule.
makeChild(Graph) - Method in class gov.nasa.javaGenes.graph.AddDirectedEdge
 
makeChild(Graph) - Method in class gov.nasa.javaGenes.graph.AddDirectedVertex
 
makeChild(Graph) - Method in class gov.nasa.javaGenes.graph.AddEdge
 
makeChild(Graph) - Method in class gov.nasa.javaGenes.graph.AddVertex
 
makeChild(Graph) - Method in class gov.nasa.javaGenes.graph.MutateEdge
 
makeChild(Graph) - Method in class gov.nasa.javaGenes.graph.MutateVertex
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.ChildMaker
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.EOSscheduling.RandomChild
 
makeChildren(ChildMaker, int[], Population) - Method in class gov.nasa.javaGenes.core.BreederSteadyState2
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.core.ChildMaker
Defaults to mutation, any subclass wanting more than one parent must over-ride.
makeChildren(Individual[]) - Method in class gov.nasa.javaGenes.core.ChildMaker
only used when the variation operator need the fitness value
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.core.ChildMakerChain
 
makeChildren(ChildMaker, int[], Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
makeChildren(Individual[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parents
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeArrayCrossover
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeCrossover
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
If this.fraction too small, can get effective infinite loop since at least one change is required for the method to complete!
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.forceFields.Mutation3Parents
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.graph.GraphGenerator
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
makeChildren(Evolvable[], int[], PermutationEvolvable) - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
makeChildren(Evolvable[]) - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
makeCompatibleWithVertices() - Method in class gov.nasa.javaGenes.chemistry.Bond
Force the type (single, double, or triple) of this bond to be compatible with the valence of its atoms.
makeCompatibleWithVertices() - Method in class gov.nasa.javaGenes.graph.Edge
Force this edge to be compatible with its vertices.
makeDirectory(String) - Static method in class gov.nasa.alsUtility.IO
 
makeDirectory(String) - Static method in class gov.nasa.alsUtility.Utility
 
makeFile(String, String) - Static method in class gov.nasa.alsUtility.Utility
make a file with a string in it, end with an additional "\n"
makeFile(String, String[]) - Static method in class gov.nasa.alsUtility.Utility
make a file with one line per string in it
makeFileNoCR(String, String) - Static method in class gov.nasa.alsUtility.Utility
 
makeFiles() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
makeFiles() - Method in class gov.nasa.javaGenes.core.FitnessFunction
create any files needed, such as a representation of a target.
makeFiles() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
tells the constituent fitness functions to makeFiles()
makeFiles() - Method in class gov.nasa.javaGenes.core.Parameters
create any files necessary to describe the parameters.
makeFiles() - Method in class gov.nasa.javaGenes.core.Weighted0to1
tells the constituent fitness functions to makeFiles()
makeFiles() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
makeFiles() - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
create a file "alleles.tsd" with the allele information in it
makeFiles() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
makeFiles() - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
creative fall column target.tsd with the target chromosome it and a file testCases.tsd with all the test cases in it
makeFiles() - Method in class gov.nasa.javaGenes.graph.CyclesSimilarity
create a mol file of the target.
makeFiles() - Method in class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity
create a mol file of the target.
makeFiles() - Method in class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity
write out the target as file target.mol
makeForceModel(jiggle.Graph) - Method in class gov.nasa.javaGenes.graph.GraphLayout
 
makeGraph(Graph) - Method in class gov.nasa.javaGenes.graph.GraphLayout
used before layout to turn a JavaGenes graph into a jiggle graph
makeIndividual(Evolvable, FitnessFunction) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation
 
makeIndividual(Evolvable, FitnessFunction) - Method in class gov.nasa.javaGenes.chemistry.MoleculePopulation
 
makeIndividual(Evolvable, FitnessFunction) - Method in class gov.nasa.javaGenes.core.Population
Meant to be a general purpose method that creates individuals of whatever type are in this population.
makeIndividual(Evolvable, FitnessFunction) - Method in class gov.nasa.javaGenes.forceFields.ChromosomePopulation
 
makeIndividual(Evolvable, FitnessFunction) - Method in class gov.nasa.javaGenes.graph.GraphPopulation
 
makeIndividual(Evolvable, FitnessFunction) - Method in class gov.nasa.javaGenes.permutation.PermutationPopulation
 
makeIndividualArray(int[]) - Method in class gov.nasa.javaGenes.core.Population
 
makeMoleculeAndBodiesFiles(String) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
makeMultipleMolecules(Molecule[]) - Static method in class gov.nasa.javaGenes.forceFields.Bodies
Converts Molecules into Bodies untested
makeOptimization(jiggle.Graph, jiggle.ForceModel) - Method in class gov.nasa.javaGenes.graph.GraphLayout
 
makePopulation(int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation
 
makePopulation(int) - Method in class gov.nasa.javaGenes.chemistry.MoleculePopulation
 
makePopulation(int) - Method in class gov.nasa.javaGenes.core.Population
 
makePopulation(int) - Method in class gov.nasa.javaGenes.forceFields.ChromosomePopulation
 
makePopulation(int) - Method in class gov.nasa.javaGenes.graph.GraphPopulation
 
makePopulation(int) - Method in class gov.nasa.javaGenes.permutation.PermutationPopulation
 
makeSequentialNumber(int) - Static method in class gov.nasa.alsUtility.Utility
Make a number that, when used as a filename, will print out sequential with others (i.e., is in ASCII order as well as numerical order) by inserting leading zeros.
makeTask(double, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest
 
makeTask(double, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
makeValenceCompatible() - Method in class gov.nasa.javaGenes.chemistry.Bond
Force the type (single, double, or triple) of this bond to be compatible with the valence of its atoms.
makeVector(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
max - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
maxEvolvableSize - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
maxLineSearchIterations - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
maxLinearTries - Variable in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
maxNumberOfSwapsPerMutation - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
maxOnTime - Variable in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
maxStandardDeviaion - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations
 
maxVariationsNeeded - Variable in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries
 
maximum - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
maximum - Variable in class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider
 
maximumGenerations - Variable in class gov.nasa.javaGenes.core.Parameters
 
maximumSlew - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
mean - Variable in class gov.nasa.alsUtility.Sample
 
mediumCopyTrail() - Method in class gov.nasa.javaGenes.graph.Trail
keeps original edges and vertices
memory - Variable in class gov.nasa.javaGenes.core.Population
memory used by the program after population generated
midPoint() - Method in class gov.nasa.alsUtility.DoubleInterval
 
min - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
minEvolvableSize - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
minStandardDeviaion - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations
 
minimizeSlewingWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
minimum - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
minimumFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
minimumNumberToSelect - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
minimumSize - Variable in class gov.nasa.javaGenes.core.ParsimonyFitness
 
minimumSlew - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
minumumEvolvableSize - Variable in class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete
 
minus(Vector3d, Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.MathUtility
 
model - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
model - Variable in class gov.nasa.javaGenes.EOSscheduling.MinimizeSlewingFitness
 
model - Variable in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
model - Variable in class gov.nasa.javaGenes.EOSscheduling.SmallSlewsFitness
 
model - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
model - Variable in class gov.nasa.javaGenes.EOSscheduling.TaskPriorityFitness
 
modulo - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
molFormat - class gov.nasa.javaGenes.chemistry.molFormat.
read and write mol files representing molecules
molFormat() - Constructor for class gov.nasa.javaGenes.chemistry.molFormat
 
molecule - Variable in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
molecules - Variable in class gov.nasa.javaGenes.chemistry.Molecules
 
molecules - Variable in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
molecules - Variable in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
molecules - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
molecules - Variable in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
more() - Method in class gov.nasa.alsUtility.IncrementIterator
 
more() - Method in class gov.nasa.alsUtility.IndexIterator
 
more() - Method in interface gov.nasa.alsUtility.Iterator
 
more() - Method in class gov.nasa.alsUtility.VectorIterator
are there any more objects to iterate over?
more() - Method in class gov.nasa.javaGenes.graph.VertexAndTrailIterator
 
more() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
moreDeservingToMoveBack(EOSschedulingEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
moreDeservingToMoveForward(EOSschedulingEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
moveAtomsIntoUnitCell() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
moveBackFraction - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
moveBackIndex - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
moveForwardFraction - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
moveForwardIndex - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
moveInside(Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
moveInside(Vertex) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
moveInsideInterval(int, double, double) - Method in class gov.nasa.javaGenes.graph.Vertex
 
mul(Quat4d) - Method in class gov.nasa.alsUtility.Quat4d
 
multiBodies - Variable in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
multiBodies - Variable in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
multiply(float) - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
multiply(int) - Method in class gov.nasa.alsUtility.ReinitializableInt
 
multiply(double[][][], double) - Static method in class gov.nasa.alsUtility.Utility
 
multiply(double[][], double) - Static method in class gov.nasa.alsUtility.Utility
 
multiply(double[], double) - Static method in class gov.nasa.alsUtility.Utility
 
multiply(Vector3d, double) - Static method in class gov.nasa.alsUtility.Vector3d
 
multiply(double) - Method in class gov.nasa.alsUtility.Vector3d
 
multiplyEnergiesBy(double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
mustBeCompatible - Variable in class gov.nasa.javaGenes.graph.AcceptableSecondBrokenEdge
 
mustBeImplementedBySubclass() - Static method in class gov.nasa.alsUtility.Error
 
mustCalculateSubtractWeightFrom - Variable in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
mustModel(ManyMultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
mustModel(ManyMultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
mustModel(MultiBody, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
mustModel(MultiBody) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
mustModel(ManyMultiBodiesForOneEnergy) - Method in class gov.nasa.javaGenes.forceFields.Tersoff
 
mustPrepareToDie - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
mustRampToEnd - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
mustToUpdateAndPropagate() - Method in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable
 
mutate(int, int, PermutationEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
shifts shift to in front of shiftBeforeMe
mutate(Evolvable) - Method in class gov.nasa.javaGenes.core.ChildMaker
mutators should over-ride, subclasses with multiple parents can ignore.
mutate(Evolvable) - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete
 
mutate(Evolvable) - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDev
 
mutate(Evolvable) - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert
 
mutate(int, int, PermutationEvolvable) - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
made public only for testing
mutateByStandardDeviation(double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
mutationProbability - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation
 
mutationStandardDeviationRange - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
mutator - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation
 
myModulo - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
myOffset - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 

N

NORMALIZE_BY_NUMBER_OF_SCHEDULED_TAKEIMAGES - Static variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
NORMALIZE_BY_SCHEDULED_TAKEIMAGES_PRIORITY - Static variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
NOT_HERE - Static variable in class gov.nasa.javaGenes.forceFields.AlleleSetup
 
NOT_SCHEDULED - Static variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
NOT_SCHEDULED - Static variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
NOT_SCHEDULED - Static variable in class gov.nasa.javaGenes.EOSscheduling.Placer
 
NOT_SCHEDULED - Static variable in class gov.nasa.javaGenes.EOSscheduling.Scheduler
Must be less than the earliest legal timestep
NOT_SCHEDULED - Static variable in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
NO_NORMALIZATION - Static variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
NO_SENSOR - Static variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
NO_WINDOW - Static variable in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
NeighboringPairsSelector - class gov.nasa.javaGenes.evolvableDoubleList.NeighboringPairsSelector.
used for type checking in Crossover.java and subclasses
NeighboringPairsSelector(Selector, int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.NeighboringPairsSelector
 
Node - class gov.nasa.javaGenes.EOSscheduling.Node.
 
Node() - Constructor for class gov.nasa.javaGenes.EOSscheduling.Node
should only be called from NodeFactory and subclasses (via NodeFactory)
NodeArrayTest - class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest.
 
NodeArrayTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
NodeFactory - class gov.nasa.javaGenes.EOSscheduling.NodeFactory.
used to reuse and avoid garbage collecting Nodes.
NodeFactory() - Constructor for class gov.nasa.javaGenes.EOSscheduling.NodeFactory
 
NodeTest - class gov.nasa.javaGenes.EOSscheduling.NodeTest.
 
NodeTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.NodeTest
 
Not - class gov.nasa.alsUtility.Not.
 
Not(Predicate) - Constructor for class gov.nasa.alsUtility.Not
 
NotApplicable - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
NotFoundException - exception gov.nasa.javaGenes.core.NotFoundException.
 
NotFoundException() - Constructor for class gov.nasa.javaGenes.core.NotFoundException
 
NumberOfTakeImagesFitness - class gov.nasa.javaGenes.EOSscheduling.NumberOfTakeImagesFitness.
 
NumberOfTakeImagesFitness(Scheduler) - Constructor for class gov.nasa.javaGenes.EOSscheduling.NumberOfTakeImagesFitness
 
name - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
name - Variable in class gov.nasa.javaGenes.EOSscheduling.SensorType
 
name - Variable in class gov.nasa.javaGenes.core.FitnessFunction
 
name - Variable in class gov.nasa.javaGenes.forceFields.Allele
 
name - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber.ChromosomeParametersData
 
names - Variable in class gov.nasa.alsUtility.LogComparisons
 
names - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
names - Variable in class gov.nasa.javaGenes.forceFields.AlleleTemplate
These names refer to the first dimension in alleles
names - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
nearWallFilename - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
nearlyEqual(Brick3d) - Method in class gov.nasa.alsUtility.Brick3d
 
nearlyEqual(DoubleInterval) - Method in class gov.nasa.alsUtility.DoubleInterval
 
nearlyEqual(Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.Utility
 
nearlyEqual(double, double) - Static method in class gov.nasa.alsUtility.Utility
 
nearlyEqual(double, double, double) - Static method in class gov.nasa.alsUtility.Utility
will always return false for values of opposite sign
nearlyEqual(double[][][], double[][][]) - Static method in class gov.nasa.alsUtility.Utility
 
nearlyEqual(double[][], double[][]) - Static method in class gov.nasa.alsUtility.Utility
 
nearlyEqual(double[], double[]) - Static method in class gov.nasa.alsUtility.Utility
 
nearlyEqual(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
nearlyEqual(ThreeBody) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
nearlyEqual(TwoBody) - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
nearlyEquals(UnitCell) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
nearlyEquals(UnitCell) - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
need(MultiBody, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
need(String, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
needToUpdateAndPropagate - Variable in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable
 
negate() - Method in class gov.nasa.alsUtility.Vector3d
 
negate(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
netChange - Variable in class gov.nasa.alsUtility.LogComparisons
 
neverUsed() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
newAvailableNode(int, Node, Node) - Method in class gov.nasa.javaGenes.EOSscheduling.NodeFactory
 
newChild(Individual) - Method in class gov.nasa.javaGenes.core.Breeder
 
newChild(Individual) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
newChildrenCreated(int) - Method in class gov.nasa.javaGenes.core.Breeder
 
newInstance(Object) - Static method in class gov.nasa.alsUtility.Utility
 
newInstance(String) - Static method in class gov.nasa.alsUtility.Utility
 
newInstance(Object, Object) - Static method in class gov.nasa.alsUtility.Utility
probably doesn't work.
newSSRNode(int, int, Node, Node) - Method in class gov.nasa.javaGenes.EOSscheduling.NodeFactory
 
newSlewNode(SlewRequirement, boolean, int, Node, Node) - Method in class gov.nasa.javaGenes.EOSscheduling.NodeFactory
 
newUnAvailableNode(int, Node, Node) - Method in class gov.nasa.javaGenes.EOSscheduling.NodeFactory
 
next() - Method in interface gov.nasa.alsUtility.Iterator
move to the next object
next() - Method in class gov.nasa.alsUtility.VectorIterator
move to the next element
next - Variable in class gov.nasa.javaGenes.EOSscheduling.Node
 
next() - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
next() - Method in class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider
 
next() - Method in class gov.nasa.javaGenes.graph.VertexAndTrailIterator
move to the next trail
next - Variable in class gov.nasa.javaGenes.weightNetwork.Weight
 
nextAvailableNode() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
nextUnAvailableNode() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
noEvolution - Variable in class gov.nasa.javaGenes.forceFields.Allele
 
noThreeTermParameters(String) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
nodeArray - Variable in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
nodeFactory - Static variable in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
nodeList - Variable in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
nodeTypePairsShortestTrailCounts - Variable in class gov.nasa.javaGenes.graph.Graph
cache the results of all-pairs-shortest-path since this operation is compute intensive.
normalNumber(double) - Static method in class gov.nasa.alsUtility.Utility
is this number a regular number? I.e., not NaN or infinity.
normalization - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
normalize(double) - Method in class gov.nasa.alsUtility.Sample
divides every value with by
normalize() - Method in class gov.nasa.alsUtility.Vector3d
 
normalizeByWeight - Variable in class gov.nasa.javaGenes.core.WeightedSumFitness
 
normalizedFitness(double, EOSschedulingEvolvable, EOSModel) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
notApplicable() - Static method in class gov.nasa.alsUtility.Error
 
notImplemented() - Static method in class gov.nasa.alsUtility.Error
 
nullhyp1 - Static variable in class gov.nasa.alsUtility.ComparativeStatistics
 
number - Variable in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
number - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
number - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
number - Variable in class gov.nasa.javaGenes.EOSscheduling.Task
 
number - Variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
number - Variable in class gov.nasa.javaGenes.forceFields.Immigrant
 
number - Variable in class gov.nasa.javaGenes.graph.Vertex
used to number vertices for various purposes
numberOfAccessWindows() - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
numberOfArrays() - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
numberOfArrays() - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
numberOfChildMakers - Variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
numberOfGetsPerGeneration - Variable in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
numberOfGetsSoFar - Variable in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
numberOfIndices() - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
numberOfObjectives() - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
numberOfObjectives() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
numberOfObjectives() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjectiveToOne
 
numberOfParameters() - Method in class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew
 
numberOfParameters() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
numberOfParameters() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewRequirement
 
numberOfParents() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.ChildMaker
 
numberOfParents() - Method in class gov.nasa.javaGenes.EOSscheduling.RandomChild
 
numberOfParents() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
numberOfParents() - Method in class gov.nasa.javaGenes.core.ChildMakerChain
 
numberOfParents() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Crossover
 
numberOfParents() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
numberOfParents() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval
 
numberOfParents() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne
 
numberOfParents() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parents
 
numberOfParents() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeCrossover
 
numberOfParents() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
numberOfParents() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
numberOfParents() - Method in class gov.nasa.javaGenes.forceFields.Mutation3Parents
 
numberOfParents() - Method in class gov.nasa.javaGenes.graph.GraphGenerator
 
numberOfParents() - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
 
numberOfParents() - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
numberOfParents() - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
numberOfParents() - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
numberOfSaves - Variable in class gov.nasa.alsUtility.Saver
 
numberOfSegments - Variable in class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
numberOfSubBreeders() - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
numberOfSwaps - Variable in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
numberOfTaskPriorityLevels - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
numberOfThisCharInString(String, char) - Static method in class gov.nasa.alsUtility.Utility
 
numberOfThreeBodyParameters - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
numberOfTimelines - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
numberOfTwoBodyParameters - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
numberOfWeightsRemoved - Variable in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
numberSatellites() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
numberTasksAndAccessWindows() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
numberToChoose - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
numberToInsert - Variable in class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert
 
numberToKill - Variable in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
numberToSelect - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumber
 
numberVertices(int) - Method in class gov.nasa.javaGenes.graph.Graph
Number the vertices starting with int start.
numberVerticesReverse(int) - Method in class gov.nasa.javaGenes.graph.Graph
 

O

ObjectCache - class gov.nasa.alsUtility.ObjectCache.
cache objects to avoid object re-allocation.
ObjectCache(String) - Constructor for class gov.nasa.alsUtility.ObjectCache
 
ObjectCacheTest - class gov.nasa.alsUtility.ObjectCacheTest.
 
