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jkappa-master
src
license
com
plectix
license
client
License.java
LicenseException.java
License_V1.java
SecurityUtil.java
server
KeyGenerator.java
LicenseGenerator.java
ServerSecurityUtil.java
main
com
plectix
simulator
BuildConstants.java
SimulationMain.java
api
CommandLineRunner.java
controller
SimulationService.java
SimulatorCallable.java
SimulatorCallableExitReport.java
SimulatorCallableListener.java
SimulatorFactoryInterface.java
SimulatorFutureTask.java
SimulatorInputData.java
SimulatorInterface.java
SimulatorProgressMonitor.java
SimulatorResultsData.java
SimulatorStatusInterface.java
gui
lib
AWTExceptionHandler.java
ColorMap.java
DialogPanel.java
GUIMain.java
GradientPanelUI.java
GridBagPanel.java
HorizontalLinePanel.java
MainPanel.java
MainWindow.java
PromptDialogs.java
Settings.java
SplitPanel.java
UIProperties.java
WaitingEventQueue.java
panel
ChartZoomInfo.java
ConsolePrintStream.java
ControlPanel.java
ControlPanelListener.java
GraphPanel.java
MainPanel.java
SimulationSettings.java
interfaces
ActivationMapInterface.java
ConnectedComponentInterface.java
ObservableConnectedComponentInterface.java
ObservableInterface.java
ObservableRuleInterface.java
RandomInterface.java
SolutionElementInterface.java
SolutionInterface.java
io
ConsoleOutputManager.java
SimulationDataOutputUtil.java
SimulationDataReader.java
xml
ContactMapXMLWriter.java
InfluenceMapXMLWriter.java
LocalViewsXMLWriter.java
OurXMLWriter.java
RuleCompressionXMLWriter.java
SimulationDataXMLWriter.java
SpeciesXMLWriter.java
StoriesXMLWriter.java
SubviewsXMLWriter.java
parser
BadOptionException.java
DocumentFormatException.java
EasyReader.java
FileReadingException.java
GeneralReader.java
IncompletesDisabledException.java
KappaFile.java
KappaFileLine.java
KappaFileParagraph.java
KappaFileReader.java
KappaParagraphModifier.java
KappaSystemParser.java
ParseErrorException.java
ParseErrorMessage.java
SimulationDataFormatException.java
abstractmodel
KappaModel.java
ModelAgent.java
ModelLink.java
ModelPerturbation.java
ModelRule.java
ModelSite.java
ModelSolution.java
ModelStories.java
SolutionLineData.java
observables
ModelObservableRule.java
ModelObservables.java
ObservableComponentLineData.java
ObservableRuleLineData.java
ObservablesLineData.java
perturbations
LinearExpressionMonome.java
LinearModification.java
ModelLinearExpression.java
RateExpressionParser.java
SpeciesConditionExpression.java
SpeciesExpressionParser.java
SpecifiedLinearModificationParser.java
conditions
ConditionType.java
ModelConjuctionCondition.java
ModelSpeciesCondition.java
ModelTimeCondition.java
PerturbationCondition.java
modifications
AbstractOnceModification.java
ModelAddOnceModification.java
ModelDeleteOnceModification.java
ModelRateModification.java
ModificationType.java
PerturbationModification.java
reader
KappaModelCreator.java
KappaParagraphReader.java
ModelParseHelper.java
ObservablesParagraphReader.java
PerturbationsParagraphReader.java
RulesParagraphReader.java
SolutionParagraphReader.java
StoriesParagraphReader.java
util
ModelSolutionManager.java
builders
KappaSystemBuilder.java
MasterSolutionModel.java
ObservablesBuilder.java
PerturbationsBuilder.java
RuleBuilder.java
SolutionBuilder.java
StoriesBuilder.java
SubstanceBuilder.java
util
AgentFactory.java
AgentFormatChecker.java
ParserUtil.java
SiteProperty.java
SitePropertyKey.java
simulationclasses
action
Action.java
ActionObserverInteface.java
ActionType.java
AddAction.java
BoundAction.java
BreakAction.java
DefaultAction.java
DeleteAction.java
ModifyAction.java
bologna
Reaction.java
ReactionClass.java
injections
Injection.java
InjectionsUtil.java
LiftElement.java
perturbations
AbstractModification.java
