Model

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase
  - - org.sbml.jsbml.AbstractNamedSBase
    - - org.sbml.jsbml.Model

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, IdManager, TreeNodeWithChangeSupport

Direct Known Subclasses:

ModelDefinition
```
public class Model
extends AbstractNamedSBase
implements UniqueNamedSBase, IdManager
```
JSBML implementation of SBML's Model construct.

In an SBML model definition, a single object of class Model serves as the overall container for the lists of the various model components. All of the lists are optional, but if a given list container is present within the model, the list must not be empty; that is, it must have length one or more.

Since:

0.8

Version:

$Rev: 1982 $

Author:

Andreas Dräger, Marine Dumousseau, Nicolas Rodriguez

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`private java.lang.String`	`areaUnitsID` Represents the 'areaUnits' XML attribute of a model element.
`private java.lang.String`	`conversionFactorID` Represents the 'conversionFactor' XML attribute of a model element.
`private static java.lang.String`	`COULD_NOT_CREATE_ELEMENT_MSG` Error message to indicate that an element could not be created.
`private java.lang.String`	`extentUnitsID` Represents the 'extentUnits' XML attribute of a model element.
`private java.lang.String`	`lengthUnitsID` Represents the 'lengthUnits' XML attribute of a model element.
`private ListOf<Compartment>`	`listOfCompartments` Represents the listOfCompartments subnode of a model element.
`private ListOf<CompartmentType>`	`listOfCompartmentTypes` Deprecated. only valid in SBML Level 2 for Versions 2 through 4.
`private ListOf<Constraint>`	`listOfConstraints` Represents the listOfConstraints subnode of a model element.
`private ListOf<Event>`	`listOfEvents` Represents the listOfEvents subnode of a model element.
`private ListOf<FunctionDefinition>`	`listOfFunctionDefinitions` Represents the listOfFunctionDefinitions subnode of a model element.
`private ListOf<InitialAssignment>`	`listOfInitialAssignments` Represents the listOfInitialAssignments subnode of a model element.
`private ListOf<Parameter>`	`listOfParameters` Represents the listOfParameters subnode of a model element.
`private java.util.List<UnitDefinition>`	`listOfPredefinedUnitDefinitions` Represents the list of predefined UnitDefinitions for a given SBML level and version.
`private ListOf<Reaction>`	`listOfReactions` Represents the listOfReactions subnode of a model element.
`private ListOf<Rule>`	`listOfRules` Represents the listOfRules subnode of a model element.
`private ListOf<Species>`	`listOfSpecies` Represents the listOfSpecies subnode of a model element.
`private ListOf<SpeciesType>`	`listOfSpeciesTypes` Deprecated. only valid in SBML Level 2 for Versions 2 through 4.
`private ListOf<UnitDefinition>`	`listOfUnitDefinitions` Represents the listOfUnitDefinitions sub-node of a model element.
`private static org.apache.log4j.Logger`	`logger` A `Logger` for this class.
`private java.util.Map<java.lang.String,java.util.List<Reaction>>`	`mapOfLocalParameters` A mapping between the identifiers of `LocalParameter`s and the containing `Reaction` objects.
`private java.util.Map<java.lang.String,UniqueNamedSBase>`	`mapOfUniqueNamedSBases` For internal computation: a mapping between their identifiers and the `UniqueNamedSBase`s in `Model`s themselves:
`private java.util.Map<java.lang.String,UnitDefinition>`	`mapOfUnitDefinitions` A mapping between their identifiers and associated `UnitDefinition` objects.
`private static long`	`serialVersionUID` Generated serial version identifier.
`private java.lang.String`	`substanceUnitsID` Represents the 'substanceUnits' XML attribute of a model element.
`private java.lang.String`	`timeUnitsID` Represents the 'timeUnits' XML attribute of a model element.
`private java.lang.String`	`volumeUnitsID` Represents the 'volumeUnits' XML attribute of a model element.

Fields inherited from class org.sbml.jsbml.AbstractSBase
ignoredExtensions, ignoredXMLElements, lv

Fields inherited from class org.sbml.jsbml.AbstractTreeNode
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors
Constructor and Description
`Model()` Creates a Model instance.
`Model(int level, int version)` Creates a Model instance.
`Model(Model model)` Creates a Model instance from a Model.
`Model(java.lang.String id)` Creates a Model instance from an id.
`Model(java.lang.String id, int level, int version)` Creates a Model instance from an id, level and version.

