JavaGenes, NASA Ames. Written largely by Al Globus

Serialized Form


Package gov.nasa.alsUtility

Class gov.nasa.alsUtility.AllTests extends TestSuite implements Serializable

Class gov.nasa.alsUtility.AmericanWireGaugeTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.And extends java.lang.Object implements Serializable

Serialized Fields

left

Predicate left

right

Predicate right

Class gov.nasa.alsUtility.Brick3d extends java.lang.Object implements Serializable

Serialized Fields

intervals

DoubleInterval[] intervals

Class gov.nasa.alsUtility.Brick3dTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.Brick3dWithSegments extends Brick3d implements Serializable

Serialized Fields

segmentCoordinates

double[][] segmentCoordinates

Class gov.nasa.alsUtility.Brick3dWithSegmentsTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ComparativeStatistics extends java.lang.Object implements Serializable

Class gov.nasa.alsUtility.ComparativeStatisticsTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.DataTable extends java.util.Hashtable implements Serializable

Class gov.nasa.alsUtility.DoubleInterval extends java.lang.Object implements Serializable

Serialized Fields

bottom

double bottom
the lowest value in the interval


top

double top
the highest value in the interval


includeBottom

boolean includeBottom
does this interval include the bottom most value?


includeTop

boolean includeTop
does this interval include to most value?

Class gov.nasa.alsUtility.DoubleIntervalTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.DoublesListTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ExtendedTreeSet extends java.util.TreeSet implements Serializable

Class gov.nasa.alsUtility.ExtendedTreeSetTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ExtendedVector extends java.util.Vector implements Serializable

Class gov.nasa.alsUtility.ExtendedVectorTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.FieldRecordTextTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.GrowOnlyArray extends java.lang.Object implements Serializable

Serialized Fields

growBy

int growBy

array

java.lang.Object[] array

currentSize

int currentSize

Class gov.nasa.alsUtility.GrowOnlyArrayTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.IncrementIterator extends java.lang.Object implements Serializable

Serialized Fields

Start

double Start

End

double End

Number

int Number

Current

int Current

Increment

double Increment

Class gov.nasa.alsUtility.IndexIterator extends java.lang.Object implements Serializable

Serialized Fields

_limit

int _limit

_current

int _current

Class gov.nasa.alsUtility.integer extends java.lang.Object implements Serializable

Serialized Fields

value

int value

Class gov.nasa.alsUtility.IntegerInterval extends java.lang.Object implements Serializable

Serialized Fields

bottom

int bottom

top

int top

Class gov.nasa.alsUtility.IntegerIntervalTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.IOTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.IsEqual extends java.lang.Object implements Serializable

Serialized Fields

object

java.lang.Object object

Class gov.nasa.alsUtility.IsInstanceOf extends java.lang.Object implements Serializable

Serialized Fields

theClass

java.lang.Class theClass

Class gov.nasa.alsUtility.IsMarked extends java.lang.Object implements Serializable

Serialized Fields

value

boolean value

Class gov.nasa.alsUtility.KeyCounter extends java.util.Hashtable implements Serializable

Class gov.nasa.alsUtility.KeyCounterTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.LogComparisons extends java.lang.Object implements Serializable

Serialized Fields

names

java.lang.String[] names

up

int[] up

between

int[] between

down

int[] down

netChange

double[] netChange

Class gov.nasa.alsUtility.LogComparisonsTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ManySamples extends java.util.Hashtable implements Serializable

Class gov.nasa.alsUtility.MarkIsSet extends java.lang.Object implements Serializable

Serialized Fields

value

boolean value

Class gov.nasa.alsUtility.MathUtilityTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.Matrix3d extends java.lang.Object implements Serializable

Serialized Fields

m00

double m00

m01

double m01

m02

double m02

m10

double m10

m11

double m11

m12

double m12

m20

double m20

m21

double m21

m22

double m22

Class gov.nasa.alsUtility.MinMaxesTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.Not extends java.lang.Object implements Serializable

Serialized Fields

predicate

Predicate predicate
predicate to execute on objects

Class gov.nasa.alsUtility.ObjectCache extends java.lang.Object implements Serializable

Serialized Fields

cache

java.util.Vector cache

nextIndex

int nextIndex

theClass

java.lang.Class theClass

Class gov.nasa.alsUtility.ObjectCacheTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ObjectCompatible extends java.lang.Object implements Serializable

Serialized Fields

object

Compatible object
object to be compatible with

Class gov.nasa.alsUtility.ObjectEquals extends java.lang.Object implements Serializable

Serialized Fields

object

java.lang.Object object
object to be equal to

Class gov.nasa.alsUtility.Or extends java.lang.Object implements Serializable

Serialized Fields

left

Predicate left

right

Predicate right

Class gov.nasa.alsUtility.PropertiesListTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.Quat4d extends java.lang.Object implements Serializable

Serialized Fields

x

double x

y

double y

z

double z

w

double w

Class gov.nasa.alsUtility.RandomNumberTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ReinitializableFloat extends java.lang.Object implements Serializable

Serialized Fields

value

float value

initialValue

float initialValue

Class gov.nasa.alsUtility.ReinitializableFloatTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ReinitializableFloatWithFactor extends ReinitializableFloat implements Serializable

Serialized Fields

factor

float factor

Class gov.nasa.alsUtility.ReinitializableFloatWithFactorTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.ReinitializableInt extends java.lang.Object implements Serializable

Serialized Fields

value

int value

initialValue

int initialValue

Class gov.nasa.alsUtility.ReinitializableIntTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.RootMeanSquaresTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.Sample extends java.lang.Object implements Serializable

Serialized Fields

data

java.util.Vector data

statisticsCorrect

boolean statisticsCorrect

mean

double mean

variance

double variance

standardDeviation

double standardDeviation

range

DoubleInterval range

Class gov.nasa.alsUtility.SampleTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.Saver extends java.lang.Object implements Serializable

Serialized Fields

directoryName

java.lang.String directoryName
directory to save data in


numberOfSaves

int numberOfSaves

data

java.util.Vector data

Class gov.nasa.alsUtility.Timer extends java.lang.Object implements Serializable

Serialized Fields

timeAllocated

long timeAllocated

timeUsed

long timeUsed

lastStart

long lastStart

running

boolean running

Class gov.nasa.alsUtility.UtilityTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.VecMathTest extends junit.framework.TestCase implements Serializable

Class gov.nasa.alsUtility.Vector3d extends java.lang.Object implements Serializable

Serialized Fields

x

double x

y

double y

z

double z

Class gov.nasa.alsUtility.Vector3dTest extends TestCase implements Serializable

Class gov.nasa.alsUtility.WeightedStatistics extends java.lang.Object implements Serializable

Serialized Fields

sum

double sum

sumSquares

double sumSquares

weightSum

double weightSum

count

int count

countOfNonNormalNumbers

int countOfNonNormalNumbers

min

double min

max

double max

Class gov.nasa.alsUtility.WeightedStatisticsTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.chemistry

Class gov.nasa.javaGenes.chemistry.Atom extends Vertex implements Serializable

Serialized Fields

element

Element element

Class gov.nasa.javaGenes.chemistry.Atom.ExtendedTypeKey extends java.lang.Object implements Serializable

Serialized Fields

bondCounts

int[] bondCounts

atomicNumber

int atomicNumber

Class gov.nasa.javaGenes.chemistry.AtomTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.chemistry.Benzene extends Molecule implements Serializable

Class gov.nasa.javaGenes.chemistry.Bond extends Edge implements Serializable

Serialized Fields

valence

int valence

Class gov.nasa.javaGenes.chemistry.Element extends java.lang.Object implements Serializable

Serialized Fields

atomicNumber

int atomicNumber

atomicWeight

double atomicWeight

symbol

java.lang.String symbol

group

int group

period

int period

valence

int valence

Class gov.nasa.javaGenes.chemistry.Molecule extends Graph implements Serializable

Serialized Fields

comment

java.lang.String comment

_energy

double _energy

hasDimerForce

boolean hasDimerForce

dimerForce

double dimerForce

unitCell

UnitCell unitCell

Class gov.nasa.javaGenes.chemistry.MoleculeIndividual extends GraphIndividual implements Serializable