AddOnceModification.java
ComplexCondition.java
ComplexPerturbation.java
ConditionInterface.java
DeleteOnceModification.java
OnceModification.java
PerturbationRule.java
RateModification.java
SpeciesCondition.java
TimeCondition.java
util
LinearExpression.java
Monome.java
Vector.java
VectorObservable.java
VectorRule.java
probability
SkipListItem.java
SkipListSelector.java
WeightedItem.java
WeightedItemSelector.java
solution
AbstractComplexSolution.java
AbstractSolutionForHigherModes.java
OperationMode.java
RuleApplicationPoolInterface.java
SolutionAdapter.java
SolutionFactory.java
SolutionFifthMode.java
SolutionFirstMode.java
SolutionFourthMode.java
SolutionLine.java
SolutionSecondMode.java
SolutionThirdMode.java
StandardRuleApplicationPool.java
StorageInterface.java
StraightStorage.java
SuperStorage.java
SuperSubstance.java
TransparentRuleApplicationPool.java
simulator
CompiledKappaFile.java
DefaultRandom.java
DefaultSimulatorFactory.java
KappaSystem.java
KappaSystemInterface.java
ObservablesLiveDataSource.java
SimulationArguments.java
SimulationClock.java
SimulationData.java
SimulationState.java
Simulator.java
SimulatorCommandLine.java
SimulatorMessage.java
SimulatorStatus.java
ThreadLocalData.java
UpdatesPerformer.java
api
OperationType.java
SimulatorAPI.java
SimulatorAPIInterface.java
SimulatorState.java
steps
AbstractOperation.java
ActivationMapComputationOperation.java
CommandLineDefinedWorkflow.java
ContactMapComputationOperation.java
DeadRuleDetectionOperation.java
DumpHelpOperation.java
DumpVersionOperation.java
ExperimentWorkflow.java
InfluenceMapComputationOperation.java
InhibitionMapComputationOperation.java
InjectionBuildingOperation.java
KappaFileCompilationOperation.java
KappaFileLoadingOperation.java
KappaModelBuildingOperation.java
LocalViewsComputationOperation.java
NoKappaInputException.java
OperationManager.java
OutputCompiledFileOperation.java
ReportErrorOperation.java
RuleCompressionOperation.java
SimulationOperation.java
SimulatorInitializationOperation.java
SolutionInitializationOperation.java
SpeciesEnumerationOperation.java
StoriesComputationOperation.java
SubviewsComputationOperation.java
XMLOutputOperation.java
experiments
AbstractExperimentRunner.java
ConnectedComponentPattern.java
Experiment.java
ExperimentListener.java
ExperimentRunner.java
ExperimentRunnerListener.java
Pattern.java
RulePattern.java
SimulationDataProcessor.java
initialization
InjectionSettingStrategy.java
InjectionsBuilder.java
StraightInjectionSettingStrategy.java
SuperInjectionSettingStrategy.java
options
CommandLineParametersManager.java
OptionsSetSingleton.java
SimulationArgumentsCreator.java
SimulatorArgumentsDefaultValues.java
SimulatorFlagOption.java
SimulatorOption.java
SimulatorParameter.java
SimulatorParameterType.java
SimulatorParameterizedOption.java
SimulatorUnusedOption.java
staticanalysis
Agent.java
ChangedSite.java
ConnectedComponent.java
InternalState.java
Link.java
LinkRank.java
LinkStatus.java
NamedEntity.java
ObservableConnectedComponent.java
ObservableRuleComponent.java
Rule.java
RuleApplicator.java
Site.java
Snapshot.java
SnapshotElement.java
SpanningTree.java
StaticAnalysisException.java
abstracting
AbstractAgent.java
AbstractLinkState.java
AbstractSite.java
contactmap
ContactMap.java
ContactMapAbstractEdge.java
ContactMapAbstractSolution.java
ContactMapChangedSite.java
ContactMapMode.java
cycledetection
Detector.java
EdgeFromContactMap.java
NodeFromContactMap.java
graphs
Edge.java
Graph.java
Vertex.java
influencemap
InfluenceMap.java
InfluenceMapEdge.java
future
InfluenceMapWithFuture.java
MarkAgentWithFuture.java
nofuture
InfluenceMapWithoutFuture.java
MarkAgentWithoutFuture.java
MarkSiteWithoutFuture.java
Quark.java