ObjectCacheTest(String) - Constructor for class gov.nasa.alsUtility.ObjectCacheTest
 
ObjectCompatible - class gov.nasa.alsUtility.ObjectCompatible.
 
ObjectCompatible(Object) - Constructor for class gov.nasa.alsUtility.ObjectCompatible
 
ObjectEquals - class gov.nasa.alsUtility.ObjectEquals.
 
ObjectEquals(Object) - Constructor for class gov.nasa.alsUtility.ObjectEquals
 
OneBody - class gov.nasa.javaGenes.forceFields.OneBody.
represents a single body in a multibody potential.
OneBody(Species) - Constructor for class gov.nasa.javaGenes.forceFields.OneBody
 
Or - class gov.nasa.alsUtility.Or.
implements logical or
Or(Predicate, Predicate) - Constructor for class gov.nasa.alsUtility.Or
predicates to implement the logical or of
OrderMutation - class gov.nasa.javaGenes.EOSscheduling.OrderMutation.
 
OrderMutation() - Constructor for class gov.nasa.javaGenes.EOSscheduling.OrderMutation
 
object - Variable in class gov.nasa.alsUtility.IsEqual
 
object() - Method in interface gov.nasa.alsUtility.Iterator
 
object - Variable in class gov.nasa.alsUtility.ObjectCompatible
object to be compatible with
object - Variable in class gov.nasa.alsUtility.ObjectEquals
object to be equal to
object() - Method in class gov.nasa.alsUtility.VectorIterator
 
objectToCheckpoint - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
offset - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
ok() - Static method in class gov.nasa.javaGenes.core.Checkpointer
called by a Checkpointable.
okBackward(AvailabilityTimeline, AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
starting at 'endTime', check backward 'totalTime' to see if there is no more than 'maxOnTimeForSearch' UnAvailable time
okForward(AvailabilityTimeline, AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
starting at 'startTime', check forward 'totalTime' to see if there is no more than 'maxOnTimeForSearch' UnAvailable time
okLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
onTimeArrayElementDuration - Variable in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
onTimes - Variable in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
oneBody - Variable in class gov.nasa.javaGenes.forceFields.Bodies
this is public for fast access.
originalEnergyInterval - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
otherVertex(Vertex) - Method in class gov.nasa.javaGenes.graph.Edge
 
outOfOrder(double[]) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
outOfOrder(double[]) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness
 
outOfOrderPenalty - Variable in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness
 
outputEdges - Variable in class gov.nasa.javaGenes.graph.DirectedVertex
 
outputFile(String) - Static method in class gov.nasa.alsUtility.Utility
 
outputFilename - Static variable in class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
overlapInTimeWith(AccessWindow) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 

P

Parameters - class gov.nasa.javaGenes.core.Parameters.
stores parameters for a run
Parameters() - Constructor for class gov.nasa.javaGenes.core.Parameters
 
Parameters - class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters.
 
Parameters() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
Parameters2tsd - class gov.nasa.javaGenes.core.utility.Parameters2tsd.
 
Parameters2tsd() - Constructor for class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
ParametersAndLog2tsd - class gov.nasa.javaGenes.core.utility.ParametersAndLog2tsd.
 
ParametersAndLog2tsd() - Constructor for class gov.nasa.javaGenes.core.utility.ParametersAndLog2tsd
 
ParametersSerializationTest - class gov.nasa.javaGenes.core.ParametersSerializationTest.
 
ParametersSerializationTest(String) - Constructor for class gov.nasa.javaGenes.core.ParametersSerializationTest
 
ParsimonyFitness - class gov.nasa.javaGenes.core.ParsimonyFitness.
this fitness function is used penalizes large evolvables.
ParsimonyFitness() - Constructor for class gov.nasa.javaGenes.core.ParsimonyFitness
 
ParsimonyFitness(int, double) - Constructor for class gov.nasa.javaGenes.core.ParsimonyFitness
 
PeriodicCheckpoints - class gov.nasa.javaGenes.core.PeriodicCheckpoints.
causes another thread to checkpoint periodically
PermutationChildMaker - class gov.nasa.javaGenes.permutation.PermutationChildMaker.
 
PermutationChildMaker() - Constructor for class gov.nasa.javaGenes.permutation.PermutationChildMaker
 
PermutationEvolvable - class gov.nasa.javaGenes.permutation.PermutationEvolvable.
 
PermutationEvolvable(int) - Constructor for class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
PermutationEvolvable(int, String) - Constructor for class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
PermutationIndividual - class gov.nasa.javaGenes.permutation.PermutationIndividual.
 
PermutationIndividual(Evolvable, FitnessFunction) - Constructor for class gov.nasa.javaGenes.permutation.PermutationIndividual
Sets the evolvable to e and calculates the fitness using FitnessFunction f.
PermutationKCutMutation - class gov.nasa.javaGenes.permutation.PermutationKCutMutation.
Think of a permutation as a graph where the nodes are the integers and neighboring nodes share an edge.
PermutationKCutMutation(int) - Constructor for class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
PermutationKCutMutationTest - class gov.nasa.javaGenes.permutation.PermutationKCutMutationTest.
 
PermutationKCutMutationTest(String) - Constructor for class gov.nasa.javaGenes.permutation.PermutationKCutMutationTest
 
PermutationOrderMutation - class gov.nasa.javaGenes.permutation.PermutationOrderMutation.
Gilbert Sysweda's order based mutation
PermutationOrderMutation() - Constructor for class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
PermutationOrderMutation(int) - Constructor for class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
PermutationOrderMutationTest - class gov.nasa.javaGenes.permutation.PermutationOrderMutationTest.
 
PermutationOrderMutationTest(String) - Constructor for class gov.nasa.javaGenes.permutation.PermutationOrderMutationTest
 
PermutationParameters - class gov.nasa.javaGenes.permutation.PermutationParameters.
 
PermutationParameters() - Constructor for class gov.nasa.javaGenes.permutation.PermutationParameters
 
PermutationPopulation - class gov.nasa.javaGenes.permutation.PermutationPopulation.
 
PermutationPopulation(PermutationParameters) - Constructor for class gov.nasa.javaGenes.permutation.PermutationPopulation
 
PermutationPopulation(int, int, FitnessFunction) - Constructor for class gov.nasa.javaGenes.permutation.PermutationPopulation
 
PermutationPopulation(int) - Constructor for class gov.nasa.javaGenes.permutation.PermutationPopulation
create an empty population with int size members
PermutationPositionCrossover - class gov.nasa.javaGenes.permutation.PermutationPositionCrossover.
Gilbert Sysweda's position based crossover
PermutationPositionCrossover() - Constructor for class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
PermutationPositionCrossoverTest - class gov.nasa.javaGenes.permutation.PermutationPositionCrossoverTest.
 
PermutationPositionCrossoverTest(String) - Constructor for class gov.nasa.javaGenes.permutation.PermutationPositionCrossoverTest
 
PermutationTestFitness - class gov.nasa.javaGenes.permutation.PermutationTestFitness.
 
PermutationTestFitness() - Constructor for class gov.nasa.javaGenes.permutation.PermutationTestFitness
 
PhenotypeChanger - interface gov.nasa.javaGenes.core.PhenotypeChanger.
is used by fitness functions that must calculate the fitness of several variants of the phenotype to simulatate potential manufacturing errors.
PhenotypeChangerDummy - class gov.nasa.javaGenes.core.PhenotypeChangerDummy.
Used for testing and as a placeholder.
PhenotypeChangerDummy() - Constructor for class gov.nasa.javaGenes.core.PhenotypeChangerDummy
 
Placer - class gov.nasa.javaGenes.EOSscheduling.Placer.
 
Placer() - Constructor for class gov.nasa.javaGenes.EOSscheduling.Placer
 
PointingRequirement - class gov.nasa.javaGenes.EOSscheduling.PointingRequirement.
 
PointingRequirement(int, double, double, double) - Constructor for class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
PointingRequirementTest - class gov.nasa.javaGenes.EOSscheduling.PointingRequirementTest.
 
PointingRequirementTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.PointingRequirementTest
 
Population - class gov.nasa.javaGenes.core.Population.
Represents a population of evolvable Graph objects
Population(int) - Constructor for class gov.nasa.javaGenes.core.Population
create an empty population with int size members
PopulationTest - class gov.nasa.javaGenes.core.PopulationTest.
 
PopulationTest(String) - Constructor for class gov.nasa.javaGenes.core.PopulationTest
 
PositionCrossover - class gov.nasa.javaGenes.EOSscheduling.PositionCrossover.
 
PositionCrossover() - Constructor for class gov.nasa.javaGenes.EOSscheduling.PositionCrossover
 
Potential - class gov.nasa.javaGenes.forceFields.Potential.
this classes used to find energy of a multibody system given a particular Chromosome for the potential parameters.
Potential() - Constructor for class gov.nasa.javaGenes.forceFields.Potential
 
PotentialEnergyFitness - class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness.
fitness function based on RMS distance of potential energies between the target and candidate Chromosome
PotentialEnergyFitness(Potential, Chromosome) - Constructor for class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
 
PotentialEnergyTestCase - class gov.nasa.javaGenes.forceFields.PotentialEnergyTestCase.
 
PotentialEnergyTestCase(double[], Bodies[]) - Constructor for class gov.nasa.javaGenes.forceFields.PotentialEnergyTestCase
 
Predicate - interface gov.nasa.alsUtility.Predicate.
a predicate object is used to test other objects for truth or falsehood.
PrintIMat(int[][]) - Static method in class gov.nasa.javaGenes.graph.apsp
Print a two dimensional integer matrix
PrintTabSeparatedData - class gov.nasa.alsUtility.PrintTabSeparatedData.
print things out in ASCII with tabs separating each print on a line
PrintTabSeparatedData(OutputStream) - Constructor for class gov.nasa.alsUtility.PrintTabSeparatedData
 
Procedure - interface gov.nasa.alsUtility.Procedure.
a procedure object is used to execute a procedure on several objects in a collection
ProductFitnessFunction - class gov.nasa.javaGenes.core.ProductFitnessFunction.
this fitness function is a product of fitness functions times their weights with one added to the fitness.
ProductFitnessFunction() - Constructor for class gov.nasa.javaGenes.core.ProductFitnessFunction
 
ProductFitnessFunctionTest - class gov.nasa.javaGenes.core.ProductFitnessFunctionTest.
 
ProductFitnessFunctionTest(String) - Constructor for class gov.nasa.javaGenes.core.ProductFitnessFunctionTest
 
PropertiesList - class gov.nasa.alsUtility.PropertiesList.
 
PropertiesList(String) - Constructor for class gov.nasa.alsUtility.PropertiesList
 
PropertiesListTest - class gov.nasa.alsUtility.PropertiesListTest.
 
PropertiesListTest(String) - Constructor for class gov.nasa.alsUtility.PropertiesListTest
 
Purine - class gov.nasa.javaGenes.chemistry.Purine.
 
Purine() - Constructor for class gov.nasa.javaGenes.chemistry.Purine
 
PutPotentialEnergiesAndForces - class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces.
 
PutPotentialEnergiesAndForces(Potential, Chromosome) - Constructor for class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
Pyridine - class gov.nasa.javaGenes.chemistry.Pyridine.
 
Pyridine() - Constructor for class gov.nasa.javaGenes.chemistry.Pyridine
 
p_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
parameterNames - Static variable in class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
parameters - Variable in class gov.nasa.javaGenes.core.Reporter
 
parameters - Variable in class gov.nasa.javaGenes.core.Run
 
parameters - Variable in class gov.nasa.javaGenes.graph.GraphGenerator
 
parametersFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
parentChooser - Variable in class gov.nasa.javaGenes.core.BreederSteadyState2
 
parentChooser - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
parentsOfPromoted(int[], Population) - Method in class gov.nasa.javaGenes.core.HFC.BottomSubBreeder
 
parentsOfPromoted(int[], Population) - Method in class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder
 
parentsOfPromoted(int[], Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
parentsOfPromoted(int[], Population) - Method in class gov.nasa.javaGenes.core.HFC.TopSubBreeder
 
paretoFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
paretoFitness - Variable in class gov.nasa.javaGenes.core.Parameters
 
permanentKeys - Static variable in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
permanentKeys - Static variable in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
permutation - Variable in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
permutationLength - Variable in class gov.nasa.javaGenes.permutation.PermutationParameters
 
phenotypeChanger - Variable in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
pick() - Method in class gov.nasa.javaGenes.core.Population
 
pick(Individual) - Method in class gov.nasa.javaGenes.core.Population
 
pick(Individual, Individual) - Method in class gov.nasa.javaGenes.core.Population
 
pickOne(Population) - Method in class gov.nasa.javaGenes.core.Breeder
 
pickOnePart(EvolvableDoubleList, EvolvableDoubleList[], Indices) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
place - Variable in class gov.nasa.alsUtility.VectorIterator
the index of the next element
placeInTimelines(TaskPlacementData, Task) - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
placeInTimelines(TaskPlacementData, Task) - Method in class gov.nasa.javaGenes.EOSscheduling.Placer
 
placementData - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
placers - Variable in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
pointingRequirements - Variable in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
poolsigmas - Static variable in class gov.nasa.alsUtility.ComparativeStatistics
 
pop() - Method in class gov.nasa.alsUtility.CircularIntQueue
 
popIndex - Variable in class gov.nasa.alsUtility.CircularIntQueue
 
population - Variable in class gov.nasa.javaGenes.core.Population
 
population - Variable in class gov.nasa.javaGenes.core.Run
 
population - Variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
populationDirectory - Static variable in class gov.nasa.javaGenes.core.Reporter
 
populationSize - Variable in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
populationSize - Variable in class gov.nasa.javaGenes.core.Parameters
minimum 3 to allow tournament selection
position - Variable in class gov.nasa.javaGenes.graph.GraphLayout.CoordinateProvider
 
potential - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
potential - Variable in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
potential - Variable in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
potential - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
potential - Variable in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
 
power(double, int) - Static method in class gov.nasa.alsUtility.Utility
 
predicate - Variable in class gov.nasa.alsUtility.Not
predicate to execute on objects
predicate - Variable in class gov.nasa.javaGenes.graph.AddDirectedVertex
 
prepareForEvaluator(Parameters) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
prepareForEvaluator(Parameters) - Method in class gov.nasa.javaGenes.core.Evolvable
Used when special setup is needed to calculate the evaluation fitness Reporter.java does when each generation is complete.
prepareForSpin(double) - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
prepareForSpinCalled - Variable in class gov.nasa.javaGenes.core.RouletteWheel
 
prepareToDie() - Static method in class gov.nasa.javaGenes.core.Checkpointer
Called by an external agency.
prepareToDieLocal() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
preservedNumber - Variable in class gov.nasa.javaGenes.core.BreederElitist
 
previous - Variable in class gov.nasa.javaGenes.EOSscheduling.Node
 
previous() - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
previous - Variable in class gov.nasa.javaGenes.weightNetwork.Weight
 
previousAvailableNode() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
previousUnAvailableNode() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
print(String) - Method in class gov.nasa.alsUtility.EasyFile
 
print(String) - Method in class gov.nasa.alsUtility.LogFile
 
print(String) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(boolean) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(int) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(long) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(float) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(double) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(Object) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(char) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
print(char[]) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
printCheckpointStatistics() - Method in class gov.nasa.javaGenes.core.Checkpointer
creates checkpoint_filename.statistics.txt and puts mean, standard deviation, highest, and lowest time between checkpoints.
printComaSeparated(double) - Method in class gov.nasa.alsUtility.EasyFile
print d with a comma between it and all other entries
printComaSeparated(double) - Method in class gov.nasa.alsUtility.LogFile
print d with a comma between it and all other entries
printComaSeparatedXYLine(double, double) - Method in class gov.nasa.alsUtility.EasyFile
print a with the form x,y
printComaSeparatedXYLine(double, double) - Method in class gov.nasa.alsUtility.LogFile
print a with the form x,y
printData2tsd(String, String[], String[], String) - Static method in class gov.nasa.javaGenes.core.utility.CoreUtility
 
printData2tsd(PrintWriter, String[], String[], String) - Static method in class gov.nasa.javaGenes.core.utility.CoreUtility
 
printIntArray(int[]) - Static method in class gov.nasa.alsUtility.Utility
 
printSeed() - Static method in class gov.nasa.alsUtility.Error
print out the seed for the random number generator.
printTo(EasyFile) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyTestCase
 
printToTsd(String) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
printToTsd(String) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
printToTsd(String) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
printToTsd(String) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
printToTsd(PrintWriter) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
printUnexecutableTasks(String) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
println(String) - Method in class gov.nasa.alsUtility.EasyFile
 
println() - Method in class gov.nasa.alsUtility.EasyFile
 
println(String) - Method in class gov.nasa.alsUtility.LogFile
 
println() - Method in class gov.nasa.alsUtility.LogFile
 
println() - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(String) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(boolean) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(int) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(long) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(float) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(double) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(Object) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(char) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
println(char[]) - Method in class gov.nasa.alsUtility.PrintTabSeparatedData
 
priority - Variable in class gov.nasa.javaGenes.EOSscheduling.Task
 
priorityWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
probability - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
probabilityToBeat(double) - Method in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
processArguments(String[]) - Static method in class gov.nasa.javaGenes.core.utility.Parameters2tsd
 
processInitialBrokenEdge(Graph, BrokenEdge, BrokenGraph) - Method in class gov.nasa.javaGenes.chemistry.MoleculeTwoVertexCrossover
find and connect a second broken edge
processInitialBrokenEdge(Graph, BrokenEdge, BrokenGraph) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
find and connect a second broken edge
promote(Individual, Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
promote(Individual, Population) - Method in class gov.nasa.javaGenes.core.HFC.TopSubBreeder
 
promoteTooFitIndividuals(Population) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
promoteTooFitIndividuals(Population) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
promoteTooFitIndividuals(Population) - Method in class gov.nasa.javaGenes.core.HFC.TopSubBreeder
 
promotionsTo - Variable in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
proportionDown() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
provider - Variable in class gov.nasa.javaGenes.graph.AddDirectedEdge
 
provider - Variable in class gov.nasa.javaGenes.graph.AddDirectedVertex
 
provider - Variable in class gov.nasa.javaGenes.graph.AddEdge
 
provider - Variable in class gov.nasa.javaGenes.graph.AddVertex
 
provider - Variable in class gov.nasa.javaGenes.graph.GraphParameters
will provide random vertices and edges for random GraphPopulation construction.
provider - Variable in class gov.nasa.javaGenes.graph.MutateEdge
provides the edges to mutate to
provider - Variable in class gov.nasa.javaGenes.graph.MutateVertex
provides the vertex to mutate to
push(int) - Method in class gov.nasa.alsUtility.CircularIntQueue
 
pushIndex - Variable in class gov.nasa.alsUtility.CircularIntQueue
 
put(Object, Object) - Method in class gov.nasa.alsUtility.KeyCounter
overrides Hashtable.put to insure that the element is always a integer object
putBoolean(boolean) - Method in class gov.nasa.javaGenes.core.TokenizeOutput
 
putDatum(String, int, double) - Method in class gov.nasa.alsUtility.DataTable
 
putDatum(String, double) - Method in class gov.nasa.alsUtility.DataTable
adds datum to end of vector
putDouble(double) - Method in class gov.nasa.javaGenes.core.TokenizeOutput
 
putInteger(int) - Method in class gov.nasa.javaGenes.core.TokenizeOutput
 
putLong(long) - Method in class gov.nasa.javaGenes.core.TokenizeOutput
 
putProperty(String, String) - Method in class gov.nasa.alsUtility.PropertiesList
 
putString(String) - Method in class gov.nasa.javaGenes.core.TokenizeOutput
 
putThreeBody(String, Atom, Atom, Atom, int) - Method in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
putTwoBody(String, Atom, Atom, int) - Method in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
putTwoBodyEnergies(String, Atom, Atom, int) - Method in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 

Q

QUARTIC_NOISE - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
Quat4d - class gov.nasa.alsUtility.Quat4d.
meant to replace a minimal subset of javax.vecmath.Quat4d to eliminate JavaGenes dependence on Java3d
Quat4d() - Constructor for class gov.nasa.alsUtility.Quat4d
 
Quat4d(Quat4d) - Constructor for class gov.nasa.alsUtility.Quat4d
 
Quat4d(double, double, double, double) - Constructor for class gov.nasa.alsUtility.Quat4d
 
q_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
quadraticPart(EvolvableDoubleList, double[], EvolvableDoubleList[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
quarticNoise(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
min = f(0,...,0) == 0 originally for list.getSize() = 30
quarticNoiseRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 

R

ROSENBROCK - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
RandomChild - class gov.nasa.javaGenes.EOSscheduling.RandomChild.
 