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`accept(SBase sbase)` Returns true if this `IdManager` can register or unregister the given `SBase`.
`boolean`	`addCompartment(Compartment compartment)` Adds a Compartment instance to the listOfCompartments of this Model.
`boolean`	`addCompartmentType(CompartmentType compartmentType)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`boolean`	`addConstraint(Constraint constraint)` Adds a `Constraint` instance to the listOfConstraints of this `Model`.
`boolean`	`addEvent(Event event)` Adds an `Event` instance to the listOfEvents of this Model.
`boolean`	`addFunctionDefinition(FunctionDefinition functionDefinition)` Adds a `FunctionDefinition` instance to the listOfFunctionDefinitions of this `Model`.
`boolean`	`addInitialAssignment(InitialAssignment initialAssignment)` Adds an InitialAssignment instance to the listOfInitialAssignments of this Model.
`boolean`	`addParameter(Parameter parameter)` Adds a Parameter instance to the listOfParameters of this Model.
`private void`	`addPredefinedUnits()` Adds all the possible unit kinds as `UnitDefinition`, so that the method `getUnitDefinition(String)` would be able to return a valid `UnitDefinition` even if one of these kinds is passed as parameter.
`boolean`	`addReaction(Reaction reaction)` Adds a Reaction instance to the listOfReactions of this Model.
`boolean`	`addRule(Rule rule)` Adds a Rule instance to the listOfRules of this Model.
`boolean`	`addSpecies(Species spec)` Adds a Species instance to the listOfSpecies of this Model.
`boolean`	`addSpeciesType(SpeciesType speciesType)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`boolean`	`addUnitDefinition(UnitDefinition unitDefinition)` Adds an `UnitDefinition` instance to the `listOfUnitDefinitions` of this `Model`.
`java.lang.String`	`addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition units)` Checks whether an identical `UnitDefinition` like the given `UnitDefinition` is already in this `Model`'s `listOfUnitDefinitions`.
`Model`	`clone()` Creates a deep copy of this object, i.e., a new `SBase` with the same properties like this one.
`boolean`	`containsCompartment(java.lang.String id)` Returns `true` if this model contains a reference to a `Compartment` with the given identifier.
`boolean`	`containsFunctionDefinition(java.lang.String id)` Returns `true` if this model contains a reference to a `FunctionDefinition` with the given identifier.
`boolean`	`containsParameter(java.lang.String id)` Returns `true` if this model contains a reference to a `Parameter` with the given identifier.
`boolean`	`containsQuantity(Quantity quantity)` Returns `true` if this `Model` contains a reference to the given `Quantity`.
`boolean`	`containsReaction(java.lang.String id)` Returns `true` if this `Model` contains a reference to the given `Reaction`.
`boolean`	`containsSpecies(java.lang.String id)` Returns `true` if this `Model` contains a reference to the given `Species`.
`boolean`	`containsUniqueNamedSBase(java.lang.String id)` Returns `true` if this `Model` contains a reference to the given `UniqueNamedSBase`.
`boolean`	`containsUnitDefinition(java.lang.String units)` Returns `true` if this `Model` contains a reference to the given `UnitDefinition`.
`AlgebraicRule`	`createAlgebraicRule()` Creates a new `AlgebraicRule` inside this `Model` and returns it.
`AssignmentRule`	`createAssignmentRule()` Creates a new `AssignmentRule` inside this `Model` and returns it.
`Compartment`	`createCompartment()` Creates a new `Compartment` inside this `Model` and returns it.
`Compartment`	`createCompartment(java.lang.String id)` Creates a new `Compartment` inside this `Model` and returns it.
`CompartmentType`	`createCompartmentType()` Deprecated. `CompartmentType`s should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
`CompartmentType`	`createCompartmentType(java.lang.String id)` Deprecated. `CompartmentType`s should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
`Constraint`	`createConstraint()` Creates a new `Constraint` inside this `Model` and returns it.
`Delay`	`createDelay()` Creates a new `Delay` inside the last `Event` object created in this `Model`, and returns a pointer to it.
`Event`	`createEvent()` Creates a new `Event` inside this `Model` and returns it.
`Event`	`createEvent(java.lang.String id)` Creates a new `Event` inside this `Model` and returns it.
`EventAssignment`	`createEventAssignment()` Creates a new `EventAssignment` inside the last `Event` object created in this `Model`, and returns a pointer to it.
`FunctionDefinition`	`createFunctionDefinition()` Creates a new `FunctionDefinition` inside this `Model` and returns it.
`FunctionDefinition`	`createFunctionDefinition(java.lang.String id)` Creates a new `FunctionDefinition` inside this `Model` and returns it.
`InitialAssignment`	`createInitialAssignment()` Creates a new `InitialAssignment` inside this `Model` and returns it.
`KineticLaw`	`createKineticLaw()` Creates a new `KineticLaw` inside the last `Reaction` object created in this `Model`, and returns a pointer to it.
`LocalParameter`	`createKineticLawParameter()` Creates a new local `LocalParameter` inside the `KineticLaw` object of the last `Reaction` created inside this `Model`, and returns a pointer to it.
`LocalParameter`	`createKineticParameter(java.lang.String id)` Creates a new local `LocalParameter` inside the `KineticLaw` object of the last `Reaction` created inside this `Model`, and returns a pointer to it.
`ModifierSpeciesReference`	`createModifier()` Creates a new `ModifierSpeciesReference` object for a modifier species inside the last `Reaction` object in this `Model`, and returns a pointer to it.
`ModifierSpeciesReference`	`createModifier(java.lang.String id)` Creates a new `ModifierSpeciesReference` with the specified 'id'.
`Parameter`	`createParameter()` Creates a new `Parameter` inside this `Model` and returns it.
`Parameter`	`createParameter(java.lang.String id)` Creates a new `Parameter`.
`SpeciesReference`	`createProduct()` Creates a new `SpeciesReference` object for a product inside the last `Reaction` object in this `Model`, and returns a pointer to it.
`SpeciesReference`	`createProduct(java.lang.String id)` Creates an instance of `SpeciesReference` and adds it to the last `Reaction` element that has been added to this `Model`.
`RateRule`	`createRateRule()` Creates a new `RateRule` inside this `Model` and returns it.
`SpeciesReference`	`createReactant()` Creates a new `SpeciesReference` object for a reactant inside the last `Reaction` object in this `Model`, and returns a pointer to it.
`SpeciesReference`	`createReactant(java.lang.String id)` Creates a new `SpeciesReference` object, with the specified 'id', for a reactant inside the last `Reaction` object in this `Model`, and returns a pointer to it.
`Reaction`	`createReaction()` Creates a new `Reaction` inside this `Model` and returns it.
`Reaction`	`createReaction(java.lang.String id)` Creates a new `Reaction` inside this `Model` and returns it.
`Species`	`createSpecies()` Creates a new `Species` inside this `Model` and returns it.
`Species`	`createSpecies(java.lang.String id)` Creates a new `Species` inside this `Model` and returns it.
`Species`	`createSpecies(java.lang.String id, Compartment c)` Creates a new `Species` inside this `Model` and returns it.
`Species`	`createSpecies(java.lang.String id, java.lang.String name, Compartment c)` Creates a new `Species` inside this `Model` and returns it.
`SpeciesType`	`createSpeciesType()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`SpeciesType`	`createSpeciesType(java.lang.String id)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`Trigger`	`createTrigger()` Creates a new `Trigger` inside the last `Event` object created in this `Model`, and returns a pointer to it.
`Unit`	`createUnit()` Creates a new `Unit` object within the last `UnitDefinition` object created in this model and returns a pointer to it.
`Unit`	`createUnit(Unit.Kind kind)` Creates a new `Unit` object within the last `UnitDefinition` object created in this model and returns a pointer to it.
`UnitDefinition`	`createUnitDefinition()` Creates a new `UnitDefinition` inside this `Model` and returns it.
`UnitDefinition`	`createUnitDefinition(java.lang.String id)` Creates a new `UnitDefinition` inside this `Model` and returns it.
`boolean`	`equals(java.lang.Object object)` Returns `true` if and only if the given `SBase` has exactly the same properties like this `SBase` instance.
`CallableSBase`	`findCallableSBase(java.lang.String id)` Returns a `CallableSBase` element of the `Model` that has the given 'id' as identifier or `null` if no element is found.
`UnitDefinition`	`findIdentical(UnitDefinition unitDefinition)` Searches the first `UnitDefinition` within this `Model`'s `listOfUnitDefinitions` that is identical to the given `UnitDefinition`.
`java.util.List<LocalParameter>`	`findLocalParameters(java.lang.String id)` Finds all instances of `LocalParameter` in this `Model` and adds them to a `List`.
`ModifierSpeciesReference`	`findModifierSpeciesReference(java.lang.String id)` Returns the `ModifierSpeciesReference` with all `Reaction`s of this `Model` that has 'id' as id.
