org.primordion.cellontro.app
Class AppLife

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

public class AppLife
extends Application

Life.

This simulation extends the basic cell model. Many instances of the cell are embedded within multiple subsystems of an organism, which in turn is embedded within an ecosystem. This demonstrates a deeply nested hierarchical structure, and the ability to reuse structures.

Which version of the model actually executes depends on which configuration file is selected.

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
AppLife()
          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)
          This is the main entry point for the Xholon application.
 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

AppLife

public AppLife()
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)
This is the main entry point for the Xholon application.

Parameters:
args - Any arguments that your application may need.

arg[0] could be any of the following:

./config/cellontro/Cell/Cell_xhn.xml

./config/cellontro/Life3d/Life3d_SingleCells_xhn.xml

./config/cellontro/Cell/Cell_BioSystems_Jul03_xhn.xml

./config/cellontro/Cell/Cell_BioSystems_Oct03_xhn.xml

./config/cellontro/Cell/Cell_BioSystems_Plus01_xhn.xml

./config/cellontro/Life/Life_xhn.xml