RandomChild() - Constructor for class gov.nasa.javaGenes.EOSscheduling.RandomChild
 
RandomDistribution - class gov.nasa.alsUtility.RandomDistribution.
this class produces random numbers from an interval.
RandomDistribution(int, DoubleInterval) - Constructor for class gov.nasa.alsUtility.RandomDistribution
 
RandomEvolvableDoubleListProducer - class gov.nasa.javaGenes.evolvableDoubleList.RandomEvolvableDoubleListProducer.
 
RandomEvolvableDoubleListProducer(IntegerInterval) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.RandomEvolvableDoubleListProducer
 
RandomEvolvableProducer - class gov.nasa.javaGenes.core.RandomEvolvableProducer.
 
RandomEvolvableProducer() - Constructor for class gov.nasa.javaGenes.core.RandomEvolvableProducer
 
RandomGaussianDistribution - class gov.nasa.alsUtility.RandomGaussianDistribution.
this class produces random numbers from an interval according to a Gaussian distribution.
RandomGaussianDistribution(int, DoubleInterval, double, double) - Constructor for class gov.nasa.alsUtility.RandomGaussianDistribution
 
RandomNumber - class gov.nasa.alsUtility.RandomNumber.
single random number generator for the whole program.
RandomNumber() - Constructor for class gov.nasa.alsUtility.RandomNumber
 
RandomNumberTest - class gov.nasa.alsUtility.RandomNumberTest.
 
RandomNumberTest(String) - Constructor for class gov.nasa.alsUtility.RandomNumberTest
 
ReinitializableFloat - class gov.nasa.alsUtility.ReinitializableFloat.
 
ReinitializableFloat() - Constructor for class gov.nasa.alsUtility.ReinitializableFloat
 
ReinitializableFloatTest - class gov.nasa.alsUtility.ReinitializableFloatTest.
 
ReinitializableFloatTest(String) - Constructor for class gov.nasa.alsUtility.ReinitializableFloatTest
 
ReinitializableFloatWithFactor - class gov.nasa.alsUtility.ReinitializableFloatWithFactor.
 
ReinitializableFloatWithFactor() - Constructor for class gov.nasa.alsUtility.ReinitializableFloatWithFactor
 
ReinitializableFloatWithFactorTest - class gov.nasa.alsUtility.ReinitializableFloatWithFactorTest.
 
ReinitializableFloatWithFactorTest(String) - Constructor for class gov.nasa.alsUtility.ReinitializableFloatWithFactorTest
 
ReinitializableInt - class gov.nasa.alsUtility.ReinitializableInt.
 
ReinitializableInt() - Constructor for class gov.nasa.alsUtility.ReinitializableInt
 
ReinitializableInt(int) - Constructor for class gov.nasa.alsUtility.ReinitializableInt
 
ReinitializableIntTest - class gov.nasa.alsUtility.ReinitializableIntTest.
 
ReinitializableIntTest(String) - Constructor for class gov.nasa.alsUtility.ReinitializableIntTest
 
Reporter - class gov.nasa.javaGenes.core.Reporter.
Create files and directories describing a genetic run.
Reporter(Parameters) - Constructor for class gov.nasa.javaGenes.core.Reporter
 
Reporter(Parameters, TokenizeInput) - Constructor for class gov.nasa.javaGenes.core.Reporter
restore state from checkpoint file
RestartAfterNChildrenWithoutAcceptance - class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptance.
 
RestartAfterNChildrenWithoutAcceptance(int) - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptance
 
RestartAfterNChildrenWithoutAcceptanceTest - class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptanceTest.
 
RestartAfterNChildrenWithoutAcceptanceTest(String) - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptanceTest
 
RestartAfterNChildrenWithoutImprovement - class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovement.
 
RestartAfterNChildrenWithoutImprovement(int) - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovement
 
RestartAfterNChildrenWithoutImprovementTest - class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovementTest.
 
RestartAfterNChildrenWithoutImprovementTest(String) - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovementTest
 
RestartEveryNChildren - class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildren.
 
RestartEveryNChildren(int) - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildren
 
RestartEveryNChildrenTest - class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildrenTest.
 
RestartEveryNChildrenTest(String) - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildrenTest
 
RestartNever - class gov.nasa.javaGenes.hillClimbing.RestartNever.
 
RestartNever() - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartNever
 
RestartPolicy - class gov.nasa.javaGenes.hillClimbing.RestartPolicy.
 
RestartPolicy() - Constructor for class gov.nasa.javaGenes.hillClimbing.RestartPolicy
 
RootMeanSquares - class gov.nasa.alsUtility.RootMeanSquares.
class to calculate RMS values
RootMeanSquares() - Constructor for class gov.nasa.alsUtility.RootMeanSquares
 
RootMeanSquaresTest - class gov.nasa.alsUtility.RootMeanSquaresTest.
 
RootMeanSquaresTest(String) - Constructor for class gov.nasa.alsUtility.RootMeanSquaresTest
 
RouletteWheel - class gov.nasa.javaGenes.core.RouletteWheel.
Implements a weighted roulette wheel with changable weights
RouletteWheel() - Constructor for class gov.nasa.javaGenes.core.RouletteWheel
 
RouletteWheel - class gov.nasa.javaGenes.weightNetwork.RouletteWheel.
 
RouletteWheel() - Constructor for class gov.nasa.javaGenes.weightNetwork.RouletteWheel
 
RouletteWheelChooseLowWeight - class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight.
 
RouletteWheelChooseLowWeight() - Constructor for class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
RouletteWheelChooseLowWeightTest - class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeightTest.
 
RouletteWheelChooseLowWeightTest(String) - Constructor for class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeightTest
 
RouletteWheelTest - class gov.nasa.javaGenes.core.RouletteWheelTest.
 
RouletteWheelTest(String) - Constructor for class gov.nasa.javaGenes.core.RouletteWheelTest
 
RouletteWheelTest - class gov.nasa.javaGenes.weightNetwork.RouletteWheelTest.
 
RouletteWheelTest(String) - Constructor for class gov.nasa.javaGenes.weightNetwork.RouletteWheelTest
 
Run - class gov.nasa.javaGenes.core.Run.
run JavaGenes under control of a Checkpointer object
Run() - Constructor for class gov.nasa.javaGenes.core.Run
 
Run - class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Run.
 
Run() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Run
 
RunChromosome - class gov.nasa.javaGenes.forceFields.RunChromosome.
run a genetic algorithm with a Chromosome (two-dimensional array) representation
RunChromosome() - Constructor for class gov.nasa.javaGenes.forceFields.RunChromosome
 
RunMolecule - class gov.nasa.javaGenes.chemistry.RunMolecule.
run a genetic algorithm on a Molecule represented as a graph
RunMolecule() - Constructor for class gov.nasa.javaGenes.chemistry.RunMolecule
 
RunPermutation - class gov.nasa.javaGenes.permutation.RunPermutation.
 
RunPermutation() - Constructor for class gov.nasa.javaGenes.permutation.RunPermutation
 
radialDistance - Variable in class gov.nasa.javaGenes.forceFields.SecondBody
distance to the first body
radialDistance - Variable in class gov.nasa.javaGenes.forceFields.ThirdBody
the distance of the last body to the first body
radians2degrees(double) - Static method in class gov.nasa.alsUtility.Utility
 
random() - Method in class gov.nasa.alsUtility.DoubleInterval
choose a random number in the interval (including the high and low values)
random() - Method in class gov.nasa.alsUtility.IntegerInterval
 
randomChildMaker - Variable in class gov.nasa.javaGenes.hillClimbing.Breeder
 
randomDivision(Graph) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
Randomly rip a copy of this in two.
randomGaussian(double, double) - Method in class gov.nasa.alsUtility.DoubleInterval
choose a random number in the interval from a Gaussian distribution
randomIndividualTriesPerSpecification - Variable in class gov.nasa.javaGenes.core.Parameters
 
randomLog() - Method in class gov.nasa.alsUtility.DoubleInterval
choose a random number in the interval (including the high and low values) from a log distribution
randomLogFromBothEnds() - Method in class gov.nasa.alsUtility.DoubleInterval
choose a random number in the interval (including the high and low values) from a log distribution whether you start from the top or the bottom
randomMerge(BrokenGraph, BrokenGraph) - Method in class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
merge two BrokenGraph objects and return the resulting graph.
randomize(int[]) - Static method in class gov.nasa.alsUtility.Utility
will be slow on large arrays.
randomizeAtomicPositions() - Method in class gov.nasa.javaGenes.chemistry.Molecule
set the positions of atoms to random numbers
randomizeAtomicPositionsBy(double) - Method in class gov.nasa.javaGenes.chemistry.Molecule
set the positions of atoms to random numbers
randomizeAtomicPositionsBy(double, boolean) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
randomizeAtomicPositionsBy(double, boolean, int) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
randomizeManyMolecules - class gov.nasa.javaGenes.chemistry.randomizeManyMolecules.
 
randomizeManyMolecules() - Constructor for class gov.nasa.javaGenes.chemistry.randomizeManyMolecules
 
randomizeXYZ - class gov.nasa.javaGenes.chemistry.randomizeXYZ.
 
randomizeXYZ() - Constructor for class gov.nasa.javaGenes.chemistry.randomizeXYZ
 
randomized(String, boolean, DutyCycleConstraint[]) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
randomized(boolean) - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
randomizedDC1(DutyCycleConstraint[]) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
randomlyChooseDefaultModulo - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
range - Variable in class gov.nasa.alsUtility.Sample
 
range - Variable in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
rate - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
read(String) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
read a mol file
read(String) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
read an xyz file
read(BufferedReader) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
read an xyz file
readFile(String, String) - Static method in class gov.nasa.alsUtility.FieldRecordText
 
readLine() - Method in class gov.nasa.alsUtility.FieldRecordText
 
readLine(BufferedReader) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
 
readMolecules(String) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
read many molecules from a xyz file
readOneLineFile(String) - Static method in class gov.nasa.alsUtility.Utility
 
readTsdFile(String) - Static method in class gov.nasa.alsUtility.FieldRecordText
 
readaTask() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
reader - Variable in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
readyToDieNow - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
reduceBy - Variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
referenceEnergy - Variable in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
referenceEnergyUncertainty - Variable in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
reinitialize() - Method in class gov.nasa.alsUtility.GrowOnlyArray
 
reinitialize() - Method in class gov.nasa.alsUtility.ObjectCache
Call when it's ok to reuse all of the objects in the cache.
reinitialize() - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
reinitialize() - Method in class gov.nasa.alsUtility.ReinitializableInt
 
reinitialize() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
reinitialize() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
reinitialize() - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
reinitialize() - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
turn intialWeights into a doubly linked list for easy deletion
remainingCapacity - Variable in class gov.nasa.javaGenes.EOSscheduling.SSRNode
 
remainingValence() - Method in class gov.nasa.javaGenes.chemistry.Atom
return the amount of valence unused by existing bonds
remove(int) - Method in class gov.nasa.alsUtility.ExtendedTreeSet
 
remove(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
remove(EvolvableDouble) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
remove(int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
remove(Edge) - Method in class gov.nasa.javaGenes.graph.Graph
Removes Edge e from graph.
remove(Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
Removes Vertex v from graph.
removeAll(Predicate) - Method in class gov.nasa.alsUtility.ExtendedVector
remove all elements that satisfy Predicate p
removeAll() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
removeBodiesAboveCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
removeBodiesAboveCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
removeCapacity(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRNode
 
removeDuplicates(String[]) - Static method in class gov.nasa.alsUtility.Utility
 
removeEdge(Edge) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
removeEdge(Edge) - Method in class gov.nasa.javaGenes.graph.Vertex
 
removeFile(String) - Static method in class gov.nasa.alsUtility.IO
 
removeFile(String) - Static method in class gov.nasa.alsUtility.Utility
 
removeFromWeightList(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
removeFromWeightList() - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
removeFromWeightList(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
removeInternalElementsOutsideOfCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
removeInternalElementsOutsideOfCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.OneBody
 
removeInternalElementsOutsideOfCutoff(Potential, int) - Method in class gov.nasa.javaGenes.forceFields.SecondBody
 
removeLastChildMaker() - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
removeLastNAtoms(int) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
removeLastNVertices(int) - Method in class gov.nasa.javaGenes.graph.Graph
 
removeUnexecutableTasks() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
removeVertices() - Method in class gov.nasa.javaGenes.graph.Edge
sets the vertices to null
renameFile(String, String) - Static method in class gov.nasa.alsUtility.IO
 
replaceEdge(Edge, Edge) - Method in class gov.nasa.javaGenes.graph.Graph
 
replaceVertex(Vertex, Vertex) - Method in class gov.nasa.javaGenes.graph.Edge
replace oldVertex with newVertex
replaceVertex(Vertex, Vertex) - Method in class gov.nasa.javaGenes.graph.Graph
 
report(String) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
report(Population) - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
report(PrintWriter) - Method in class gov.nasa.javaGenes.core.Population
Write out an ASCII version of the population
report(Parameters) - Method in class gov.nasa.javaGenes.core.Reporter
 
report(Population, Breeder) - Method in class gov.nasa.javaGenes.core.Reporter
Report on a population
report() - Method in class gov.nasa.javaGenes.core.Run
 
report(Population) - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
report(Population) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
report(Population) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
report(Population) - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
Prints out a file called difference.tsd with the target chromosome in it and the difference between the best and target chromosomes.
reportAccessWindowsWindowsTo(int, PrintWriter) - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
reportGroundStationAccessWindowsTo(PrintWriter) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
reportOnGeneration(int, String) - Method in class gov.nasa.javaGenes.core.Breeder
 
reportOnGeneration(int, String) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
reportTo(int, PrintWriter) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
reportTo(PrintWriter) - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
reportVariationOperatorPerformanceEachGeneration - Variable in class gov.nasa.javaGenes.core.Parameters
 
reporter - Variable in class gov.nasa.javaGenes.core.Run
 
reporter - Variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
requiredPopulationSize() - Static method in class gov.nasa.javaGenes.hillClimbing.Breeder
 
requiresSWextraParameters - Variable in class gov.nasa.javaGenes.forceFields.ThreeBody
 
requiresStillingWeberFFFform() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
rescheduleFromPermutation(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
rescheduleFromPermutationOver() - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
reset() - Method in class gov.nasa.alsUtility.CircularIntQueue
 
reset() - Method in class gov.nasa.alsUtility.IndexIterator
 
reset(long) - Method in class gov.nasa.alsUtility.Timer
resets the timer and stops
reset() - Method in class gov.nasa.alsUtility.Timer
resets the timer and stops
restart() - Method in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
restart() - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
restart() - Method in class gov.nasa.javaGenes.core.Run
start the run after having read any checkpoint file
restartPolicy - Variable in class gov.nasa.javaGenes.hillClimbing.Breeder
 
restartThreshold - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
results(double[], double[][]) - Method in class gov.nasa.alsUtility.LogComparisons
 
results(Individual, Individual[]) - Method in class gov.nasa.javaGenes.core.ChildMaker
 
retestStudents(StudentFitnessFunction) - Method in class gov.nasa.javaGenes.core.Population
 
right - Variable in class gov.nasa.alsUtility.And
 
right - Variable in class gov.nasa.alsUtility.Or
 
rms() - Method in class gov.nasa.alsUtility.RootMeanSquares
 
rosenbrock(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
min = f(1,...1) = 0.
rosenbrockRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
rouletteWheel - Variable in class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
 
run() - Method in class gov.nasa.javaGenes.core.PeriodicCheckpoints
 
run() - Method in class gov.nasa.javaGenes.core.Run
called by start and restart to run the genetic algorithm
runEOSscheduling - class gov.nasa.javaGenes.EOSscheduling.runEOSscheduling.
 
runEOSscheduling() - Constructor for class gov.nasa.javaGenes.EOSscheduling.runEOSscheduling
 
running - Variable in class gov.nasa.alsUtility.Timer
 

S

SEPARATOR - Static variable in class gov.nasa.javaGenes.core.Parameters
 
SHEKEL_FOXHOLES - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
SPHERE - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
SSRNode - class gov.nasa.javaGenes.EOSscheduling.SSRNode.
 
SSRNode() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SSRNode
 
SSRNodeTest - class gov.nasa.javaGenes.EOSscheduling.SSRNodeTest.
 
SSRNodeTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SSRNodeTest
 
SSRTimeline - class gov.nasa.javaGenes.EOSscheduling.SSRTimeline.
 
SSRTimeline() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
SSRTimeline(Horizon, int, Satellite) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
SSRTimelineNone - class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone.
 
SSRTimelineNone() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone
 
SSRTimelineTest - class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest.
 
SSRTimelineTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
SSRcapacity - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
SSRcapacity - Variable in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
SSRcapacity - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
SSRindex - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
SSRtimeline - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
SSRuse - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
SSRuse - Variable in class gov.nasa.javaGenes.EOSscheduling.TakeImage
 
STEP - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
STILLINGER_WEBER - Static variable in class gov.nasa.javaGenes.forceFields.Potential
 
STKAccessFile - class gov.nasa.javaGenes.EOSscheduling.STKAccessFile.
 
STKAccessFile(String, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
STKAccessFileTest - class gov.nasa.javaGenes.EOSscheduling.STKAccessFileTest.
 
STKAccessFileTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.STKAccessFileTest
 
Sample - class gov.nasa.alsUtility.Sample.
holds doubles (called "datums") from a statistical sample and does simple statistics on them
Sample() - Constructor for class gov.nasa.alsUtility.Sample
 
SampleTest - class gov.nasa.alsUtility.SampleTest.
 
SampleTest(String) - Constructor for class gov.nasa.alsUtility.SampleTest
 
Satellite - class gov.nasa.javaGenes.EOSscheduling.Satellite.
 
Satellite(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.Satellite
 
Saver - class gov.nasa.alsUtility.Saver.
This class is intended to buffer up many timesteps or generations of data and then save them as an array using java serialization.
Saver(String) - Constructor for class gov.nasa.alsUtility.Saver
 
Scheduler - class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler.
Assumes that AccessWindow.getDuration() == Task.getDuration()
Scheduler(EOSModel) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
only for use of subclasses
Scheduler(EOSModel, float, float, float) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
NOTE: requires that there are no tasks with 0 accessWindows BUG: in the evaluation function used by JavaGenes.Reporter.java the best schedule cannot be regenerated, so some of the objective values (e.g., MinimizeSlewingFitness and SmallSlewsFitness) will have values form a new HBSS run, not the actual best run! Need to figure out how to fix this.
Scheduler - class gov.nasa.javaGenes.EOSscheduling.Scheduler.
 