Class gov.nasa.javaGenes.chemistry.MoleculeParameters extends GraphParameters implements Serializable

Class gov.nasa.javaGenes.chemistry.MoleculePopulation extends GraphPopulation implements Serializable

Class gov.nasa.javaGenes.chemistry.MoleculeTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.chemistry.MoleculeTwoVertexCrossover extends TwoVertexGraphCrossover implements Serializable

Class gov.nasa.javaGenes.chemistry.Purine extends Molecule implements Serializable

Class gov.nasa.javaGenes.chemistry.Pyridine extends Molecule implements Serializable

Class gov.nasa.javaGenes.chemistry.RunMolecule extends Run implements Serializable

Class gov.nasa.javaGenes.chemistry.UnitCell extends java.lang.Object implements Serializable

Serialized Fields

cell

double[][] cell

halfDistance

double[] halfDistance

fullDistance

double[] fullDistance

Class gov.nasa.javaGenes.chemistry.UnitCellNone extends UnitCell implements Serializable

Class gov.nasa.javaGenes.chemistry.UnitCellTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.core

Class gov.nasa.javaGenes.core.AbstractCheckpointable extends java.lang.Object implements Serializable

Serialized Fields

checkpointer

Checkpointer checkpointer

Class gov.nasa.javaGenes.core.AntiTournament extends Tournament implements Serializable

Class gov.nasa.javaGenes.core.AntiTournamentLocal extends AntiTournament implements Serializable

Serialized Fields

extendFromFirstParentIndices

int extendFromFirstParentIndices

Class gov.nasa.javaGenes.core.AntiTournamentLocalTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.AntiTournamentTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Breeder extends java.lang.Object implements Serializable

Serialized Fields

childMakerProvider

ChildMakerProvider childMakerProvider

tournamentProbability

double tournamentProbability

fitnessFunction

FitnessFunction fitnessFunction

index

int index

totalNumberOfKidsProduced

int totalNumberOfKidsProduced

Class gov.nasa.javaGenes.core.BreederElitist extends Breeder implements Serializable

Serialized Fields

children

Population children

preservedNumber

int preservedNumber

internalGenerationsPerExternalGeneration

int internalGenerationsPerExternalGeneration

internalGeneration

int internalGeneration

Class gov.nasa.javaGenes.core.BreederSteadyState extends Breeder implements Serializable

Class gov.nasa.javaGenes.core.BreederSteadyState2 extends Breeder implements Serializable

Serialized Fields

parentChooser

ChooseParents parentChooser

grimReaper

ChooseForDeath grimReaper

Class gov.nasa.javaGenes.core.BreederWithTeachers extends BreederSteadyState implements Serializable

Serialized Fields

_teacherIndex

int _teacherIndex

_numberOfTeachers

int _numberOfTeachers

_newTeachersPerGeneration

int _newTeachersPerGeneration

_teacherPopulation

TeacherPopulation _teacherPopulation

_teacherFitnessFunction

TeacherFitnessFunction _teacherFitnessFunction

_teacherChildMakers

ChildMakerProvider _teacherChildMakers

Class gov.nasa.javaGenes.core.ChangeFunctionByGeneration extends FitnessFunction implements Serializable

Serialized Fields

lastGenerations

ExtendedVector lastGenerations

fitnessFunctions

ExtendedVector fitnessFunctions

Class gov.nasa.javaGenes.core.ChangeFunctionByGenerationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ChangingWeightsObject extends java.lang.Object implements Serializable

Serialized Fields

start

double start

slope

double slope

currentWeight

double currentWeight

weightedObject

java.lang.Object weightedObject

Class gov.nasa.javaGenes.core.ChangingWeightsObjectTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Checkpointer extends java.lang.Object implements Serializable

Serialized Fields

objectToCheckpoint

Checkpointable objectToCheckpoint

excessiveTimeBetweenCheckpointOKs

int excessiveTimeBetweenCheckpointOKs

timeBetweenCheckpoints

long timeBetweenCheckpoints

lastCheckpointDate

java.util.Date lastCheckpointDate

lastOkToCheckpoint

long lastOkToCheckpoint

checkpointASAP

boolean checkpointASAP

mustPrepareToDie

boolean mustPrepareToDie

readyToDieNow

boolean readyToDieNow

Class gov.nasa.javaGenes.core.ChildMaker extends java.lang.Object implements Serializable

Serialized Fields

cumulative

LogComparisons cumulative

last

LogComparisons last

forEvolution

LogComparisons forEvolution

Class gov.nasa.javaGenes.core.ChildMakerChain extends ChildMaker implements Serializable

Serialized Fields

initialChildMaker

ChildMaker initialChildMaker

chain

java.util.Vector chain

Class gov.nasa.javaGenes.core.ChildMakerChain.ChainElement extends java.lang.Object implements Serializable

Serialized Fields

childMaker

ChildMaker childMaker

probability

double probability

Class gov.nasa.javaGenes.core.ChildMakerDownFractionComparatorTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider extends ChildMakerProvider implements Serializable

Class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2 extends ChildMakerProvider implements Serializable

Serialized Fields

numberOfGetsPerGeneration

int numberOfGetsPerGeneration

numberToKill

double numberToKill

childMakerCreator

ChildMakerRandomCreator childMakerCreator

numberOfGetsSoFar

int numberOfGetsSoFar

evolutionScaleFactor

double evolutionScaleFactor

downFractionComparator

ChildMakerDownFractionComparator downFractionComparator

Class gov.nasa.javaGenes.core.ChildMakerEvolvingProvider2Test extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ChildMakerEvolvingProviderTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ChildMakerProvider extends java.lang.Object implements Serializable

Serialized Fields

childMakers

ExtendedVector childMakers

Class gov.nasa.javaGenes.core.ChildMakerProviderTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ChildMakerProviderWeighted extends ChildMakerProvider implements Serializable

Serialized Fields

rouletteWheel

RouletteWheel rouletteWheel

Class gov.nasa.javaGenes.core.ChildMakerTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.DescendingWeightsComparator extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.core.DescendingWeightsComparatorTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Evolvable extends java.lang.Object implements Serializable

Serialized Fields

childMakersUsed

KeyCounter childMakersUsed

Class gov.nasa.javaGenes.core.EvolvableTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Fitness extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.core.FitnessBad extends Fitness implements Serializable

Class gov.nasa.javaGenes.core.FitnessDouble extends Fitness implements Serializable

Serialized Fields

fitness

double fitness

Class gov.nasa.javaGenes.core.FitnessFunction extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

Class gov.nasa.javaGenes.core.FitnessFunctionBadSize extends FitnessFunction implements Serializable

Serialized Fields

goodSize

IntegerInterval goodSize

Class gov.nasa.javaGenes.core.FitnessFunctionBadSizeTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.FitnessFunctionFixed extends FitnessFunction implements Serializable

Serialized Fields

fitness

Fitness fitness

Class gov.nasa.javaGenes.core.FitnessFunctionMultiObjective extends FitnessFunction implements Serializable

Serialized Fields

weights

ExtendedVector weights

fitnessFunctions

ExtendedVector fitnessFunctions

Class gov.nasa.javaGenes.core.FitnessFunctionMultiObjectiveToOne extends FitnessFunctionMultiObjective implements Serializable

Class gov.nasa.javaGenes.core.FitnessFunctionRandom extends FitnessFunction implements Serializable

Serialized Fields

range

DoubleInterval range

Class gov.nasa.javaGenes.core.FitnessFunctionWorstFitness extends FitnessFunction implements Serializable

Serialized Fields

fitnessFunction

FitnessFunction fitnessFunction

phenotypeChanger

PhenotypeChanger phenotypeChanger

Class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTries extends FitnessFunctionWorstFitness implements Serializable

Serialized Fields

maxVariationsNeeded

int maxVariationsNeeded

threshold

Fitness threshold

Class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessManyTriesTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.FitnessFunctionWorstFitnessTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.FitnessMultiObjective extends Fitness implements Serializable

Serialized Fields

function

FitnessFunctionMultiObjective function

fitness

ExtendedVector fitness

Class gov.nasa.javaGenes.core.FitnessMultiObjectiveTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Individual extends java.lang.Object implements Serializable

