org.primordion.xholon.mech.petrinet

Class Transition

java.lang.Object

org.primordion.xholon.base.Xholon

org.primordion.xholon.base.XholonWithPorts

org.primordion.xholon.mech.petrinet.Transition

All Implemented Interfaces:

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

public class Transition
extends XholonWithPorts
implements IKinetics

Transition

Since:

0.8.1 (Created on July 20, 2012)

See Also:

Xholon Project website, Serialized Form

Field Summary

Fields inherited from class org.primordion.xholon.base.XholonWithPorts

port

Fields inherited from interface org.primordion.xholon.mech.petrinet.IKinetics

K_UNSPECIFIED, KINETICS_BASIC_PTNET, KINETICS_CUSTOM, KINETICS_DEFAULT, KINETICS_DIFFUSION, KINETICS_GRID, KINETICS_LOGIC_AND, KINETICS_LOGIC_NOT, KINETICS_LOGIC_OR, KINETICS_MASS_ACTION, KINETICS_MAX_VALID, KINETICS_MAXIMAL_PARALLELISM, KINETICS_MICHAELIS_MENTEN, KINETICS_MIN_VALID, KINETICS_NULL, KINETICS_UNSPECIFIED, KM_UNSPECIFIED, LOGIC_FALSE, LOGIC_TRUE, P_UNSPECIFIED, VMAX_UNSPECIFIED

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
Transition()

Method Summary

Methods

Modifier and Type	Method and Description
void	actNr() This method is intended to be called by QueueTransitions.
boolean	couldUseDiffusion() Could this transition use diffusion kinetics? // TODO should the in/out arcs have the same weight ?
void	decVal(double dec) Decrement an internal double value by a specified amount.
java.util.List	getAllPorts() Get a list of all ports exiting from this xholon.
double	getCount()
double	getDt()
IXholon	getInputArcs()
double	getK() Get reaction rate/constant k.
int	getKineticsType() Get kinetics type.
double	getKm() Get Michaelis-Menten Km.
IXholon	getOutputArcs()
double	getP() Get probability p.
java.lang.String	getRoleName() Get name of the role played by this Xholon within a specific context.
java.lang.String	getSymbol()
int	getVal_int() Get the value of a "int" maintained by this xholon instance.
double	getVal() Get the value of a "double" maintained by this xholon instance.
double	getVmax() Get Michaelis-Menten Vmax.
void	incVal(double inc) Increment an internal double value by a specified amount.
static boolean	isShouldWriteSequenceDiagram()
void	postConfigure() Perform some action, typically once at start up; MAY be overridden.
int	setAttributeVal(java.lang.String attrName, java.lang.String attrVal) Set the value of an attribute, given it's name.
void	setCount(double count)
void	setDt(double dt) This should only be called by the Petri net (QueueTransitions).
void	setInputArcs(IXholon inputArcs)
void	setK(double k) Set reaction rate/constant k.
void	setKineticsType(int kineticsType) Set kinetics type.
void	setKm(double km) Set Michaelis-Menten Km.
void	setOutputArcs(IXholon outputArcs)
void	setP(double p) Set probability p.
void	setRoleName(java.lang.String roleName) Set name of the role played by this Xholon within a specific context.
static void	setShouldWriteSequenceDiagram(boolean shouldWriteSequenceDiagram)
void	setSymbol(java.lang.String symbol)
void	setVal(double val) Set the value of a "double" maintained by this xholon instance.
void	setVal(int val) Set the value of a "int" maintained by this xholon instance.
void	setVal(java.lang.String val) Set the value of a "String" maintained by this xholon instance.
void	setVmax(double vmax) Set Michaelis-Menten Vmax.
void	toXmlAttributes(IXholon2Xml xholon2xml, IXmlWriter xmlWriter) Write a set of attributes formatted as XML.

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

configure, configurePorts, getPort, getPort, initialize, isActiveObject, isBound, isContainer, isPassiveObject, setPort, setPort, setPorts, terminate, toString

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

act, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, compareTo, configure, consoleLog, decVal, depth, doAction, equals, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, getActionList, 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, getPreviousSibling, getRootNode, getSelfAndSiblings, getSelfAndSiblingsIndex, getService, getSiblings, getSystemMsgQ, getUid, getUri, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXholon2Xml, getXhType, getXml2Xholon, getXPath, handleNodeSelection, handleNodeSelection, hasAncestor, hasAnnotation, hasAttributeXh, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, hasSiblingNodes, height, incVal, initStatics, inOrderPrint, insertAfter, insertAfter, insertAfter, insertBefore, insertBefore, insertBefore, insertFirstChild, isAttributeHandler, isExternal, isInternal, isLeaf, isRootNode, isUniqueSibling, isUniqueSiblingRoleName, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, 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, setAttributeXh, setFirstChild, setId, setName, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, 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, setXhc, showAnnotation, swapNode, toXml, toXmlAttribute, toXmlText, treeSize, visit

Methods inherited from class java.lang.Object

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

Constructor Detail

Transition

public Transition()

Method Detail

setRoleName

public void setRoleName(java.lang.String roleName)

Description copied from interface: IXholon

Set name of the role played by this Xholon within a specific context.

Specified by:

setRoleName in interface IXholon

Overrides:

setRoleName in class Xholon

Parameters:

roleName - An optional name that identifies the role.

getRoleName

public java.lang.String getRoleName()

Description copied from interface: IXholon

Get name of the role played by this Xholon within a specific context.

Specified by:

getRoleName in interface IXholon

Overrides:

getRoleName in class Xholon

Returns:

A name that identifies the role, or null.

setVal

public void setVal(double val)

Description copied from interface: IXholon

Set the value of a "double" maintained by this xholon instance.