Scheduler(EOSModel) - Constructor for class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
SchedulerTest - class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest.
 
SchedulerTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest
 
SchedulingData - class gov.nasa.javaGenes.EOSscheduling.SchedulingData.
 
SchedulingData() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
SchedulingFitnessFunction - class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction.
 
SchedulingFitnessFunction(Scheduler) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
SecondBody - class gov.nasa.javaGenes.forceFields.SecondBody.
represents the second body and relevant parameters of a three-body.
SecondBody(Species, double) - Constructor for class gov.nasa.javaGenes.forceFields.SecondBody
 
SecondBody(Species, double, boolean) - Constructor for class gov.nasa.javaGenes.forceFields.SecondBody
 
SelectAll - class gov.nasa.javaGenes.evolvableDoubleList.SelectAll.
 
SelectAll() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectAll
 
SelectAllTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectAllTest.
 
SelectAllTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectAllTest
 
SelectByProbability - class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability.
 
SelectByProbability(double, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
SelectByProbabilityTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbabilityTest.
 
SelectByProbabilityTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbabilityTest
 
SelectChunk - class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk.
 
SelectChunk(int[]) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
SelectChunk(int[], int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
SelectChunk(int[], int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
SelectChunk(Selector, int[], int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
SelectChunkTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectChunkTest.
 
SelectChunkTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectChunkTest
 
SelectFixedIndices - class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndices.
 
SelectFixedIndices(int[]) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndices
 
SelectFixedIndicesTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndicesTest.
 
SelectFixedIndicesTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndicesTest
 
SelectFixedNumber - class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumber.
selects a fixed number of indices, or all of them if there aren't enough
SelectFixedNumber(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumber
 
SelectFixedNumberTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumberTest.
 
SelectFixedNumberTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumberTest
 
SelectModulo - class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo.
 
SelectModulo(Selector, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
SelectModulo(Selector, int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
SelectModuloTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectModuloTest.
 
SelectModuloTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectModuloTest
 
SelectOne - class gov.nasa.javaGenes.evolvableDoubleList.SelectOne.
 
SelectOne() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectOne
 
SelectOneNeighboringPair - class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair.
 
SelectOneNeighboringPair() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair
 
SelectOneNeighboringPair(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair
 
SelectOneNeighboringPair(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair
 
SelectOneNeighboringPairTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPairTest.
 
SelectOneNeighboringPairTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPairTest
 
SelectOneTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectOneTest.
 
SelectOneTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectOneTest
 
SelectTwoNeighboringPairs - class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs.
 
SelectTwoNeighboringPairs() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs
 
SelectTwoNeighboringPairs(int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs
 
SelectTwoNeighboringPairs(int, int) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs
 
SelectTwoNeighboringPairsTest - class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairsTest.
 
SelectTwoNeighboringPairsTest(String) - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairsTest
 
Selector - class gov.nasa.javaGenes.evolvableDoubleList.Selector.
 
Selector() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.Selector
 
Sensor - class gov.nasa.javaGenes.EOSscheduling.Sensor.
 
Sensor(Satellite, SensorType, Horizon, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.Sensor
must be called by all Sensor and subclass constructors to assign numbers and maintain allSensor's list
SensorTest - class gov.nasa.javaGenes.EOSscheduling.SensorTest.
 
SensorTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SensorTest
 
SensorType - class gov.nasa.javaGenes.EOSscheduling.SensorType.
 
SensorType(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SensorType
 
SetMark - class gov.nasa.alsUtility.SetMark.
 
SetMark(boolean) - Constructor for class gov.nasa.alsUtility.SetMark
 
SiCutoff - Static variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
SimpleCubicLatticConstant - Static variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
SlewIndex - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
SlewMotor - class gov.nasa.javaGenes.EOSscheduling.SlewMotor.
 
SlewMotor() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
SlewMotor(double, double, double, Horizon, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
SlewMotorNone - class gov.nasa.javaGenes.EOSscheduling.SlewMotorNone.
 
SlewMotorNone() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewMotorNone
 
SlewMotorTest - class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest.
 
SlewMotorTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest
 
SlewNode - class gov.nasa.javaGenes.EOSscheduling.SlewNode.
 
SlewNode() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
SlewNone - class gov.nasa.javaGenes.EOSscheduling.SlewNone.
 
SlewNone() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewNone
 
SlewRequirement - class gov.nasa.javaGenes.EOSscheduling.SlewRequirement.
 
SlewRequirement() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewRequirement
 
SlewTimeline - class gov.nasa.javaGenes.EOSscheduling.SlewTimeline.
 
SlewTimeline() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
SlewTimeline(Horizon, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
SlewTimelineNone - class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone.
 
SlewTimelineNone() - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
SlewTimelineTest - class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest.
 
SlewTimelineTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
Slewable - class gov.nasa.javaGenes.EOSscheduling.Slewable.
 
Slewable() - Constructor for class gov.nasa.javaGenes.EOSscheduling.Slewable
 
SmallSlewsFitness - class gov.nasa.javaGenes.EOSscheduling.SmallSlewsFitness.
 
SmallSlewsFitness(Scheduler, EOSModel) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SmallSlewsFitness
 
Species - class gov.nasa.javaGenes.forceFields.Species.
superclass for objects representing the species of the body for many body problems.
Species() - Constructor for class gov.nasa.javaGenes.forceFields.Species
 
Species2IndexMap - class gov.nasa.javaGenes.forceFields.Species2IndexMap.
used to convert a Species object to a array index for fast processing.
Species2IndexMap() - Constructor for class gov.nasa.javaGenes.forceFields.Species2IndexMap
 
SqueakyWheelPlacedTSM - class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM.
Same as SqueakyWheelTournamentSwapMutation except that moveForwardIndex is forced to be near the end of the permutation and moveBackIndex is forced to be closer to the front of the permutation.
SqueakyWheelPlacedTSM(EOSModel, int, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
SqueakyWheelPlacedTSM(EOSModel, int, int, double, double) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
SqueakyWheelPlacedTSMTest - class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSMTest.
 
SqueakyWheelPlacedTSMTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSMTest
 
SqueakyWheelShiftForward - class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward.
 
SqueakyWheelShiftForward(EOSModel, int, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
SqueakyWheelShiftForward(EOSModel, int, int, double, double) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
SqueakyWheelShiftForwardTest - class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest.
 
SqueakyWheelShiftForwardTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest
 
SqueakyWheelTournamentSwapMutation - class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation.
 
SqueakyWheelTournamentSwapMutation(EOSModel, int, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
Do numberOfSwaps swaps.
SqueakyWheelTournamentSwapMutationTest - class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest.
 
SqueakyWheelTournamentSwapMutationTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest
 
SteadyStateDiscreteBreeder - class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder.
implements a version of the Hierarchical Fair Competition Model (HFC, see http://www.egr.msu.edu/~hujianju/HFC.htm) with steady state breeding in discrete sub-popuations.
SteadyStateDiscreteBreeder(Parameters, Population, double, int, ChildMakerProvider, FitnessFunction, boolean, RandomEvolvableProducer, Fitness) - Constructor for class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
SteadyStateDiscreteBreeder(Parameters, Population, double, SubBreeder[], RandomEvolvableProducer, Fitness) - Constructor for class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
SteadyStateDiscreteBreederTest - class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreederTest.
 
SteadyStateDiscreteBreederTest(String) - Constructor for class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreederTest
 
StillingerWeber - class gov.nasa.javaGenes.forceFields.StillingerWeber.
Implements Thomas A.
StillingerWeber() - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeber
 
StillingerWeber(DoubleInterval, DoubleInterval, DoubleInterval) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeber
 
StillingerWeber(AtomicSpecies[], DoubleInterval, DoubleInterval, DoubleInterval) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeber
 
StillingerWeber.ChromosomeParametersData - class gov.nasa.javaGenes.forceFields.StillingerWeber.ChromosomeParametersData.
 
StillingerWeber.ChromosomeParametersData(String) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeber.ChromosomeParametersData
 
StillingerWeberEnergies - class gov.nasa.javaGenes.forceFields.StillingerWeberEnergies.
 
StillingerWeberEnergies() - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberEnergies
 
StillingerWeberPartialSiF - class gov.nasa.javaGenes.forceFields.StillingerWeberPartialSiF.
 
StillingerWeberPartialSiF(String[], DoubleInterval, DoubleInterval, DoubleInterval) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberPartialSiF
 
StillingerWeberPrintEnergiesAndForces - class gov.nasa.javaGenes.forceFields.StillingerWeberPrintEnergiesAndForces.
 
StillingerWeberPrintEnergiesAndForces() - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberPrintEnergiesAndForces
 
StillingerWeberSi - class gov.nasa.javaGenes.forceFields.StillingerWeberSi.
 
StillingerWeberSi() - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberSi
 
StillingerWeberSiF - class gov.nasa.javaGenes.forceFields.StillingerWeberSiF.
 
StillingerWeberSiF() - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
StillingerWeberSiF(DoubleInterval, DoubleInterval, DoubleInterval) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
StillingerWeberSiFTest - class gov.nasa.javaGenes.forceFields.StillingerWeberSiFTest.
 
StillingerWeberSiFTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberSiFTest
 
StillingerWeberSiTest - class gov.nasa.javaGenes.forceFields.StillingerWeberSiTest.
 
StillingerWeberSiTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberSiTest
 
StillingerWeberTest - class gov.nasa.javaGenes.forceFields.StillingerWeberTest.
 
StillingerWeberTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.StillingerWeberTest
 
StudentFitness - class gov.nasa.javaGenes.core.StudentFitness.
 
StudentFitness(StudentFitnessFunction) - Constructor for class gov.nasa.javaGenes.core.StudentFitness
 
StudentFitnessFunction - class gov.nasa.javaGenes.core.StudentFitnessFunction.
 
StudentFitnessFunction() - Constructor for class gov.nasa.javaGenes.core.StudentFitnessFunction
 
StudentTeacherTest - class gov.nasa.javaGenes.core.StudentTeacherTest.
 
StudentTeacherTest(String) - Constructor for class gov.nasa.javaGenes.core.StudentTeacherTest
 
SubBreeder - class gov.nasa.javaGenes.core.HFC.SubBreeder.
 
SubBreeder(ChildMakerProvider, FitnessFunction) - Constructor for class gov.nasa.javaGenes.core.HFC.SubBreeder
 
sameDimensions(double[][][], double[][][]) - Static method in class gov.nasa.alsUtility.Utility
 
sameDimensions(double[][], double[][]) - Static method in class gov.nasa.alsUtility.Utility
 
sameDimensions(double[], double[]) - Static method in class gov.nasa.alsUtility.Utility
 
satellite - Variable in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
satellite - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
satellites - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
save() - Method in class gov.nasa.alsUtility.Saver
save an array of objects that were buffered
save(Serializable) - Method in class gov.nasa.alsUtility.Saver
save an single object
scale(double) - Method in class gov.nasa.alsUtility.Vector3d
 
scale(double, Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
scaleBy(double) - Method in class gov.nasa.alsUtility.LogComparisons
used to scale down current values for evolution of ChildMakers
scaleBy(double) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
scaleBy(double) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
scaleBy(double) - Method in class gov.nasa.javaGenes.graph.Vertex
 
scaleEnergiesTo(DoubleInterval) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
scaleIntBy(int, double) - Method in class gov.nasa.alsUtility.LogComparisons
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.Body
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.OneBody
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
scaleLengthsBy(double) - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
scaleLengthsByAndReturnThis(double) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
scaleTo - Variable in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
scheduleTask(EOSschedulingEvolvable, TaskWeight) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
 
scheduleTask(TaskPlacementData, int) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
scheduleTaskFromEvolvableData(Task, TaskPlacementData) - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
scheduled(AccessWindowWeight) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
scheduler - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
scheduler - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
schedulingData - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
scramble(jiggle.Graph, double) - Method in class gov.nasa.javaGenes.graph.GraphLayout
set the xyz locations of vertices in a graph to random values
secondBody - Variable in class gov.nasa.javaGenes.forceFields.OneBody
the twoBody(s) this is involved with in a public array for fast access.
seed - Static variable in class gov.nasa.alsUtility.RandomNumber
 
selectionProbabilityRange - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
selector - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMaker
 
selector - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
sensor - Variable in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
sensor - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
sensorType - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
sensorType - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
sensorType - Variable in class gov.nasa.javaGenes.EOSscheduling.TakeImage
 
sensors - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
sensors - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
separateLogAndEvolvableFiles - Variable in class gov.nasa.javaGenes.core.Parameters
 
separator - Static variable in class gov.nasa.alsUtility.DoublesList
 
separator - Variable in class gov.nasa.alsUtility.FieldRecordText
 
separator() - Static method in class gov.nasa.alsUtility.PropertiesList
 
serialize(Serializable, String) - Static method in class gov.nasa.alsUtility.Utility
serialize object and put it in filename
set(double, double) - Method in class gov.nasa.alsUtility.DoubleInterval
set the high and low values of the interval.
set(DoubleInterval) - Method in class gov.nasa.alsUtility.DoubleInterval
make this equal to interval
set(double, boolean, double, boolean) - Method in class gov.nasa.alsUtility.DoubleInterval
 
set(int, int) - Method in class gov.nasa.alsUtility.IntegerInterval
sets the interval from x to y or y to x depending on which is lower
set(Quat4d) - Method in class gov.nasa.alsUtility.Matrix3d
set this matrix to the equivalent of quaternion q
set(Quat4d) - Method in class gov.nasa.alsUtility.Quat4d
 
set(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
setAcceptRandomIndividualFitnessThreshold(Fitness) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setAll(double, double, double, double, double, double) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
setAllMarks(boolean) - Method in class gov.nasa.javaGenes.graph.Graph
set marks on all edges and vertices
setAllele(Allele, int, int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
setAlleles(AlleleTemplate) - Method in class gov.nasa.javaGenes.forceFields.AssumedParameters
 
setAngle(double) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
setAtomicNumber(int) - Method in class gov.nasa.javaGenes.chemistry.Element
perform alchemy, transmute this element.
setAvailable(boolean) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNode
 
setBestFitnessAllowed(double) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
assumes best fitness is lower value
setBondLengthInterval(DoubleInterval) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setBreeder(Breeder) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setCapacity(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SSRNode
 
setCheckpointer(Checkpointer) - Method in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
setChromosome(Chromosome) - Method in class gov.nasa.javaGenes.forceFields.Potential
 
setChromosome(Chromosome) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setChromosome(Chromosome) - Method in class gov.nasa.javaGenes.forceFields.Tersoff
put the chromosome parameters in for future getEnergy calls
setComment(String) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
setCommentFromProperties() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
setCurrent(float) - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
setCutoff(MultiBody, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setCutoff(TwoBody, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
value is in angstoms
setCutoff(ThreeBody, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
value is in angstoms
setCutoff(ThreeBody, double, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
values are in angstoms
setCutoff(TwoBody, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
setCutoff(ThreeBody, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
setCutoff(ThreeBody, double, double) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
setCutoffInterval(DoubleInterval) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setDefaultCrossoverIntervalRange(DoubleInterval) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
setDefaultMutationStandardDeviationRange(DoubleInterval) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
setDefaultSelectionProbabilityRange(DoubleInterval) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
setDefaultWeightRange(DoubleInterval) - Static method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
setDerivedValues() - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
setDimension(int, double, double) - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
setDimerForce(double) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
setDirectedVertices(DirectedVertex, DirectedVertex) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
setDoPerAtomEnergies(boolean) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
setDoubleValue(int, double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
setDuration(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
setDutyCycles(DutyCycleConstraint[]) - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
setDutyCycles(DutyCycleConstraint[]) - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
setEdgeMarks(boolean) - Method in class gov.nasa.javaGenes.graph.Graph
 
setEnd(int) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
setEnd(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
setEnergy(double) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
setEnergy(int, double) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
setExponentInterval(DoubleInterval) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setExtension(double) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
setFactor(float) - Method in class gov.nasa.alsUtility.ReinitializableFloatWithFactor
 
setFactorInterval(DoubleInterval) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setFilename(String) - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
setFilename(String) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
setFilename(String) - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
setFirst(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
setFitness(double) - Method in class gov.nasa.javaGenes.core.Fitness
 
setFitness(double) - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
setFitnessFunction(FitnessFunction) - Method in class gov.nasa.javaGenes.core.Breeder
 
setFitnessFunction(FitnessFunction) - Method in class gov.nasa.javaGenes.core.ChildMaker
 
setFitnessFunction(FitnessFunction) - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
setFitnessFunctionNames(String[]) - Method in class gov.nasa.javaGenes.core.ChildMaker
 
setFitnessFunctionNames(String[]) - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
setFrom(TaskPlacementData) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setGeneration(int) - Method in class gov.nasa.javaGenes.core.Population
 
setGenerationIndex(int) - Method in class gov.nasa.javaGenes.core.Breeder
 
setGrade(double) - Method in class gov.nasa.javaGenes.core.StudentFitness
 
setGrimReaper(AntiTournament) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setGroundStationAccessWindows(AccessWindow[]) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
for testing
setHasBeenScheduled(boolean) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
setHigh(double) - Method in class gov.nasa.alsUtility.DoubleInterval
 
setHigh(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
setHorizon(Horizon) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
setHorizon(Horizon) - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
setHowMany(double) - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
setInVertex(DirectedVertex) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
setIndexAt(int, int) - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
setIndexRange(int, int) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setIndices() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setIndividual(Population, int, Individual) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setIndividual(int, Individual) - Method in class gov.nasa.javaGenes.core.Population
 
setInitial(float) - Method in class gov.nasa.alsUtility.ReinitializableFloat
 
setInitial(int) - Method in class gov.nasa.alsUtility.ReinitializableInt
 
setInterval(double) - Method in class gov.nasa.javaGenes.forceFields.Allele
set the interval to only include value
setLastNodes(Node, Node) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
for testing only
setLimit(int) - Method in class gov.nasa.alsUtility.IndexIterator
 
setLimitToOriginalInterval(boolean) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
setLimitToOriginalInterval(boolean) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
setLimitToOriginalInterval(boolean) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation
 
setLow(double) - Method in class gov.nasa.alsUtility.DoubleInterval
 
setLow(int) - Method in class gov.nasa.alsUtility.IntegerInterval
 
setMap(Species, int) - Method in class gov.nasa.javaGenes.forceFields.Species2IndexMap
enter a species and index into the map
setMark(boolean) - Method in class gov.nasa.alsUtility.Mark
 
setMemory(long) - Method in class gov.nasa.javaGenes.core.Population
 
setMillisecondsPerTimestep(int) - Static method in class gov.nasa.javaGenes.EOSscheduling.Horizon
changes all time calculations.
setMustRampToEnd(boolean) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
setName(String) - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
setName(String, int) - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
setName(String) - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
setNext(Node) - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
setNext(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
setNoEvolution(double) - Method in class gov.nasa.javaGenes.forceFields.Allele
 
setNormalization(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction
 
setNormalizeByWeight(boolean) - Method in class gov.nasa.javaGenes.core.WeightedSumFitness
 
setNumber(int) - Method in class gov.nasa.alsUtility.Saver
set the number used to name files
setNumber(int) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
setNumber(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
setNumber(int) - Method in class gov.nasa.javaGenes.forceFields.Immigrant
 
