public class ModelDefinition extends Model
Models.
However, modelDefinitions are non-instantiated models
that can be called by submodels within the Model
class of an SBML document, or can be called externally
with references stored in ExternalModelDefinitions.
ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageNamelistOfListeners, parent, resourceBundle| Constructor and Description |
|---|
ModelDefinition()
Creates a new
ModelDefinition instance. |
ModelDefinition(int level,
int version)
Creates a new
ModelDefinition instance. |
ModelDefinition(Model model)
Creates a new
ModelDefinition instance cloned from the given core Model instance. |
ModelDefinition(String id)
Creates a new
ModelDefinition instance. |
ModelDefinition(String id,
int level,
int version)
Creates a new
ModelDefinition instance. |
| Modifier and Type | Method and Description |
|---|---|
ModelDefinition |
clone() |
void |
init() |
accept, addCompartment, addCompartmentType, addConstraint, addEvent, addFunctionDefinition, addInitialAssignment, addParameter, addReaction, addRule, addSpecies, addSpeciesType, addUnitDefinition, addUnitDefinitionOrReturnIdenticalUnit, containsCompartment, containsFunctionDefinition, containsParameter, containsQuantity, containsReaction, containsSpecies, containsUniqueNamedSBase, containsUnitDefinition, createAlgebraicRule, createAssignmentRule, createCompartment, createCompartment, createCompartmentType, createCompartmentType, createConstraint, createDelay, createEvent, createEvent, createEventAssignment, createFunctionDefinition, createFunctionDefinition, createInitialAssignment, createKineticLaw, createKineticLawParameter, createKineticParameter, createModifier, createModifier, createParameter, createParameter, createProduct, createProduct, createRateRule, createReactant, createReactant, createReaction, createReaction, createSpecies, createSpecies, createSpecies, createSpecies, createSpeciesType, createSpeciesType, createTrigger, createUnit, createUnit, createUnitDefinition, createUnitDefinition, equals, findCallableSBase, findIdentical, findLocalParameters, findModifierSpeciesReference, findNamedSBase, findNamedSBaseWithDerivedUnit, findQuantity, findQuantityWithUnit, findReactionsForLocalParameter, findSimpleSpeciesReference, findSpeciesReference, findSymbol, findUniqueNamedSBase, findUniqueSBase, findUnitDefinition, findVariable, getAllowsChildren, getAreaUnits, getAreaUnitsInstance, getAssignmentRuleByVariable, getChildAt, getChildCount, getCompartment, getCompartment, getCompartmentCount, getCompartmentType, getCompartmentType, getCompartmentTypeCount, getConstraint, getConstraintCount, getConversionFactor, getConversionFactorInstance, getDelayCount, getElementBySId, getEvent, getEvent, getEventAssignmentCount, getEventCount, getExtentUnits, getExtentUnitsInstance, getFunctionDefinition, getFunctionDefinition, getFunctionDefinitionCount, getInitialAssignment, getInitialAssignment, getInitialAssignmentById, getInitialAssignmentBySymbol, getInitialAssignmentCount, getKineticLawCount, getLengthUnits, getLengthUnitsInstance, getListOfCompartments, getListOfCompartmentTypes, getListOfConstraints, getListOfCount, getListOfEvents, getListOfFunctionDefinitions, getListOfInitialAssignments, getListOfParameters, getListOfPredefinedUnitDefinitions, getListOfReactions, getListOfRules, getListOfSpecies, getListOfSpeciesTypes, getListOfUnitDefinitions, getLocalParameterCount, getMathContainerCount, getModelHistory, getModifierSpeciesReferenceCount, getModifierSpeciesReferences, getNamedSBaseCount, getNamedSBaseWithDerivedUnitCount, getNumCompartments, getNumCompartmentTypes, getNumConstraints, getNumDelays, getNumEventAssignments, getNumEvents, getNumFunctionDefinitions, getNumInitialAssignments, getNumKineticLaws, getNumListsOf, getNumLocalParameters, getNumMathContainers, getNumModifierSpeciesReferences, getNumNamedSBases, getNumNamedSBasesWithDerivedUnit, getNumParameters, getNumQuantities, getNumQuantitiesWithUnit, getNumReactions, getNumRules, getNumSBases, getNumSBasesWithDerivedUnit, getNumSpecies, getNumSpeciesReferences, getNumSpeciesTypes, getNumSpeciesWithBoundaryCondition, getNumStoichiometryMath, getNumSymbols, getNumTriggers, getNumUnitDefinitions, getNumUnits, getNumVariables