localviews
LocalViewsMain.java
observables
MaxStateFinder.java
ObservableComponentsManager.java
ObservableState.java
Observables.java
ObservablesStatesHandler.java
ObservablesStatesVisitor.java
rulecompression
CompressionResults.java
QualitativeCompressor.java
QuantitativeCompressor.java
RootedRule.java
RootedRulesGroup.java
RuleCompressionType.java
RuleCompressionUtils.java
RuleCompressor.java
RuleMaster.java
ShadowAgent.java
speciesenumeration
Species.java
SpeciesEnumeration.java
stories
ActionOfAEvent.java
MarkOfEvent.java
State.java
Stories.java
TypeOfWire.java
compressions
BoundFreeSateIterator.java
CompressionPassport.java
Compressor.java
LinkStateIterator.java
QueueEntry.java
StackEntry.java
StrongCompression.java
WeakCompression.java
graphs
BoundedCouple.java
Connection.java
Connections.java
MergeStoriesGraphs.java
Site.java
StoriesGraphs.java
UniqueGraph.java
storage
AbstractState.java
AbstractStorage.java
AtomicEvent.java
Event.java
EventBuilder.java
EventInterface.java
EventIteratorInterface.java
EventIteratorOnWire.java
IteratorAtomicEventWithinEvent.java
MasterInformationAboutWires.java
NullEvent.java
PointRound.java
ReLinker.java
StateOfLink.java
StoragePassport.java
StoriesAgentTypesStorage.java
StoryBuilder.java
StoryStorageException.java
SwapRecord.java
Utils.java
WireHashKey.java
WireStorageInterface.java
subviews
AllSubViewsOfAllAgentsInterface.java
MainSubViews.java
SubViewClass.java
WrapperTwoSet.java
base
AbstractAction.java
AbstractActionType.java
AbstractClassSubViewBuilder.java
AbstractionRule.java
storage
SubViewsException.java
SubViewsInterface.java
SubViewsLinkedlist.java
streaming
AbstractLiveDataConsumer.java
DensityDependantLiveDataConsumer.java
InterpolatingLiveDataConsumer.java
LiveData.java
LiveDataConsumerInterface.java
LiveDataPoint.java
LiveDataSourceInterface.java
LiveDataStreamer.java
RawLiveDataConsumer.java
SegmentCovering.java
util
BoundContactMap.java
CommandLineUtils.java
DecimalFormatter.java
ExponentialMovingAverage.java
IdGenerator.java
InequalitySign.java
Info.java
MemoryUtil.java
NameDictionary.java
OutputUtils.java
PersistenceUtils.java
PlxTimer.java
PrimeNumbers.java
PrimeNumbers2.java
RunningMetric.java
SpeciesManager.java
StatsComputer.java
io
PlxLogger.java
StringBufferReader.java
StringBufferWriter.java
string
AgentInvariant.java
ConnectedComponentToSmilesString.java
ConnectedComponentToStringInterface.java
SiteComparator.java
test
acceptance
com
plectix
simulator
DirectoryTestsRunner.java
FileNameCollectionGenerator.java
Initializator.java
OperationModeCollectionGenerator.java
RunAllAcceptanceTests.java
SimulatorTestOptions.java
Test.java
TestRunner.java
consoleOutput
TestConsoleOutput.java
controller
SimulationServiceTest.java
Simulator1.java
cyclesdetection
InitData.java
InitTestDetectionOfCycles.java
TestDetectionOfCycles.java
events
TestEvents.java
experiments
ExperimentFailedException.java
ExperimentTestSuite.java
TestExponentielleExperiment.java
harness
RunTest.java
SimulatorTest.java
contactmap
InitData.java
InitTestContactMap.java
TestContactMap.java
injections
RunInjectionsTests.java
TestInjections.java
TestInjectionsAgentLinking.java
TestInjectionsCorrection.java
TestInjectionsLifts.java
TestInjectionsQuantity.java
localviews
InitData.java
InitTestLocalViews.java
InitTestLocalViewsCompareXML.java
LocalViewsParserXMLHandler.java
TestLocalViews.java
TestLocalViewsCompareXML.java
miscellaneous
TestInitTime.java
parser
ExceptionsTest.java
RunParserTests.java
TestParser.java
TestSimulationData.java
perturbations
RunPerturbationsTests.java
TestPerturbation.java
TestTimeCondition.java
triggering
TestPerturbationsTriggering.java
random
TalkingAlotSimulationOperation.java