setNumber(int) - Method in class gov.nasa.javaGenes.graph.Vertex
 
setNumberInfinit(boolean) - Method in class gov.nasa.javaGenes.forceFields.Immigrant
 
setNumbers(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
setOutOfOrderPenalty(double) - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness
 
setOutVertex(DirectedVertex) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
setParentChooser(Tournament) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setPermissions(String, String) - Static method in class gov.nasa.alsUtility.Utility
sets the permissions of file to permissions using chmod.
setPreserved(Population, Population, int) - Method in class gov.nasa.javaGenes.core.BreederElitist
the best parents become children without modifications
setPrevious(Node) - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
setPrevious(Weight) - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
setPriority(double) - Method in class gov.nasa.javaGenes.EOSscheduling.Task
 
setPromotionsTo(SubBreeder) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
setPropertiesFromComment() - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
setQuickCheckArrays(Horizon) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
setR(double) - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
setRJI(double) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
setRJK(double) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
setResults(int, int, int, int) - Method in class gov.nasa.alsUtility.LogComparisons
for testing only
setSSR(int, Horizon, int) - Method in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
setSSRuse(int) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
setScheduled(boolean) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setScheduledAtStartOf(AccessWindow) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setSeed(long) - Static method in class gov.nasa.alsUtility.RandomNumber
set the random number generator seed.
setSensor(Sensor) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
setSensor(Sensor) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
setSensorNumber(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
setSensorNumber(int) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setSlew(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
setSlewMotor(SlewMotor) - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
setSlewRequirement(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
setSlewRequirement(int, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
setSlewRequirement(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
setSlewRequirement(SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setSlewable(Slewable) - Method in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
setSlewingToLargestPointing(Sensor) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
setSlop(double) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
setSpeciesIndex(Species2IndexMap) - Method in class gov.nasa.javaGenes.forceFields.Body
used to set the species index
setSpeciesIndices(Species2IndexMap) - Method in class gov.nasa.javaGenes.forceFields.Bodies
set the species indices in all the bodies for fast access
setSpeciesIndices(Species2IndexMap) - Method in class gov.nasa.javaGenes.forceFields.OneBody
converts the species of this and the SecondBody(s) to an integer for fast access
setSpeciesIndices(Species2IndexMap) - Method in class gov.nasa.javaGenes.forceFields.SecondBody
sets the array index for the species for each body for fast access
setStart(int) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
setStart(int) - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
setStartTime(int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
setStartTime(int) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setStudents(Population) - Method in class gov.nasa.javaGenes.core.TeacherFitnessFunction
 
setTaskPlacement(int, TaskPlacementData) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
setTaskPlacement(int, EOSschedulingEvolvable, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
setTaskPriorities(double, double, int) - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
setTeachers(TeacherPopulation) - Method in class gov.nasa.javaGenes.core.StudentFitnessFunction
 
setTime(long) - Method in class gov.nasa.javaGenes.core.Population
 
setTimeAndNeighbors(int, Node, Node) - Method in class gov.nasa.javaGenes.EOSscheduling.Node
 
setToAscending() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
used for testing
setToConstant(double[][][], double) - Static method in class gov.nasa.alsUtility.Utility
 
setToConstant(double[][], double) - Static method in class gov.nasa.alsUtility.Utility
 
setToConstant(double[], double) - Static method in class gov.nasa.alsUtility.Utility
 
setToExtremes(double[]) - Method in class gov.nasa.alsUtility.DoubleInterval
set the bounds to the extreme values in array
setToExtremes(Vector) - Method in class gov.nasa.alsUtility.DoubleInterval
 
setToExtremes(int[]) - Method in class gov.nasa.alsUtility.IntegerInterval
sets the interval to the low and high values of array
setToLog() - Method in class gov.nasa.alsUtility.DoubleInterval
convert the top and bottom values to their natural logarithm
setTotalNumberOfKidsProduced(int) - Method in class gov.nasa.javaGenes.core.Breeder
 
setUnitCell(UnitCell) - Method in class gov.nasa.javaGenes.chemistry.Molecule
 
setUp() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
setUp() - Method in class gov.nasa.alsUtility.FieldRecordTextTest
 
setUp() - Method in class gov.nasa.alsUtility.SampleTest
 
setUp() - Method in class gov.nasa.alsUtility.Vector3dTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFileTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.SensorTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSMTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest
 
setUp() - Method in class gov.nasa.javaGenes.EOSscheduling.TimelineTest
 
setUp() - Method in class gov.nasa.javaGenes.chemistry.AtomTest
 
setUp() - Method in class gov.nasa.javaGenes.chemistry.MoleculeTest
 
setUp() - Method in class gov.nasa.javaGenes.core.AntiTournamentLocalTest
 
setUp() - Method in class gov.nasa.javaGenes.core.AntiTournamentTest
 
setUp() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest
 
setUp() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProviderTest
 
setUp() - Method in class gov.nasa.javaGenes.core.ChildMakerTest
 
setUp() - Method in class gov.nasa.javaGenes.core.FitnessMultiObjectiveTest
 
setUp() - Method in class gov.nasa.javaGenes.core.PopulationTest
 
setUp() - Method in class gov.nasa.javaGenes.core.RouletteWheelTest
 
setUp() - Method in class gov.nasa.javaGenes.core.StudentTeacherTest
 
setUp() - Method in class gov.nasa.javaGenes.core.TournamentLocalTest
 
setUp() - Method in class gov.nasa.javaGenes.core.TournamentTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplateTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.AlleleTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.AssumedParametersTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.BodiesTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossoverTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutationTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.ForceFitnessRMSTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.ImmigrantTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.ImmigrantsTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMSTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiFTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.TersoffTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.ThreeBodyTest
 
setUp() - Method in class gov.nasa.javaGenes.forceFields.TwoBodyTest
 
setUp() - Method in class gov.nasa.javaGenes.graph.GraphTest
 
setUp() - Method in class gov.nasa.javaGenes.graph.VertexTest
 
setUp() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeightTest
 
setUp() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelTest
 
setUp() - Method in class gov.nasa.javaGenes.weightNetwork.WeightListTest
 
setUpForRescheduleFromPermutation() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
 
setUpForRescheduleFromPermutation() - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
setUpIndices(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
setUpIndices(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
setUpIndicesFromArray(EOSschedulingEvolvable) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
testing purposes only, has no randomization here!
setUpMolecule() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
setUpNodeList() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline
 
setUpNodeList() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimeline
 
setUpNodeList() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimeline
 
setUpNodeList() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone
 
setUpNodeList() - Method in class gov.nasa.javaGenes.EOSscheduling.Timeline
 
setValue(int) - Method in class gov.nasa.alsUtility.integer
 
setValue(double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
setValue(double, int, int) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
set the value at the indicated indices
setValue(double, int, int) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setVertexMarks(boolean) - Method in class gov.nasa.javaGenes.graph.Graph
 
setVertices(Vertex, Vertex) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
not implemented
setVertices(Vertex, Vertex) - Method in class gov.nasa.javaGenes.graph.Edge
removes existing vertices removes "this" from edge list of existing vertices sets the vertices forces itself to be compatible (subclass responsibility)
setWeight(float) - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
setWeightAndPropagate(float) - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
setWeightList(WeightList) - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
setWindowNumber(int) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
setX(double) - Method in class gov.nasa.alsUtility.Vector3d
 
setXyz(double[]) - Method in class gov.nasa.javaGenes.graph.Vertex
set the physical location of the vertex
setXyz(double, double, double) - Method in class gov.nasa.javaGenes.graph.Vertex
set the physical location of the vertex
setY(double) - Method in class gov.nasa.alsUtility.Vector3d
 
setZ(double) - Method in class gov.nasa.alsUtility.Vector3d
 
setupAllelesAndChromosome() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setupChromosome(Chromosome, AlleleTemplate) - Method in class gov.nasa.javaGenes.forceFields.Immigrant
 
setupChromosomeFromPaper() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setupChromosomeFromPaper() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSi
 
setupChromosomeFromPaper(String) - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiF
 
setupComplete - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
setupOk() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
shallowClone() - Method in class gov.nasa.javaGenes.graph.Graph
copy the graph and don't make copies of all edges and vertices
shallowCopyBrokenEdge() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
 
shallowCopyEdge() - Method in class gov.nasa.javaGenes.graph.Edge
 
shallowCopyVertex() - Method in class gov.nasa.javaGenes.graph.Vertex
don't make copies of the edges
shekelFoxholes(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
min = f(-32,-32) -- and four others ~= 1, the numbers are in a strange space, see code originally for list.getSize() = 2 with 25 local minima
shekelFoxholesRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
shiftFraction - Variable in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
shouldChooseSecondOne(Fitness, Fitness) - Method in class gov.nasa.javaGenes.core.AntiTournament
 
shouldChooseSecondOne(Fitness, Fitness) - Method in class gov.nasa.javaGenes.core.Tournament
 
shouldPromote(Individual) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
shouldSecondGoForward(EOSschedulingEvolvable, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
shouldStop() - Method in class gov.nasa.javaGenes.core.Run
 
shouldWrite(int, int) - Method in class gov.nasa.javaGenes.core.Reporter
 
shrinkAroundMiddle(int) - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
signOf(double) - Static method in class gov.nasa.alsUtility.Utility
 
simpleClassName(String) - Static method in class gov.nasa.alsUtility.Utility
probably doesn't work.
simpleLighting() - Static method in class gov.nasa.alsUtility.VRMLUtility
 
simpleSelector - Variable in class gov.nasa.javaGenes.evolvableDoubleList.NeighboringPairsSelector
 
simpleSelector - Variable in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
size() - Method in class gov.nasa.alsUtility.Distribution
number of values available
size() - Method in class gov.nasa.alsUtility.DoublesList
 
size() - Method in class gov.nasa.alsUtility.GrowOnlyArray
 
size() - Method in class gov.nasa.alsUtility.MinMaxes
 
size() - Method in class gov.nasa.alsUtility.PropertiesList
 
size - Variable in class gov.nasa.alsUtility.RandomDistribution
the number of numbers in the distribution.
size() - Method in class gov.nasa.alsUtility.RandomDistribution
 
size - Variable in class gov.nasa.alsUtility.RandomGaussianDistribution
the number of numbers in the distribution.
size() - Method in class gov.nasa.alsUtility.RandomGaussianDistribution
 
size() - Method in class gov.nasa.javaGenes.chemistry.Molecules
 
size() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
size() - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
size - Variable in class gov.nasa.javaGenes.core.Tournament
 
size() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Indices
 
size() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
size() - Method in class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy
 
size() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
size() - Method in class gov.nasa.javaGenes.forceFields.Species2IndexMap
 
sizeRange - Variable in class gov.nasa.javaGenes.evolvableDoubleList.RandomEvolvableDoubleListProducer
 
slewMotor - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
slewMotors - Variable in class gov.nasa.javaGenes.EOSscheduling.Satellite
 
slewRate - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
slewRequirement - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
slewRequirement - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewNode
 
slewTime(SlewRequirement, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
slewTime(SlewRequirement, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorNone
 
slewTime(SlewRequirement, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.Slewable
 
slewTimeAdequate(int, SlewRequirement, SlewRequirement) - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
slewTimeline - Variable in class gov.nasa.javaGenes.EOSscheduling.Slewable
 
slewable - Variable in class gov.nasa.javaGenes.EOSscheduling.SchedulingData
 
slop - Variable in class gov.nasa.javaGenes.EOSscheduling.SlewMotor
 
slope - Variable in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
slowFits(AvailabilityTimeline, AvailableNode, int, int) - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
if a period of 'duration' length starting at startTime became UnAvailable, would the timeline be consistant with the dutycycle constraint? Algorithm: - subtract duration to maxOnTime to get the maximum ontime acceptable - check from the beginning of the duration forward - check from the end of the duration backward - for UnAvailable nodes before the duration, check from it's beginning forward - for UnAvailable nodes after the duration, check from it's end backward
smallSlewFactor - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
smallSlewNormalizedWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
smallSlewWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
sort() - Method in class gov.nasa.alsUtility.DataTable
 
sort(int[]) - Static method in class gov.nasa.alsUtility.Utility
sort array using a bubble sort
sortArray(long[]) - Static method in class gov.nasa.alsUtility.Utility
sort array using a bubble sort
sortByString() - Method in class gov.nasa.alsUtility.ExtendedVector
sorts elements according to their string representations
sortVectorOfDouble(Vector) - Static method in class gov.nasa.alsUtility.Utility
 
specialLog(double) - Method in class gov.nasa.javaGenes.core.Reporter
will always return a number.
specialThreeBodyParametersIncrement - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
species - Variable in class gov.nasa.javaGenes.forceFields.Body
the species of this body (second body in TwoBody, third body in ThreeBody)
species - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
speciesIndex - Variable in class gov.nasa.javaGenes.forceFields.Body
the species index.
speciesMap - Variable in class gov.nasa.javaGenes.forceFields.Tersoff
 
speedOfLightMetersPerSecond - Static variable in class gov.nasa.alsUtility.Constants
 
sphere(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
min = f(0,...,0) == 0 originally for list.getSize() = 3
sphereRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
spinWheel(int) - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
spinWheel() - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
spinWheel() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheel
 
spinWheel(float) - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheel
 
spinWheel() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
spinWheel(float) - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
only for testing.
ssrWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
standardDeviation - Variable in class gov.nasa.alsUtility.RandomGaussianDistribution
standard deviation of the Gaussian distribution
standardDeviation - Variable in class gov.nasa.alsUtility.Sample
 
standardDeviation - Variable in class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDev
 
standardDeviation - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
The standard deviation to use expressed as a fraction of the allele interval
standardDeviationFactor - Variable in class gov.nasa.javaGenes.forceFields.Mutation3Parents
 
start() - Method in class gov.nasa.alsUtility.Timer
starts the clock
start - Variable in class gov.nasa.javaGenes.EOSscheduling.AccessWindow
 
start - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
start(String[]) - Method in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
start - Variable in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
start(String[]) - Method in class gov.nasa.javaGenes.core.Checkpointer
Not normally not called directly
start(String[]) - Method in class gov.nasa.javaGenes.core.Run
start a run.
startDate - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
startJavaEpoch - Variable in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
startPeriodicCheckpoint(Checkpointer, long) - Static method in class gov.nasa.javaGenes.core.Checkpointer
starts a thread that will execute periodic checkpoints
startSpecialized(String[]) - Method in class gov.nasa.javaGenes.EOSscheduling.runEOSscheduling
 
startSpecialized(String[]) - Method in class gov.nasa.javaGenes.chemistry.RunMolecule
create MoleculeParameters and MoleculePopulation objects
startSpecialized(String[]) - Method in class gov.nasa.javaGenes.core.Run
used to do the special processing necessary at startup by subclasses
startSpecialized(String[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Run
 
startSpecialized(String[]) - Method in class gov.nasa.javaGenes.forceFields.RunChromosome
get ChromosomeParameters and ChromosomePopulation objects
startSpecialized(String[]) - Method in class gov.nasa.javaGenes.permutation.RunPermutation
 
startTime - Variable in class gov.nasa.javaGenes.EOSscheduling.Node
 
startUpdateAndPropagate() - Method in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable
 
stateChange() - Method in class gov.nasa.javaGenes.graph.Vertex
deletes cached information.
stateRestore(TokenizeInput) - Method in class gov.nasa.javaGenes.core.Breeder
restore from a checkpoint
stateRestore(TokenizeInput) - Method in class gov.nasa.javaGenes.core.Population
write to a checkpoint file
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.core.AbstractCheckpointable
 
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.core.Breeder
checkpoint
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.core.Evolvable
 
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.core.Individual
 
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.core.Population
read from a checkpoint file
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.core.Reporter
save state to checkpoint file
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.forceFields.Chromosome
Save the state of a chromosome to a checkpoint file
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIndividual
checkpoint
stateSave(TokenizeOutput) - Method in class gov.nasa.javaGenes.forceFields.ChromosomePopulation
checkpoint
statisticsCorrect - Variable in class gov.nasa.alsUtility.Sample
 
statisticsString() - Method in class gov.nasa.alsUtility.Sample
 
statisticsString() - Method in class gov.nasa.alsUtility.WeightedStatistics
 
stealEdges(Vertex) - Method in class gov.nasa.javaGenes.graph.DirectedVertex
if an error to call this
stealEdges(Vertex) - Method in class gov.nasa.javaGenes.graph.Vertex
 
stealVertices(Edge) - Method in class gov.nasa.javaGenes.graph.DirectedEdge
it is an error to call this
stealVertices(Edge) - Method in class gov.nasa.javaGenes.graph.Edge
 
step(EvolvableDoubleList) - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
min = f({-5.12,-5],...,[-5.12,-5]) == 0 originally for list.getSize() = 5 Again the references disagree, but this time I use the second one since the min is always 0 regarless of dimensionality
stepRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
stkDateString2Date(String) - Static method in class gov.nasa.alsUtility.Utility
 
stop() - Method in class gov.nasa.alsUtility.Timer
stops the clock and remembers the time used
stopAtPerfection - Variable in class gov.nasa.javaGenes.core.Parameters
if true, end run when best fitness equals 0
stopFile - Variable in class gov.nasa.javaGenes.core.Parameters
after each generation check for this file.
string2boolean(String) - Static method in class gov.nasa.alsUtility.Utility
 
string2double(String) - Static method in class gov.nasa.alsUtility.Utility
 
string2integer(String) - Static method in class gov.nasa.alsUtility.Utility
 
string2long(String) - Static method in class gov.nasa.alsUtility.Utility
 
stringSeparator() - Static method in class gov.nasa.alsUtility.Utility
 
sub(Vector3d, Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
subBreeders - Variable in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
subClassMeasures() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
subClassMeasures() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
subClassMeasures() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
subClassMeasures() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
subtract(Vector3d, Vector3d) - Static method in class gov.nasa.alsUtility.Vector3d
 
subtract(Vector3d) - Method in class gov.nasa.alsUtility.Vector3d
 
subtractWeightFrom - Variable in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight
 
suite() - Static method in class gov.nasa.alsUtility.AllTests
 
sum - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
sumSquares - Variable in class gov.nasa.alsUtility.RootMeanSquares
 
sumSquares - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
suspendFile - Variable in class gov.nasa.javaGenes.core.Parameters
after each generation check for this file.
suspendTime - Variable in class gov.nasa.javaGenes.core.Parameters
 
symbolSize - Static variable in class gov.nasa.javaGenes.chemistry.molFormat
 

T

TERSOFF - Static variable in class gov.nasa.javaGenes.forceFields.Potential
 
TakeImage - class gov.nasa.javaGenes.EOSscheduling.TakeImage.
 
TakeImage(int, SensorType, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TakeImage
 
TakeImage(int, SensorType) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TakeImage
 
Tanimoto - class gov.nasa.alsUtility.Tanimoto.
calculates the Tanimoto coefficient for different data structures.
Tanimoto() - Constructor for class gov.nasa.alsUtility.Tanimoto
 
TanimotoDistance(double, double) - Static method in class gov.nasa.alsUtility.Utility
 
TanimotoDistanceOneSideOfZero(double, double) - Static method in class gov.nasa.alsUtility.Utility
 
Task - class gov.nasa.javaGenes.EOSscheduling.Task.
 
Task(int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.Task
 
TaskAndAccessWindowGenerator - class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator.
 
TaskAndAccessWindowGenerator(Horizon, int, int) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
TaskAndAccessWindowGeneratorTest - class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest.
 
TaskAndAccessWindowGeneratorTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest
 
TaskList - class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskList.
 