Serialized Fields

fitness

Fitness fitness

evolvable

Evolvable evolvable

Class gov.nasa.javaGenes.core.MultiStageFitnessFunction extends FitnessFunctionMultiObjectiveToOne implements Serializable

Class gov.nasa.javaGenes.core.MultiStageFitnessFunctionTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.NotFoundException extends java.lang.Exception implements Serializable

Class gov.nasa.javaGenes.core.Parameters extends java.lang.Object implements Serializable

Serialized Fields

populationSize

int populationSize
minimum 3 to allow tournament selection


kidsPerGeneration

int kidsPerGeneration

maximumGenerations

int maximumGenerations

tournamentProbability

double tournamentProbability

fitnessFunction

FitnessFunction fitnessFunction

evaluationFunction

FitnessFunction evaluationFunction

paretoFitness

FitnessFunction paretoFitness

breeder

Breeder breeder

childMakerProvider

ChildMakerProvider childMakerProvider

separateLogAndEvolvableFiles

boolean separateLogAndEvolvableFiles

logBestEvolvableEachGeneration

boolean logBestEvolvableEachGeneration

reportVariationOperatorPerformanceEachGeneration

boolean reportVariationOperatorPerformanceEachGeneration

randomIndividualTriesPerSpecification

int randomIndividualTriesPerSpecification

frequencyOfASCIIPopulations

int frequencyOfASCIIPopulations

stopFile

java.io.File stopFile
after each generation check for this file. If exists, end the run.


suspendFile

java.io.File suspendFile
after each generation check for this file. If exists, suspend for suspendTime milliseconds.


suspendTime

int suspendTime

stopAtPerfection

boolean stopAtPerfection
if true, end run when best fitness equals 0

Class gov.nasa.javaGenes.core.ParametersSerializationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ParsimonyFitness extends FitnessFunction implements Serializable

Serialized Fields

minimumSize

int minimumSize

factor

double factor

Class gov.nasa.javaGenes.core.PhenotypeChangerDummy extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.core.Population extends java.lang.Object implements Serializable

Serialized Fields

population

Individual[] population

generation

int generation

time

long time
time to generate this population


memory

long memory
memory used by the program after population generated

Class gov.nasa.javaGenes.core.PopulationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.ProductFitnessFunction extends FitnessFunctionMultiObjectiveToOne implements Serializable

Class gov.nasa.javaGenes.core.ProductFitnessFunctionTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.RandomEvolvableProducer extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.core.Reporter extends java.lang.Object implements Serializable

Serialized Fields

parameters

Parameters parameters

Class gov.nasa.javaGenes.core.RouletteWheel extends java.lang.Object implements Serializable

Serialized Fields

weights

java.util.Vector weights

comparator

java.util.Comparator comparator

totalWeight

double totalWeight

prepareForSpinCalled

boolean prepareForSpinCalled

Class gov.nasa.javaGenes.core.RouletteWheelTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Run extends AbstractCheckpointable implements Serializable

Serialized Fields

parameters

Parameters parameters

population

Population population

foundPerfection

boolean foundPerfection

generationTimer

Timer generationTimer

generation

int generation

reporter

Reporter reporter

timeRun

boolean timeRun

Class gov.nasa.javaGenes.core.StudentFitness extends FitnessMultiObjective implements Serializable

Serialized Fields

_grade

double _grade

Class gov.nasa.javaGenes.core.StudentFitnessFunction extends FitnessFunctionMultiObjective implements Serializable

Serialized Fields

_teachers

TeacherPopulation _teachers

Class gov.nasa.javaGenes.core.StudentTeacherTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.TeacherFitnessFunction extends FitnessFunction implements Serializable

Serialized Fields

_students

Population _students

Class gov.nasa.javaGenes.core.TeacherPopulation extends ChromosomePopulation implements Serializable

Class gov.nasa.javaGenes.core.Tournament extends java.lang.Object implements Serializable

Serialized Fields

size

int size

Class gov.nasa.javaGenes.core.TournamentLocal extends Tournament implements Serializable

Serialized Fields

extendFromFirstParentIndex

int extendFromFirstParentIndex

Class gov.nasa.javaGenes.core.TournamentLocalTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.TournamentTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.Weighted0to1 extends FitnessFunction implements Serializable

Serialized Fields

weights

ExtendedVector weights

fitnessFunctions

ExtendedVector fitnessFunctions

Class gov.nasa.javaGenes.core.WeightedSumFitness extends FitnessFunctionMultiObjectiveToOne implements Serializable

Serialized Fields

normalizeByWeight

boolean normalizeByWeight

Class gov.nasa.javaGenes.core.WeightedSumFitnessTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.core.HFC

Class gov.nasa.javaGenes.core.HFC.BottomSubBreeder extends SubBreeder implements Serializable

Serialized Fields

killParents

boolean killParents

Class gov.nasa.javaGenes.core.HFC.Breeder extends Breeder implements Serializable

Serialized Fields

randomEvolvableProducer

RandomEvolvableProducer randomEvolvableProducer

Class gov.nasa.javaGenes.core.HFC.MiddleSubBreeder extends SubBreeder implements Serializable

Serialized Fields

killParents

boolean killParents

Class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreeder extends Breeder implements Serializable

Serialized Fields

subBreeders

SubBreeder[] subBreeders

considerOnlyHigherFitness

Fitness considerOnlyHigherFitness

populationSize

int populationSize

Class gov.nasa.javaGenes.core.HFC.SteadyStateDiscreteBreederTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.core.HFC.SubBreeder extends java.lang.Object implements Serializable

Serialized Fields

breeder

Breeder breeder

childMakerProvider

ChildMakerProvider childMakerProvider

fitnessFunction

FitnessFunction fitnessFunction

promotionsTo

SubBreeder promotionsTo

bestFitnessAllowed

Fitness bestFitnessAllowed

indicesRange

IntegerInterval indicesRange

deathRow

java.util.TreeSet deathRow

parentChooser

ChooseParents parentChooser

grimReaper

ChooseForDeath grimReaper

acceptRandomIndividualFitnessThreshold

Fitness acceptRandomIndividualFitnessThreshold

Class gov.nasa.javaGenes.core.HFC.TopSubBreeder extends SubBreeder implements Serializable


Package gov.nasa.javaGenes.core.utility

Class gov.nasa.javaGenes.core.utility.CoreUtilityTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.EOSscheduling

Class gov.nasa.javaGenes.EOSscheduling.AccessWindow extends java.lang.Object implements Serializable

Serialized Fields

sensor

Sensor sensor

start

int start

end

int end

duration

int duration

pointingRequirements

java.util.Vector pointingRequirements

debug

boolean debug

slewRequirement

SlewRequirement slewRequirement

number

int number

Class gov.nasa.javaGenes.EOSscheduling.AccessWindowTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimeline extends Timeline implements Serializable

Serialized Fields

dutyCycle

DutyCycleConstraint[] dutyCycle

dutyCycleMask

boolean[] dutyCycleMask

lastNodeFound

AvailableNode lastNodeFound

Class gov.nasa.javaGenes.EOSscheduling.AvailabilityTimelineTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.AvailableNode extends Node implements Serializable

Serialized Fields

isAvailable

boolean isAvailable

Class gov.nasa.javaGenes.EOSscheduling.AvailableNodeTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlew extends SlewRequirement implements Serializable

Serialized Fields

angleInDegrees

double angleInDegrees

Class gov.nasa.javaGenes.EOSscheduling.CrossTrackSlewTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraint extends java.lang.Object implements Serializable

Serialized Fields

totalTime

int totalTime

maxOnTime

int maxOnTime

onTimeArrayElementDuration

int onTimeArrayElementDuration

onTimes

int[] onTimes

Class gov.nasa.javaGenes.EOSscheduling.DutyCycleConstraintTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacer extends Placer implements Serializable

Serialized Fields

numberOfTimelines

int numberOfTimelines
See Also:
Constant Field Values

timelines

Timeline[] timelines

AvailableIndex

int AvailableIndex
See Also:
Constant Field Values

SlewIndex

int SlewIndex
See Also:
Constant Field Values

SSRindex

int SSRindex
See Also:
Constant Field Values

placementData

TaskPlacementData placementData

schedulingData

SchedulingData schedulingData

Class gov.nasa.javaGenes.EOSscheduling.EarliestFirstPlacerTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EarliestFromChosenWindowPlacer extends EarliestFirstPlacer implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EarliestFromRandomWindowPlacer extends EarliestFirstPlacer implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EOSModel extends java.lang.Object implements Serializable

