public class AppCell extends Application
This simulation of a biological cell includes enzymes that continuously transform substrate chemicals into products, and lipid bilayers and transport proteins that move chemicals between compartments.
For more information on this model, see:
Webb, K., & White, T. (2005). UML as a cell and biochemistry modeling language. BioSystems, 80, 283�302.
Webb, K., & White, T. (2004). Cell Modeling using Agent-based Formalisms. AAMAS 2004, New York.
DEFAULT_SIZE_MSG_Q, DEFAULT_SIZE_SYSTEM_MSG_Q, GETNAME_DEFAULT, GETNAME_LOCALPART_ID, GETNAME_NOROLENAME, GETNAME_ROLENAME_OR_CLASSNAME, GETNAME_ROLENAMESEP_, GETNAME_SIZE_TEMPLATE, NINCLUDE_PSC, NINCLUDE_PSx, NINCLUDE_PxC, NINCLUDE_Pxx, NINCLUDE_xSC, NINCLUDE_xSx, NINCLUDE_xxC, NINCLUDE_xxx, XHOLON_ID_DEFAULT, XHOLON_ID_NULL
Constructor and Description |
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AppCell()
Constructor.
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Modifier and Type | Method and Description |
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void |
about()
Display brief information about Xholon and the application.
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void |
initialize(java.lang.String configFileName)
Initialize the application.
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static void |
main(java.lang.String[] args)
main
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void |
wrapup()
Only invoke a viewer on wrapup if:
- the unconditional INVOKE_VIEWERS_ON_WRAPUP is set to true, or
- the viewer is non-graphical and writes to a file or stdout
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appMain, cacheIXholonAttributes, clearConsole, createChart, createGridViewer, createInteractions, findAppSpecificClass, findAppSpecificConstantValue, findGwtClientBundle, getAbout, getApp, getApplication, getApplication, getApplication, getApplicationNames, getApplicationOther, getApplicationOther, getApplications, getAppM, getAppRoot, getAppSpecificAttribute, getAppSpecificAttributes, getAppSpecificObjectVal, getAppSpecificObjectValNames, getAppSpecificObjectVals, getAttributePostConfigAction, getChartViewer, getClassDetailsFile, getClassNode, getClassNode, getCompositeStructureHierarchyFile, getConfigAppName, getConfigFileName, getConfigPathName, getControllerState, getControllerStateName, getControlRoot, getDataPlotterParams, getDebugM, getDefaultMechanism, getErrorM, getFactory, getGraphicalNetworkViewerClassName, getGraphicalNetworkViewerParams, getGraphicalTreeViewerParams, getGridPanelClassName, getGridViewer, getHistogramPlotterParams, getHistogramViewer, getHostPageBaseURL, getImageFile, getInfoM, getInformationFile, getInherHier, getInheritanceHierarchyFile, getInitialControllerState, getInteraction, getInteractionParams, getIQueueImplName, getJavaActivityClassName, getJavaClassName, getJavaXhClassClassName, getJavaXhClassName, getJdbcParams, getJpaParams, getLastInsertedApplication, getMaxActivities, getMaxPorts, getMaxProcessLoops, getMaxStateMachineEntities, getMaxXholonClasses, getMaxXholons, getMechRoot, getModelName, getMsgQ, getName, getNetworkViewerJung, getNextId, getNextXholonClassId, getNumApplications, getParam, getRandomNumberSeed, getRoleName, getRoot, getSaveSnapshots, getScriptParams, getService, getSizeMessageQueue, getSnapshotParams, getSrvRoot, getSystemMsgQ, getTimeStep, getTimeStepInterval, getTreeNodeFactoryDynamic, getTreeViewerJung, getUri, getUseC3, getUseD3_Hist, getUseDataPlotter, getUseGnuplot_Hist, getUseGnuplot, getUseGoogle, getUseGoogle2_Hist, getUseGoogle2, getUseGraphicalNetworkViewer, getUseGraphicalTreeViewer, getUseGridViewer, getUseHistogramPlotter, getUseInteractions, getUseJdbc, getUseJFreeChart_Hist, getUseJFreeChart, getUseJpa, getUseNVD3, getUseTextTree, getUseVrml, getUseXholon2Gui, getView, getVrmlParams, getVrmlWriterClassName, getWorkbookBundle, getWorkbookFileName, getWorkbookId, getXhcName, getXhcRoot, getXholon2GuiClassName, getXholon2GuiParams, getXhymAgent, getXincludePath, image, information, initControl, initGui, initViewers, invokeDataPlotter, invokeGraphicalNetworkViewer, invokeGraphicalNetworkViewer, invokeGraphicalTreeViewer, invokeGraphicalTreeViewer, invokeHistogramPlotter, invokeInteraction, invokeXholon2Gui, isAllowConfigSrv, isApplet, isAppSpecificAttribute, isAppSpecificClassFindable, isShouldStepView, isUseAppOut, isUseGwt, loadWorkbook, makeAppSpecificNode, makeDefaultConsoles, makeSvgClient, process, processOnce, rcConfig, rcConfig, readConfigFromFileXml, readParameters, resetNextId, resetNextXholonClassId, resetStaticVariables, resetViewers, restoreIXholonAttributes, runApp, saveSnapshot, setAllowConfigSrv, setApplet, setApplication, setAppM, setAppRoot, setAppSpecificAttribute, setAppSpecificObjectArrayVal, setAppSpecificObjectVal, setAttributePostConfigAction, setClassDetailsFile, setCompositeStructureHierarchyFile, setConfigFileName, setControllerState, setControlRoot, setDataPlotterParams, setDebugM, setDefaultMechanism, setErrorM, setGraphicalNetworkViewerClassName, setGraphicalNetworkViewerParams, setGraphicalTreeViewerParams, setGridPanelClassName, setGridViewerParams, setHistogramPlotterParams, setHostPageBaseURL, setHtmlTitles, setImageFile, setInfoM, setInformationFile, setInheritanceHierarchyFile, setInitialControllerState, setInteractionParams, setIQueueImplName, setJavaActivityClassName, setJavaClassName, setJavaXhClassClassName, setJavaXhClassName, setJdbcParams, setJpaParams, setMaxActivities, setMaxPorts, setMaxProcessLoops, setMaxStateMachineEntities, setMaxXholonClasses, setMaxXholons, setMechRoot, setModelName, setNextId, setNextXholonClassId, setParam, setRandomNumberSeed, setRoleName, setRoot, setSaveSnapshots, setScriptParams, setShouldStepView, setSizeMessageQueue, setSnapshotParams, setSrvRoot, setTimeStep, setTimeStepInterval, setTreeNodeFactoryDynamic, setUseAppOut, setUseDataPlotter, setUseGraphicalNetworkViewer, setUseGraphicalTreeViewer, setUseGridViewer, setUseGwt, setUseHistogramPlotter, setUseInteractions, setUseTextTree, setUseVrml, setUseXholon2Gui, setView, setVrmlParams, setVrmlWriterClassName, setWorkbookBundle, setWorkbookFileName, setWorkbookId, setXhcRoot, setXholon2GuiClassName, setXholon2GuiParams, setXhymAgent, setXincludePath, toString, toXmlAttribute, toXmlAttributes, wbCallback
