org.sbml.jsbml.ext.comp
public class ModelDefinition extends Model
Model
class of an SBML document, or can be called externally
with references stored in ExternalModelDefinitions.| Modifier and Type | Field and Description |
|---|---|
private static long |
serialVersionUID
Generated serial version identifier.
|
ignoredExtensions, ignoredXMLElementslistOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS| Constructor and Description |
|---|
ModelDefinition() |
ModelDefinition(int level,
int version) |
ModelDefinition(Model model) |
ModelDefinition(java.lang.String id) |
ModelDefinition(java.lang.String id,
int level,
int version) |
| Modifier and Type | Method and Description |
|---|---|
ModelDefinition |
clone()
Creates a deep copy of this object, i.e., a new
SBase with the same properties
like this one. |
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, findUnitDefinition, findVariable, getAllowsChildren, getAreaUnits, getAreaUnitsInstance, getChildAt, getChildCount, getCompartment, getCompartment, getCompartmentCount, getCompartmentType, getCompartmentType, getCompartmentTypeCount, getConstraint, getConstraintCount, getConversionFactor, getConversionFactorInstance, getDelayCount, getEvent, getEvent, getEventAssignmentCount, getEventCount, getExtentUnits, getExtentUnitsInstance, getFunctionDefinition, getFunctionDefinition, getFunctionDefinitionCount, getInitialAssignment, getInitialAssignment, 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, getReaction, getReaction, getReactionCount, getRule, getRule, getRuleCount, getSBaseCount, getSBaseWithDerivedUnitCount, getSpecies, getSpecies, getSpeciesCount, getSpeciesReferenceCount, getSpeciesType, getSpeciesType, getSpeciesTypeCount, getSpeciesWithBoundaryConditionCount, getStoichiometryMathCount, getSubstanceUnits, getSubstanceUnitsInstance, getSymbolCount, getTimeUnits, getTimeUnitsInstance, getTriggerCount, getUnitCount, getUnitDefinition, getUnitDefinition, getUnitDefinitionCount, getVariableCount, getVolumeUnits, getVolumeUnitsInstance, hashCode, hasUnit, initDefaults, initDefaults, isIdMandatory, 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, writeXMLAttributesgetId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetNameaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, 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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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, userObjectKeySetprivate static final long serialVersionUID
public ModelDefinition()
public ModelDefinition(int level,
int version)
public ModelDefinition(Model model)
public ModelDefinition(java.lang.String id)
public ModelDefinition(java.lang.String id,
int level,
int version)
public ModelDefinition clone()
SBaseSBase with the same properties
like this one.public void init()