TaskList() - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskList
 
TaskList(EOSModel, float, float, float) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskList
 
TaskPlacementData - class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData.
just holds data to simplify returning it.
TaskPlacementData() - Constructor for class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
TaskPriorityFitness - class gov.nasa.javaGenes.EOSscheduling.TaskPriorityFitness.
assumes larger priorities are more important (e.g., priorty 1 more important that 2)
TaskPriorityFitness(Scheduler, EOSModel) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TaskPriorityFitness
 
TaskTest - class gov.nasa.javaGenes.EOSscheduling.TaskTest.
 
TaskTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TaskTest
 
TaskWeight - class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight.
 
TaskWeight() - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
TaskWeight(Task, float, float, float) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
assumes Task requires SSR
TaskWeightTest - class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest.
 
TaskWeightTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
TeacherFitnessFunction - class gov.nasa.javaGenes.core.TeacherFitnessFunction.
 
TeacherFitnessFunction() - Constructor for class gov.nasa.javaGenes.core.TeacherFitnessFunction
 
TeacherPopulation - class gov.nasa.javaGenes.core.TeacherPopulation.
 
TeacherPopulation(int, AlleleTemplate, TeacherFitnessFunction) - Constructor for class gov.nasa.javaGenes.core.TeacherPopulation
 
Tersoff - class gov.nasa.javaGenes.forceFields.Tersoff.
Implements the Tersoff potential.
Tersoff(AtomicSpecies[]) - Constructor for class gov.nasa.javaGenes.forceFields.Tersoff
 
Tersoff() - Constructor for class gov.nasa.javaGenes.forceFields.Tersoff
only use for C, Si
TersoffTest - class gov.nasa.javaGenes.forceFields.TersoffTest.
 
TersoffTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.TersoffTest
 
TestFitnessFunction1 - class gov.nasa.javaGenes.evolvableDoubleList.TestFitnessFunction1.
 
TestFitnessFunction1() - Constructor for class gov.nasa.javaGenes.evolvableDoubleList.TestFitnessFunction1
 
TetrahedronAngle - Static variable in class gov.nasa.javaGenes.chemistry.Constants
 
ThirdBody - class gov.nasa.javaGenes.forceFields.ThirdBody.
represents the last body and relevant parameters of a three-body.
ThirdBody(Species, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.ThirdBody
 
ThreeBody - class gov.nasa.javaGenes.forceFields.ThreeBody.
 
ThreeBody(String, String, String, double, double, double) - Constructor for class gov.nasa.javaGenes.forceFields.ThreeBody
middle atom is center of the three body.
ThreeBody(String, String, String) - Constructor for class gov.nasa.javaGenes.forceFields.ThreeBody
 
ThreeBody(Atom, Atom, Atom) - Constructor for class gov.nasa.javaGenes.forceFields.ThreeBody
middle atom is center of the three body
ThreeBody(Atom, Atom, Atom, UnitCell) - Constructor for class gov.nasa.javaGenes.forceFields.ThreeBody
middle atom is center of the three body
ThreeBodyTest - class gov.nasa.javaGenes.forceFields.ThreeBodyTest.
 
ThreeBodyTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.ThreeBodyTest
 
TimeInterval - class gov.nasa.javaGenes.EOSscheduling.TimeInterval.
 
TimeInterval() - Constructor for class gov.nasa.javaGenes.EOSscheduling.TimeInterval
 
Timeline - class gov.nasa.javaGenes.EOSscheduling.Timeline.
This class must be very fast.
Timeline() - Constructor for class gov.nasa.javaGenes.EOSscheduling.Timeline
must be called by all Timeline and subclass constructors reinitialize timelines for next scheduling execution.
Timeline(Horizon) - Constructor for class gov.nasa.javaGenes.EOSscheduling.Timeline
 
TimelineTest - class gov.nasa.javaGenes.EOSscheduling.TimelineTest.
 
TimelineTest(String) - Constructor for class gov.nasa.javaGenes.EOSscheduling.TimelineTest
 
Timer - class gov.nasa.alsUtility.Timer.
time things using wallclock time.
Timer() - Constructor for class gov.nasa.alsUtility.Timer
 
Timer(long) - Constructor for class gov.nasa.alsUtility.Timer
 
TokenizeInput - class gov.nasa.javaGenes.core.TokenizeInput.
used to read files created by TokenizeOutput.
TokenizeInput(String) - Constructor for class gov.nasa.javaGenes.core.TokenizeInput
 
TokenizeOutput - class gov.nasa.javaGenes.core.TokenizeOutput.
used to write files that will be read by TokenizeInput.
TokenizeOutput(String) - Constructor for class gov.nasa.javaGenes.core.TokenizeOutput
 
TopSubBreeder - class gov.nasa.javaGenes.core.HFC.TopSubBreeder.
 
TopSubBreeder(ChildMakerProvider, FitnessFunction) - Constructor for class gov.nasa.javaGenes.core.HFC.TopSubBreeder
 
Tournament - class gov.nasa.javaGenes.core.Tournament.
assumes that the tournament size is usually quite a bit smaller than the index interval from which the indices are chosen
Tournament(int) - Constructor for class gov.nasa.javaGenes.core.Tournament
 
TournamentLocal - class gov.nasa.javaGenes.core.TournamentLocal.
 
TournamentLocal(int, int) - Constructor for class gov.nasa.javaGenes.core.TournamentLocal
 
TournamentLocalTest - class gov.nasa.javaGenes.core.TournamentLocalTest.
 
TournamentLocalTest(String) - Constructor for class gov.nasa.javaGenes.core.TournamentLocalTest
 
TournamentTest - class gov.nasa.javaGenes.core.TournamentTest.
 
TournamentTest(String) - Constructor for class gov.nasa.javaGenes.core.TournamentTest
 
Trail - class gov.nasa.javaGenes.graph.Trail.
A trail of edges between ends[0] and ends[1].
Trail(Vertex) - Constructor for class gov.nasa.javaGenes.graph.Trail
 
TwoBody - class gov.nasa.javaGenes.forceFields.TwoBody.
 
TwoBody(String, String, double) - Constructor for class gov.nasa.javaGenes.forceFields.TwoBody
 
TwoBody(String, String) - Constructor for class gov.nasa.javaGenes.forceFields.TwoBody
 
TwoBody(Atom, Atom) - Constructor for class gov.nasa.javaGenes.forceFields.TwoBody
 
TwoBody(Atom, Atom, UnitCell) - Constructor for class gov.nasa.javaGenes.forceFields.TwoBody
 
TwoBodyTest - class gov.nasa.javaGenes.forceFields.TwoBodyTest.
 
TwoBodyTest(String) - Constructor for class gov.nasa.javaGenes.forceFields.TwoBodyTest
 
TwoVertexGraphCrossover - class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover.
implements the crossover operator described in "JavaGenes: Evolving Graphs with Crossover," Al Globus, Sean Atsatt, John Lawton, and Todd Wipke and found at http://www.nas.nasa.gov/~globus/papers/JavaGenes/paper.html
TwoVertexGraphCrossover() - Constructor for class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover
 
tabSeparatedResults() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
tabSeparatedString(Vector) - Static method in class gov.nasa.alsUtility.Utility
 
tabSeparatedString() - Method in class gov.nasa.javaGenes.forceFields.Body
 
tabSeparatedString() - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
tabSeparatedString() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
tabSeparatedString() - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
table - Variable in class gov.nasa.alsUtility.PropertiesList
 
table - Variable in class gov.nasa.javaGenes.forceFields.Species2IndexMap
 
takeImageTime - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
tanimotoDistance(KeyCounter) - Method in class gov.nasa.alsUtility.KeyCounter
BUG: only works for counts that fit in an int.
target - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeDistanceFitness
target chromosome
target - Variable in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
 
target - Variable in class gov.nasa.javaGenes.graph.CyclesSimilarity
the target graph against which Individuals will be measured
target - Variable in class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity
 
target - Variable in class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity
target graph
targetReferenceEnergy - Variable in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS
 
task - Variable in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
taskList - Variable in class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler
 
taskPlacements - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
taskPriorityIncrement - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
taskPriorityWeight - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
taskSSRuse - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
taskSSRuse - Variable in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
tasks - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
tearDown() - Method in class gov.nasa.alsUtility.FieldRecordTextTest
 
tearDown() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeTest
 
tearDown() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFileTest
 
tearDown() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest
 
tearDown() - Method in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMSTest
 
tearDown() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
temperatureChange - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
temporary - Static variable in class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey
 
temporary - Static variable in class gov.nasa.javaGenes.graph.Graph.TrailKey
 
terpolate0to1(double) - Method in class gov.nasa.alsUtility.DoubleInterval
interpolate or exterpolate to a 0-1 space
test() - Method in class gov.nasa.alsUtility.AmericanWireGaugeTest
 
test() - Method in class gov.nasa.alsUtility.Brick3dWithSegmentsTest
 
test() - Static method in class gov.nasa.alsUtility.RandomNumber
for testing run: java RandomNumber buckets trials
test() - Method in class gov.nasa.alsUtility.RootMeanSquaresTest
 
test(String[]) - Static method in class gov.nasa.alsUtility.Timer
 
test() - Method in class gov.nasa.alsUtility.VecMathTest
 
test() - Method in class gov.nasa.alsUtility.WeightedStatisticsTest
 
test(String[]) - Static method in class gov.nasa.javaGenes.chemistry.Element
 
test(String[]) - Static method in class gov.nasa.javaGenes.chemistry.MoleculeLayout
 
test() - Method in class gov.nasa.javaGenes.core.ChildMakerDownFractionComparatorTest
 
test() - Method in class gov.nasa.javaGenes.core.FitnessFunctionBadSizeTest
 
test() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEachTest
 
test() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectAllTest
 
test() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectOneTest
 
test(String[]) - Static method in class gov.nasa.javaGenes.graph.apsp
 
testAdd() - Method in class gov.nasa.alsUtility.KeyCounterTest
 
testAdd() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testAdd() - Method in class gov.nasa.javaGenes.weightNetwork.WeightListTest
 
testAddAll() - Method in class gov.nasa.javaGenes.evolvableDoubleList.IndicesTest
 
testAddIndex() - Method in class gov.nasa.javaGenes.evolvableDoubleList.IndicesTest
 
testAddRemoveSize() - Method in class gov.nasa.javaGenes.core.ChildMakerProviderTest
 
testAll() - Method in class gov.nasa.alsUtility.MinMaxesTest
 
testAll() - Method in class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetterTest
 
testAll() - Method in class gov.nasa.javaGenes.hillClimbing.AcceptImprovementTest
 
testAll() - Method in class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptanceTest
 
testAll() - Method in class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovementTest
 
testAll() - Method in class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildrenTest
 
testAlleleTemplate() - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplateTest
 
testAngle() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testAreDifferent() - Method in class gov.nasa.alsUtility.UtilityTest
 
testAreDifferentIntArrayToLimit() - Method in class gov.nasa.alsUtility.UtilityTest
 
testArrayLength() - Method in class gov.nasa.alsUtility.GrowOnlyArrayTest
 
testArraySum() - Method in class gov.nasa.alsUtility.UtilityTest
 
testArrayToTabSeparated() - Method in class gov.nasa.alsUtility.UtilityTest
 
testArrayValues() - Method in class gov.nasa.alsUtility.GrowOnlyArrayTest
 
testCalculateDistance() - Method in class gov.nasa.javaGenes.forceFields.MMEFreferenceRMSTest
 
testCalculateTranslations() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testCapacity() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRNodeTest
 
testCases - Variable in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
 
testClosestLineSegmentPoints() - Method in class gov.nasa.alsUtility.MathUtilityTest
 
testCompare() - Method in class gov.nasa.javaGenes.core.DescendingWeightsComparatorTest
 
testConcatentateStringArrays() - Method in class gov.nasa.alsUtility.UtilityTest
 
testConstructor() - Method in class gov.nasa.alsUtility.Brick3dTest
 
testConstructor() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testConstructor() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testConstructor() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
testConstructor() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testConstructor() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
testConstructor() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testConstructor() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testConstructor() - Method in class gov.nasa.javaGenes.core.ChangingWeightsObjectTest
 
testConstructor() - Method in class gov.nasa.javaGenes.forceFields.AssumedParametersTest
 
testConstructor() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
testConstructor() - Method in class gov.nasa.javaGenes.forceFields.ThreeBodyTest
 
testConstructor() - Method in class gov.nasa.javaGenes.forceFields.TwoBodyTest
 
testConstructorAndCutoffRemoval() - Method in class gov.nasa.javaGenes.forceFields.BodiesTest
 
testConstructorWithElements() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberTest
 
testConvertBack() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModuloTest
 
testCopy() - Method in class gov.nasa.alsUtility.UtilityTest
 
testCopy() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testCopy() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testCopy() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest
 
testCopyForEvolution() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
testCoulbBeScheduledWith() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
testCoverage() - Method in class gov.nasa.javaGenes.core.AntiTournamentLocalTest
 
testCreateSchedule() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest
 
testCrossover() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEachTest
 
testCrossover() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointTest
 
testCrossover() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEachTest
 
testCrossover() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsTest
 
testCrossover() - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossoverTest
 
testCrossoverIntervalTest() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverIntervalTest
 
testDefinitelyFits() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testDelta() - Method in class gov.nasa.javaGenes.simulatedAnnealing.AccepterTest
 
testDistance() - Method in class gov.nasa.alsUtility.MathUtilityTest
 
testDistance() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testDistanceFrom() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testDistanceFrom() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testDistanceTo() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testDistanceToSquared() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testDouble() - Method in class gov.nasa.alsUtility.RandomNumberTest
 
testDoubleArraySum() - Method in class gov.nasa.alsUtility.UtilityTest
 
testDoubleLessThanOrEqual() - Method in class gov.nasa.alsUtility.UtilityTest
 
testDoublesList() - Method in class gov.nasa.alsUtility.DoublesListTest
 
testDuration() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
testDurationBucketCalcs() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testDutyCycles() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testDutyCyclesSpeedCheck() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testEndTimeOK() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testEnergiesDifferent() - Method in class gov.nasa.javaGenes.forceFields.TersoffTest
 
testEquals() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testEqualsExtremes() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testEqualsIntArray() - Method in class gov.nasa.alsUtility.UtilityTest
 
testEquivalent() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTriesTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.core.FitnessMultiObjectiveTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.core.MultiStageFitnessFunctionTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.core.ProductFitnessFunctionTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.core.WeightedSumFitnessTest
 
testEvaluateFitness() - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunctionTest
 
testEvolve() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2Test
 
testExpand() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testExpandByAddition() - Method in class gov.nasa.alsUtility.Brick3dTest
 
testExpandByAddition() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testExpandToInclude() - Method in class gov.nasa.alsUtility.Brick3dTest
 
testExtendIfNecessary() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testFactor() - Method in class gov.nasa.javaGenes.simulatedAnnealing.AccepterTest
 
testFastVsSlowBug() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testFile2StringArray() - Method in class gov.nasa.alsUtility.UtilityTest
 
testFillRandomly() - Method in class gov.nasa.alsUtility.RandomNumberTest
 
testFindEarliest() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
testFindEarliest() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testFindObject() - Method in class gov.nasa.javaGenes.core.RouletteWheelTest
 
testFits() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testFits() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testFits() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
testFits() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testFixedIndices() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOneTest
 
testForCrash() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest
 
testForceInsideAlleleLimits() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutationTest
 
testGenerateMany() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest
 
testGenerateOne() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest
 
testGet() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testGet() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2Test
 
testGetAllAtoms() - Method in class gov.nasa.javaGenes.chemistry.MoleculeTest
 
testGetAngleBetween() - Method in class gov.nasa.javaGenes.graph.VertexTest
 
testGetArrayOfAllValues() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testGetAtom() - Method in class gov.nasa.javaGenes.chemistry.MoleculeTest
 
testGetAvailableNodeAtOrAfter() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testGetDeathRowIndexRandom() - Method in class gov.nasa.javaGenes.core.AntiTournamentLocalTest
 
testGetDistanceTo() - Method in class gov.nasa.javaGenes.graph.VertexTest
 
testGetDoubleInInterval() - Method in class gov.nasa.alsUtility.RandomNumberTest
 
testGetDoubleModule() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
testGetDummyForSize() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModuloTest
 
testGetDurationOf() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testGetEarliestStartTimeInNode() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testGetFirstLineOfFile() - Method in class gov.nasa.alsUtility.UtilityTest
 
testGetFirstLineOfFile(int, String, String) - Method in class gov.nasa.alsUtility.UtilityTest
 
testGetFunction() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest
 
testGetImmigrant() - Method in class gov.nasa.javaGenes.forceFields.ImmigrantsTest
 
testGetIndex() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testGetIndicesArray() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModuloTest
 
testGetIntegerInInterval() - Method in class gov.nasa.alsUtility.RandomNumberTest
 
testGetIntegerTimeAt() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testGetLastGeneration() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest
 
testGetLastLineOfFile() - Method in class gov.nasa.alsUtility.UtilityTest
 
testGetLastLineOfFile(int, String, String) - Method in class gov.nasa.alsUtility.UtilityTest
 
testGetLinearValue() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest
 
testGetMaxAbsoluteSlew() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest
 
testGetMaxSlewTimeFrom() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest
 
testGetNodeAtTime() - Method in class gov.nasa.javaGenes.EOSscheduling.TimelineTest
 
testGetNumberOfSSRsegments() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
testGetParameterValues() - Method in class gov.nasa.javaGenes.core.utility.CoreUtilityTest
 
testGetParentIndices() - Method in class gov.nasa.javaGenes.core.TournamentTest
 
testGetParentIndicesRandom() - Method in class gov.nasa.javaGenes.core.TournamentLocalTest
 
testGetParetoFront() - Method in class gov.nasa.javaGenes.core.PopulationTest
 
testGetParetoFront2() - Method in class gov.nasa.javaGenes.core.PopulationTest
 
testGetProbability() - Method in class gov.nasa.alsUtility.RandomNumberTest
 
testGetQuadraticFactorsFailure() - Method in class gov.nasa.alsUtility.MathUtilityTest
 
testGetQuadraticFactorsRandom() - Method in class gov.nasa.alsUtility.MathUtilityTest
 
testGetRandomUniqueIndices() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testGetSeparation() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testGetSmallerParent() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTest
 
testGetSmallest() - Method in class gov.nasa.javaGenes.core.EvolvableTest
 
testGetTimeAtMiddle() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
testGetTotalSlewTime() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testGetUniqueIndex() - Method in class gov.nasa.alsUtility.RandomNumberTest
 
testHasVertexPairCloserThan() - Method in class gov.nasa.javaGenes.graph.GraphTest
 
testImmigrate() - Method in class gov.nasa.javaGenes.forceFields.ImmigrantsTest
 
testIncludes() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testIncludes() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeTest
 
testIncludes() - Method in class gov.nasa.javaGenes.EOSscheduling.TimelineTest
 
testIncompatibleSlewInMiddle() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testIndexInPrevious() - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutationTest
 
testIndexOnUnschedulable() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvableTest
 
testIndexofGreatest() - Method in class gov.nasa.alsUtility.UtilityTest
 
testIndexofLeast() - Method in class gov.nasa.alsUtility.UtilityTest
 
testInitializeTo() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testInsert() - Method in class gov.nasa.alsUtility.ExtendedVectorTest
 
testInsert(String, int[], int[], int, int[], int[]) - Method in class gov.nasa.alsUtility.ExtendedVectorTest
 
testInsert() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
testInsert(String, double[], double[], int, double[], double[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
testInsertAt() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
testInsertAt1() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt1() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt2() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt2() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt3() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt3() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt4() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt4() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt5() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt5() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt6() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt6() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt7() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt7() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt8() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAt8() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest
 
