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