A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

C

CCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
CLASSID_NOT_FOUND - Static variable in interface org.primordion.xholon.base.IInheritanceHierarchy
 
CNPT_OUTGOING1 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING10 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING2 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING3 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING4 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING5 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING6 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING7 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING8 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_OUTGOING9 - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CNPT_TARGET - Static variable in class org.primordion.xholon.base.StateMachineEntity
 
CO2CE - Static variable in interface org.primordion.cellontro.app.sbml.CeYeastGly
 
CO2CE - Static variable in interface org.primordion.cellontro.app.sbml.CeYeastGlyPritchardKel
 
COMMANDID_HATCH - Static variable in class org.primordion.user.app.WolfSheepGrass.WolfSheep
 
COMMANDID_NONE - Static variable in interface org.primordion.xholon.base.IPatch
 
COMMANDID_NONE - Static variable in interface org.primordion.xholon.base.ITurtle
 
COMMENT_CHAR - Static variable in interface org.primordion.xholon.base.IContainmentHierarchy
 
CS_INITIALIZED - Static variable in class org.primordion.xholon.base.Control
 
CS_LOADED - Static variable in class org.primordion.xholon.base.Control
 
CS_NO_MODEL_LOADED - Static variable in class org.primordion.xholon.base.Control
 
CS_PAUSED - Static variable in class org.primordion.xholon.base.Control
 
CS_RESETTING - Static variable in class org.primordion.xholon.base.Control
 
CS_RUNNING - Static variable in class org.primordion.xholon.base.Control
 
CS_STEPPING - Static variable in class org.primordion.xholon.base.Control
 
CS_STOPPED - Static variable in class org.primordion.xholon.base.Control
 
C_dilutionCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
C_transport_backwardCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
C_transport_forwardCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
CaCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CallActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CallBehaviorActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CallButtonCE - Static variable in interface org.primordion.xholon.xmiapps.CeElevator
 
CallButtonCE - Static variable in interface org.primordion.xholon.xmiappsTc.CeElevator
 
CallOperationActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CapillaryCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CarCE - Static variable in interface org.primordion.dynsys.app.CeTrain
 
CarbonDioxideCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CarboxylGroupCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CartCE - Static variable in interface org.primordion.ealontro.app.CeCartCentering
 
CartCentering - class org.primordion.ealontro.ec.app.cartcentering.CartCentering.
 
CartCentering() - Constructor for class org.primordion.ealontro.ec.app.cartcentering.CartCentering
 
CartCenteringCE - Static variable in interface org.primordion.ealontro.app.CeCartCentering
 
CartCenteringSystemCE - Static variable in interface org.primordion.ealontro.app.CeCartCentering
 
Ce09SpatialGames - interface org.primordion.xholon.samples.Ce09SpatialGames.
 
Ce1dSimple - interface org.primordion.xholon.samples.Ce1dSimple.
 
CeAdapSysLab - interface org.primordion.ctrnn.app.CeAdapSysLab.
 
CeAntForaging - interface org.primordion.ealontro.app.CeAntForaging.
 
CeAntTrail - interface org.primordion.ealontro.app.CeAntTrail.
 
CeBehavior - interface org.primordion.xholon.common.mechanism.CeBehavior.
 
CeBraneCalc1 - interface org.primordion.memcomp.app.CeBraneCalc1.
 
CeBrenda - interface org.primordion.user.app.CeBrenda.
 
CeBrusselator - interface org.primordion.cellontro.app.sbml.CeBrusselator.
 
CeCartCentering - interface org.primordion.ealontro.app.CeCartCentering.
 
CeCellModel - interface org.primordion.cellontro.app.sbml.CeCellModel.
 
CeCircadianClock - interface org.primordion.cellontro.app.sbml.CeCircadianClock.
 
CeCombo - interface org.primordion.xholon.samples.CeCombo.
 
CeCoopPSys00ex0 - interface org.primordion.memcomp.app.CeCoopPSys00ex0.
 
CeCoopSys02ex32_1 - interface org.primordion.memcomp.app.CeCoopSys02ex32_1.
 
CeCoopSys02ex343_1 - interface org.primordion.memcomp.app.CeCoopSys02ex343_1.
 
CeCoopSys02ex343_2 - interface org.primordion.memcomp.app.CeCoopSys02ex343_2.
 
