org.primordion.cellontro.app
Class AppSbml

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

public class AppSbml
extends Application

SBML Application. Use this class if you're developing an application that executes a model read from a Systems Biology Markup Language (SBML) file. SBML is used to exchange models between different software packages.

Since:
0.2 (Created on December 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
AppSbml()
          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 setConcreteClass(java.lang.String concreteClass)
          Set what the concrete XH class will be.
 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

AppSbml

public AppSbml()
Constructor.

Method Detail

setConcreteClass

public void setConcreteClass(java.lang.String concreteClass)
Set what the concrete XH class will be.

Parameters:
concreteClass - The name of the concrete Xh class, including the complete dotted package name.

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.