Serialized Fields

tasks

ExtendedVector tasks

satellites

java.util.Vector satellites

horizon

Horizon horizon

Class gov.nasa.javaGenes.EOSscheduling.EOSModelTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvable extends PermutationEvolvable implements Serializable

Serialized Fields

hasBeenScheduledAlready

boolean hasBeenScheduledAlready

taskPlacements

TaskPlacementData[] taskPlacements

Class gov.nasa.javaGenes.EOSscheduling.EOSschedulingEvolvableTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EOSschedulingIndividual extends PermutationIndividual implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EOSschedulingParameters extends PermutationParameters implements Serializable

Serialized Fields

model

EOSModel model

scheduler

Scheduler scheduler

takeImageTime

int takeImageTime

timeBetweenSamples

int timeBetweenSamples

slewRate

double slewRate

SSRcapacity

int SSRcapacity

taskSSRuse

int taskSSRuse

timeBetweenGroundStationDownload

int timeBetweenGroundStationDownload

inputDirectory

java.lang.String inputDirectory

maxNumberOfSwapsPerMutation

int maxNumberOfSwapsPerMutation

initialTemperature

double initialTemperature

temperatureChange

double temperatureChange

callsPerTermperatureChange

int callsPerTermperatureChange

lowestTaskPriority

double lowestTaskPriority

taskPriorityIncrement

double taskPriorityIncrement

numberOfTaskPriorityLevels

int numberOfTaskPriorityLevels

taskPriorityWeight

double taskPriorityWeight

minimizeSlewingWeight

double minimizeSlewingWeight

smallSlewFactor

double smallSlewFactor

smallSlewWeight

double smallSlewWeight

smallSlewNormalizedWeight

double smallSlewNormalizedWeight

priorityWeight

float priorityWeight

accessWindowWeight

float accessWindowWeight

ssrWeight

float ssrWeight

sensorType

SensorType sensorType

Class gov.nasa.javaGenes.EOSscheduling.EOSschedulingPopulation extends Population implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.EOSschedulingReporter extends Reporter implements Serializable

Serialized Fields

fitnessEachGenerationFilename

java.lang.String fitnessEachGenerationFilename
See Also:
Constant Field Values

Class gov.nasa.javaGenes.EOSscheduling.Horizon extends TimeInterval implements Serializable

Serialized Fields

startDate

java.util.Date startDate

endDate

java.util.Date endDate

startJavaEpoch

long startJavaEpoch

endJavaEpoch

long endJavaEpoch

start

int start

end

int end

duration

int duration

Class gov.nasa.javaGenes.EOSscheduling.HorizonTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.MinimizeSlewingFitness extends SchedulingFitnessFunction implements Serializable

Serialized Fields

model

EOSModel model

Class gov.nasa.javaGenes.EOSscheduling.Node extends TimeInterval implements Serializable

Serialized Fields

startTime

int startTime

previous

Node previous

next

Node next

Class gov.nasa.javaGenes.EOSscheduling.NodeArrayTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.NodeFactory extends java.lang.Object implements Serializable

Serialized Fields

availableNodeCache

ObjectCache availableNodeCache

slewNodeCache

ObjectCache slewNodeCache

SSRNodeCache

ObjectCache SSRNodeCache

Class gov.nasa.javaGenes.EOSscheduling.NodeTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.NumberOfTakeImagesFitness extends SchedulingFitnessFunction implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.OrderMutation extends PermutationOrderMutation implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.Placer extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.PointingRequirement extends java.lang.Object implements Serializable

Serialized Fields

time

int time

azimuth

double azimuth

elevation

double elevation

range

double range

Class gov.nasa.javaGenes.EOSscheduling.PointingRequirementTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.PositionCrossover extends PermutationPositionCrossover implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.RandomChild extends PermutationChildMaker implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.runEOSscheduling extends Run implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.Satellite extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

SSRcapacity

int SSRcapacity

SSRtimeline

SSRTimeline SSRtimeline

sensors

java.util.Vector sensors

slewMotors

java.util.Vector slewMotors

groundStationAccessWindows

AccessWindow[] groundStationAccessWindows

number

int number

Class gov.nasa.javaGenes.EOSscheduling.Scheduler extends java.lang.Object implements Serializable

Serialized Fields

model

EOSModel model

placers

ExtendedVector placers

Class gov.nasa.javaGenes.EOSscheduling.SchedulingData extends java.lang.Object implements Serializable

Serialized Fields

duration

int duration

slewRequirement

SlewRequirement slewRequirement

slewable

Slewable slewable

sensor

Sensor sensor

SSRuse

int SSRuse

Class gov.nasa.javaGenes.EOSscheduling.SchedulingFitnessFunction extends FitnessFunction implements Serializable

Serialized Fields

scheduler

Scheduler scheduler

normalization

int normalization

Class gov.nasa.javaGenes.EOSscheduling.Sensor extends java.lang.Object implements Serializable

Serialized Fields

satellite

Satellite satellite

sensorType

SensorType sensorType

number

int number

availableTimeline

AvailabilityTimeline availableTimeline

slewMotor

SlewMotor slewMotor

horizon

Horizon horizon

typicalTakeImageTime

int typicalTakeImageTime

Class gov.nasa.javaGenes.EOSscheduling.SensorTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SensorType extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

Class gov.nasa.javaGenes.EOSscheduling.Slewable extends java.lang.Object implements Serializable

Serialized Fields

slewTimeline

SlewTimeline slewTimeline

Class gov.nasa.javaGenes.EOSscheduling.SlewMotor extends Slewable implements Serializable

Serialized Fields

rate

double rate

minimum

double minimum

maximum

double maximum

minimumSlew

CrossTrackSlew minimumSlew

maximumSlew

CrossTrackSlew maximumSlew

slop

double slop

sensors

java.util.Vector sensors

Class gov.nasa.javaGenes.EOSscheduling.SlewMotorNone extends SlewMotor implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SlewMotorTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SlewNode extends Node implements Serializable

Serialized Fields

slewRequirement

SlewRequirement slewRequirement

mustRampToEnd

boolean mustRampToEnd

Class gov.nasa.javaGenes.EOSscheduling.SlewNone extends SlewRequirement implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SlewRequirement extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SlewTimeline extends Timeline implements Serializable

Serialized Fields

lastStartNode

SlewNode lastStartNode

lastEndNode

SlewNode lastEndNode

Class gov.nasa.javaGenes.EOSscheduling.SlewTimelineNone extends SlewTimeline implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SlewTimelineTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SmallSlewsFitness extends SchedulingFitnessFunction implements Serializable

Serialized Fields

model

EOSModel model

Class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSM extends SqueakyWheelTournamentSwapMutation implements Serializable

Serialized Fields

moveForwardFraction

double moveForwardFraction

moveBackFraction

double moveBackFraction

goodMoves

int goodMoves

badMoves

int badMoves

Class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelPlacedTSMTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForward extends SqueakyWheelPlacedTSM implements Serializable

Serialized Fields

shiftFraction

double shiftFraction

Class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelShiftForwardTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutation extends PermutationOrderMutation implements Serializable

Serialized Fields

indices

int[] indices

legalRange

IntegerInterval legalRange

moveForwardIndex

int moveForwardIndex

moveBackIndex

int moveBackIndex

model

EOSModel model

indexDifferenceSum

int indexDifferenceSum

backSmallerThanForward

int backSmallerThanForward

backLargerThanForward

int backLargerThanForward

backSameAsForward

int backSameAsForward

Class gov.nasa.javaGenes.EOSscheduling.SqueakyWheelTournamentSwapMutationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SSRNode extends Node implements Serializable

Serialized Fields

remainingCapacity

int remainingCapacity

Class gov.nasa.javaGenes.EOSscheduling.SSRNodeTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SSRTimeline extends Timeline implements Serializable

