public class AnalysisMemComp extends XholonWithPorts
Correspondences between PN and Membrane Computing terminology:
Petri net Membrane Computing ------------- ------------------ membrane place object transition rule marking weight rate
To add an Analysis node to a running Petri net app, paste the following as last child of PetriNet node:
<AnalysisMemComp/>
port
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 and Description |
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AnalysisMemComp() |
Modifier and Type | Method and Description |
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void |
doAction(java.lang.String action)
Do a specific action that this xholon knows how to do.
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java.lang.String[] |
getActionList()
Get a list of actions that this xholon can do.
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java.util.List<java.lang.Object> |
getConcentrations(java.lang.Class<?> clazz)
Get list/vector of current concentrations of species in the CRN
= list/vector of current markings of places in the PN.
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java.util.Set<java.lang.String> |
getMembranes()
Get set of membranes.
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java.util.List<java.lang.String> |
getObjects()
Get list of species in the CRN = list of places in the PN.
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java.util.List<java.lang.String> |
getRules()
Get list of reactions in the CRN = list of transitions in the PN.
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void |
setActionList(java.lang.String[] actionList)
Set the list of actions that this xholon can do.
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configure, configurePorts, getPort, getPort, initialize, isActiveObject, isBound, isContainer, isPassiveObject, postConfigure, setPort, setPort, setPorts, terminate, toString
act, actNr, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, compareTo, configure, consoleLog, decVal, decVal, depth, equals, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, 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, 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, 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, setAnnotation, setApp, setAttributeNodeXh, setAttributeVal, setAttributeXh, setFirstChild, setId, setName, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, 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, toXml, toXmlAttribute, toXmlAttributes, toXmlText, treeSize, visit
public java.lang.String[] getActionList()
IXholon
getActionList
in interface IXholon
getActionList
in class Xholon
public void setActionList(java.lang.String[] actionList)
IXholon
setActionList
in interface IXholon
setActionList
in class Xholon
actionList
- A list of actions, or null.public void doAction(java.lang.String action)
IXholon
public java.util.List<java.lang.Object> getConcentrations(java.lang.Class<?> clazz)
"(instantaneous) values of the molar concentrations of the species" "we abbreviate this list of numbers by the 'composition vector' c(t)" example of a vector: c_A(t),c_B(t),c_C(t),c_D(t),c_E(t) (Feinberg 1-2)
This returns values only for "the set of species which are actually present in the reactor" (Feinberg 2-4). If there are no instances of a species, then that species does not appear in the list returned.
clazz
- The desired class of the items in the returned list.public java.util.Set<java.lang.String> getMembranes()
public java.util.List<java.lang.String> getObjects()
public java.util.List<java.lang.String> getRules()