Specified by:

setVal in interface IXholon

Overrides:

setVal in class Xholon

Parameters:

val - The new value.

setVal

public void setVal(int val)

Description copied from interface: IXholon

Set the value of a "int" maintained by this xholon instance.

Specified by:

setVal in interface IXholon

Overrides:

setVal in class Xholon

setVal

public void setVal(java.lang.String val)

Description copied from interface: IXholon

Set the value of a "String" maintained by this xholon instance.

Specified by:

setVal in interface IXholon

Overrides:

setVal in class Xholon

getVal

public double getVal()

Description copied from interface: IXholon

Get the value of a "double" maintained by this xholon instance. If a class that implements this interface does not maintain such a value, it should return 0.0 This method can be used in place of getVal_double()

Specified by:

getVal in interface IXholon

Overrides:

getVal in class Xholon

Returns:

A double value.

getVal_int

public int getVal_int()

Description copied from interface: IXholon

Get the value of a "int" maintained by this xholon instance.

Specified by:

getVal_int in interface IXholon

Overrides:

getVal_int in class Xholon

incVal

public void incVal(double inc)

Description copied from interface: IXholon

Increment an internal double value by a specified amount. This is a convenience method.

Specified by:

incVal in interface IXholon

Overrides:

incVal in class Xholon

Parameters:

inc - Increment amount.

decVal

public void decVal(double dec)

Description copied from interface: IXholon

Decrement an internal double value by a specified amount. This is a convenience method.

Specified by:

decVal in interface IXholon

Overrides:

decVal in class Xholon

Parameters:

dec - Decrement amount.

postConfigure

public void postConfigure()

Description copied from interface: IXholon

Perform some action, typically once at start up; MAY be overridden. Recursive; application should call this only for root.

Specified by:

postConfigure in interface IXholon

Overrides:

postConfigure in class XholonWithPorts

getAllPorts

public java.util.List getAllPorts()

Description copied from interface: IXholon

Get a list of all ports exiting from this xholon.

Specified by:

getAllPorts in interface IXholon

Overrides:

getAllPorts in class Xholon

Returns:

A list of the IXholon instances referenced by ports. The list will contain duplicate entries if more than one port references the same IXholon instance. The IXholons firstChild, nextSibling, and parentNode nodes are NOT included in the list. If there are no ports, then an empty List is returned.

actNr

public void actNr()

This method is intended to be called by QueueTransitions.

Specified by:

actNr in interface IXholon

Overrides:

actNr in class Xholon

See Also:

Xholon.actNr()

couldUseDiffusion

public boolean couldUseDiffusion()

Could this transition use diffusion kinetics? // TODO should the in/out arcs have the same weight ?

Returns:

true if

- there are the same number of inputPlace and outputPlace, and

- all inputPlace and outputPlace are the same type

else false

setAttributeVal

public int setAttributeVal(java.lang.String attrName,
                  java.lang.String attrVal)

Description copied from interface: IXholon

Set the value of an attribute, given it's name. The default implementation of this should handle any variable with the name "val". Concrete subclasses may handle any other variables, which would be required if using JavaMicro reflection.

Specified by:

setAttributeVal in interface IXholon

Overrides:

setAttributeVal in class Xholon

Parameters:

attrName - The name of an attribute.

attrVal - The intended value of the attribute.

Returns:

The Java class type of the input val. Returns JAVACLASS_UNKNOWN if the attribute cannot be set.

toXmlAttributes

public void toXmlAttributes(IXholon2Xml xholon2xml,
                   IXmlWriter xmlWriter)

Description copied from interface: IXholon

Write a set of attributes formatted as XML.

Specified by:

toXmlAttributes in interface IXholon

Overrides:

toXmlAttributes in class Xholon

xmlWriter - The XML writer.

getInputArcs

public IXholon getInputArcs()

setInputArcs

public void setInputArcs(IXholon inputArcs)

getOutputArcs

public IXholon getOutputArcs()

setOutputArcs

public void setOutputArcs(IXholon outputArcs)

getP

public double getP()

Get probability p.

Returns:

setP

public void setP(double p)

Set probability p.

Parameters:

p -

getK

public double getK()

Get reaction rate/constant k.

Returns:

setK

public void setK(double k)

Set reaction rate/constant k.

Parameters:

k -

getCount

public double getCount()

setCount

public void setCount(double count)

isShouldWriteSequenceDiagram

public static boolean isShouldWriteSequenceDiagram()

setShouldWriteSequenceDiagram

public static void setShouldWriteSequenceDiagram(boolean shouldWriteSequenceDiagram)

getKineticsType

public int getKineticsType()

Description copied from interface: IKinetics

Get kinetics type.

Specified by:

getKineticsType in interface IKinetics

Returns:

setKineticsType

public void setKineticsType(int kineticsType)

Description copied from interface: IKinetics

Set kinetics type.

Specified by:

setKineticsType in interface IKinetics

getVmax

public double getVmax()

Get Michaelis-Menten Vmax.

Returns:

setVmax

public void setVmax(double vmax)

Set Michaelis-Menten Vmax.

Parameters:

vmax -

getKm

public double getKm()

Get Michaelis-Menten Km.

Returns:

setKm

public void setKm(double km)

Set Michaelis-Menten Km.

Parameters:

km -

getDt

public double getDt()

setDt

public void setDt(double dt)

This should only be called by the Petri net (QueueTransitions).

Parameters:

dt -

getSymbol

public java.lang.String getSymbol()

setSymbol

public void setSymbol(java.lang.String symbol)