`NamedSBase`	`findNamedSBase(java.lang.String id)` Returns a `NamedSBase` element of the model that has the given 'id' as id or `null` if no element is found.
`NamedSBaseWithDerivedUnit`	`findNamedSBaseWithDerivedUnit(java.lang.String id)` Returns a `NamedSBaseWithDerivedUnit` element of the `Model` that has the given 'id' as id or `null` if no element is found.
`Quantity`	`findQuantity(java.lang.String id)` Searches for an instance of `Quantity` within all of this `Model`'s components that has the given identifier or name attribute and returns it.
`QuantityWithUnit`	`findQuantityWithUnit(java.lang.String idOrName)` Searches for an instance of `QuantityWithUnit` within all of this `Model`'s components that has the given identifier or name attribute and returns it.
`java.util.SortedSet<java.lang.String>`	`findReactionsForLocalParameter(java.lang.String id)` Returns a `SortedSet` of identifiers of all `Reaction` elements within this `Model` whose `KineticLaw`s contain a `LocalParameter` that has the given 'id' or `null` if no element cannot be found.
`SimpleSpeciesReference`	`findSimpleSpeciesReference(java.lang.String id)` Returns the `SimpleSpeciesReference` within all `Reaction`s of this `Model` that has 'id' as id.
`SpeciesReference`	`findSpeciesReference(java.lang.String id)` Returns the `SpeciesReference` with all `Reaction`s of this `Model` that has 'id' as id.
`Symbol`	`findSymbol(java.lang.String id)` Searches in the list of `Compartment`s, `Species`, and `Parameter`s for the element with the given identifier.
`UniqueNamedSBase`	`findUniqueNamedSBase(java.lang.String id)` Returns a `UniqueNamedSBase` element that has the given 'id' within this `Model` or `null` if no such element can be found.
`UnitDefinition`	`findUnitDefinition(java.lang.String id)` Returns a `UnitDefinition` element that has the given 'id' within this `Model` or `null` if no such element can be found.
`Variable`	`findVariable(java.lang.String id)` Searches the `Variable` with the given identifier in this model.
`boolean`	`getAllowsChildren()`
`java.lang.String`	`getAreaUnits()` Returns the area units ID of this `Model`.
`UnitDefinition`	`getAreaUnitsInstance()` Returns the `UnitDefinition` instance which has the `areaUnitsID` of this `Model` as id.
`javax.swing.tree.TreeNode`	`getChildAt(int index)`
`int`	`getChildCount()`
`Compartment`	`getCompartment(int n)` Gets the n^th `Compartment` instance of the listOfCompartments.
`Compartment`	`getCompartment(java.lang.String id)` Gets the `Compartment` of the listOfCompartments which has 'id' as id.
`int`	`getCompartmentCount()` Returns the number of `Compartment`s of this `Model`.
`CompartmentType`	`getCompartmentType(int n)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`CompartmentType`	`getCompartmentType(java.lang.String id)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`int`	`getCompartmentTypeCount()` Deprecated. using `CompartmentType` is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
`Constraint`	`getConstraint(int n)` Gets the n^th Constraint object in this Model.
`int`	`getConstraintCount()` Returns the number of `Constraint`s of this `Model`.
`java.lang.String`	`getConversionFactor()` Returns the conversionFactor ID of this `Model`.
`Parameter`	`getConversionFactorInstance()` Returns the Parameter instance which has the conversionFactorID of this Model as id.
`int`	`getDelayCount()` Returns the number of `Delay`s of this `Model`.
`Event`	`getEvent(int n)` Gets the n^th Event object in this Model.
`Event`	`getEvent(java.lang.String id)` Gets the `Event` which as the given `id` as id.
`int`	`getEventAssignmentCount()` Returns the number of `EventAssignment`s of this `Model`.
`int`	`getEventCount()` Returns the number of `Event`s of this `Model`.
`java.lang.String`	`getExtentUnits()` Returns the extent units ID of this `Model`.
`UnitDefinition`	`getExtentUnitsInstance()` Returns the `UnitDefinition` instance which has the extent units ID of this Model as id.
`FunctionDefinition`	`getFunctionDefinition(int n)` Gets the n^th `FunctionDefinition` instance of the listOfFunstionDefinitions.
`FunctionDefinition`	`getFunctionDefinition(java.lang.String id)` Returns the `FunctionDefinition` of the `listOfFunctionDefinitions` which has 'id' as id.
`int`	`getFunctionDefinitionCount()` Returns the number of `FunctionDefinition`s of this `Model`.
`InitialAssignment`	`getInitialAssignment(int n)` Gets the n^th `InitialAssignment` object in this `Model`.
`InitialAssignment`	`getInitialAssignment(java.lang.String variable)` Returns the `InitialAssignment` of the `listOfInitialAssignments` whose `symbol` attribute, i.e., whose `Variable` has the given `variable` as identifier.
`int`	`getInitialAssignmentCount()` Returns the number of `InitialAssignment`s of this `Model`.
`int`	`getKineticLawCount()` Returns the number of `KineticLaw`s of this `Model`.
`private <T> T`	`getLastElementOf(ListOf<? extends T> listOf)` Returns the last element added in the given list.
`java.lang.String`	`getLengthUnits()` Returns the length units ID of this `Model`.
`UnitDefinition`	`getLengthUnitsInstance()` Returns the length units of this `Model` as a `UnitDefinition`.
`ListOf<Compartment>`	`getListOfCompartments()` Returns the listOfCompartments of this `Model`.
`ListOf<CompartmentType>`	`getListOfCompartmentTypes()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`ListOf<Constraint>`	`getListOfConstraints()` Returns the listOfConstraints of this `Model`.
`int`	`getListOfCount()` Returns the number of `ListOf`s of this `Model`.
`ListOf<Event>`	`getListOfEvents()` Returns the listOfEvents of this `Model`.
`ListOf<FunctionDefinition>`	`getListOfFunctionDefinitions()` Returns the listOfFunctionDefinitions of this `Model`.
`ListOf<InitialAssignment>`	`getListOfInitialAssignments()` Returns the listOfInitialAssignments of this `Model`.
`ListOf<Parameter>`	`getListOfParameters()` Returns the `listOfParameters` of this `Model`.
`java.util.List<UnitDefinition>`	`getListOfPredefinedUnitDefinitions()`
`ListOf<Reaction>`	`getListOfReactions()` Returns the listOfReactions of this `Model`.
`ListOf<Rule>`	`getListOfRules()` Returns the listOfRules of this `Model`.
`ListOf<Species>`	`getListOfSpecies()` Returns the `listOfSpecies` of this `Model`.
`ListOf<SpeciesType>`	`getListOfSpeciesTypes()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`ListOf<UnitDefinition>`	`getListOfUnitDefinitions()` Returns the listOfUnitDefinitions of this `Model`.
`int`	`getLocalParameterCount()` Returns the number of parameters that are contained within kineticLaws in the reactions of this model.
`int`	`getMathContainerCount()` Returns the number of elements that can contain math in the `Model` .
`History`	`getModelHistory()` Deprecated. use `SBase.getHistory()`
`int`	`getModifierSpeciesReferenceCount()` Returns the number of `ModifierSpeciesReference`s in the `Model`.
`java.util.Set<ModifierSpeciesReference>`	`getModifierSpeciesReferences()` Returns all `ModifierSpeciesReference`s, registered in any `Reaction`.
`int`	`getNamedSBaseCount()` Returns the number of `NamedSBase`s in the `Model`, so elements that can have a name.
`int`	`getNamedSBaseWithDerivedUnitCount()`
`int`	`getNumCompartments()` Returns the number of `Compartment`s of this `Model`.
`int`	`getNumCompartmentTypes()` Deprecated.
`int`	`getNumConstraints()` Returns the number of `Constraint`s of this `Model`.
`int`	`getNumDelays()` Returns the number of `Delay`s of this `Model`.
`int`	`getNumEventAssignments()` Returns the number of `EventAssignment`s of this `Model`.
`int`	`getNumEvents()` Returns the number of `Event`s of this `Model`.
`int`	`getNumFunctionDefinitions()` Returns the number of `FunctionDefinition`s of this `Model`.
`int`	`getNumInitialAssignments()` Returns the number of `InitialAssignment`s of this `Model`.
`int`	`getNumKineticLaws()` Returns the number of `KineticLaw`s of this `Model`.
`int`	`getNumListsOf()` Returns the number of `ListOf`s of this `Model`.
`int`	`getNumLocalParameters()` Returns the number of parameters that are contained within kineticLaws in the reactions of this model.
`int`	`getNumMathContainers()` Returns the number of elements that can contain math in the `Model` .
`int`	`getNumModifierSpeciesReferences()` Returns the number of `ModifierSpeciesReference`s in the `Model`.
`int`	`getNumNamedSBases()` Returns the number of `NamedSBase`s in the `Model`, so elements that can have a name.
`int`	`getNumNamedSBasesWithDerivedUnit()` Returns the number of `NamedSBaseWithDerivedUnit`s in the `Model`, so elements that can have a name and a unit that can be derived.
`int`	`getNumParameters()` Returns the number of `Parameter`s of this `Model`.
`int`	`getNumQuantities()` Returns the number of `Quantity`s of this `Model`.
`int`	`getNumQuantitiesWithUnit()` Returns the number of `QuantityWithUnit`s of this `Model`.
`int`	`getNumReactions()` Returns the number of `Reaction`s of this `Model`.
`int`	`getNumRules()` Returns the number of `Rule`s of this `Model`.
`int`	`getNumSBases()` Returns the number of `SBase`s of this `Model`.