TestSimulationIdentity.java
ruleapplication
InitTestAction.java
RunActionTest.java
rulecompression
InitData.java
InitTestRuleCompressions.java
TestQualitative.java
TestQualitativeCompressions.java
TestQuantitativeCompressions.java
rulestudio
TestRuleStudioOptionsSets.java
simulationclasses
probability
TestSelector.java
TestWeightedItemSelector.java
WeightedItemWithId.java
smoke
SmokeTest.java
SmokeTestMain.java
TestENG229.java
TestENG310.java
TestENG325.java
TestENG345.java
TestENG388.java
TestENG413.java
TestENG415.java
TestENG423.java
speciesenumeration
EnumOfSpeciesParserXMLHandler.java
InitData.java
InitTestEnumOfSpecies.java
InitTestEnumOfSpeciesCompareXML.java
TestEnumOfSpecies.java
TestEnumOfSpeciesCompareXML.java
util
Entry.java
Reachables.java
Set.java
stories
InitStoriesTests.java
RunTestStories.java
StoryCorrectness.java
TestPassportCorrectness.java
TestStoryCorrectness.java
graphs
TestIntro.java
TestStoryTrees.java
TestTransitivity.java
TestTree.java
strongcompression
TestStrong.java
weakcompression
BruteForseByWires.java
BruteForseWithGreyCode.java
BruteForseWithMarksGenerator.java
RunTestWeakCompression.java
RunTestWeakWithSeed.java
TestWeakCompressionBrute.java
TestWeakCompressionByWires.java
util
Correctness.java
GreyCode.java
Maps.java
MarksGenerator.java
StoragePrinter.java
subviews
InitData.java
InitTestSubView.java
InitTestSubViewsCompareXML.java
ParserFileTesterSubViews.java
SubViewsParserXMLHandler.java
TestSubViews.java
TestSubViewsCompareXML.java
util
Entry.java
Set.java
Tag.java
updates
RunUpdateTests.java
TestNegativeUpdate.java
TestPositiveUpdate.java
TestUpdate.java
util
BasicTestByModel.java
CComponentComparator.java
CollectionsComparator.java
Converter.java
CorrectionsDataCommand.java
CorrectionsDataParser.java
DefaultPropertiesForTest.java
Failer.java
FileComparator.java
FileDirComparator.java
GenerateXMLByModel.java
GreatFileUtility.java
Memory.java
MessageConstructor.java
NumberQueryParser.java
Piece.java
QuantityDataParser.java
ReadAndParserFile.java
RuleCCDataParser.java
RuleStructure.java
SetUtilities.java
SilentPrintStream.java
SimulatorRenewer.java
SubstanceConstructor.java
Timer.java
io
BackingUpPrintStream.java
SmokeKappaSystemWriter.java
XMLOutputOracle.java
xmlcompare
JavaXMLMaker.java
PathFinder.java
SimplxBatFileCreator.java
TestJavaXMLCompare.java
xmlmap
Agent.java
Bond.java
Connection.java
InitTestContactMap.java
InitTestInfluenceMap.java
Node.java
RunTestXml.java
SAXHandler.java
Site.java
TestContactMap.java
TestInfluenceMap.java
TestRuleCompressionMap.java
TestXmlFile.java
rulecompression
Association.java
InitTestRuleCompression.java
RuleTag.java
SAXHandler.java
slow
com
plectix
simulator
RunAllSlowTests.java
smiles
FullereneCreator.java
FusedRingsCreator.java
PolyhedraCreator.java
RunSmilesTest.java
SmilesTest.java
unit
com
plectix
simulator
RunAllUnitTests.java
commandline
TestCommandLineHandling.java
TestCommandLineOptionsToBeSet.java
experiments
TestSimulationDataProcessor.java
injections
RunUnitInjectionTest.java
parser
TestParserSites.java
incomplete
TestIncompleteSubstance.java
regex
TestAgentFormatChecker.java
simulationdata
TestSimulationData.java
simulator
MockKappaSystemForRules.java
staticanalysis
LibraryOfRules.java
LibraryOfSpecies.java
ObservableMock.java
TestObservables.java
TestRule.java
graphs
EdgeTest.java
GraphsTest.java
VertexTest.java
influencemap
TestInfluenceMap.java
localviews
LibraryOfLocalViews.java
rulecompression
TestQualitativeCompression.java
TestQuantitativeCompression.java
TestRootedRule.java
TestRootedRulesGroup.java
TestRuleMaster.java
TestRuleUtils.java
TestsRuleCompressions.java
stories
storage
TestRelinker.java
package com.plectix.simulator; public interface Test { }