org.primordion.cellontro.app
Class AppCell

java.lang.Object
  extended byorg.primordion.xholon.base.Xholon
      extended byorg.primordion.xholon.app.Application
          extended byorg.primordion.cellontro.app.AppCell
All Implemented Interfaces:
IApplication, IXholon

public class AppCell
extends Application

Cell Model.

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, 283302.

Webb, K., & White, T. (2004). Cell Modeling using Agent-based Formalisms. AAMAS 2004, New York.

Since:
0.1 (Created on Jun 8, 2005)
Author:
Ken Webb

Nested Class Summary
 
Nested classes inherited from class org.primordion.xholon.app.Application
Application.GridViewerDetails
 
Field Summary
 
Fields inherited from class org.primordion.xholon.base.Xholon
DEFAULT_LEVEL, interaction, interactionsEnabled
 
Fields inherited from interface org.primordion.xholon.base.IXholon
DEFAULT_SIZE_MSG_Q, NINCLUDE_PSC, NINCLUDE_PSx, NINCLUDE_PxC, NINCLUDE_Pxx, NINCLUDE_xSC, NINCLUDE_xSx, NINCLUDE_xxC, NINCLUDE_xxx
 
Constructor Summary
AppCell()
          Constructor.
 
Method Summary
 void about()
          Display brief information about Xholon and the application.
 void initialize(java.lang.String configFileName)
          Initialize the application.
static void main(java.lang.String[] args)
          main
 void wrapup()
          Wrapup any unfinished business in the application.
 
Methods inherited from class org.primordion.xholon.app.Application
appMain, getApplication, getAppM, getAppRoot, getClass, getClassDetailsFile, getCompositeStructureHierarchyFile, getControllerState, getDataPlotterParams, getErrorM, getGraphicalNetworkViewerClassName, getGraphicalNetworkViewerParams, getGraphicalTreeViewerParams, getGridPanelClassName, getHistogramPlotterParams, getInfoM, getInformationFile, getInheritanceHierarchyFile, getInteractionParams, getJavaActivityClassName, getJavaClassName, getJavaXhClassClassName, getJavaXhClassName, getMaxActivities, getMaxPorts, getMaxProcessLoops, getMaxStateMachineEntities, getMaxXholonClasses, getMaxXholons, getModelName, getRandomNumberSeed, getRoot, getSaveSnapshots, getSizeMessageQueue, getSnapshotParams, getTimeStepInterval, getTreeNodeFactoryDynamic, getUseDataPlotter, getUseGnuplot_Hist, getUseGnuplot, getUseGraphicalNetworkViewer, getUseGraphicalTreeViewer, getUseGridViewer, getUseHistogramPlotter, getUseInteractions, getUseJFreeChart_Hist, getUseJFreeChart, getUseTextTree, getUseVrml, getVrmlParams, getVrmlWriterClassName, getXhymAgent, getXincludePath, information, initControl, initGui, initViewers, invokeDataPlotter, invokeGraphicalNetworkViewer, invokeGraphicalNetworkViewer, invokeGraphicalTreeViewer, invokeGraphicalTreeViewer, invokeHistogramPlotter, invokeInteraction, process, readConfigFromFileXml, resetViewers, saveSnapshot, setApplication, setAppM, setClassDetailsFile, setCompositeStructureHierarchyFile, setControllerState, setDataPlotterParams, setErrorM, setGraphicalNetworkViewerClassName, setGraphicalNetworkViewerParams, setGraphicalTreeViewerParams, setGridPanelClassName, setGridViewerParams, setHistogramPlotterParams, setInfoM, setInformationFile, setInheritanceHierarchyFile, setInteractionParams, setJavaActivityClassName, setJavaClassName, setJavaXhClassClassName, setJavaXhClassName, setMaxActivities, setMaxPorts, setMaxProcessLoops, setMaxStateMachineEntities, setMaxXholonClasses, setMaxXholons, setModelName, setParam, setRandomNumberSeed, setSaveSnapshots, setSizeMessageQueue, setSnapshotParams, setTimeStepInterval, setTreeNodeFactoryDynamic, setUseDataPlotter, setUseGraphicalNetworkViewer, setUseGraphicalTreeViewer, setUseGridViewer, setUseHistogramPlotter, setUseInteractions, setUseTextTree, setUseVrml, setVrmlParams, setVrmlWriterClassName, setXhymAgent, setXincludePath
 
Methods inherited from class org.primordion.xholon.base.Xholon
act, appendChild, appendChild, appendChild, cleanup, configure, configure, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextId, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPort, getPreviousSibling, getRoleName, getRootNode, getSiblings, getSizeMessageQ, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getVal, getXhc, getXhcId, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initialize, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isActiveObject, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preAct, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, reconfigure, remove, removeChild, resetNextId, sendMessage, sendMessage, sendMessage, setAttributeVal, setFactory, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPorts, setRoleName, setSizeMessageQ, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, terminate, toString, treeSize, writeXml
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.primordion.xholon.base.IXholon
act, appendChild, appendChild, appendChild, cleanup, configure, configure, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPort, getPreviousSibling, getRoleName, getRootNode, 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, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initialize, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isActiveObject, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preAct, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, reconfigure, remove, removeChild, sendMessage, sendMessage, sendMessage, setAttributeVal, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPorts, setRoleName, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, terminate, treeSize, writeXml
 

Constructor Detail

AppCell

public AppCell()
Constructor.

Method Detail

initialize

public void initialize(java.lang.String configFileName)
Description copied from interface: IApplication
Initialize the application.

Specified by:
initialize in interface IApplication
Overrides:
initialize in class Application

wrapup

public void wrapup()
Description copied from interface: IApplication
Wrapup any unfinished business in the application.

Specified by:
wrapup in interface IApplication
Overrides:
wrapup in class Application

about

public void about()
Description copied from interface: IApplication
Display brief information about Xholon and the application.

Specified by:
about in interface IApplication
Overrides:
about in class Application

main

public static void main(java.lang.String[] args)
main

Parameters:
args - One optional command line argument.