CeDataPlotter - interface org.primordion.xholon.common.viewer.CeDataPlotter.
 
CeDimericMWCstiff - interface org.primordion.cellontro.app.sbml.CeDimericMWCstiff.
 
CeElevator - interface org.primordion.xholon.xmiapps.CeElevator.
 
CeElevator - interface org.primordion.xholon.xmiappsTc.CeElevator.
 
CeEpo2 - interface org.primordion.user.app.Epo2.CeEpo2.
 
CeFibonacci - interface org.primordion.dynsys.app.CeFibonacci.
 
CeFsm06ex1 - interface org.primordion.memcomp.app.CeFsm06ex1.
 
CeFsm06ex1_Fsm - interface org.primordion.memcomp.app.CeFsm06ex1_Fsm.
 
CeFsm06ex1_Fsm - interface org.primordion.xholon.xmiapps.CeFsm06ex1_Fsm.
 
CeGameOfLife - interface org.primordion.xholon.samples.CeGameOfLife.
 
CeGlyHunThouBilayer - interface org.primordion.cellontro.app.sbml.CeGlyHunThouBilayer.
 
CeGlyHunThouInhibit - interface org.primordion.cellontro.app.sbml.CeGlyHunThouInhibit.
 
CeGlyMillion - interface org.primordion.cellontro.app.sbml.CeGlyMillion.
 
CeGlyTenThou - interface org.primordion.cellontro.app.sbml.CeGlyTenThou.
 
CeGlycolysis - interface org.primordion.cellontro.app.sbml.CeGlycolysis.
 
CeGlycolysisTESTXML - class org.primordion.cellontro.app.sbml.CeGlycolysisTESTXML.
 
CeGlycolysisTESTXML() - Constructor for class org.primordion.cellontro.app.sbml.CeGlycolysisTESTXML
 
CeGlycolysisTESTXML2 - interface org.primordion.cellontro.app.sbml.CeGlycolysisTESTXML2.
 
CeGlycolysis_Test - interface org.primordion.cellontro.app.sbml.CeGlycolysis_Test.
 
CeGraphicalNetworkViewer - interface org.primordion.xholon.common.viewer.CeGraphicalNetworkViewer.
 
CeGraphicalTreeViewer - interface org.primordion.xholon.common.viewer.CeGraphicalTreeViewer.
 
CeGravity1 - interface org.primordion.dynsys.app.CeGravity1.
 
CeGridViewer - interface org.primordion.xholon.common.viewer.CeGridViewer.
 
CeHelloWorld - interface org.primordion.xholon.tutorials.CeHelloWorld.
 
CeHelloWorldTutorial - interface org.primordion.xholon.xmiapps.CeHelloWorldTutorial.
 
CeHelloWorldTutorial - interface org.primordion.xholon.xmiappsArgoUML.CeHelloWorldTutorial.
 
CeHelloWorldTutorial - interface org.primordion.xholon.xmiappsTc.CeHelloWorldTutorial.
 
CeHelloWorldTutorialSysML - interface org.primordion.xholon.xmiappsTcSysML.CeHelloWorldTutorialSysML.
 
CeHelloWorldTutorial_multiWorld - interface org.primordion.xholon.xmiapps.CeHelloWorldTutorial_multiWorld.
 
CeHelloWorldTutorial_multiWorld - interface org.primordion.xholon.xmiappsTc.CeHelloWorldTutorial_multiWorld.
 
CeHelloWorldTutorial_plus - interface org.primordion.xholon.xmiapps.CeHelloWorldTutorial_plus.
 
CeHelloWorldTutorial_universe - interface org.primordion.xholon.xmiapps.CeHelloWorldTutorial_universe.
 
CeHex - interface org.primordion.xholon.samples.CeHex.
 
CeHistogramViewer - interface org.primordion.xholon.common.viewer.CeHistogramViewer.
 
CeInteractions - interface org.primordion.xholon.common.viewer.CeInteractions.
 
CeInterest - interface org.primordion.dynsys.app.CeInterest.
 
CeLife - interface org.primordion.cellontro.app.CeLife.
 
CePort - interface org.primordion.xholon.common.mechanism.CePort.
Port.
CeProvidedRequiredTest - interface org.primordion.xholon.xmiapps.CeProvidedRequiredTest.
 