`int`	`getNumSBasesWithDerivedUnit()` Returns the number of `SBaseWithDerivedUnit`s of this `Model`.
`int`	`getNumSpecies()` Returns the number of `Species` of this `Model`.
`int`	`getNumSpeciesReferences()` Returns the number of `SpeciesReference`s of this `Model`.
`int`	`getNumSpeciesTypes()` Deprecated.
`int`	`getNumSpeciesWithBoundaryCondition()` Returns the number of `Species` whose boundary condition is set to `true`.
`int`	`getNumStoichiometryMath()` Returns the number of `StoichiometryMath` in the `Model`.
`int`	`getNumSymbols()` Returns the number of all instances of `Symbol` referenced within the model.
`int`	`getNumTriggers()` Returns the number of `Trigger` of this `Model`.
`int`	`getNumUnitDefinitions()` Returns the number of `UnitDefinition`s of this `Model`.
`int`	`getNumUnits()` Returns the number of `Unit`s of this `Model`.
`int`	`getNumVariables()` Returns the number of `Variable`s of this `Model`.
`Parameter`	`getParameter(int n)` Gets the n^th `Parameter` object in this `Model`.
`Parameter`	`getParameter(java.lang.String id)` Returns the `Parameter` of the `listOfParameters` which has 'id' as id
`int`	`getParameterCount()` Returns the number of `Parameter`s of this `Model`.
`UnitDefinition`	`getPredefinedUnitDefinition(java.lang.String unitKind)` Returns a `UnitDefinition` representing one of the predefined units of SBML, returns `null` if the given unit kind is not a valid one for the SBML level and version of this `Model`.
`int`	`getQuantityCount()` Returns the number of `Quantity`s of this `Model`.
`int`	`getQuantityWithUnitCount()` Returns the number of `QuantityWithUnit`s of this `Model`.
`Reaction`	`getReaction(int n)` Gets the n-th `Reaction` object in this Model.
`Reaction`	`getReaction(java.lang.String id)` Returns the `Reaction` of the `listOfReactions` which has 'id' as id.
`int`	`getReactionCount()` Returns the number of `Reaction`s of this `Model`.
`Rule`	`getRule(int n)` Gets the n^th `Rule` of the listOfRules.
`ExplicitRule`	`getRule(java.lang.String variable)` Searches for the first instance of `ExplicitRule` within this `Model`'s `listOfRules`, whose variable attribute is set to the value passed to this method.
`int`	`getRuleCount()` Returns the number of `Rule`s of this `Model`.
`int`	`getSBaseCount()` Returns the number of `SBase`s of this `Model`.
`int`	`getSBaseWithDerivedUnitCount()` Returns the number of `SBaseWithDerivedUnit`s of this `Model`.
`Species`	`getSpecies(int n)` Gets the n-th `Species` object in this Model.
`Species`	`getSpecies(java.lang.String id)` Gets the `Species` of the `listOfSpecies` which has 'id' as id.
`int`	`getSpeciesCount()` Returns the number of `Species` of this `Model`.
`int`	`getSpeciesReferenceCount()` Returns the number of `SpeciesReference`s of this `Model`.
`SpeciesType`	`getSpeciesType(int n)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`SpeciesType`	`getSpeciesType(java.lang.String id)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`int`	`getSpeciesTypeCount()` Deprecated. the use of `SpeciesType` is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
`int`	`getSpeciesWithBoundaryConditionCount()` Returns the number of `Species` whose boundary condition is set to `true`.
`int`	`getStoichiometryMathCount()` Returns the number of `StoichiometryMath` in the `Model`.
`java.lang.String`	`getSubstanceUnits()` Returns the substance units ID of this model.
`UnitDefinition`	`getSubstanceUnitsInstance()` Returns the `UnitDefinition` which has the `substanceUnitsID` of this `Model` as id.
`int`	`getSymbolCount()` Returns the number of all instances of `Symbol` referenced within the model.
`java.lang.String`	`getTimeUnits()` Returns the time units ID of this `Model`.
`UnitDefinition`	`getTimeUnitsInstance()` Gets the `UnitDefinition` representing the time units of this `Model`.
`int`	`getTriggerCount()` Returns the number of `Trigger` of this `Model`.
`int`	`getUnitCount()` Returns the number of `Unit`s of this `Model`.
`UnitDefinition`	`getUnitDefinition(int n)` Gets the n^th `UnitDefinition` object in this `Model`.
`UnitDefinition`	`getUnitDefinition(java.lang.String id)` Returns the `UnitDefinition` of the `listOfUnitDefinitions` which has 'id' as id.
`int`	`getUnitDefinitionCount()` Returns the number of `UnitDefinition`s of this `Model`.
`int`	`getVariableCount()` Returns the number of `Variable`s of this `Model`.
`java.lang.String`	`getVolumeUnits()` Returns the volume units ID of this `Model`.
`UnitDefinition`	`getVolumeUnitsInstance()` Returns the `UnitDefinition` instance which has the `volumeUnitsID` of this `Model` as id.
`int`	`hashCode()` Returns a hash code value for this `SBase` instance.
`boolean`	`hasUnit(java.lang.String id)` Returns `true` if this model has a reference to the unit with the given identifier.
`void`	`initDefaults()` Initializes the default values using the current Level/Version configuration.
`void`	`initDefaults(int level, int version)` Initializes the default values of the attributes of the `Model`
`boolean`	`isIdMandatory()` This method can be used to query if the identifier of this `NamedSBase` is required to be defined (i.e., not `null`) in the definition of SBML.
`boolean`	`isSetAreaUnits()` Returns `true` if the area units ID of this `Model` is not `null`.
`boolean`	`isSetAreaUnitsInstance()` Returns `true` if the `UnitDefinition` which has the area units ID of this `Model` as id is not `null`.
`boolean`	`isSetConversionFactor()` Returns `true` if the `conversionFactorID` of this `Model` is not `null`.
`boolean`	`isSetConversionFactorInstance()` Returns `true` if the Parameter which has the conversionFactorID of this Model as id is not `null`.
`boolean`	`isSetExtentUnits()` Returns `true` if the extentUnitsID of this Model is not `null`.
`boolean`	`isSetExtentUnitsInstance()` Returns `true` if the UnitDefinition which has the extentUnitsID of this Model as id is not `null`.
`boolean`	`isSetLengthUnits()` Returns `true` if the lengthUnitsID of this Model is not `null`.
`boolean`	`isSetLengthUnitsInstance()` Returns `true` if the UnitDefinition which has the lengthUnitsID of this Model as id is not `null`.
`boolean`	`isSetListOfCompartments()` Returns `true` if the listOfCompartments of this Model is not `null` and not empty.
`boolean`	`isSetListOfCompartmentTypes()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`boolean`	`isSetListOfConstraints()` Returns `true` if the listOfConstraints of this Model is not `null` and not empty.
`boolean`	`isSetListOfEvents()` Returns `true` if the listOfEvents of this Model is not `null` and not empty.
`boolean`	`isSetListOfFunctionDefinitions()` Returns `true` if the listOfFunctionDefinitions of this Model is not `null` and not empty.
`boolean`	`isSetListOfInitialAssignments()` Returns `true` if the listOfInitialAssignments of this Model is not `null` and not empty.
`boolean`	`isSetListOfParameters()` Returns `true` if the listOfParameters of this Model is not `null` and not empty.
`boolean`	`isSetListOfReactions()` Returns `true` if the listOfReactions of this Model is not `null` and not empty.
`boolean`	`isSetListOfRules()` Returns `true` if the listOfRules of this Model is not `null` and not empty.
`boolean`	`isSetListOfSpecies()` Returns `true` if the listOfSpecies of this Model is not `null` and not empty.
`boolean`	`isSetListOfSpeciesTypes()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`boolean`	`isSetListOfUnitDefinitions()` Returns `true` if the listOfUnitDefinitions of this Model is not `null` and not empty.
`boolean`	`isSetModelHistory()` Deprecated. use `SBase.isSetHistory()`
`boolean`	`isSetSubstanceUnits()` Returns `true` if the substanceUnitsID of this Model is not `null`.
`boolean`	`isSetSubstanceUnitsInstance()` Returns `true` if the UnitDefinition which has the substanceUnitsID of this Model as id is not `null`.
`boolean`	`isSetTimeUnits()` Returns `true` if the timeUnitsID of this `Model` is not `null`.
`boolean`	`isSetTimeUnitsInstance()` Returns `true` if the UnitsDefinition which has the timeUnistID of this Model as id is not `null`.
`boolean`	`isSetVolumeUnits()` Returns `true` if the volumeUnitsID of this Model is not `null`.
`boolean`	`isSetVolumeUnitsInstance()` Returns `true` if the UnitDefinition which has the volumeUnitsID of this Model as id is not `null`.
`boolean`	`readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)` Sets the given attribute in this `SBase`.
`boolean`	`register(SBase sbase)` Registers the given `SBase` element and all of it's children in this `IdManager`.
`private boolean`	`registerId(KineticLaw kl, LocalParameter lp, boolean delete, boolean alreadyRegisteredInKL)` Registration of `LocalParameter` instances in the `Model`.
`private boolean`	`registerId(UniqueNamedSBase unsb, boolean delete)`
`private boolean`	`registerId(UnitDefinition ud, boolean add)` Registers the identifier and the corresponding `UnitDefinition` itself in this `Model`.
`private boolean`	`registerIds(SBase parent, SBase newElem, boolean recursively, boolean delete, java.util.List<IdManager> idManagerList)` Registers the given element in this `Model`.
