org.primordion.ef.petrinet

Class Xholon2Sbgn4PetriNets

java.lang.Object

org.primordion.xholon.base.Xholon

org.primordion.ef.AbstractXholon2ExternalFormat

org.primordion.ef.petrinet.Xholon2Sbgn4PetriNets

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, IXholon, XholonMarker, IXholon2ExternalFormat

public class Xholon2Sbgn4PetriNets
extends AbstractXholon2ExternalFormat
implements IXholon2ExternalFormat

Export a Xholon Petri net model in Systems Biology Graphical Notation (SBGN) XML format. The resulting file can be viewed and edited by SBGN-ED, a Visualization and Analysis of Networks containing Experimental Data (VANTED) add-on.

Since:

0.8.1 (Created on August 5, 2012)

See Also:

Xholon Project website, SBGN website, SBGN-ED website, VANTED website, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	SBGN_PLACE_CLONE_LIST For use with BlackboardService.

Fields inherited from interface org.primordion.xholon.service.ef.IXholon2ExternalFormat

STRING_WRITER

Fields inherited from interface org.primordion.xholon.base.IXholon

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 Summary

Constructors

Constructor and Description
Xholon2Sbgn4PetriNets() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getModelName()
java.lang.String	getNameTemplate()
java.lang.String	getOutFileName()
java.lang.String	getOutPath()
IXholon	getRoot()
boolean	initialize(java.lang.String mmFileName, java.lang.String modelName, IXholon root) Initialize.
void	setModelName(java.lang.String modelName)
void	setNameTemplate(java.lang.String nameTemplate)
void	setOutFileName(java.lang.String outFileName)
void	setOutPath(java.lang.String outPath)
void	setRoot(IXholon root)
void	writeAll() Create a list of Places, and optionally a list of Transitions.

Methods inherited from class org.primordion.ef.AbstractXholon2ExternalFormat

adjustOptions, adjustOptionsNative, canAdjustOptions, getEfParamsAsJsonString, setEfParamsFromJsonString

Methods inherited from class org.primordion.xholon.base.Xholon

act, actNr, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, compareTo, configure, configure, consoleLog, decVal, decVal, depth, doAction, equals, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, getActionList, getAllPorts, getAnnotation, getApp, getAttributeNodeXh, getAttributeXh, getChildNodes, getClassNode, getClassNode, getFactory, getFirstChild, getFirstSibling, getId, getInteraction, getInteractionsEnabled, getIQueueImplName, getLastChild, getLastSibling, getLogger, getMsgQ, getName, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumLevels, getNumSiblings, getParentNode, getPort, getPort, getPreviousSibling, getRoleName, getRootNode, getSelfAndSiblings, getSelfAndSiblingsIndex, getService, getSiblings, getSystemMsgQ, getUid, getUri, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getVal, getXhc, getXhcId, getXhcName, 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, setRoleName, 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, toString, toXml, toXmlAttribute, toXmlAttributes, toXmlText, treeSize, visit

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.primordion.xholon.service.ef.IXholon2ExternalFormat

adjustOptions, canAdjustOptions, getEfParamsAsJsonString, setEfParamsFromJsonString

Field Detail

SBGN_PLACE_CLONE_LIST

public static final java.lang.String SBGN_PLACE_CLONE_LIST

For use with BlackboardService.

See Also:

Constant Field Values

Constructor Detail

Xholon2Sbgn4PetriNets

public Xholon2Sbgn4PetriNets()

Constructor.

Method Detail

initialize

public boolean initialize(java.lang.String mmFileName,
                 java.lang.String modelName,
                 IXholon root)

Description copied from interface: IXholon2ExternalFormat

Initialize.

Specified by:

initialize in interface IXholon2ExternalFormat

Parameters:

mmFileName - Name of the output file.

modelName - Name of the model.

root - Root of the hierarchy to write out (composite or inheritance structure).

Returns:

Whether or not the initialization succeeded.

writeAll

public void writeAll()

Create a list of Places, and optionally a list of Transitions.

Specified by:

writeAll in interface IXholon2ExternalFormat

getOutFileName

public java.lang.String getOutFileName()

setOutFileName

public void setOutFileName(java.lang.String outFileName)

getModelName

public java.lang.String getModelName()

setModelName

public void setModelName(java.lang.String modelName)

getRoot

public IXholon getRoot()

setRoot

public void setRoot(IXholon root)

getNameTemplate

public java.lang.String getNameTemplate()

setNameTemplate

public void setNameTemplate(java.lang.String nameTemplate)

getOutPath

public java.lang.String getOutPath()

setOutPath

public void setOutPath(java.lang.String outPath)