CeRcs1 - interface org.primordion.xholon.tutorials.rcs.CeRcs1.
 
CeRcs2 - interface org.primordion.xholon.tutorials.rcs.CeRcs2.
 
CeRcs_GP_FSM - interface org.primordion.xholon.xmiapps.CeRcs_GP_FSM.
 
CeRcs_GP_FSM_Grid - interface org.primordion.xholon.xmiapps.CeRcs_GP_FSM_Grid.
 
CeRcs_GP_MM - interface org.primordion.xholon.xmiapps.CeRcs_GP_MM.
 
CeRcs_GP_MM_NoSymbols - interface org.primordion.xholon.xmiapps.CeRcs_GP_MM_NoSymbols.
 
CeSnapshot - interface org.primordion.xholon.common.viewer.CeSnapshot.
 
CeStateMachineEntity - interface org.primordion.xholon.common.mechanism.CeStateMachineEntity.
 
CeStateMachineOnly - interface org.primordion.xholon.xmiappsTc.CeStateMachineOnly.
 
CeStopWatch - interface org.primordion.xholon.xmiapps.CeStopWatch.
 
CeStopWatch_Xhym - interface org.primordion.xholon.xmiapps.CeStopWatch_Xhym.
 
CeStupidModel1 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel1.
 
CeStupidModel10 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel10.
 
CeStupidModel11 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel11.
 
CeStupidModel12 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel12.
 
CeStupidModel13 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel13.
 
CeStupidModel14 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel14.
 
CeStupidModel15 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel15.
 
CeStupidModel16 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel16.
 
CeStupidModel16nl - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel16nl.
 
CeStupidModel2 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel2.
 
CeStupidModel3 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel3.
 
CeStupidModel4 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel4.
 
CeStupidModel5 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel5.
 
CeStupidModel5tg - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel5tg.
 
CeStupidModel6 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel6.
 
CeStupidModel7 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel7.
 
CeStupidModel8 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel8.
 
CeStupidModel9 - interface org.primordion.xholon.tutorials.StupidModel.CeStupidModel9.
 
CeSymAnti02ex41 - interface org.primordion.memcomp.app.CeSymAnti02ex41.
 
CeTestFsm - interface org.primordion.xholon.samples.CeTestFsm.
 
CeTestFsm - interface org.primordion.xholon.xmiapps.CeTestFsm.
 
CeTestFsm - interface org.primordion.xholon.xmiappsTc.CeTestFsm.
 
CeTestFsmForkJoin - interface org.primordion.xholon.xmiapps.CeTestFsmForkJoin.
 
CeTestFsmHistory - interface org.primordion.xholon.xmiapps.CeTestFsmHistory.
 
CeTestFsmJunction - interface org.primordion.xholon.xmiapps.CeTestFsmJunction.
 
CeTestFsmKW - interface org.primordion.xholon.samples.CeTestFsmKW.
 
CeTestFsmOrthogonal - interface org.primordion.xholon.xmiapps.CeTestFsmOrthogonal.
 
CeTextTree - interface org.primordion.xholon.common.viewer.CeTextTree.
 
CeTrain - interface org.primordion.dynsys.app.CeTrain.
 
CeTurtleExample1 - interface org.primordion.user.app.CeTurtleExample1.
 
CeTutorial4 - interface org.primordion.ealontro.app.CeTutorial4.
 
CeUMLActionEntity - interface org.primordion.xholon.common.mechanism.CeUMLActionEntity.
 
CeUMLActivityEntity - interface org.primordion.xholon.common.mechanism.CeUMLActivityEntity.
 
CeVrml - interface org.primordion.xholon.common.viewer.CeVrml.
 
CeWatch - interface org.primordion.xholon.xmiapps.CeWatch.
 
CeWolfSheepGrass - interface org.primordion.user.app.WolfSheepGrass.CeWolfSheepGrass.
 
CeXhym - interface org.primordion.xholon.common.viewer.CeXhym.
 
CeYeastGly - interface org.primordion.cellontro.app.sbml.CeYeastGly.
 
CeYeastGlyPritchardKel - interface org.primordion.cellontro.app.sbml.CeYeastGlyPritchardKel.
 
Ce__XholonTemplate__ - interface org.primordion.xholon.xmiapps.Ce__XholonTemplate__.
 
CelestialBodyCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CeliacGanglionCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CellBilayerCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CellBilayerCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCellModel
 
CellBilayerCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlyHunThouBilayer
 
CellLocations - class org.primordion.cellontro.io.vrml.CellLocations.
VRML CellLocations.
CellLocations() - Constructor for class org.primordion.cellontro.io.vrml.CellLocations
Constructor.
CellMembraneCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CellMembraneCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCellModel
 
CellMembraneCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlyHunThouBilayer
 
CellWallCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
Cellontro2Sbml - class org.primordion.cellontro.io.sbml.Cellontro2Sbml.
Cellontro2Sbml transforms Xholon runtime models into SBML Level 2 files.
Cellontro2Sbml() - Constructor for class org.primordion.cellontro.io.sbml.Cellontro2Sbml
Constructor.
Cellontro2Sbml(String, String, IXholon) - Constructor for class org.primordion.cellontro.io.sbml.Cellontro2Sbml
Constructor.
CellularAutomaton1DCE - Static variable in interface org.primordion.xholon.samples.Ce1dSimple
 
CellularSolutionCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CellularSpaceCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CentralBufferNodeCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActivityEntity
 
CentralNervousSystemCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CentralNeuronCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CerebellumCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CerebralCortexCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CerebrumCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChartViewerGnuplot - class org.primordion.xholon.io.ChartViewerGnuplot.
Captures data, and creates a script to display the data in a gnuplot chart.
ChartViewerGnuplot(IXholon, int, String, String, int) - Constructor for class org.primordion.xholon.io.ChartViewerGnuplot
constructor
ChartViewerJFreeChart - class org.primordion.xholon.io.ChartViewerJFreeChart.
Captures data, and creates a chart using JFreeChart.
ChartViewerJFreeChart() - Constructor for class org.primordion.xholon.io.ChartViewerJFreeChart
default constructor
ChartViewerJFreeChart(IXholon, int) - Constructor for class org.primordion.xholon.io.ChartViewerJFreeChart
constructor
ChloroplastBilayerCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChloroplastCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChloroplastDualMembraneCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChloroplastFluidCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChloroplastIntermembraneSpaceCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChloroplastMembraneCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CholesterolCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CholineCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChromosomeCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ChronographControlCE - Static variable in interface org.primordion.xholon.xmiapps.CeWatch
 
CirculatorySystemCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CisternaeCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CisternalSpaceCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CitrateCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CitrateCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCellModel
 
CitrateSynthaseCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CitrateSynthaseCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCellModel
 
ClassACE - Static variable in interface org.primordion.xholon.xmiapps.CeProvidedRequiredTest
 
ClassBCE - Static variable in interface org.primordion.xholon.xmiapps.CeProvidedRequiredTest
 
ClassCCE - Static variable in interface org.primordion.xholon.xmiapps.CeProvidedRequiredTest
 
ClearStructuralFeatureActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
ClearVariableActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CmpCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CnCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
Cn_dilutionCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
ColonCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ComboCE - Static variable in interface org.primordion.xholon.samples.CeCombo
 
Complete - Static variable in class org.primordion.user.app.Epo2.PurchaseOrder
 
CompletionDetectorCE - Static variable in interface org.primordion.memcomp.app.CeCoopPSys00ex0
 
CompletionDetectorCE - Static variable in interface org.primordion.memcomp.app.CeCoopSys02ex32_1
 
CompletionDetectorCE - Static variable in interface org.primordion.memcomp.app.CeCoopSys02ex343_1
 
CompletionDetectorCE - Static variable in interface org.primordion.memcomp.app.CeCoopSys02ex343_2
 
CompletionDetectorCE - Static variable in interface org.primordion.memcomp.app.CeFsm06ex1
 
CompletionDetectorCE - Static variable in interface org.primordion.memcomp.app.CeSymAnti02ex41
 
ConditionalNodeCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
ConeCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ConeOuterSegmentCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ConfigurationAgentCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
ConnectionCE - Static variable in interface org.primordion.ctrnn.app.CeAdapSysLab
 
ConnectionPointReferenceCE - Static variable in interface org.primordion.xholon.common.mechanism.CeStateMachineEntity
 