testInsertAt9() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertAtAndInitialize() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testInsertDumpAt() - Method in class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest
 
testInsertEarliest0() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest01() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest1() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest2() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest4() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest5() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest6() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliest7() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertEarliestRandomized() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest
 
testInsertIntoTimelines() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest
 
testInteractive() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest
 
testInterpolateInto() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest
 
testIntervalInclusive() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testIsBetween() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testIsCutoffInBounds() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testIsDominatedBy() - Method in class gov.nasa.javaGenes.core.FitnessMultiObjectiveTest
 
testIsDurationAvailable() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeTest
 
testIsElement() - Method in class gov.nasa.javaGenes.chemistry.AtomTest
 
testIsEqual() - Method in class gov.nasa.alsUtility.ExtendedVectorTest
 
testIsEqual() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest
 
testIsEqual() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest
 
testIsExecutable() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskTest
 
testIsIn() - Method in class gov.nasa.javaGenes.chemistry.AtomTest
 
testIsInside() - Method in class gov.nasa.alsUtility.Brick3dTest
 
testIsInside() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testIsNewFunction() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest
 
testIsNonNegative() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testIsPositive() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testIsPositiveDoubleArray() - Method in class gov.nasa.alsUtility.UtilityTest
 
testIsWithin() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
testIsWithinLimits() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest
 
testLastReporting() - Method in class gov.nasa.javaGenes.core.ChildMakerTest
 
testLength() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testLessThanOrEqual() - Method in class gov.nasa.alsUtility.UtilityTest
 
testLimitTo() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testLimitToDouble() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testLinearPart() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest
 
testList2String() - Method in class gov.nasa.alsUtility.UtilityTest
 
testMakeChildren() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossoverTest
 
testMakeChildren() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutationTest
 
testMakeChildren() - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutationTest
 
testMakeChildren() - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutationTest
 
testMakeChildren() - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossoverTest
 
testMakeChildrenCreatesPermutation() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest
 
testMakeChildrenCreatesPermutation() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest
 
testMakeFile() - Method in class gov.nasa.alsUtility.UtilityTest
 
testMakeIndividualArray() - Method in class gov.nasa.javaGenes.core.PopulationTest
 
testMakeVector() - Method in class gov.nasa.alsUtility.UtilityTest
 
testMeanAndN() - Method in class gov.nasa.alsUtility.SampleTest
 
testMidPoint() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testMinus() - Method in class gov.nasa.alsUtility.MathUtilityTest
 
testMoreDeserving() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest
 
testMoveInside() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testMoveInside() - Method in class gov.nasa.javaGenes.graph.VertexTest
 
testMultipleChunks() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunkTest
 
testMultipleInsertions() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationInsertTest
 
testMultiply() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testMutate() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest
 
testMutation3parents() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parentsTest
 
testMutation3parents(double, int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parentsTest
 
testMutationDelete() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest
 
testMutationDelete(String, int[], int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest
 
testMutationDelete2() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest
 
testMutationFixedStdDevTest() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDevTest
 
testMutationFixedStdDevTest(double, int, int, double) - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDevTest
 
testMutationInsert() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationInsertTest
 
testMutationInsert(String, int[], int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationInsertTest
 
testNames() - Method in class gov.nasa.javaGenes.core.ProductFitnessFunctionTest
 
testNames() - Method in class gov.nasa.javaGenes.core.WeightedSumFitnessTest
 
testNearlyEqual() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testNearlyEqual() - Method in class gov.nasa.alsUtility.UtilityTest
 
testNearlyEqual() - Method in class gov.nasa.javaGenes.forceFields.ThreeBodyTest
 
testNearlyEqual() - Method in class gov.nasa.javaGenes.forceFields.TwoBodyTest
 
testNearlyEqualVector3d() - Method in class gov.nasa.alsUtility.UtilityTest
 
testNextPreviousAvailableNode() - Method in class gov.nasa.javaGenes.EOSscheduling.AvailableNodeTest
 
testNormalize() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testNumberOfObjectives() - Method in class gov.nasa.javaGenes.core.ProductFitnessFunctionTest
 
testNumberOfObjectives() - Method in class gov.nasa.javaGenes.core.WeightedSumFitnessTest
 
testNumberOfThisCharInString() - Method in class gov.nasa.alsUtility.UtilityTest
 
testOjbect() - Method in class gov.nasa.alsUtility.ObjectCacheTest
 
testOkBackward() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testOkForward() - Method in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest
 
testOutOfOrder() - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitnessTest
 
testOutOfOrder() - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitnessTest
 
testOverlapInTimeWith() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
testParentIndicesArray() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTest
 
testPermutationParameters() - Method in class gov.nasa.javaGenes.core.ParametersSerializationTest
 
testPickOnePart() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest
 
testPlaceInTimelines() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
testPlaceInTimelinesBig() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
testPlaceInTimelinesRandomized() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
testPlaceInTimelinesSSR() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest
 
testPotential() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiFTest
 
testPotential() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberSiTest
 
testProbabilityToBeat() - Method in class gov.nasa.javaGenes.simulatedAnnealing.AccepterTest
 
testProperties() - Method in class gov.nasa.alsUtility.PropertiesListTest
 
testPropertiesFromCommentAndPropertiesCopy() - Method in class gov.nasa.javaGenes.chemistry.MoleculeTest
 
testQuadraticPart() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest
 
testRMS() - Method in class gov.nasa.alsUtility.WeightedStatisticsTest
 
testRandom() - Method in class gov.nasa.alsUtility.IntegerIntervalTest
 
testRandom() - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreederTest
 
testRandom() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOneTest
 
testRandom(int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOneTest
 
testRandom() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest
 
testRandom() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunkTest
 
testRandom() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPairTest
 
testRandom() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairsTest
 
testRandom() - Method in class gov.nasa.javaGenes.forceFields.AlleleTest
 
testRandomGaussian() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testRandomizeIntArray() - Method in class gov.nasa.alsUtility.UtilityTest
 
testReadFile() - Method in class gov.nasa.alsUtility.FieldRecordTextTest
 
testReadLine() - Method in class gov.nasa.alsUtility.FieldRecordTextTest
 
testReinitializableFloat() - Method in class gov.nasa.alsUtility.ReinitializableFloatTest
 
testReinitializableFloatWithFactor() - Method in class gov.nasa.alsUtility.ReinitializableFloatWithFactorTest
 
testReinitializableInt() - Method in class gov.nasa.alsUtility.ReinitializableIntTest
 
testRemoval() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeightTest
 
testRemoval() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelTest
 
testRemove() - Method in class gov.nasa.alsUtility.ExtendedTreeSetTest
 
testRemove() - Method in class gov.nasa.javaGenes.weightNetwork.WeightListTest
 
testRemoveBodiesAboveCutoff() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
testRemoveDuplicates() - Method in class gov.nasa.alsUtility.UtilityTest
 
testRemoveUnexecutableTasks() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModelTest
 
testRenameFile() - Method in class gov.nasa.alsUtility.IOTest
 
testReporting() - Method in class gov.nasa.alsUtility.LogComparisonsTest
 
testReporting() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProviderTest
 
testReporting() - Method in class gov.nasa.javaGenes.core.ChildMakerTest
 
testRosenbrock() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest
 
testSD() - Method in class gov.nasa.alsUtility.SampleTest
 
testSTKAccessFile() - Method in class gov.nasa.javaGenes.EOSscheduling.STKAccessFileTest
 
testScaleBy() - Method in class gov.nasa.alsUtility.LogComparisonsTest
 
testScaleBy() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testScaleBy() - Method in class gov.nasa.javaGenes.graph.VertexTest
 
testScaleIntBy() - Method in class gov.nasa.alsUtility.LogComparisonsTest
 
testScaleLengthsBy() - Method in class gov.nasa.javaGenes.forceFields.ThreeBodyTest
 
testScaleLengthsBy() - Method in class gov.nasa.javaGenes.forceFields.TwoBodyTest
 
testScheduleTask() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest
 
testScheduling() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
testSelectByProbability(double, int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectAllTest
 
testSelectByProbability() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbabilityTest
 
testSelectByProbability(double, int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbabilityTest
 
testSelectFixedChunk() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunkTest
 
testSelectFixedIndices() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndicesTest
 
testSelectFixedIndices(String, int, int[], int[]) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndicesTest
 
testSelectFixedNumber() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumberTest
 
testSelectFixedNumber(int, int) - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumberTest
 
testSetAlleles() - Method in class gov.nasa.javaGenes.forceFields.AssumedParametersTest
 
testSetCutoff() - Method in class gov.nasa.javaGenes.forceFields.StillingerWeberTest
 
testSetTaskPlacement() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvableTest
 
testSetTaskPriorities() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModelTest
 
testSetToExtremes() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testSetUpIndices() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSMTest
 
testSetUpIndices() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest
 
testSetUpIndicesFromArray() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest
 
testSetupChromosome() - Method in class gov.nasa.javaGenes.forceFields.ImmigrantTest
 
testShekelFoxholes() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest
 
testShortFileIO() - Method in class gov.nasa.alsUtility.UtilityTest
 
testShrinkAroundMiddle() - Method in class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest
 
testSideLength() - Method in class gov.nasa.alsUtility.Brick3dTest
 
testSignOf() - Method in class gov.nasa.alsUtility.UtilityTest
 
testSlewTime() - Method in class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest
 
testSlewTimeAdequate() - Method in class gov.nasa.javaGenes.EOSscheduling.SensorTest
 
testSortIntegerArrays() - Method in class gov.nasa.alsUtility.UtilityTest
 
testSortVectorOfDouble() - Method in class gov.nasa.alsUtility.UtilityTest
 
testSortingAccessWindows() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskTest
 
testSphere() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest
 
testSpinWheel() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeightTest
 
testSpinWheel() - Method in class gov.nasa.javaGenes.weightNetwork.RouletteWheelTest
 
testStep() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest
 
testString2Integer() - Method in class gov.nasa.alsUtility.UtilityTest
 
testStudent(StudentFitness) - Method in class gov.nasa.javaGenes.core.StudentFitnessFunction
 
testStudents() - Method in class gov.nasa.javaGenes.core.StudentTeacherTest
 
testSubtract() - Method in class gov.nasa.alsUtility.Vector3dTest
 
testTanimotoDistance() - Method in class gov.nasa.alsUtility.UtilityTest
 
testTanimotoDistanceOneSideOfZero() - Method in class gov.nasa.alsUtility.UtilityTest
 
testTeachers() - Method in class gov.nasa.javaGenes.core.StudentTeacherTest
 
testTerpolate0to1() - Method in class gov.nasa.alsUtility.DoubleIntervalTest
 
testTheSame() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testToString() - Method in class gov.nasa.javaGenes.chemistry.UnitCellTest
 
testTournament() - Method in class gov.nasa.javaGenes.core.AntiTournamentTest
 
testTournament() - Method in class gov.nasa.javaGenes.core.TournamentTest
 
testTranslate() - Method in class gov.nasa.javaGenes.graph.VertexTest
 
testTranslateWithNeighbors() - Method in class gov.nasa.javaGenes.chemistry.AtomTest
 
testTtest() - Method in class gov.nasa.alsUtility.ComparativeStatisticsTest
 
testTwoNearlyEqual() - Method in class gov.nasa.alsUtility.UtilityTest
 
testUnitCell() - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest
 
testUnscheduling() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest
 
testUpdateWith1() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testUpdateWith2() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testUpdateWith3() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testUpdateWith4() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testUpdateWith5() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testUpdateWith6() - Method in class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest
 
testWeight() - Method in class gov.nasa.javaGenes.core.ChangingWeightsObjectTest
 
testWeightChanged() - Method in class gov.nasa.javaGenes.weightNetwork.WeightListTest
 
testWindowIncludes() - Method in class gov.nasa.javaGenes.EOSscheduling.HorizonTest
 
testWithinCutoff() - Method in class gov.nasa.javaGenes.forceFields.ThreeBodyTest
 
testWithinCutoff() - Method in class gov.nasa.javaGenes.forceFields.TwoBodyTest
 
testWorstFitness() - Method in class gov.nasa.javaGenes.core.PopulationTest
 
testfitness() - Method in class gov.nasa.javaGenes.forceFields.ForceFitnessRMSTest
 
theClass - Variable in class gov.nasa.alsUtility.IsInstanceOf
 
theSame(Horizon) - Method in class gov.nasa.javaGenes.EOSscheduling.Horizon
 
theSameAs(TaskPlacementData) - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
theta0_index - Variable in class gov.nasa.javaGenes.forceFields.StillingerWeber
 
thirdBody - Variable in class gov.nasa.javaGenes.forceFields.SecondBody
don't access until after createArrays has been called
threshold - Variable in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries
 
time - Variable in class gov.nasa.javaGenes.EOSscheduling.PointingRequirement
 
time - Variable in class gov.nasa.javaGenes.core.PeriodicCheckpoints
 
time - Variable in class gov.nasa.javaGenes.core.Population
time to generate this population
timeAllocated - Variable in class gov.nasa.alsUtility.Timer
 
timeAvailable() - Method in class gov.nasa.alsUtility.Timer
how much allocated time is still available?
timeBetweenCheckpoints - Variable in class gov.nasa.javaGenes.core.Checkpointer
 
timeBetweenGroundStationDownload - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
timeBetweenSamples - Variable in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters
 
timeBetweenSamples - Variable in class gov.nasa.javaGenes.EOSscheduling.STKAccessFile
 
timeElapsed() - Method in class gov.nasa.alsUtility.Timer
 
timeUsed - Variable in class gov.nasa.alsUtility.Timer
 
timelines - Variable in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
timelinesOk() - Method in class gov.nasa.javaGenes.EOSscheduling.Sensor
 
toArrayOfDoubleValues(Vector) - Static method in class gov.nasa.alsUtility.Utility
 
toDeathRow(int[]) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
toDeathRow(int) - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
toInnerCutoff - Variable in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
toString() - Method in class gov.nasa.alsUtility.Brick3d
in tsd (tab separated data) format
toString() - Method in class gov.nasa.alsUtility.DoubleInterval
 
toString() - Method in class gov.nasa.alsUtility.IntegerInterval
 
toString() - Method in class gov.nasa.alsUtility.KeyCounter
 
toString() - Method in class gov.nasa.alsUtility.LogComparisons
 
toString(Sample[]) - Static method in class gov.nasa.alsUtility.Sample
 
toString(Sample[][]) - Static method in class gov.nasa.alsUtility.Sample
 
toString() - Method in class gov.nasa.alsUtility.Timer
 
toString(Object[]) - Static method in class gov.nasa.alsUtility.Utility
 
toString(boolean[]) - Static method in class gov.nasa.alsUtility.Utility
 
toString(int[]) - Static method in class gov.nasa.alsUtility.Utility
 
toString(double[][][][]) - Static method in class gov.nasa.alsUtility.Utility
 
toString(double[][][]) - Static method in class gov.nasa.alsUtility.Utility
 
toString(double[][]) - Static method in class gov.nasa.alsUtility.Utility
 
toString(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
toString() - Method in class gov.nasa.alsUtility.integer
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSModel
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFromChosenWindowPlacer
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.EarliestFromRandomWindowPlacer
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.ChildMaker
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.MinimizeSlewingFitness
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.NumberOfTakeImagesFitness
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.OrderMutation
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.PositionCrossover
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.RandomChild
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.Scheduler
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.SensorType
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.SmallSlewsFitness
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
toString() - Method in class gov.nasa.javaGenes.EOSscheduling.TaskPriorityFitness
 
toString() - Method in class gov.nasa.javaGenes.chemistry.Atom
 
toString() - Method in class gov.nasa.javaGenes.chemistry.Bond
 
toString() - Method in class gov.nasa.javaGenes.chemistry.Element
 
toString() - Method in class gov.nasa.javaGenes.chemistry.UnitCell
 
toString() - Method in class gov.nasa.javaGenes.chemistry.UnitCellNone
 
toString(Graph) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
 
toString() - Method in class gov.nasa.javaGenes.core.AntiTournament
 
toString() - Method in class gov.nasa.javaGenes.core.AntiTournamentLocal
 
toString() - Method in class gov.nasa.javaGenes.core.BreederElitist
 
toString() - Method in class gov.nasa.javaGenes.core.BreederSteadyState
 
toString() - Method in class gov.nasa.javaGenes.core.BreederSteadyState2
 
toString() - Method in class gov.nasa.javaGenes.core.ChangeFunctionByGeneration
 
toString() - Method in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMaker
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMakerChain.ChainElement
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMakerChain
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMakerProvider
 
toString() - Method in class gov.nasa.javaGenes.core.ChildMakerProviderWeighted
 
toString() - Method in class gov.nasa.javaGenes.core.Fitness
 
toString() - Method in class gov.nasa.javaGenes.core.FitnessBad
 
toString() - Method in class gov.nasa.javaGenes.core.FitnessDouble
 
toString() - Method in class gov.nasa.javaGenes.core.FitnessFunctionBadSize
 
toString() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
toString() - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness
 
toString() - Method in class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries
 
toString() - Method in class gov.nasa.javaGenes.core.HFC.BottomSubBreeder
 
toString() - Method in class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder
 
toString() - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
toString() - Method in class gov.nasa.javaGenes.core.HFC.SubBreeder
 
toString() - Method in class gov.nasa.javaGenes.core.HFC.TopSubBreeder
 
toString() - Method in class gov.nasa.javaGenes.core.Individual
 
toString() - Method in class gov.nasa.javaGenes.core.NotFoundException
 
toString() - Method in class gov.nasa.javaGenes.core.Parameters
does not be to be changed when fields are changed, but has a bug that occurs when a field is a interface
toString() - Method in class gov.nasa.javaGenes.core.ParsimonyFitness
 
toString() - Method in class gov.nasa.javaGenes.core.Reporter
 
toString() - Method in class gov.nasa.javaGenes.core.RouletteWheel
 
toString() - Method in class gov.nasa.javaGenes.core.StudentFitness
 
toString() - Method in class gov.nasa.javaGenes.core.Tournament
 
toString() - Method in class gov.nasa.javaGenes.core.TournamentLocal
 
toString() - Method in class gov.nasa.javaGenes.core.Weighted0to1
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parents
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDev
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectAll
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndices
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumber
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectOne
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair
 
toString() - Method in class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs
 
toString() - Method in class gov.nasa.javaGenes.forceFields.Allele
 
toString() - Method in class gov.nasa.javaGenes.forceFields.AlleleTemplate
 
toString() - Method in class gov.nasa.javaGenes.forceFields.AtomicSpecies
 
toString() - Method in class gov.nasa.javaGenes.forceFields.Bodies
 
toString() - Method in class gov.nasa.javaGenes.forceFields.Chromosome
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeDistanceFitness
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeMutation
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation
 
toString() - Method in class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction
 
toString() - Method in class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
 
toString() - Method in class gov.nasa.javaGenes.forceFields.Mutation3Parents
 
toString() - Method in class gov.nasa.javaGenes.forceFields.OneBody
 
toString() - Method in class gov.nasa.javaGenes.forceFields.Potential
 
toString() - Method in class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness
 
toString() - Method in class gov.nasa.javaGenes.forceFields.SecondBody
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ThirdBody
 
toString() - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
toString() - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
toString() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
 
toString() - Method in class gov.nasa.javaGenes.graph.BrokenGraph
 
toString() - Method in class gov.nasa.javaGenes.graph.CyclesSimilarity
 
toString() - Method in class gov.nasa.javaGenes.graph.DirectedEdge
 
toString() - Method in class gov.nasa.javaGenes.graph.DirectedVertex
 
toString() - Method in class gov.nasa.javaGenes.graph.Edge
 
toString() - Method in class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity
 