`private <T extends UniqueNamedSBase> T`	`remove(java.lang.Class<T> clazz, java.lang.String id)` Removes the element with the given id from this model if such an element can be found.
`<T extends UniqueNamedSBase> T`	`remove(java.lang.String id)` Removes any `UniqueNamedSBase` with the given identifier from this `Model` and returns the removed element if the operation was successfull.
`Compartment`	`removeCompartment(int i)` Removes the i-th `Compartment` of the `Model`.
`Compartment`	`removeCompartment(java.lang.String id)` Removes the `Compartment` of the `Model` with 'id' as id.
`CompartmentType`	`removeCompartmentType(int n)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`CompartmentType`	`removeCompartmentType(java.lang.String id)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`Constraint`	`removeConstraint(int n)` Removes the n-th `Constraint` of the `Model`.
`Event`	`removeEvent(int n)` Removes the n-th `Event` of the `Model`.
`Event`	`removeEvent(java.lang.String id)` Removes the `Event` of the `Model` with 'id' as id.
`FunctionDefinition`	`removeFunctionDefinition(int n)` Removes the n-th `FunctionDefinition` of the `Model`.
`FunctionDefinition`	`removeFunctionDefinition(java.lang.String id)` Removes the `FunctionDefinition` of the `Model` with 'id' as id.
`InitialAssignment`	`removeInitialAssignment(int n)` Removes the n-th `InitialAssignment` of the `Model`.
`Parameter`	`removeParameter(int n)` Removes the n-th `Parameter` of the `Model`.
`boolean`	`removeParameter(Parameter parameter)` Removes the Parameter 'parameter' from this Model.
`Parameter`	`removeParameter(java.lang.String id)` Removes the `Parameter` of the `Model` with 'id' as id.
`Reaction`	`removeReaction(int n)` Removes the n-th `Reaction` of the `Model`.
`boolean`	`removeReaction(Reaction reac)` Removes a reaction from the model.
`Reaction`	`removeReaction(java.lang.String id)` Removes the `Reaction` of the `Model` with 'id' as id.
`Rule`	`removeRule(int i)` Removes the i-th `Rule` of the `Model`.
`boolean`	`removeRule(Rule rule)` Removes a `Rule` from the `Model`.
`Rule`	`removeRule(java.lang.String variableId)` Removes the `Rule` of the `Model` with 'variableId' as variable.
`Species`	`removeSpecies(int i)` Removes the i-th `Species` of the `Model`.
`boolean`	`removeSpecies(Species spec)` Removes a species from the model.
`Species`	`removeSpecies(java.lang.String id)` Removes the `Species` of the `Model` with 'id' as id.
`SpeciesType`	`removeSpeciesType(int n)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`SpeciesType`	`removeSpeciesType(java.lang.String id)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`UnitDefinition`	`removeUnitDefinition(int n)` Removes the n-th `UnitDefinition` of the `Model`.
`UnitDefinition`	`removeUnitDefinition(java.lang.String id)` Removes the `UnitDefinition` of the `Model` with 'id' as id.
`boolean`	`removeUnitDefinition(UnitDefinition unitDefininition)` Removes a `UnitDefinition` of the `Model`.
`void`	`setAreaUnits(java.lang.String areaUnitsID)` Sets the areaUnitsID of this `Model` to 'areaUnitsID'
`void`	`setAreaUnits(Unit.Kind kind)`
`void`	`setAreaUnits(UnitDefinition areaUnits)` Sets the areaUnitsID of this `Model` to the id of the `UnitDefinition` 'areaUnits'.
`void`	`setConversionFactor(Parameter conversionFactor)` Sets the conversionFactorID of this `Model` to the id of the `Parameter` 'conversionFactor'.
`void`	`setConversionFactor(java.lang.String conversionFactorID)` Sets the conversionFactorID of this `Model` to 'conversionFactorID'.
`void`	`setExtentUnits(java.lang.String extentUnitsID)` Sets the extendUnitsID of this `Model` to 'extentUnitsID'.
`void`	`setExtentUnits(Unit.Kind kind)`
`void`	`setExtentUnits(UnitDefinition extentUnits)` Sets the extentUnitsID of this `Model` to the id of the `UnitDefinition` 'extentUnits'.
`void`	`setLengthUnits(java.lang.String lengthUnitsID)` Sets the lengthUnitsID of this `Model` to 'lengthUnitsID'.
`void`	`setLengthUnits(Unit.Kind kind)`
`void`	`setLengthUnits(UnitDefinition lengthUnits)` Sets the lengthUnitsID of this `Model` to the id of the UnitDefinition 'lengthUnits'.
`void`	`setListOfCompartments(ListOf<Compartment> listOfCompartments)` Sets the listOfCompartments of this `Model` to 'listOfCompartments'.
`void`	`setListOfCompartmentTypes(ListOf<CompartmentType> listOfCompartmentTypes)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`void`	`setListOfConstraints(ListOf<Constraint> listOfConstraints)` Sets the listOfConstraints of this `Model` to 'listOfConstraints'.
`void`	`setListOfEvents(ListOf<Event> listOfEvents)` Sets the listOfEvents of this `Model` to 'listOfEvents'.
`void`	`setListOfFunctionDefinitions(ListOf<FunctionDefinition> listOfFunctionDefinitions)` Sets the listOfFunctionDefinitions of this `Model` to 'listOfFunctionDefinitions'.
`void`	`setListOfInitialAssignments(ListOf<InitialAssignment> listOfInitialAssignments)` Sets the `listOfInitialAssignments` of this `Model` to 'listOfInitialAssignments'.
`void`	`setListOfParameters(ListOf<Parameter> listOfParameters)` Sets the `listOfParameters` of this `Model` to 'listOfParameters'.
`void`	`setListOfReactions(ListOf<Reaction> listOfReactions)` Sets the `listOfReactions` of this `Model` to 'listOfReactions'.
`void`	`setListOfRules(ListOf<Rule> listOfRules)` Sets the `listOfRules` of this `Model` to 'listOfRules'.
`void`	`setListOfSpecies(ListOf<Species> listOfSpecies)` Sets the listOfSpecies of this `Model` to 'listOfSpecies'.
`void`	`setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes)` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`void`	`setListOfUnitDefinitions(ListOf<UnitDefinition> listOfUnitDefinitions)` Sets the listOfUnitDefinitions of this `Model` to 'listOfUnitDefinitions'.
`void`	`setModelHistory(History history)` Deprecated. use `AbstractSBase.setHistory(History)`
`void`	`setSubstanceUnits(java.lang.String substanceUnitsID)` Sets the `substanceUnitsID` of this `Model` to 'substanceUnitsID'
`void`	`setSubstanceUnits(Unit.Kind kind)`
`void`	`setSubstanceUnits(UnitDefinition substanceUnits)` Sets the substanceUnitsID of this `Model` to the id of 'substanceUnits'.
`void`	`setTimeUnits(java.lang.String timeUnitsID)` Sets the timeUnits of this `Model` to 'timeUnistID'
`void`	`setTimeUnits(Unit.Kind kind)` Sets the `timeUnitsID` of this `Model` to the given unit kind.
`void`	`setTimeUnits(UnitDefinition timeUnits)` Sets the timeUnitsID of this `Model` to the id of the `UnitDefinition` 'timeUnits'.
`void`	`setVolumeUnits(java.lang.String volumeUnitsID)` Sets the volumeUnitsID of this `Model` to 'volumeUnitsID'
`void`	`setVolumeUnits(Unit.Kind kind)`
`void`	`setVolumeUnits(UnitDefinition volumeUnits)` Sets the volumeUnitsID of this `Model` to the id of the `UnitDefinition` 'volumeUnits'.
`boolean`	`unregister(SBase sbase)` Unregisters the given `SBase` element and all of it's children in this `IdManager`.
`void`	`unsetAreaUnits()` Sets the `areaUnitsID` of this `Model` to `null`.
`void`	`unsetConversionFactor()` Sets the `conversionFactorID` of this `Model` to `null`.
`void`	`unsetExtentUnits()` Sets the `extentUnitsID` of this `Model` to `null`.
`void`	`unsetLengthUnits()` Sets the `lengthUnitsID` of this `Model` to `null`.
`boolean`	`unsetListOfCompartments()` Removes the `listOfCompartments` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfCompartmentTypes()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`boolean`	`unsetListOfConstraints()` Removes the `listOfConstraints` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfEvents()` Removes the `listOfEvents` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfFunctionDefinitions()` Removes the `listOfFunctionDefinitions` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfInitialAssignments()` Removes the `listOfInitialAssignments` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfParameters()` Removes the `listOfParameters` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfReactions()` Removes the `listOfReactions` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfRules()` Removes the `listOfRules` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfSpecies()` Removes the `listOfSpecies` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfSpeciesTypes()` Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
`boolean`	`unsetListOfUnitDefinitions()` Removes the `listOfUnitDefinitions` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`void`	`unsetModelHistory()` Deprecated. use `AbstractSBase.unsetHistory()`.
`void`	`unsetSubstanceUnits()` Sets the `substanceUnitsID` of this `Model` to `null`.
`void`	`unsetTimeUnits()` Sets the timeUnitsID of this `Model` to `null`.
`void`	`unsetVolumeUnits()` Sets the `volumeUnitsID` of this `Model` to `null`.
`java.util.Map<java.lang.String,java.lang.String>`	`writeXMLAttributes()` Returns a map with all the attributes of this `SBase` that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase
checkIdentifier, getId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase
addCVTerm, 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, setLevelAndVersion, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase
addCVTerm, 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, unsetSBOTerm