ContainmentData - class org.primordion.xholon.base.ContainmentData.
ContainmentData is used at configuration time as a temporary holding place for data read in from a CompositeStructureHierarchy.xml file.
ContainmentData() - Constructor for class org.primordion.xholon.base.ContainmentData
 
ContainmentHierarchy - class org.primordion.xholon.base.ContainmentHierarchy.
A ContainmentHierarchy represents a hierarchy (tree) of Xholon nodes contained within other Xholon nodes.
ContainmentHierarchy(int) - Constructor for class org.primordion.xholon.base.ContainmentHierarchy
Constructor.
Control - class org.primordion.xholon.base.Control.
Control for a Xholon application.
Control() - Constructor for class org.primordion.xholon.base.Control
 
ControlFlowCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActivityEntity
 
ControlNodeCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActivityEntity
 
CouplerCE - Static variable in interface org.primordion.dynsys.app.CeTrain
 
CreateClassEnum - class org.primordion.xholon.util.CreateClassEnum.
Creates a Java class enumeration file from an InheritanceHierarchy file.
CreateClassEnum() - Constructor for class org.primordion.xholon.util.CreateClassEnum
 
CreateLinkActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CreateLinkObjectActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CreateObjectActionCE - Static variable in interface org.primordion.xholon.common.mechanism.CeUMLActionEntity
 
CreatureCE - Static variable in interface org.primordion.xholon.samples.CeCombo
 
CreatureCE - Static variable in interface org.primordion.xholon.samples.CeHex
 
CtfCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CtrnnCE - Static variable in interface org.primordion.ctrnn.app.CeAdapSysLab
 
CtrnnEntityCE - Static variable in interface org.primordion.ctrnn.app.CeAdapSysLab
 
Customer - class org.primordion.user.app.Epo2.Customer.
Extended Purchase Order example.
Customer() - Constructor for class org.primordion.user.app.Epo2.Customer
 
CustomerCE - Static variable in interface org.primordion.user.app.Epo2.CeEpo2
 
CwasCCE - Static variable in interface org.primordion.xholon.samples.Ce09SpatialGames
 
CwasDCE - Static variable in interface org.primordion.xholon.samples.Ce09SpatialGames
 
CysCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CytoSkeletonCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CytoplasmCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CytoplasmCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCellModel
 
CytoplasmLocations - class org.primordion.cellontro.io.vrml.CytoplasmLocations.
VRML CytoplasmLocations.
CytoplasmLocations() - Constructor for class org.primordion.cellontro.io.vrml.CytoplasmLocations
Constructor.
CytosineCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.CeLife
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCellModel
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlyHunThouBilayer
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlyHunThouInhibit
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlyMillion
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlyTenThou
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlycolysis
 
CytosolCE - Static variable in class org.primordion.cellontro.app.sbml.CeGlycolysisTESTXML
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlycolysisTESTXML2
 
CytosolCE - Static variable in interface org.primordion.cellontro.app.sbml.CeGlycolysis_Test
 
cCE - Static variable in interface org.primordion.memcomp.app.CeCoopPSys00ex0
 
cCE - Static variable in interface org.primordion.memcomp.app.CeCoopSys02ex32_1
 
cCE - Static variable in interface org.primordion.memcomp.app.CeCoopSys02ex343_2
 
cCE - Static variable in interface org.primordion.memcomp.app.CeFsm06ex1
 
cCE - Static variable in interface org.primordion.memcomp.app.CeSymAnti02ex41
 
ca() - Method in class org.primordion.xholon.base.PatchOwner
Clear patches, turtles, etc.
caRuleNumber - Static variable in class org.primordion.xholon.samples.Xh1dSimple
 
canExecute(File) - Static method in class org.primordion.xholon.util.Misc
Can this existing file be executed? A similar function has been added to Java 6.
canMove(double) - Method in interface org.primordion.xholon.base.ITurtle
Can this turtle legally move the specified distance, given its current heading?
canMove(double) - Method in class org.primordion.xholon.base.Turtle
 
cancel(XholonTimerTask) - Method in interface org.primordion.xholon.base.IXholonTime
Cancel a relative, repeat or absolute timeout.
cancel(XholonTimerTask) - Method in class org.primordion.xholon.base.XholonTime
 