toString() - Method in class gov.nasa.javaGenes.graph.Graph
 
toString() - Method in class gov.nasa.javaGenes.graph.GraphLayout
 
toString() - Method in class gov.nasa.javaGenes.graph.Vertex
 
toString() - Method in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
toString() - Method in class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity
 
toString() - Method in class gov.nasa.javaGenes.hillClimbing.Breeder
 
toString() - Method in class gov.nasa.javaGenes.permutation.PermutationEvolvable
 
toString() - Method in class gov.nasa.javaGenes.permutation.PermutationKCutMutation
 
toString() - Method in class gov.nasa.javaGenes.permutation.PermutationOrderMutation
 
toString() - Method in class gov.nasa.javaGenes.permutation.PermutationPositionCrossover
 
toString() - Method in class gov.nasa.javaGenes.permutation.PermutationTestFitness
 
toString() - Method in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
toString() - Method in class gov.nasa.javaGenes.simulatedAnnealing.Breeder
 
top - Variable in class gov.nasa.alsUtility.DoubleInterval
the highest value in the interval
top - Variable in class gov.nasa.alsUtility.IntegerInterval
 
topSubPopulationReceivedNewBestIndividual(Individual) - Method in class gov.nasa.javaGenes.core.HFC.Breeder
 
topSubPopulationReceivedNewBestIndividual(Individual) - Method in class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder
 
totalEvolvableSize() - Method in class gov.nasa.javaGenes.core.Population
 
totalTime - Variable in class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint
 
totalTime(long) - Method in class gov.nasa.javaGenes.core.Reporter
 
totalTimeFilename - Static variable in class gov.nasa.javaGenes.core.Reporter
 
totalWeight - Variable in class gov.nasa.javaGenes.core.RouletteWheel
 
tournament(Population, Individual) - Method in class gov.nasa.javaGenes.core.Breeder
implements a two-way tournament.
tournament(int[], Population) - Method in class gov.nasa.javaGenes.core.Tournament
 
tournamentProbability - Variable in class gov.nasa.javaGenes.core.Breeder
 
tournamentProbability - Variable in class gov.nasa.javaGenes.core.Parameters
 
trail() - Method in class gov.nasa.javaGenes.graph.VertexAndTrailIterator
 
transform(Vector3d) - Method in class gov.nasa.alsUtility.Matrix3d
 
translate(double) - Method in class gov.nasa.alsUtility.DoubleInterval
add distance to the top and bottom
translate(Vector3d) - Method in class gov.nasa.javaGenes.graph.Vertex
 
translateWithNeighbors(Vector3d, Atom[]) - Method in class gov.nasa.javaGenes.chemistry.Atom
 
ttest(Sample, Sample) - Static method in class gov.nasa.alsUtility.ComparativeStatistics
implements and t-test between two Samples.
ttest(int, int, double, double, double, double) - Static method in class gov.nasa.alsUtility.ComparativeStatistics
 
twoBodyTermMatters - Variable in class gov.nasa.javaGenes.forceFields.SecondBody
used to turn of calculation off two body energies so the three body terms will be more important.
twoNearlyEqual(double[]) - Static method in class gov.nasa.alsUtility.Utility
 
typicalTakeImageTime - Variable in class gov.nasa.javaGenes.EOSscheduling.Sensor
 

U

UnitCell - class gov.nasa.javaGenes.chemistry.UnitCell.
 
UnitCell() - Constructor for class gov.nasa.javaGenes.chemistry.UnitCell
 
UnitCell(double) - Constructor for class gov.nasa.javaGenes.chemistry.UnitCell
 
UnitCell(double, double, double) - Constructor for class gov.nasa.javaGenes.chemistry.UnitCell
 
UnitCell(double, double, double, double, double, double) - Constructor for class gov.nasa.javaGenes.chemistry.UnitCell
 
UnitCell(String) - Constructor for class gov.nasa.javaGenes.chemistry.UnitCell
 
UnitCellNone - class gov.nasa.javaGenes.chemistry.UnitCellNone.
a 'unit cell' that is not a unit cell at all.
UnitCellNone() - Constructor for class gov.nasa.javaGenes.chemistry.UnitCellNone
 
UnitCellTest - class gov.nasa.javaGenes.chemistry.UnitCellTest.
 
UnitCellTest(String) - Constructor for class gov.nasa.javaGenes.chemistry.UnitCellTest
 
UpdateAndPropagatable - class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable.
 
UpdateAndPropagatable() - Constructor for class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable
 
UpdateAndPropagateList - class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList.
 
UpdateAndPropagateList() - Constructor for class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
 
UpdateAndPropagateList(int) - Constructor for class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
used when same objects in multiple lists with different processing
Utility - class gov.nasa.alsUtility.Utility.
Miscellaneous useful functions.
Utility() - Constructor for class gov.nasa.alsUtility.Utility
 
UtilityTest - class gov.nasa.alsUtility.UtilityTest.
 
UtilityTest(String) - Constructor for class gov.nasa.alsUtility.UtilityTest
 
unitCellPropertyName - Static variable in class gov.nasa.javaGenes.chemistry.Molecule
 
universalRange - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
universalRangeSize - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
unschedulable(AccessWindowWeight) - Method in class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight
 
up - Variable in class gov.nasa.alsUtility.LogComparisons
 
updateAndPropagate(int) - Method in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable
 
updateAndPropagate() - Method in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
 
updateAndPropagateDone() - Method in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable
 
updatePositions(jiggle.Graph, Graph) - Method in class gov.nasa.javaGenes.graph.GraphLayout
called after layout to move xyz locations to a JavaGenes graph
useLocalBreeder - Static variable in class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters
 
useTournament() - Method in class gov.nasa.javaGenes.core.Breeder
 
userAssert(boolean, String) - Static method in class gov.nasa.alsUtility.Error
 

V

VRMLUtility - class gov.nasa.alsUtility.VRMLUtility.
 
VRMLUtility() - Constructor for class gov.nasa.alsUtility.VRMLUtility
 
VecMathTest - class gov.nasa.alsUtility.VecMathTest.
compare Vector3d, Matrix3d, and Quat4d with Java3d's javax.vecmath to make sure they give similar results
VecMathTest(String) - Constructor for class gov.nasa.alsUtility.VecMathTest
 
Vector3d - class gov.nasa.alsUtility.Vector3d.
 
Vector3d() - Constructor for class gov.nasa.alsUtility.Vector3d
 
Vector3d(Vector3d) - Constructor for class gov.nasa.alsUtility.Vector3d
 
Vector3d(double, double, double) - Constructor for class gov.nasa.alsUtility.Vector3d
 
Vector3d(double[]) - Constructor for class gov.nasa.alsUtility.Vector3d
 
Vector3dTest - class gov.nasa.alsUtility.Vector3dTest.
 
Vector3dTest(String) - Constructor for class gov.nasa.alsUtility.Vector3dTest
 
VectorIterator - class gov.nasa.alsUtility.VectorIterator.
 
VectorIterator(Vector) - Constructor for class gov.nasa.alsUtility.VectorIterator
 
Vertex - class gov.nasa.javaGenes.graph.Vertex.
a vertex in a graph.
Vertex() - Constructor for class gov.nasa.javaGenes.graph.Vertex
 
VertexAcceptsEdge - class gov.nasa.javaGenes.graph.VertexAcceptsEdge.
predicate that determines when vertices can accept an additional edge
VertexAcceptsEdge(Edge) - Constructor for class gov.nasa.javaGenes.graph.VertexAcceptsEdge
 
VertexAcceptsEdge() - Constructor for class gov.nasa.javaGenes.graph.VertexAcceptsEdge
used when asking if any edge may be accepted
VertexAcceptsInputEdge - class gov.nasa.javaGenes.graph.VertexAcceptsInputEdge.
predicate that determines when vertices can accept an input edge.
VertexAcceptsInputEdge() - Constructor for class gov.nasa.javaGenes.graph.VertexAcceptsInputEdge
 
VertexAcceptsOutputEdge - class gov.nasa.javaGenes.graph.VertexAcceptsOutputEdge.
predicate that determines when vertices can accept an output edge.
VertexAcceptsOutputEdge() - Constructor for class gov.nasa.javaGenes.graph.VertexAcceptsOutputEdge
 
VertexAndEdgeProvider - class gov.nasa.javaGenes.graph.VertexAndEdgeProvider.
holds a set of vertices and a set of edges.
VertexAndEdgeProvider() - Constructor for class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
 
VertexAndTrailIterator - class gov.nasa.javaGenes.graph.VertexAndTrailIterator.
This iterator will return each vertex in g starting with the neighbors of v using a breadth first search.
VertexAndTrailIterator(Graph, Vertex) - Constructor for class gov.nasa.javaGenes.graph.VertexAndTrailIterator
 
VertexIterator - class gov.nasa.javaGenes.graph.VertexIterator.
iterate over a Vector containing Vertex objects
VertexIterator(Vector) - Constructor for class gov.nasa.javaGenes.graph.VertexIterator
 
VertexPairsDistanceSimilarity - class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity.
fitness is the distance from a target graph.
VertexPairsDistanceSimilarity(Graph) - Constructor for class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity
 
VertexPairsDistanceSimilarity() - Constructor for class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity
set the target to a test molecule
VertexTest - class gov.nasa.javaGenes.graph.VertexTest.
 
VertexTest(String) - Constructor for class gov.nasa.javaGenes.graph.VertexTest
 
valence - Variable in class gov.nasa.javaGenes.chemistry.Bond
 
valid() - Method in class gov.nasa.alsUtility.Sample
is there enough data to calculate descriptive statistics?
value() - Method in class gov.nasa.alsUtility.IncrementIterator
 
value - Variable in class gov.nasa.alsUtility.IsMarked
 
value - Variable in class gov.nasa.alsUtility.MarkIsSet
 
value - Variable in class gov.nasa.alsUtility.ReinitializableFloat
 
value - Variable in class gov.nasa.alsUtility.ReinitializableInt
 
value - Variable in class gov.nasa.alsUtility.SetMark
 
value - Variable in class gov.nasa.alsUtility.integer
 
value - Variable in class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble
 
valueFits(double) - Method in class gov.nasa.javaGenes.forceFields.Allele
 
valueToSet - Variable in class gov.nasa.javaGenes.forceFields.Allele
 
values - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues
 
variance - Variable in class gov.nasa.alsUtility.Sample
 
variationOperatorDirectory - Static variable in class gov.nasa.javaGenes.core.Reporter
 
vector - Variable in class gov.nasa.alsUtility.VectorIterator
the vector to iterate over
vector - Variable in class gov.nasa.javaGenes.forceFields.OneBody
 
vector - Variable in class gov.nasa.javaGenes.forceFields.SecondBody
 
vertex - Variable in class gov.nasa.javaGenes.graph.AcceptableSecondVertex
vertex seeking a vertex to have an edge with
vertex - Variable in class gov.nasa.javaGenes.graph.BrokenEdge
 
vertex - Variable in class gov.nasa.javaGenes.graph.HasInputEdgeFrom
 
vertex - Variable in class gov.nasa.javaGenes.graph.HasOutputEdgesTo
 
vertex() - Method in class gov.nasa.javaGenes.graph.VertexAndTrailIterator
 
vertex() - Method in class gov.nasa.javaGenes.graph.VertexIterator
 
vertexSize - Variable in class gov.nasa.javaGenes.graph.GraphLayout
 
vertices - Variable in class gov.nasa.javaGenes.graph.Edge
the vertices this edge connects
vertices - Variable in class gov.nasa.javaGenes.graph.Graph
 
vertices - Variable in class gov.nasa.javaGenes.graph.VertexAndEdgeProvider
the vertices to be provided.
verticesInterval - Variable in class gov.nasa.javaGenes.graph.GraphParameters
an interval to choose a random number of Graph vertices from.

W

Weight - class gov.nasa.javaGenes.weightNetwork.Weight.
 
Weight() - Constructor for class gov.nasa.javaGenes.weightNetwork.Weight
 
WeightList - class gov.nasa.javaGenes.weightNetwork.WeightList.
 
WeightList() - Constructor for class gov.nasa.javaGenes.weightNetwork.WeightList
 
WeightListTest - class gov.nasa.javaGenes.weightNetwork.WeightListTest.
 
WeightListTest(String) - Constructor for class gov.nasa.javaGenes.weightNetwork.WeightListTest
 
Weighted0to1 - class gov.nasa.javaGenes.core.Weighted0to1.
this fitness function is a weighted sum of fitness functions that return 0 for perfection and 1 for worst possible
Weighted0to1() - Constructor for class gov.nasa.javaGenes.core.Weighted0to1
 
WeightedStatistics - class gov.nasa.alsUtility.WeightedStatistics.
holds doubles (called "datums") from a statistical sample and does simple statistics on them
WeightedStatistics() - Constructor for class gov.nasa.alsUtility.WeightedStatistics
 
WeightedStatisticsTest - class gov.nasa.alsUtility.WeightedStatisticsTest.
 
WeightedStatisticsTest(String) - Constructor for class gov.nasa.alsUtility.WeightedStatisticsTest
 
WeightedSumFitness - class gov.nasa.javaGenes.core.WeightedSumFitness.
this fitness function is a weighted sum of fitness functions
WeightedSumFitness() - Constructor for class gov.nasa.javaGenes.core.WeightedSumFitness
 
WeightedSumFitness(boolean) - Constructor for class gov.nasa.javaGenes.core.WeightedSumFitness
 
WeightedSumFitnessTest - class gov.nasa.javaGenes.core.WeightedSumFitnessTest.
 
WeightedSumFitnessTest(String) - Constructor for class gov.nasa.javaGenes.core.WeightedSumFitnessTest
 
w - Variable in class gov.nasa.alsUtility.Quat4d
 
walkAll(Procedure, Procedure) - Method in class gov.nasa.javaGenes.graph.Vertex
assumes that only already walked vertices and edges are marked true
walkVertices(Procedure) - Method in class gov.nasa.javaGenes.graph.Vertex
assumes that only already walked vertices are marked true
wantsInput() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
used with DirectedEdge
wantsOutput() - Method in class gov.nasa.javaGenes.graph.BrokenEdge
used with DirectedEdge
warning(String, String) - Static method in class gov.nasa.alsUtility.Error
 
warning(String) - Static method in class gov.nasa.alsUtility.Error
 
weight - Variable in class gov.nasa.javaGenes.weightNetwork.Weight
 
weightChanged(float, float) - Method in class gov.nasa.javaGenes.weightNetwork.Weight
 
weightChanged(float, float) - Method in class gov.nasa.javaGenes.weightNetwork.WeightList
 
weightList - Variable in class gov.nasa.javaGenes.weightNetwork.Weight
 
weightRange - Variable in class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom
 
weightSum - Variable in class gov.nasa.alsUtility.WeightedStatistics
 
weightSum - Variable in class gov.nasa.javaGenes.weightNetwork.WeightList
 
weightedObject - Variable in class gov.nasa.javaGenes.core.ChangingWeightsObject
 
weights - Variable in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
weights - Variable in class gov.nasa.javaGenes.core.RouletteWheel
 
weights - Variable in class gov.nasa.javaGenes.core.Weighted0to1
 
which - Variable in class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList
 
whichPotential - Variable in class gov.nasa.javaGenes.forceFields.ChromosomeParameters
 
whichReduction - Variable in class gov.nasa.javaGenes.simulatedAnnealing.Accepter
 
windowDuration - Variable in class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator
 
windowNumber - Variable in class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData
 
withinCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.Body
 
withinCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.MultiBody
 
withinCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.OneBody
 
withinCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
withinCutoff(double) - Method in class gov.nasa.javaGenes.forceFields.ThreeBody
 
withinCutoff(Potential) - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
withinCutoff(double) - Method in class gov.nasa.javaGenes.forceFields.TwoBody
 
worstDouble() - Method in class gov.nasa.javaGenes.core.FitnessFunction
 
worstDouble() - Method in class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective
 
worstFitness() - Method in class gov.nasa.javaGenes.core.Population
 
worstFitness(Fitness) - Method in class gov.nasa.javaGenes.core.Population
 
worstIndividual() - Method in class gov.nasa.javaGenes.core.Population
 
worstIndividual(Fitness) - Method in class gov.nasa.javaGenes.core.Population
 
worstIndividualIndex() - Method in class gov.nasa.javaGenes.core.Population
 
worstIndividualIndex(Fitness) - Method in class gov.nasa.javaGenes.core.Population
 
write(String) - Method in class gov.nasa.alsUtility.DataTable
write all the data to a tab separated ASCII file.
write(Molecule, PrintWriter) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
write the file to PrintWriter out
write(Molecule, PrintWriter) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
write the file to PrintWriter out
writeColumns(String) - Method in class gov.nasa.alsUtility.DataTable
write all the data to a tab separated ASCII file.
writeFile(Molecule, String) - Static method in class gov.nasa.javaGenes.chemistry.molFormat
 
writeMolecules(ExtendedVector, String) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
 
writeThreeBodiesToTsdFile(String) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 
writeToFile(Molecule, String) - Static method in class gov.nasa.javaGenes.chemistry.xyzFormat
 
writeTwoBodiesToTsdFile(String) - Method in class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy
 

X

x - Variable in class gov.nasa.alsUtility.Quat4d
 
x - Variable in class gov.nasa.alsUtility.Vector3d
 
xyz - Variable in class gov.nasa.javaGenes.graph.Vertex
 
xyzFormat - class gov.nasa.javaGenes.chemistry.xyzFormat.
read and write mol files representing molecules
xyzFormat() - Constructor for class gov.nasa.javaGenes.chemistry.xyzFormat
 

Y

y - Variable in class gov.nasa.alsUtility.Quat4d
 
y - Variable in class gov.nasa.alsUtility.Vector3d
 

Z

z - Variable in class gov.nasa.alsUtility.Quat4d
 
z - Variable in class gov.nasa.alsUtility.Vector3d
 

_

_angle - Variable in class gov.nasa.javaGenes.forceFields.ThreeBody
 
_chromosome - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_grade - Variable in class gov.nasa.javaGenes.core.StudentFitness
 
_jiDistance - Variable in class gov.nasa.javaGenes.forceFields.ThreeBody
 
_jkDistance - Variable in class gov.nasa.javaGenes.forceFields.ThreeBody
 
_lengthScale - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_maximumAngle - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_maximumDistance - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_minimumAngle - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_minimumDistance - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_name - Variable in class gov.nasa.javaGenes.forceFields.MultiBody
 
_newTeachersPerGeneration - Variable in class gov.nasa.javaGenes.core.BreederWithTeachers
 
_numberOfTeachers - Variable in class gov.nasa.javaGenes.core.BreederWithTeachers
 
_potential - Variable in class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces
 
_radialDistance - Variable in class gov.nasa.javaGenes.forceFields.TwoBody
 
_students - Variable in class gov.nasa.javaGenes.core.TeacherFitnessFunction
 
_teacherChildMakers - Variable in class gov.nasa.javaGenes.core.BreederWithTeachers
 
_teacherFitnessFunction - Variable in class gov.nasa.javaGenes.core.BreederWithTeachers
 
_teacherIndex - Variable in class gov.nasa.javaGenes.core.BreederWithTeachers
 
_teacherPopulation - Variable in class gov.nasa.javaGenes.core.BreederWithTeachers
 
_teachers - Variable in class gov.nasa.javaGenes.core.StudentFitnessFunction
 

A B C D E F G H I K L M N O P Q R S T U V W X Y Z _
JavaGenes, NASA Ames. Written largely by Al Globus