Serialized Fields

satellite

Satellite satellite

SSRcapacity

int SSRcapacity

firstSetUpNodeList

boolean firstSetUpNodeList

dummyLastNode

Node dummyLastNode

Class gov.nasa.javaGenes.EOSscheduling.SSRTimelineNone extends SSRTimeline implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.SSRTimelineTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.STKAccessFile extends java.lang.Object implements Serializable

Serialized Fields

horizon

Horizon horizon

reader

FieldRecordText reader

timeBetweenSamples

int timeBetweenSamples

Class gov.nasa.javaGenes.EOSscheduling.STKAccessFileTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.TakeImage extends Task implements Serializable

Serialized Fields

sensorType

SensorType sensorType

SSRuse

int SSRuse

Class gov.nasa.javaGenes.EOSscheduling.Task extends java.lang.Object implements Serializable

Serialized Fields

duration

int duration

accessWindows

ExtendedVector accessWindows

accessWindowsArray

AccessWindow[] accessWindowsArray

priority

double priority

number

int number

Class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGenerator extends java.lang.Object implements Serializable

Serialized Fields

horizon

Horizon horizon

windowDuration

int windowDuration

allTakeImages

java.util.Vector allTakeImages

taskSSRuse

int taskSSRuse

Class gov.nasa.javaGenes.EOSscheduling.TaskAndAccessWindowGeneratorTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.TaskPlacementData extends java.lang.Object implements Serializable

Serialized Fields

scheduled

boolean scheduled

startTime

int startTime

windowNumber

int windowNumber

sensorNumber

int sensorNumber

slewRequirement

SlewRequirement slewRequirement

Class gov.nasa.javaGenes.EOSscheduling.TaskPriorityFitness extends SchedulingFitnessFunction implements Serializable

Serialized Fields

model

EOSModel model

Class gov.nasa.javaGenes.EOSscheduling.TaskTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.TimeInterval extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.Timeline extends java.lang.Object implements Serializable

Serialized Fields

nodeList

Node nodeList

nodeArray

NodeArray nodeArray

horizon

Horizon horizon

Class gov.nasa.javaGenes.EOSscheduling.TimelineTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.EOSscheduling.HBSS

Class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowsList extends RouletteWheelChooseLowWeight implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.HBSS.AccessWindowWeight extends Weight implements Serializable

Serialized Fields

accessWindow

AccessWindow accessWindow

Class gov.nasa.javaGenes.EOSscheduling.HBSS.Breeder extends Breeder implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.HBSS.ChildMaker extends ChildMaker implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.HBSS.Scheduler extends Scheduler implements Serializable

Serialized Fields

taskList

TaskList taskList

schedulingData

SchedulingData schedulingData

Class gov.nasa.javaGenes.EOSscheduling.HBSS.SchedulerTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskList extends RouletteWheel implements Serializable

Class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeight extends Weight implements Serializable

Serialized Fields

task

Task task

accessWindowsList

AccessWindowsList accessWindowsList

Class gov.nasa.javaGenes.EOSscheduling.HBSS.TaskWeightTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.evolvableDoubleList

Class gov.nasa.javaGenes.evolvableDoubleList.ChildMaker extends ChildMaker implements Serializable

Serialized Fields

selector

Selector selector

Class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandom extends ChildMakerProviderWeighted implements Serializable

Serialized Fields

crossoverIntervalRange

DoubleInterval crossoverIntervalRange

mutationStandardDeviationRange

DoubleInterval mutationStandardDeviationRange

selectionProbabilityRange

DoubleInterval selectionProbabilityRange

weightRange

DoubleInterval weightRange

myModulo

int myModulo

myOffset

int myOffset

randomlyChooseDefaultModulo

boolean randomlyChooseDefaultModulo

minEvolvableSize

int minEvolvableSize

maxEvolvableSize

int maxEvolvableSize

fixedLength

boolean fixedLength

deleteSizes

int[] deleteSizes

insertSizes

int[] insertSizes

Class gov.nasa.javaGenes.evolvableDoubleList.ChildMakerProviderRandomMutations extends ChildMakerProviderRandom implements Serializable

Serialized Fields

minStandardDeviaion

double minStandardDeviaion

maxStandardDeviaion

double maxStandardDeviaion

evolvableSize

int evolvableSize

Class gov.nasa.javaGenes.evolvableDoubleList.Crossover extends ChildMaker implements Serializable

Serialized Fields

indicesArray

int[] indicesArray

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewaya extends ChildMaker implements Serializable

Serialized Fields

BAD_VALUE

double BAD_VALUE
See Also:
Constant Field Values

maxLinearTries

int maxLinearTries

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverAdewayaTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverInterval extends ChildMaker implements Serializable

Serialized Fields

expandIntervalsBy

double expandIntervalsBy

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverIntervalTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePoint extends Crossover implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEach extends CrossoverOnePoint implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointEachTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverOnePointTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOne extends ChildMaker implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverPickOneTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPoints extends Crossover implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEach extends CrossoverTwoPoints implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsEachTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.CrossoverTwoPointsTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctions extends FitnessFunction implements Serializable

Serialized Fields

number

int number

Class gov.nasa.javaGenes.evolvableDoubleList.DeJongFitnessFunctionsTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDouble extends java.lang.Object implements Serializable

Serialized Fields

value

double value

Class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleList extends Evolvable implements Serializable

Serialized Fields

list

ExtendedVector list

Class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleListTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.EvolvableDoubleTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.Indices extends java.lang.Object implements Serializable

Serialized Fields

indices

ExtendedTreeSet indices

Class gov.nasa.javaGenes.evolvableDoubleList.IndicesTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parents extends ChildMaker implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.Mutation3parentsTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.MutationDelete extends ChildMaker implements Serializable

Serialized Fields

minumumEvolvableSize

int minumumEvolvableSize

Class gov.nasa.javaGenes.evolvableDoubleList.MutationDeleteTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDev extends ChildMaker implements Serializable

Serialized Fields

standardDeviation

double standardDeviation

Class gov.nasa.javaGenes.evolvableDoubleList.MutationFixedStdDevTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.MutationInsert extends ChildMaker implements Serializable

Serialized Fields

numberToInsert

int[] numberToInsert

Class gov.nasa.javaGenes.evolvableDoubleList.MutationInsertTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.NeighboringPairsSelector extends Selector implements Serializable

Serialized Fields

simpleSelector

SelectModulo simpleSelector

Class gov.nasa.javaGenes.evolvableDoubleList.RandomEvolvableDoubleListProducer extends RandomEvolvableProducer implements Serializable

Serialized Fields

sizeRange

IntegerInterval sizeRange

Class gov.nasa.javaGenes.evolvableDoubleList.SelectAll extends Selector implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectAllTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbability extends Selector implements Serializable

Serialized Fields

probability

double probability

minimumNumberToSelect

int minimumNumberToSelect

DEFAULT_MAXIMUM_TRIES

int DEFAULT_MAXIMUM_TRIES
See Also:
Constant Field Values

Class gov.nasa.javaGenes.evolvableDoubleList.SelectByProbabilityTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectChunk extends Selector implements Serializable

Serialized Fields

simpleSelector

SelectModulo simpleSelector

numberToChoose

int[] numberToChoose

Class gov.nasa.javaGenes.evolvableDoubleList.SelectChunkTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndices extends Selector implements Serializable

Serialized Fields

indicesToSelect

int[] indicesToSelect

Class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedIndicesTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumber extends Selector implements Serializable

Serialized Fields

numberToSelect

int numberToSelect

Class gov.nasa.javaGenes.evolvableDoubleList.SelectFixedNumberTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectModulo extends Selector implements Serializable

Serialized Fields

selector

Selector selector

modulo

int modulo

offset

int offset

Class gov.nasa.javaGenes.evolvableDoubleList.SelectModuloTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectOne extends Selector implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPair extends NeighboringPairsSelector implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectOneNeighboringPairTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectOneTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.Selector extends java.lang.Object implements Serializable

Serialized Fields

MAXIMUM_TRIES

int MAXIMUM_TRIES
See Also:
Constant Field Values

Class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairs extends NeighboringPairsSelector implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.SelectTwoNeighboringPairsTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.evolvableDoubleList.TestFitnessFunction1 extends FitnessFunction implements Serializable