cancelAll() - Method in interface org.primordion.xholon.base.IXholonTime
Cancel all timeouts.
cancelAll() - Method in class org.primordion.xholon.base.XholonTime
 
capture(double) - Method in class org.primordion.xholon.io.AbstractChartViewer
 
capture(int, double, double[]) - Method in class org.primordion.xholon.io.AbstractChartViewer
 
capture(double) - Method in class org.primordion.xholon.io.ChartViewerGnuplot
 
capture(int, double, double[]) - Method in class org.primordion.xholon.io.ChartViewerGnuplot
 
capture(double) - Method in class org.primordion.xholon.io.ChartViewerJFreeChart
 
capture(int, double, double[]) - Method in class org.primordion.xholon.io.ChartViewerJFreeChart
 
capture(double) - Method in interface org.primordion.xholon.io.IChartViewer
Capture data at each timestep.
capture(int, double, double[]) - Method in interface org.primordion.xholon.io.IChartViewer
Capture specified data at each time interval.
cd() - Method in class org.primordion.xholon.base.PatchOwner
Clear the drawing surface.
cellCE - Static variable in interface org.primordion.cellontro.app.sbml.CeCircadianClock
 
cellCE - Static variable in interface org.primordion.cellontro.app.sbml.CeDimericMWCstiff
 
chart() - Method in class org.primordion.xholon.io.AbstractChartViewer
 
chart(double[]) - Method in class org.primordion.xholon.io.AbstractHistogramViewer
 
chart() - Method in class org.primordion.xholon.io.AbstractHistogramViewer
 
chart() - Method in class org.primordion.xholon.io.ChartViewerGnuplot
 
chart(boolean) - Method in class org.primordion.xholon.io.ChartViewerGnuplot
 
chart() - Method in class org.primordion.xholon.io.ChartViewerJFreeChart
 
chart(boolean) - Method in class org.primordion.xholon.io.ChartViewerJFreeChart
 
chart(double[]) - Method in class org.primordion.xholon.io.HistogramViewerGnuplot
 
chart(double[]) - Method in class org.primordion.xholon.io.HistogramViewerJFreeChart
 
chart() - Method in interface org.primordion.xholon.io.IChartViewer
Produce a chart from the captured data.
chart(boolean) - Method in interface org.primordion.xholon.io.IChartViewer
Produce a chart from the captured data.
chart(double[]) - Method in interface org.primordion.xholon.io.IHistogramViewer
Produce a histogram chart.
chart() - Method in interface org.primordion.xholon.io.IHistogramViewer
Produce a histogram chart.
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.DropPheromone
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.IfCarryingFood
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.IfFoodHere
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.MoveRandom
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.MoveToAdjacentFoodElse
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.MoveToAdjacentPheromoneElse
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.MoveToNest
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.antforaging.PickUp
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.ABS
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.Add
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.Divide
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.GT
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.Multiply
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.Subtract
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.Velocity
 
checkConstraints(EvolutionState, int, GPIndividual, Parameter) - Method in class org.primordion.ealontro.ec.app.cartcentering.XPosition
 
chiSquare - Static variable in class org.primordion.xholon.util.Random
 
city - Variable in class org.primordion.user.app.Epo2.USAddress
 
cleanup() - Method in interface org.primordion.xholon.base.IXholon
Do any required cleanup work once the application has stopped executing.
cleanup() - Method in class org.primordion.xholon.base.Xholon
 
cleanup() - Method in class org.primordion.xholon.tutorials.XhHelloWorld_TestTime
 
clearAll() - Method in class org.primordion.xholon.base.PatchOwner
Clear patches, turtles, etc.
clearDrawing() - Method in class org.primordion.xholon.base.PatchOwner
Clear the drawing surface.
clearPatches() - Method in class org.primordion.xholon.base.PatchOwner
Set all patch variables to their initial values.
clearTurtles() - Method in class org.primordion.xholon.base.PatchOwner
Kill all turtles within the scope of this PatchOwner.
clone() - Method in class org.primordion.ealontro.ec.app.antforaging.AntForaging
 
clone() - Method in class org.primordion.ealontro.ec.app.cartcentering.CartCentering
 