Methods inherited from interface javax.swing.tree.TreeNode
children, getIndex, getParent, isLeaf

- Field Detail
  - COULD_NOT_CREATE_ELEMENT_MSG
```
private static final java.lang.String COULD_NOT_CREATE_ELEMENT_MSG
```
    Error message to indicate that an element could not be created.
    
    See Also:
    Constant Field Values
  - logger
```
private static final transient org.apache.log4j.Logger logger
```
    A Logger for this class.
  - serialVersionUID
```
private static final long serialVersionUID
```
    Generated serial version identifier.
    
    See Also:
    Constant Field Values
  - areaUnitsID
```
private java.lang.String areaUnitsID
```
    Represents the 'areaUnits' XML attribute of a model element.
  - conversionFactorID
```
private java.lang.String conversionFactorID
```
    Represents the 'conversionFactor' XML attribute of a model element.
  - extentUnitsID
```
private java.lang.String extentUnitsID
```
    Represents the 'extentUnits' XML attribute of a model element.
  - lengthUnitsID
```
private java.lang.String lengthUnitsID
```
    Represents the 'lengthUnits' XML attribute of a model element.
  - listOfCompartments
```
private ListOf<Compartment> listOfCompartments
```
    Represents the listOfCompartments subnode of a model element.
  - listOfCompartmentTypes
```
@Deprecated
private ListOf<CompartmentType> listOfCompartmentTypes
```
    Deprecated. only valid in SBML Level 2 for Versions 2 through 4.
    
    Represents the listOfCompartmentTypes subnode of a model element.
  - listOfConstraints
```
private ListOf<Constraint> listOfConstraints
```
    Represents the listOfConstraints subnode of a model element.
  - listOfEvents
```
private ListOf<Event> listOfEvents
```
    Represents the listOfEvents subnode of a model element.
  - listOfFunctionDefinitions
```
private ListOf<FunctionDefinition> listOfFunctionDefinitions
```
    Represents the listOfFunctionDefinitions subnode of a model element.
  - listOfInitialAssignments
```
private ListOf<InitialAssignment> listOfInitialAssignments
```
    Represents the listOfInitialAssignments subnode of a model element.
  - listOfParameters
```
private ListOf<Parameter> listOfParameters
```
    Represents the listOfParameters subnode of a model element.
  - listOfPredefinedUnitDefinitions
```
private java.util.List<UnitDefinition> listOfPredefinedUnitDefinitions
```
    Represents the list of predefined UnitDefinitions for a given SBML level and version.
  - listOfReactions
```
private ListOf<Reaction> listOfReactions
```
    Represents the listOfReactions subnode of a model element.
  - listOfRules
```
private ListOf<Rule> listOfRules
```
    Represents the listOfRules subnode of a model element.
  - listOfSpecies
```
private ListOf<Species> listOfSpecies
```
    Represents the listOfSpecies subnode of a model element.
  - listOfSpeciesTypes
```
@Deprecated
private ListOf<SpeciesType> listOfSpeciesTypes
```
    Deprecated. only valid in SBML Level 2 for Versions 2 through 4.
    
    Represents the listOfSpeciesTypes subnode of a model element.
  - listOfUnitDefinitions
```
private ListOf<UnitDefinition> listOfUnitDefinitions
```
    Represents the listOfUnitDefinitions sub-node of a model element.
  - mapOfLocalParameters
```
private java.util.Map<java.lang.String,java.util.List<Reaction>> mapOfLocalParameters
```
    A mapping between the identifiers of LocalParameters and the containing Reaction objects.
  - mapOfUniqueNamedSBases
```
private java.util.Map<java.lang.String,UniqueNamedSBase> mapOfUniqueNamedSBases
```
    For internal computation: a mapping between their identifiers and the UniqueNamedSBases in Models themselves:
  - mapOfUnitDefinitions
```
private java.util.Map<java.lang.String,UnitDefinition> mapOfUnitDefinitions
```
    A mapping between their identifiers and associated UnitDefinition objects.
  - substanceUnitsID
```
private java.lang.String substanceUnitsID
```
    Represents the 'substanceUnits' XML attribute of a model element.
  - timeUnitsID
```
private java.lang.String timeUnitsID
```
    Represents the 'timeUnits' XML attribute of a model element.
  - volumeUnitsID
```
private java.lang.String volumeUnitsID
```
    Represents the 'volumeUnits' XML attribute of a model element.
- Constructor Detail
  - Model
```
public Model()
```
    Creates a Model instance. By default, all the listOfxxx and xxxUnitsID are null.
  - Model
```
public Model(int level,
     int version)
```
    Creates a Model instance.
    
    Parameters:
    level -
    version -
  - Model
```
public Model(Model model)
```
    Creates a Model instance from a Model.
    
    Parameters:
    model -
  - Model
```
public Model(java.lang.String id)
```
    Creates a Model instance from an id.
    
    Parameters:
    id -
  - Model
```
public Model(java.lang.String id,
     int level,
     int version)
```
    Creates a Model instance from an id, level and version. By default, all the listOfxxx and xxxUnitsID are null.
    