act, actNr, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, compareTo, configure, configure, consoleLog, decVal, decVal, depth, doAction, equals, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, getActionList, getAllPorts, getAnnotation, getAttributeNodeXh, getAttributeXh, getChildNodes, getFirstChild, getFirstSibling, getId, getInteractionsEnabled, getLastChild, getLastSibling, getLogger, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumLevels, getNumSiblings, getParentNode, getPort, getPort, getPreviousSibling, getRootNode, getSelfAndSiblings, getSelfAndSiblingsIndex, getSiblings, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getVal, getXhc, getXhcId, getXholon2Xml, getXhType, getXml2Xholon, getXPath, handleNodeSelection, handleNodeSelection, hasAncestor, hasAnnotation, hasAttributeXh, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, hasSiblingNodes, height, incVal, incVal, initialize, initStatics, inOrderPrint, insertAfter, insertAfter, insertAfter, insertBefore, insertBefore, insertBefore, insertFirstChild, isActiveObject, isAttributeHandler, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, isUniqueSibling, isUniqueSiblingRoleName, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preAct, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, processReceivedSyncMessage, processSystemMessageQ, reconfigure, registerMessageForwardee, remove, removeAttributeNodeXh, removeAttributeXh, removeChild, replaceNode, searchForReferencingNodes, searchForReferencingNodesRecurse, sendMessage, sendMessage, sendMessage, sendSyncMessage, sendSyncMessage, sendSyncMessage, sendSystemMessage, sendSystemMessage, setActionList, setAnnotation, setApp, setAttributeNodeXh, setAttributeVal, setAttributeXh, setFirstChild, setId, setName, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPort, setPort, setPorts, setUid, setUri, setVal_boolean, setVal_byte, setVal_char, setVal_double, setVal_float, setVal_int, setVal_long, setVal_Object, setVal_short, setVal_String, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setXhc, showAnnotation, swapNode, terminate, toXml, toXmlText, treeSize, visit
getClass, hashCode, notify, notifyAll, wait, wait, wait
act, actNr, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, configure, configure, consoleLog, decVal, decVal, depth, doAction, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, getActionList, getAllPorts, getAnnotation, getAttributeNodeXh, getAttributeXh, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumLevels, getNumSiblings, getParentNode, getPort, getPort, getPreviousSibling, getRootNode, getSelfAndSiblings, getSelfAndSiblingsIndex, getSiblings, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getVal, getXhc, getXhcId, getXholon2Xml, getXhType, getXml2Xholon, handleNodeSelection, handleNodeSelection, hasAncestor, hasAnnotation, hasAttributeXh, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, hasSiblingNodes, height, incVal, incVal, initialize, initStatics, inOrderPrint, insertAfter, insertAfter, insertAfter, insertBefore, insertBefore, insertBefore, insertFirstChild, isActiveObject, isAttributeHandler, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, isUniqueSibling, isUniqueSiblingRoleName, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preAct, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, processReceivedSyncMessage, processSystemMessageQ, reconfigure, registerMessageForwardee, remove, removeAttributeNodeXh, removeAttributeXh, removeChild, replaceNode, searchForReferencingNodes, sendMessage, sendMessage, sendMessage, sendSyncMessage, sendSyncMessage, sendSyncMessage, sendSystemMessage, sendSystemMessage, setActionList, setAnnotation, setApp, setAttributeNodeXh, setAttributeVal, setAttributeXh, setFirstChild, setId, setName, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPort, setPort, setPorts, setUid, setUri, setVal_boolean, setVal_byte, setVal_char, setVal_double, setVal_float, setVal_int, setVal_long, setVal_Object, setVal_short, setVal_String, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setXhc, showAnnotation, swapNode, terminate, toXml, toXmlText, treeSize, visit
public void initialize(java.lang.String configFileName) throws XholonConfigurationException
IApplication
initialize
in interface IApplication
initialize
in class Application
configFileName
- Name of the configuration file.XholonConfigurationException
public void wrapup()
Application
wrapup
in interface IApplication
wrapup
in class Application
IApplication.wrapup()
public void about()
IApplication
about
in interface IApplication
about
in class Application
public static void main(java.lang.String[] args)
args
- One optional command line argument.