Package gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment

Class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Parameters extends Parameters implements Serializable

Serialized Fields

population

Population population

reporter

Reporter reporter

numberOfChildMakers

int numberOfChildMakers
See Also:
Constant Field Values

Class gov.nasa.javaGenes.evolvableDoubleList.DeJongExperiment.Run extends Run implements Serializable


Package gov.nasa.javaGenes.forceFields

Class gov.nasa.javaGenes.forceFields.Allele extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

noEvolution

boolean noEvolution

valueToSet

double valueToSet

interval

DoubleInterval interval
holds the maximum and minimum values for this allele

Class gov.nasa.javaGenes.forceFields.AlleleSetup extends java.lang.Object implements Serializable

Serialized Fields

intervals

java.util.Hashtable intervals

indices

java.util.Hashtable indices

Class gov.nasa.javaGenes.forceFields.AlleleTemplate extends java.lang.Object implements Serializable

Serialized Fields

alleles

Allele[][] alleles

names

java.lang.String[] names
These names refer to the first dimension in alleles

Class gov.nasa.javaGenes.forceFields.AlleleTemplateTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.AlleleTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.AssumedParameters extends ChromosomeParameterValues implements Serializable

Class gov.nasa.javaGenes.forceFields.AssumedParametersTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.Bodies extends MultiBodiesForOneEnergy implements Serializable

Serialized Fields

oneBody

OneBody[] oneBody
this is public for fast access. Access is often in an inner loop. multiBodies is converted to this.

Class gov.nasa.javaGenes.forceFields.BodiesTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.Body extends MultiBody implements Serializable

Serialized Fields

species

Species species
the species of this body (second body in TwoBody, third body in ThreeBody)


speciesIndex

int speciesIndex
the species index. Used for speed.

Class gov.nasa.javaGenes.forceFields.Chromosome extends Evolvable implements Serializable

Serialized Fields

chromosome

double[][] chromosome

Class gov.nasa.javaGenes.forceFields.ChromosomeArrayCrossover extends ChromosomeCrossover implements Serializable

Class gov.nasa.javaGenes.forceFields.ChromosomeCrossover extends ChildMaker implements Serializable

Class gov.nasa.javaGenes.forceFields.ChromosomeDistanceFitness extends FitnessFunction implements Serializable

Serialized Fields

target

Chromosome target
target chromosome

Class gov.nasa.javaGenes.forceFields.ChromosomeIndividual extends Individual implements Serializable

Class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossover extends ChildMaker implements Serializable

Serialized Fields

alleles

AlleleTemplate alleles

extension

double extension
interval crossover fraction of distance between


limitToOriginalInterval

boolean limitToOriginalInterval

Class gov.nasa.javaGenes.forceFields.ChromosomeIntervalCrossoverTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ChromosomeMutation extends ChildMaker implements Serializable

Serialized Fields

limitToOriginalInterval

boolean limitToOriginalInterval

alleles

AlleleTemplate alleles

standardDeviation

double standardDeviation
The standard deviation to use expressed as a fraction of the allele interval


frequency

double frequency
average fraction of the alleles to be used. Whether any alleles is to be used is a randomized event. If this too small, can get effective infinite loop since at least one change is required for the makeChildren() method to complete! Value defaults to 1.

Class gov.nasa.javaGenes.forceFields.ChromosomeMutationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ChromosomeParameters extends Parameters implements Serializable

Serialized Fields

alleles

AlleleTemplate alleles

lengthsAndAnglesFilename

java.lang.String lengthsAndAnglesFilename

assumed

AssumedParameters assumed

immigrants

Immigrants immigrants

species

AtomicSpecies[] species

energiesToExamineBestIndividual

ManyMultiBodiesForOneEnergy energiesToExamineBestIndividual

potential

Potential potential

whichPotential

int whichPotential

fileDirectory

java.lang.String fileDirectory
See Also:
Constant Field Values

farWallFilename

java.lang.String farWallFilename

nearWallFilename

java.lang.String nearWallFilename

minimumFilename

java.lang.String minimumFilename

forceFilename

java.lang.String forceFilename

bondLengthFilename

java.lang.String bondLengthFilename

eval

FitnessFunctionMultiObjective eval

Class gov.nasa.javaGenes.forceFields.ChromosomeParameterValues extends java.lang.Object implements Serializable

Serialized Fields

names

java.util.Vector names

values

java.util.Vector values

Class gov.nasa.javaGenes.forceFields.ChromosomePopulation extends Population implements Serializable

Serialized Fields

alleles

AlleleTemplate alleles

Class gov.nasa.javaGenes.forceFields.ChromosomeReporter extends Reporter implements Serializable

Serialized Fields

EnergiesFilename

java.lang.String EnergiesFilename

Class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutation extends ChromosomeIntervalCrossover implements Serializable

Serialized Fields

mutator

ChromosomeMutation mutator

mutationProbability

double mutationProbability

Class gov.nasa.javaGenes.forceFields.ChromosomeXoverWithMutationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunction extends FitnessFunction implements Serializable

Serialized Fields

potential

Potential potential

molecules

ManyMultiBodiesForOneEnergy molecules

filename

java.lang.String filename

cliff

double cliff

Class gov.nasa.javaGenes.forceFields.FirstClusterLowestEnergyFitnessFunctionTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ForceFitnessRMS extends ManyMoleculesEnergyFitness implements Serializable

Class gov.nasa.javaGenes.forceFields.ForceFitnessRMSTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ForceFitnessTanimoto extends ForceFitnessRMS implements Serializable

Class gov.nasa.javaGenes.forceFields.FunctionalForm extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.forceFields.Immigrant extends ChromosomeParameterValues implements Serializable

Serialized Fields

infinitNumber

boolean infinitNumber

number

int number

Class gov.nasa.javaGenes.forceFields.Immigrants extends java.lang.Object implements Serializable

Serialized Fields

immigrants

java.util.Vector immigrants

Class gov.nasa.javaGenes.forceFields.ImmigrantsTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ImmigrantTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitness extends FitnessFunction implements Serializable

Serialized Fields

potential

Potential potential

molecules

ManyMultiBodiesForOneEnergy molecules

filename

java.lang.String filename

doPerAtomEnergies

boolean doPerAtomEnergies

Class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyFitnessTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitness extends LowestToHighestEnergyFitness implements Serializable

Serialized Fields

outOfOrderPenalty

double outOfOrderPenalty

Class gov.nasa.javaGenes.forceFields.LowestToHighestEnergyGradualFitnessTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness extends FitnessFunction implements Serializable

Serialized Fields

potential

Potential potential

molecules

ManyMultiBodiesForOneEnergy molecules

energies

java.util.Vector energies

scaleTo

DoubleInterval scaleTo

originalEnergyInterval

DoubleInterval originalEnergyInterval

filename

java.lang.String filename

doPerAtomEnergies

boolean doPerAtomEnergies

Class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessRatio extends ManyMoleculesEnergyFitness implements Serializable

Class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitnessTanimotoDistance extends ManyMoleculesEnergyFitness implements Serializable

Class gov.nasa.javaGenes.forceFields.ManyMultiBodiesForOneEnergy extends java.lang.Object implements Serializable

Serialized Fields

molecules

java.util.Vector molecules

multiBodies

java.util.Vector multiBodies

Class gov.nasa.javaGenes.forceFields.MMEFreferenceRMS extends ManyMoleculesEnergyFitness implements Serializable

Serialized Fields

referenceEnergy

double referenceEnergy

referenceEnergyUncertainty

DoubleInterval referenceEnergyUncertainty

energyRangeDivideBy

double energyRangeDivideBy

targetReferenceEnergy

double targetReferenceEnergy

Class gov.nasa.javaGenes.forceFields.MMEFreferenceRMSTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.MMEFreferenceTanimoto extends MMEFreferenceRMS implements Serializable

Class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergy extends java.lang.Object implements Serializable

Serialized Fields

multiBodies

java.util.Vector multiBodies

molecule

Molecule molecule

Class gov.nasa.javaGenes.forceFields.MultiBodiesForOneEnergyTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.MultiBody extends java.lang.Object implements Serializable

