org.primordion.cellontro.app
Class AppCellAutop

java.lang.Object
  org.primordion.xholon.base.Xholon
      org.primordion.xholon.app.Application
          org.primordion.cellontro.app.AppCellAutop

All Implemented Interfaces:

IApplication, IXholon

public class AppCellAutop

extends Application

Cell Model with Autopoiesis.

This is a variation of the Cell Model in which the cell bilayer contains lipids. These lipids are created within the Cytosol. Because they are hydrophobic, the water in the cytosol tends to push them towards the cell bilayer, which gradually incorporates them. The activity of the cell bilayer is causally dependent on the quantity of lipids it contains.

For more information, see: Webb, K., & White, T. (2004). Combining Analysis and Synthesis in a Model of a Biological Cell. SAC '04, March 14-17, 2004, Nicosia, Cyprus.

Since:

0.1 (Created on Oct 20, 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

AppCellAutop()
Constructor.

Method Summary

void	about() Display brief information about Xholon and 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, initialize, 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

AppCellAutop

public AppCellAutop()

Constructor.

Method Detail

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.