clone(IXholon) - Method in class org.primordion.xholon.base.Activity
Clone this instance of Activity, with cloned children as well.
closeInputFile(Reader) - Static method in class org.primordion.xholon.util.Misc
Close input file.
closeOutputFile(Writer) - Static method in class org.primordion.xholon.util.Misc
Close output file.
color - Variable in class org.primordion.xholon.base.Turtle
 
comment - Variable in class org.primordion.user.app.Epo2.Item
 
comment - Variable in class org.primordion.user.app.Epo2.PurchaseOrder
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel10
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel11
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel12
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel13
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel14
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel15
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel16
 
compareTo(Object) - Method in class org.primordion.xholon.tutorials.StupidModel.BugStupidModel16nl
 
compartmentCE - Static variable in interface org.primordion.cellontro.app.sbml.CeBrusselator
 
compartmentCE - Static variable in interface org.primordion.cellontro.app.sbml.CeYeastGly
 
compartmentCE - Static variable in interface org.primordion.cellontro.app.sbml.CeYeastGlyPritchardKel
 
compile(String) - Method in interface org.primordion.xholon.io.IXmi2Xholon
Compile a generated Java class.
compile(String) - Method in class org.primordion.xholon.io.Xmi2Xholon
 
configInstructions - Variable in class org.primordion.xholon.base.ContainmentData
 
configure() - Method in class org.primordion.cellontro.app.XhAbstractSbml
 
configure() - Method in class org.primordion.cellontro.app.XhCell
 
configure() - Method in class org.primordion.cellontro.app.XhCellAutop
 
configure() - Method in class org.primordion.cellontro.app.XhLife
 
configure(String, int) - Method in class org.primordion.cellontro.app.XhLife
 
configure() - Method in class org.primordion.cellontro.base.BioXholonClass
 
configure() - Method in class org.primordion.ealontro.ec.app.antforaging.XhEcjAntForaging
 
configure(String, int) - Method in class org.primordion.xholon.base.AbstractGrid
 
configure() - Method in interface org.primordion.xholon.base.IXholon
Perform some action, typically once at start up; MAY be overridden.
configure(String, int) - Method in interface org.primordion.xholon.base.IXholon
Configure something based on a configure instruction.
configure() - Method in class org.primordion.xholon.base.StateMachineEntity
 
configure(String, int) - Method in class org.primordion.xholon.base.Xholon
 
configure() - Method in class org.primordion.xholon.base.Xholon
 
configure() - Method in class org.primordion.xholon.base.XholonClass
 
configure() - Method in class org.primordion.xholon.base.XholonWithPorts
 
configure() - Method in class org.primordion.xholon.samples.XhCollisions
 
configure() - Method in class org.primordion.xholon.samples.XhGeneric
 
convertHSVtoRGB(HSVType) - Method in class org.primordion.xholon.io.vrml.AbstractVrmlColor
Convert from HSV to RGB color model.
convertHSVtoRGB(HSVType) - Method in interface org.primordion.xholon.io.vrml.IVrmlColor
 
copyTo(GPData) - Method in class org.primordion.ealontro.ec.app.antforaging.BooleanData
 
copyTo(GPData) - Method in class org.primordion.ealontro.ec.app.cartcentering.DoubleData
 
countObservers() - Method in interface org.primordion.xholon.base.IObservable
Returns the number of observers of this Observable object.
countObservers() - Method in class org.primordion.xholon.base.ObservableStateMachineEntity
 
countObservers() - Method in class org.primordion.xholon.base.ObservableXholonWithPorts
 
countTokens() - Method in class org.primordion.xholon.util.StringTokenizer
Returns the number of tokens in the String.
countdown - Variable in class org.primordion.user.app.WolfSheepGrass.Grass
 
country - Variable in class org.primordion.user.app.Epo2.Address
 
cp() - Method in class org.primordion.xholon.base.PatchOwner
Set all patch variables to their initial values.
createAndShowGUI(String) - Static method in class org.primordion.xholon.io.XholonGui
Create the Xholon GUI and show it.
createBeta(double, double) - Static method in class org.primordion.xholon.util.Random
 
createBinomial(int, double) - Static method in class org.primordion.xholon.util.Random
 
createBreitWigner(double, double, double) - Static method in class org.primordion.xholon.util.Random
 
createBreitWignerMeanSquareState(double, double, double) - Static method in class org.primordion.xholon.util.Random
 
createChiSquare(double) - Static method in class org.primordion.xholon.util.Random
 