Serialized Fields

_name

java.lang.String _name

howMany

double howMany

Class gov.nasa.javaGenes.forceFields.Mutation3Parents extends ChromosomeMutation implements Serializable

Serialized Fields

standardDeviationFactor

double standardDeviationFactor

Class gov.nasa.javaGenes.forceFields.OneBody extends Body implements Serializable

Serialized Fields

vector

ExtendedVector vector

secondBody

SecondBody[] secondBody
the twoBody(s) this is involved with in a public array for fast access. Will not contain anything until createArrays() is called

Class gov.nasa.javaGenes.forceFields.PotentialEnergyFitness extends FitnessFunction implements Serializable

Serialized Fields

potential

Potential potential

testCases

java.util.Vector testCases

target

Chromosome target

Class gov.nasa.javaGenes.forceFields.PutPotentialEnergiesAndForces extends java.lang.Object implements Serializable

Serialized Fields

_potential

Potential _potential

_chromosome

Chromosome _chromosome

_minimumDistance

double _minimumDistance

_maximumDistance

double _maximumDistance

_minimumAngle

double _minimumAngle

_maximumAngle

double _maximumAngle

_lengthScale

double _lengthScale

Class gov.nasa.javaGenes.forceFields.RunChromosome extends Run implements Serializable

Class gov.nasa.javaGenes.forceFields.SecondBody extends Body implements Serializable

Serialized Fields

radialDistance

double radialDistance
distance to the first body


twoBodyTermMatters

boolean twoBodyTermMatters
used to turn of calculation off two body energies so the three body terms will be more important.


vector

java.util.Vector vector

thirdBody

ThirdBody[] thirdBody
don't access until after createArrays has been called

Class gov.nasa.javaGenes.forceFields.StillingerWeber extends Potential implements Serializable

Serialized Fields

alleleSetup

AlleleSetup alleleSetup

chromosome

Chromosome chromosome

alleles

AlleleTemplate alleles

setupComplete

boolean setupComplete

bondLengthInterval

DoubleInterval bondLengthInterval

exponentInterval

DoubleInterval exponentInterval

factorInterval

DoubleInterval factorInterval

angleInterval

DoubleInterval angleInterval

cutoffInterval

DoubleInterval cutoffInterval

A_index

int A_index
See Also:
Constant Field Values

B_index

int B_index
See Also:
Constant Field Values

C_index

int C_index
See Also:
Constant Field Values

p_index

int p_index
See Also:
Constant Field Values

q_index

int q_index
See Also:
Constant Field Values

a_index

int a_index
See Also:
Constant Field Values

numberOfTwoBodyParameters

int numberOfTwoBodyParameters
See Also:
Constant Field Values

alpha_index

int alpha_index
See Also:
Constant Field Values

lambda_index

int lambda_index
See Also:
Constant Field Values

theta0_index

int theta0_index
See Also:
Constant Field Values

gamma_index

int gamma_index
See Also:
Constant Field Values

a1_index

int a1_index
See Also:
Constant Field Values

numberOfThreeBodyParameters

int numberOfThreeBodyParameters
See Also:
Constant Field Values

flourineThreeBodyParametersIncrement

int flourineThreeBodyParametersIncrement
See Also:
Constant Field Values

specialThreeBodyParametersIncrement

int specialThreeBodyParametersIncrement
See Also:
Constant Field Values

delta_index

int delta_index
See Also:
Constant Field Values

m_index

int m_index
See Also:
Constant Field Values

beta_index

int beta_index
See Also:
Constant Field Values

a2_index

int a2_index
See Also:
Constant Field Values

NotApplicable

double NotApplicable
See Also:
Constant Field Values

cutoffs

java.util.Hashtable cutoffs

Class gov.nasa.javaGenes.forceFields.StillingerWeber.ChromosomeParametersData extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

Class gov.nasa.javaGenes.forceFields.StillingerWeberPartialSiF extends StillingerWeberSiF implements Serializable

Class gov.nasa.javaGenes.forceFields.StillingerWeberSi extends StillingerWeber implements Serializable

Class gov.nasa.javaGenes.forceFields.StillingerWeberSiF extends StillingerWeber implements Serializable

Serialized Fields

energyUnitKcalPerMol

double energyUnitKcalPerMol

energyUnitErgPerAtom

double energyUnitErgPerAtom

Class gov.nasa.javaGenes.forceFields.StillingerWeberSiFTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.StillingerWeberSiTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.StillingerWeberTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.TersoffTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.ThirdBody extends Body implements Serializable

Serialized Fields

radialDistance

double radialDistance
the distance of the last body to the first body


angle

double angle
the angle between the lines joining the second and third bodies and the first body

Class gov.nasa.javaGenes.forceFields.ThreeBody extends MultiBody implements Serializable

Serialized Fields

_jiDistance

double _jiDistance

_jkDistance

double _jkDistance

_angle

double _angle

requiresSWextraParameters

boolean requiresSWextraParameters

Class gov.nasa.javaGenes.forceFields.ThreeBodyTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.forceFields.TwoBody extends MultiBody implements Serializable

Serialized Fields

_radialDistance

double _radialDistance

Class gov.nasa.javaGenes.forceFields.TwoBodyTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.graph

Class gov.nasa.javaGenes.graph.AcceptableSecondBrokenEdge extends java.lang.Object implements Serializable

Serialized Fields

first

BrokenEdge first

mustBeCompatible

boolean mustBeCompatible

Class gov.nasa.javaGenes.graph.AcceptableSecondVertex extends java.lang.Object implements Serializable

Serialized Fields

vertex

Vertex vertex
vertex seeking a vertex to have an edge with

Class gov.nasa.javaGenes.graph.AddDirectedEdge extends gov.nasa.javaGenes.graph.GraphMutation implements Serializable

Serialized Fields

provider

VertexAndEdgeProvider provider

Class gov.nasa.javaGenes.graph.AddDirectedVertex extends gov.nasa.javaGenes.graph.GraphMutation implements Serializable

Serialized Fields

provider

VertexAndEdgeProvider provider

predicate

Predicate predicate

Class gov.nasa.javaGenes.graph.AddEdge extends gov.nasa.javaGenes.graph.GraphMutation implements Serializable

Serialized Fields

provider

VertexAndEdgeProvider provider

Class gov.nasa.javaGenes.graph.AddVertex extends gov.nasa.javaGenes.graph.GraphMutation implements Serializable

Serialized Fields

provider

VertexAndEdgeProvider provider

Class gov.nasa.javaGenes.graph.CyclesSimilarity extends FitnessFunction implements Serializable

Serialized Fields

target

Graph target
the target graph against which Individuals will be measured

Class gov.nasa.javaGenes.graph.DirectedEdge extends Edge implements Serializable

Class gov.nasa.javaGenes.graph.DirectedGraph extends Graph implements Serializable

Class gov.nasa.javaGenes.graph.DirectedGraph.SecondVertex extends java.lang.Object implements Serializable

Serialized Fields

acceptsOutput

DirectedVertex acceptsOutput

Class gov.nasa.javaGenes.graph.DirectedVertex extends Vertex implements Serializable

Serialized Fields

inputEdges

ExtendedVector inputEdges

outputEdges

ExtendedVector outputEdges

Class gov.nasa.javaGenes.graph.DissimilarEdgeCompatibleWithVertices extends java.lang.Object implements Serializable

Serialized Fields

edge

Edge edge

Class gov.nasa.javaGenes.graph.Edge extends GraphElement implements Serializable

Serialized Fields

vertices

Vertex[] vertices
the vertices this edge connects

Class gov.nasa.javaGenes.graph.ExtendedTypeSimilarity extends FitnessFunction implements Serializable

Serialized Fields

target

Graph target

Class gov.nasa.javaGenes.graph.Graph extends Evolvable implements Serializable

Serialized Fields

vertices

ExtendedVector vertices

edges

ExtendedVector edges

nodeTypePairsShortestTrailCounts

KeyCounter nodeTypePairsShortestTrailCounts
cache the results of all-pairs-shortest-path since this operation is compute intensive.