    Parameters:
    id -
    level -
    version -
- Method Detail
  - accept
```
public boolean accept(SBase sbase)
```
    Description copied from interface: IdManager
    
    Returns true if this IdManager can register or unregister the given SBase.
    
    Specified by:
    
    accept in interface IdManager
    
    Returns:
    true if this IdManager can register or unregister the given SBase.
  - addCompartment
```
public boolean addCompartment(Compartment compartment)
```
    Adds a Compartment instance to the listOfCompartments of this Model.
    
    Parameters:
    compartment -
    
    Returns:
    true if the listOfCompartments was changed as a result of this call.
  - addCompartmentType
```
@Deprecated
public boolean addCompartmentType(CompartmentType compartmentType)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Adds a CompartmentType instance to the listOfCompartmentTypes of this Model.
    
    Parameters:
    compartmentType -
    
    Returns:
    true if the listOfCompartmentTypes was changed as a result of this call.
  - addConstraint
```
public boolean addConstraint(Constraint constraint)
```
    Adds a Constraint instance to the listOfConstraints of this Model.
    
    Parameters:
    constraint -
    
    Returns:
    true if the listOfConstraints was changed as a result of this call.
  - addEvent
```
public boolean addEvent(Event event)
```
    Adds an Event instance to the listOfEvents of this Model.
    
    Parameters:
    event -
    
    Returns:
    true if the listOfEvents was changed as a result of this call.
    
    Throws:
    
    PropertyNotAvailableException - for inappropriate Level/Version combinations.
  - addFunctionDefinition
```
public boolean addFunctionDefinition(FunctionDefinition functionDefinition)
```
    Adds a FunctionDefinition instance to the listOfFunctionDefinitions of this Model.
    
    Parameters:
    functionDefinition -
    
    Returns:
    true if the listOfFunctionDefinitions was changed as a result of this call.
  - addInitialAssignment
```
public boolean addInitialAssignment(InitialAssignment initialAssignment)
```
    Adds an InitialAssignment instance to the listOfInitialAssignments of this Model.
    
    Parameters:
    initialAssignment -
    
    Returns:
    true if the listOfInitialAssignments was changed as a result of this call.
  - addParameter
```
public boolean addParameter(Parameter parameter)
```
    Adds a Parameter instance to the listOfParameters of this Model.
    
    Parameters:
    parameter -
    
    Returns:
    true if the listOfParameters was changed as a result of this call.
  - addPredefinedUnits
```
private void addPredefinedUnits()
```
    Adds all the possible unit kinds as UnitDefinition, so that the method getUnitDefinition(String) would be able to return a valid UnitDefinition even if one of these kinds is passed as parameter.
  - addReaction
```
public boolean addReaction(Reaction reaction)
```
    Adds a Reaction instance to the listOfReactions of this Model.
    
    Parameters:
    reaction -
    
    Returns:
    true if the listOfReactions was changed as a result of this call.
  - addRule
```
public boolean addRule(Rule rule)
```
    Adds a Rule instance to the listOfRules of this Model.
    
    Parameters:
    rule -
    
    Returns:
    true if the listOfRules was changed as a result of this call.
  - addSpecies
```
public boolean addSpecies(Species spec)
```
    Adds a Species instance to the listOfSpecies of this Model.
    
    Parameters:
    spec -
    
    Returns:
    true if the listOfSpecies was changed as a result of this call.
  - addSpeciesType
```
@Deprecated
public boolean addSpeciesType(SpeciesType speciesType)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Adds a SpeciesType instance to the listOfSpeciesTypes of this Model.
    
    Parameters:
    speciesType -
    
    Returns:
    true if the listOfSpeciesTypes was changed as a result of this call.
  - addUnitDefinition
```
public boolean addUnitDefinition(UnitDefinition unitDefinition)
```
    Adds an UnitDefinition instance to the listOfUnitDefinitions of this Model.
    
    Parameters:
    unitDefinition -
    
    Returns:
    true if the listOfUnitDefinitions was changed as a result of this call.
  - addUnitDefinitionOrReturnIdenticalUnit
```
public java.lang.String addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition units)
```
    Checks whether an identical UnitDefinition like the given UnitDefinition is already in this Model's listOfUnitDefinitions. If yes, the identifier of the identical UnitDefinition will be returned. Otherwise, the given unit is added to the listOfUnitDefinitions and its identifier will be returned. In any case, this method returns the identifier of a UnitDefinition that is part of this Model at least after calling this method.
    
    Parameters:
    units - The unit to be checked and added if no identical UnitDefinition can be found.
    
    Returns:
  - clone
```
public Model clone()
```
    Description copied from interface: SBase
    
    Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
    
    Specified by:
    
    clone in interface SBase
    
    Specified by:
    
    clone in class AbstractSBase
    
    Returns:
    a copy of this object
  - containsCompartment
```
public boolean containsCompartment(java.lang.String id)
```
    Returns true if this model contains a reference to a Compartment with the given identifier.
    
    Parameters:
    id -
    
    Returns:
    true if this model contains a reference to a Compartment with the given identifier.
  - containsFunctionDefinition
```
public boolean containsFunctionDefinition(java.lang.String id)
```
    Returns true if this model contains a reference to a FunctionDefinition with the given identifier.
    
    Parameters:
    id -
    
    Returns:
    true if this model contains a reference to a FunctionDefinition with the given identifier.
  - containsParameter
```
public boolean containsParameter(java.lang.String id)
```
    Returns true if this model contains a reference to a Parameter with the given identifier.
    
    Parameters:
    id -
    
    Returns:
    true if this model contains a reference to a Parameter with the given identifier.
  - containsQuantity
```
public boolean containsQuantity(Quantity quantity)
```
    Returns true if this Model contains a reference to the given Quantity.
    
    Parameters:
    quantity -
    
    Returns:
    true if this Model contains a reference to the given Quantity.
  - containsReaction
```
public boolean containsReaction(java.lang.String id)
```
    Returns true if this Model contains a reference to the given Reaction.
    
    Parameters:
    id - the identifier of a potential reaction.
    
    Returns:
    true if this Model contains a reference to the given Reaction.
  - containsSpecies
```
public boolean containsSpecies(java.lang.String id)
```
    Returns true if this Model contains a reference to the given Species.
    
    Parameters:
    id -
    
    Returns:
    true if this Model contains a reference to the given Species.
  - containsUniqueNamedSBase
```
public boolean containsUniqueNamedSBase(java.lang.String id)
```
    Returns true if this Model contains a reference to the given UniqueNamedSBase.
    
    Parameters:
    id -
    
    Returns:
    true if this Model contains a reference to the given UniqueNamedSBase.
  - containsUnitDefinition
```
public boolean containsUnitDefinition(java.lang.String units)
```
    Returns true if this Model contains a reference to the given UnitDefinition.
    
    Parameters:
    units -
    
    Returns:
    true if this Model contains a reference to the given UnitDefinition.
  - createAlgebraicRule
```
public AlgebraicRule createAlgebraicRule()
```
    Creates a new AlgebraicRule inside this Model and returns it.
    
    Returns:
    the AlgebraicRule object created
    See Also:
    addRule(Rule r)
  - createAssignmentRule
```
public AssignmentRule createAssignmentRule()
```
    Creates a new AssignmentRule inside this Model and returns it.
    
    Returns:
    the AssignmentRule object created
    See Also:
    addRule(Rule r)
  - createCompartment
```
public Compartment createCompartment()
```
    Creates a new Compartment inside this Model and returns it.
    
    Returns:
    the Compartment object created
    See Also:
    addCompartment(Compartment c)
  - createCompartment
```
public Compartment createCompartment(java.lang.String id)
```
    Creates a new Compartment inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the Compartment object created
  - createCompartmentType
```
@Deprecated
public CompartmentType createCompartmentType()
```
    Deprecated. CompartmentTypes should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
    
    Creates a new CompartmentType inside this Model and returns it.
    