createClassEnumFile(String, String, String) - Method in class org.primordion.xholon.util.CreateClassEnum
Create class enum file.
createEmpirical(double[], int) - Static method in class org.primordion.xholon.util.Random
 
createEmpiricalWalker(double[], int) - Static method in class org.primordion.xholon.util.Random
 
createExponential(double) - Static method in class org.primordion.xholon.util.Random
 
createExponentialPower(double) - Static method in class org.primordion.xholon.util.Random
 
createGamma(double, double) - Static method in class org.primordion.xholon.util.Random
 
createGraph(IXholon, String, boolean) - Method in class org.primordion.xholon.io.AbstractNetworkViewerJung
 
createGraph(IXholon, String, boolean) - Method in interface org.primordion.xholon.io.IGraphicalNetworkViewer
Create a graph using a tree layout.
createGraph(IXholon, String, boolean) - Method in interface org.primordion.xholon.io.IGraphicalTreeViewer
Create a graph using a tree layout.
createGraph(IXholon, String, boolean) - Method in class org.primordion.xholon.io.TreeViewerJung
 
createHyperGeometric(int, int, int) - Static method in class org.primordion.xholon.util.Random
 
createHyperbolic(double, double) - Static method in class org.primordion.xholon.util.Random
 
createLogarithmic(double) - Static method in class org.primordion.xholon.util.Random
 
createNegativeBinomial(int, double) - Static method in class org.primordion.xholon.util.Random
 
createNormal(double, double) - Static method in class org.primordion.xholon.util.Random
 
createNotes() - Method in class org.primordion.xholon.io.ChartViewerGnuplot
Create a notes file that can be used by a human to capture observations as the simulation is running.
createPoisson(double) - Static method in class org.primordion.xholon.util.Random
 
createPoissonSlow(double) - Static method in class org.primordion.xholon.util.Random
 
createPort(IXholon, int, int[], String[], int[], String[], boolean) - Static method in class org.primordion.xholon.base.Port
Create an instance of the Port class.
createSequenceDiagram(String) - Method in interface org.primordion.xholon.base.IInteraction
Create a sequence diagram from the interaction.
createSequenceDiagram(String) - Method in class org.primordion.xholon.base.Interaction
 
createStructure(Vector, int, ITreeNodeFactory, IInheritanceHierarchy) - Method in interface org.primordion.xholon.base.IXholon
Recursively create this Xholon and its internal part structure, as nodes within the overall composite structure tree.
createStructure(Vector, int, ITreeNodeFactory, IInheritanceHierarchy) - Method in class org.primordion.xholon.base.Xholon
 
createStudentT(double) - Static method in class org.primordion.xholon.util.Random
 
createTurtles(int) - Method in class org.primordion.xholon.base.PatchOwner
Create a given number of new turtles in the center of the grid.
createTurtles(int, String) - Method in class org.primordion.xholon.base.PatchOwner
Create a given number of new turtles in the center of the grid, of a given breed.
createUniform(double, double) - Static method in class org.primordion.xholon.util.Random
 
createUniform() - Static method in class org.primordion.xholon.util.Random
 
createUserApp(String, String, int, int) - Method in class org.primordion.xholon.io.XholonAppWizardGui
 
createUserApp(String, String) - Method in class org.primordion.xholon.util.XholonAppWizard
Create a new user application.
createVonMises(double) - Static method in class org.primordion.xholon.util.Random
 
createXySeries(int, String[]) - Method in class org.primordion.xholon.io.ChartViewerGnuplot
 
createXySeries(int, String[]) - Method in class org.primordion.xholon.io.ChartViewerJFreeChart
 
createXySeries(int, String[]) - Method in interface org.primordion.xholon.io.IChartViewer
Create one or more xy data series.
createZeta(double, double) - Static method in class org.primordion.xholon.util.Random
 
crt(int) - Method in class org.primordion.xholon.base.PatchOwner
Create a given number of new turtles in the center of the grid.
crt(int, String) - Method in class org.primordion.xholon.base.PatchOwner
Create a given number of new turtles in the center of the grid, of a given breed.
ct() - Method in class org.primordion.xholon.base.PatchOwner
Kill all turtles within the scope of this PatchOwner.
customerID - Variable in class org.primordion.user.app.Epo2.Customer
 

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