Class gov.nasa.javaGenes.graph.Graph.TrailKey extends java.lang.Object implements Serializable

Serialized Fields

end1

java.lang.Object end1

end2

java.lang.Object end2

length

int length

Class gov.nasa.javaGenes.graph.GraphElement extends Mark implements Serializable

Class gov.nasa.javaGenes.graph.GraphGenerator extends ChildMaker implements Serializable

Serialized Fields

parameters

GraphParameters parameters

Class gov.nasa.javaGenes.graph.GraphIndividual extends Individual implements Serializable

Class gov.nasa.javaGenes.graph.GraphLayout extends java.lang.Object implements Serializable

Serialized Fields

iterations

int iterations

maxLineSearchIterations

int maxLineSearchIterations

vertexSize

double vertexSize

edgeLength

double edgeLength

border

double border

BarnesHutTheta

double BarnesHutTheta

accuracyOfLineSearch

double accuracyOfLineSearch

restartThreshold

double restartThreshold

Class gov.nasa.javaGenes.graph.GraphParameters extends Parameters implements Serializable

Serialized Fields

verticesInterval

IntegerInterval verticesInterval
an interval to choose a random number of Graph vertices from. Used for generation of a random GraphPopulation.

See Also:
GraphPopulation

cyclesInterval

IntegerInterval cyclesInterval
an interval to choose a random number of Graph cycles from. Used for generation of a random GraphPopulation.

See Also:
GraphPopulation

provider

VertexAndEdgeProvider provider
will provide random vertices and edges for random GraphPopulation construction.

See Also:
GraphPopulation

layoutGraph2d

boolean layoutGraph2d

layout

GraphLayout layout

Class gov.nasa.javaGenes.graph.GraphPopulation extends Population implements Serializable

Class gov.nasa.javaGenes.graph.GraphTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.graph.HasInputEdgeFrom extends java.lang.Object implements Serializable

Serialized Fields

vertex

DirectedVertex vertex

Class gov.nasa.javaGenes.graph.HasOutputEdgesTo extends java.lang.Object implements Serializable

Serialized Fields

vertex

DirectedVertex vertex

Class gov.nasa.javaGenes.graph.MutateEdge extends gov.nasa.javaGenes.graph.GraphMutation implements Serializable

Serialized Fields

provider

VertexAndEdgeProvider provider
provides the edges to mutate to

Class gov.nasa.javaGenes.graph.MutateVertex extends gov.nasa.javaGenes.graph.GraphMutation implements Serializable

Serialized Fields

provider

VertexAndEdgeProvider provider
provides the vertex to mutate to

Class gov.nasa.javaGenes.graph.TwoVertexGraphCrossover extends ChildMaker implements Serializable

Class gov.nasa.javaGenes.graph.Vertex extends GraphElement implements Serializable

Serialized Fields

edges

ExtendedVector edges

xyz

double[] xyz

extendedTypeCache

java.lang.String extendedTypeCache

number

int number
used to number vertices for various purposes

Class gov.nasa.javaGenes.graph.VertexAcceptsEdge extends java.lang.Object implements Serializable

Serialized Fields

edge

Edge edge
the edge to be accepted

Class gov.nasa.javaGenes.graph.VertexAcceptsInputEdge extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.graph.VertexAcceptsOutputEdge extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.graph.VertexAndEdgeProvider extends java.lang.Object implements Serializable

Serialized Fields

vertices

ExtendedVector vertices
the vertices to be provided.


edges

ExtendedVector edges
the edges to be provided

Class gov.nasa.javaGenes.graph.VertexPairsDistanceSimilarity extends FitnessFunction implements Serializable

Serialized Fields

target

Graph target
target graph

Class gov.nasa.javaGenes.graph.VertexTest extends TestCase implements Serializable


Package gov.nasa.javaGenes.hillClimbing

Class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetter extends Accepter implements Serializable

Class gov.nasa.javaGenes.hillClimbing.AcceptEqualOrBetterTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.hillClimbing.Accepter extends java.lang.Object implements Serializable

Class gov.nasa.javaGenes.hillClimbing.AcceptImprovement extends Accepter implements Serializable

Class gov.nasa.javaGenes.hillClimbing.AcceptImprovementTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.hillClimbing.Breeder extends Breeder implements Serializable

Serialized Fields

CURRENT

int CURRENT
See Also:
Constant Field Values

BEST_SO_FAR

int BEST_SO_FAR
See Also:
Constant Field Values

accepter

Accepter accepter

restartPolicy

RestartPolicy restartPolicy

randomChildMaker

ChildMaker randomChildMaker

Class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptance extends RestartEveryNChildren implements Serializable

Class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutAcceptanceTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovement extends RestartEveryNChildren implements Serializable

Class gov.nasa.javaGenes.hillClimbing.RestartAfterNChildrenWithoutImprovementTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildren extends RestartPolicy implements Serializable

Serialized Fields

limit

int limit

count

int count

Class gov.nasa.javaGenes.hillClimbing.RestartEveryNChildrenTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.hillClimbing.RestartNever extends RestartPolicy implements Serializable

Class gov.nasa.javaGenes.hillClimbing.RestartPolicy extends java.lang.Object implements Serializable


Package gov.nasa.javaGenes.permutation

Class gov.nasa.javaGenes.permutation.PermutationChildMaker extends ChildMaker implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationEvolvable extends Evolvable implements Serializable

Serialized Fields

permutation

int[] permutation

Class gov.nasa.javaGenes.permutation.PermutationIndividual extends Individual implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationKCutMutation extends PermutationChildMaker implements Serializable

Serialized Fields

numberOfSegments

int numberOfSegments

Class gov.nasa.javaGenes.permutation.PermutationKCutMutationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationOrderMutation extends PermutationChildMaker implements Serializable

Serialized Fields

numberOfSwaps

int numberOfSwaps

Class gov.nasa.javaGenes.permutation.PermutationOrderMutationTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationParameters extends Parameters implements Serializable

Serialized Fields

permutationLength

int permutationLength

Class gov.nasa.javaGenes.permutation.PermutationPopulation extends Population implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationPositionCrossover extends PermutationChildMaker implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationPositionCrossoverTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.permutation.PermutationTestFitness extends FitnessFunction implements Serializable

Class gov.nasa.javaGenes.permutation.RunPermutation extends Run implements Serializable


Package gov.nasa.javaGenes.simulatedAnnealing

Class gov.nasa.javaGenes.simulatedAnnealing.Accepter extends Accepter implements Serializable

Serialized Fields

reduceBy

double reduceBy

currentTemperature

double currentTemperature

callsPerStaticTemperature

int callsPerStaticTemperature

callsAtThisTemperature

int callsAtThisTemperature

whichReduction

int whichReduction

Class gov.nasa.javaGenes.simulatedAnnealing.AccepterTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.simulatedAnnealing.Breeder extends Breeder implements Serializable


Package gov.nasa.javaGenes.weightNetwork

Class gov.nasa.javaGenes.weightNetwork.RouletteWheel extends WeightList implements Serializable

Class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeight extends WeightList implements Serializable

Serialized Fields

subtractWeightFrom

float subtractWeightFrom

mustCalculateSubtractWeightFrom

boolean mustCalculateSubtractWeightFrom

numberOfWeightsRemoved

int numberOfWeightsRemoved

Class gov.nasa.javaGenes.weightNetwork.RouletteWheelChooseLowWeightTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.weightNetwork.RouletteWheelTest extends TestCase implements Serializable

Class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagatable extends java.lang.Object implements Serializable

Serialized Fields

needToUpdateAndPropagate

boolean needToUpdateAndPropagate

Class gov.nasa.javaGenes.weightNetwork.UpdateAndPropagateList extends GrowOnlyArray implements Serializable

Serialized Fields

which

int which

Class gov.nasa.javaGenes.weightNetwork.Weight extends UpdateAndPropagatable implements Serializable

Serialized Fields

weight

float weight

weightList

WeightList weightList

next

Weight next

previous

Weight previous

Class gov.nasa.javaGenes.weightNetwork.WeightList extends UpdateAndPropagatable implements Serializable

Serialized Fields

initialWeights

java.util.Vector initialWeights

currentWeights

Weight currentWeights

weightSum

ReinitializableFloat weightSum

Class gov.nasa.javaGenes.weightNetwork.WeightListTest extends TestCase implements Serializable


JavaGenes, NASA Ames. Written largely by Al Globus