, getParameter, getParameter, getParameterCount, getPredefinedUnitDefinition, getQuantityCount, getQuantityWithUnitCount, getRateRuleByVariable, getReaction, getReaction, getReactionCount, getRule, getRule, getRuleById, getRuleByVariable, getRuleCount, getSBaseById, getSBaseCount, getSBaseWithDerivedUnitCount, getSpecies, getSpecies, getSpeciesCount, getSpeciesReferenceCount, getSpeciesType, getSpeciesType, getSpeciesTypeCount, getSpeciesWithBoundaryConditionCount, getStoichiometryMathCount, getSubstanceUnits, getSubstanceUnitsInstance, getSymbolCount, getTimeUnits, getTimeUnitsInstance, getTriggerCount, getUnitCount, getUnitDefinition, getUnitDefinition, getUnitDefinitionById, getUnitDefinitionCount, getVariableCount, getVolumeUnits, getVolumeUnitsInstance, hashCode, hasUnit, initDefaults, initDefaults, isIdMandatory, isListOfCompartmentsEmpty, isListOfCompartmentTypesEmpty, isListOfConstraintsEmpty, isListOfEventsEmpty, isListOfFunctionDefinitionsEmpty, isListOfInitialAssignmentsEmpty, isListOfParametersEmpty, isListOfReactionsEmpty, isListOfRulesEmpty, isListOfSpeciesEmpty, isListOfSpeciesTypesEmpty, isListOfUnitDefinitionEmpty, isSetAreaUnits, isSetAreaUnitsInstance, isSetConversionFactor, isSetConversionFactorInstance, isSetExtentUnits, isSetExtentUnitsInstance, isSetLengthUnits, isSetLengthUnitsInstance, isSetListOfCompartments, isSetListOfCompartmentTypes, isSetListOfConstraints, isSetListOfEvents, isSetListOfFunctionDefinitions, isSetListOfInitialAssignments, isSetListOfParameters, isSetListOfReactions, isSetListOfRules, isSetListOfSpecies, isSetListOfSpeciesTypes, isSetListOfUnitDefinitions, isSetModelHistory, isSetSubstanceUnits, isSetSubstanceUnitsInstance, isSetTimeUnits, isSetTimeUnitsInstance, isSetVolumeUnits, isSetVolumeUnitsInstance, readAttribute, register, remove, removeCompartment, removeCompartment, removeCompartmentType, removeCompartmentType, removeConstraint, removeEvent, removeEvent, removeFunctionDefinition, removeFunctionDefinition, removeInitialAssignment, removeParameter, removeParameter, removeParameter, removeReaction, removeReaction, removeReaction, removeRule, removeRule, removeRule, removeSpecies, removeSpecies, removeSpecies, removeSpeciesType, removeSpeciesType, removeUnitDefinition, removeUnitDefinition, removeUnitDefinition, setAreaUnits, setAreaUnits, setAreaUnits, setConversionFactor, setConversionFactor, setExtentUnits, setExtentUnits, setExtentUnits, setLengthUnits, setLengthUnits, setLengthUnits, setListOfCompartments, setListOfCompartmentTypes, setListOfConstraints, setListOfEvents, setListOfFunctionDefinitions, setListOfInitialAssignments, setListOfParameters, setListOfReactions, setListOfRules, setListOfSpecies, setListOfSpeciesTypes, setListOfUnitDefinitions, setModelHistory, setSubstanceUnits, setSubstanceUnits, setSubstanceUnits, setTimeUnits, setTimeUnits, setTimeUnits, setVolumeUnits, setVolumeUnits, setVolumeUnits, unregister, unsetAreaUnits, unsetConversionFactor, unsetExtentUnits, unsetLengthUnits, unsetListOfCompartments, unsetListOfCompartmentTypes, unsetListOfConstraints, unsetListOfEvents, unsetListOfFunctionDefinitions, unsetListOfInitialAssignments, unsetListOfParameters, unsetListOfReactions, unsetListOfRules, unsetListOfSpecies, unsetListOfSpeciesTypes, unsetListOfUnitDefinitions, unsetModelHistory, unsetSubstanceUnits, unsetTimeUnits, unsetVolumeUnits, writeXMLAttributesisValidIdaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySetfinalize, getClass, notify, notifyAll, wait, wait, waitgetId, getName, isSetId, isSetName, setId, setName, unsetId, unsetNameaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySetpublic ModelDefinition()
ModelDefinition instance.public ModelDefinition(int level,
int version)
ModelDefinition instance.level - the SBML levelversion - the SBML versionpublic ModelDefinition(Model model)
ModelDefinition instance cloned from the given core Model instance.model - the core Model to clonepublic ModelDefinition(String id)
ModelDefinition instance.id - the idpublic ModelDefinition(String id, int level, int version)
ModelDefinition instance.id - the idlevel - the SBML levelversion - the SBML versionpublic ModelDefinition clone()
public void init()
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