    Returns:
    the CompartmentType object created
    See Also:
    addCompartmentType(CompartmentType ct)
  - createCompartmentType
```
@Deprecated
public CompartmentType createCompartmentType(java.lang.String id)
```
    Deprecated. CompartmentTypes should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
    
    Creates a new CompartmentType inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the CompartmentType object created
  - createConstraint
```
public Constraint createConstraint()
```
    Creates a new Constraint inside this Model and returns it.
    
    Returns:
    the Constraint object created
    See Also:
    addConstraint(Constraint c)
  - createDelay
```
public Delay createDelay()
```
    Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
    The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Delay is not created and null is returned instead.
    
    Returns:
    the Delay object created
  - createEvent
```
public Event createEvent()
```
    Creates a new Event inside this Model and returns it.
    
    Returns:
    the Event object created
  - createEvent
```
public Event createEvent(java.lang.String id)
```
    Creates a new Event inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the Event object created
  - createEventAssignment
```
public EventAssignment createEventAssignment()
```
    Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
    The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and null is returned instead.
    
    Returns:
    the EventAssignment object created
  - createFunctionDefinition
```
public FunctionDefinition createFunctionDefinition()
```
    Creates a new FunctionDefinition inside this Model and returns it.
    
    Returns:
    the FunctionDefinition object created
    See Also:
    addFunctionDefinition(FunctionDefinition fd)
  - createFunctionDefinition
```
public FunctionDefinition createFunctionDefinition(java.lang.String id)
```
    Creates a new FunctionDefinition inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the FunctionDefinition object created
  - createInitialAssignment
```
public InitialAssignment createInitialAssignment()
```
    Creates a new InitialAssignment inside this Model and returns it.
    
    Returns:
    the InitialAssignment object created
    See Also:
    addInitialAssignment(InitialAssignment ia)
  - createKineticLaw
```
public KineticLaw createKineticLaw()
```
    Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
    The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and null is returned instead.
    
    Returns:
    the KineticLaw object created
  - createKineticLawParameter
```
public LocalParameter createKineticLawParameter()
```
    Creates a new local LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
    The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new LocalParameter is not created and null is returned instead.
    
    Returns:
    the LocalParameter object created
  - createKineticParameter
```
public LocalParameter createKineticParameter(java.lang.String id)
```
    Creates a new local LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the LocalParameter object created
  - createModifier
```
public ModifierSpeciesReference createModifier()
```
    Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
    The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new ModifierSpeciesReference is not created and null is returned instead.
    
    Returns:
    the SpeciesReference object created
  - createModifier
```
public ModifierSpeciesReference createModifier(java.lang.String id)
```
    Creates a new ModifierSpeciesReference with the specified 'id'.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the SpeciesReference object created
  - createParameter
```
public Parameter createParameter()
```
    Creates a new Parameter inside this Model and returns it.
    
    Returns:
    the Parameter object created
    See Also:
    addParameter(Parameter p)
  - createParameter
```
public Parameter createParameter(java.lang.String id)
```
    Creates a new Parameter.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the Parameter object created
  - createProduct
```
public SpeciesReference createProduct()
```
    Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
    The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and null is returned instead.
    
    Returns:
    the SpeciesReference object created
  - createProduct
```
public SpeciesReference createProduct(java.lang.String id)
```
    Creates an instance of SpeciesReference and adds it to the last Reaction element that has been added to this Model.
    
    Parameters:
    id -
    
    Returns:
  - createRateRule
```
public RateRule createRateRule()
```
    Creates a new RateRule inside this Model and returns it.
    
    Returns:
    the RateRule object created
    See Also:
    addRule(Rule r)
  - createReactant
```
public SpeciesReference createReactant()
```
    Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
    The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and null is returned instead.
    
    Returns:
    the SpeciesReference object created
  - createReactant
```
public SpeciesReference createReactant(java.lang.String id)
```
    Creates a new SpeciesReference object, with the specified 'id', for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the SpeciesReference object created.
  - createReaction
```
public Reaction createReaction()
```
    Creates a new Reaction inside this Model and returns it.
    
    Returns:
    the Reaction object created
    See Also:
    addReaction(Reaction r)
  - createReaction
```
public Reaction createReaction(java.lang.String id)
```
    Creates a new Reaction inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the Reaction object created
  - createSpecies
```
public Species createSpecies()
```
    Creates a new Species inside this Model and returns it.
    
    Returns:
    the Species object created
    See Also:
    addSpecies(Species s)
  - createSpecies
```
public Species createSpecies(java.lang.String id)
```
    Creates a new Species inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the Species object created
  - createSpecies
```
public Species createSpecies(java.lang.String id,
                    Compartment c)
```
    Creates a new Species inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    c - the Compartment of the new Species
    
    Returns:
    the Species object created
  - createSpecies
```
public Species createSpecies(java.lang.String id,
                    java.lang.String name,
                    Compartment c)
```
    Creates a new Species inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    name - the name of the new element to create
    c - the Compartment of the new Species
    
    Returns:
    the Species object created
  - createSpeciesType
```
@Deprecated
public SpeciesType createSpeciesType()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Creates a new SpeciesType inside this Model and returns it.
    
    Returns:
    the SpeciesType object created
    See Also:
    addSpeciesType(SpeciesType st)
  - createSpeciesType
```
@Deprecated
public SpeciesType createSpeciesType(java.lang.String id)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Creates a new SpeciesType inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the SpeciesType object created
  - createTrigger
```
public Trigger createTrigger()
```
    Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
    The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Trigger is not created and null is returned instead.
    
    Returns:
    the Trigger object created
  - createUnit
```
public Unit createUnit()
```
    Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
    The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and null is returned instead.
    
    Returns:
    the Unit object created
    See Also:
    addUnitDefinition(UnitDefinition ud)
  - createUnit
```
public Unit createUnit(Unit.Kind kind)
```
    Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
    
    Parameters:
    kind - the kind of the new unit.
    
    Returns:
    the Unit object created
  - createUnitDefinition
```
public UnitDefinition createUnitDefinition()
```
    Creates a new UnitDefinition inside this Model and returns it.
    
    Returns:
    the UnitDefinition object created
    See Also:
    addUnitDefinition(UnitDefinition ud)
  - createUnitDefinition
```
public UnitDefinition createUnitDefinition(java.lang.String id)
```
    Creates a new UnitDefinition inside this Model and returns it.
    
    Parameters:
    id - the id of the new element to create
    
    Returns:
    the UnitDefinition object created
  - equals
```
public boolean equals(java.lang.Object object)
```
    Description copied from interface: SBase
    
    Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
    
    Specified by:
    
    equals in interface SBase
    
    Overrides:
    
    equals in class AbstractNamedSBase
    
    Parameters:
    object - the SBase to be compared to.
    
    Returns:
    true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.
  - findCallableSBase
```
public CallableSBase findCallableSBase(java.lang.String id)
```
    Returns a CallableSBase element of the Model that has the given 'id' as identifier or null if no element is found.
    
    Parameters:
    id - an identifier indicating an element of the Model.
    
    Returns:
    a CallableSBase element of the Model that has the given 'id' as id or null if no element is found.
  - findIdentical
```
public UnitDefinition findIdentical(UnitDefinition unitDefinition)
```
    Searches the first UnitDefinition within this Model's listOfUnitDefinitions that is identical to the given UnitDefinition. If no element can be found that satisfies the method UnitDefinition.areIdentical(UnitDefinition, UnitDefinition), null will be returned.
    
    Parameters:
    unitDefinition -
    
    Returns:
    A UnitDefinition object that is already part of this Model's listOfUnitDefinitions and satisfies the condition of UnitDefinition.areIdentical(UnitDefinition, UnitDefinition) in comparison to the given UnitDefinition, or null if no such element can be found.
  - findLocalParameters
```
public java.util.List<LocalParameter> findLocalParameters(java.lang.String id)
```
    Finds all instances of LocalParameter in this Model and adds them to a List.
    
    Parameters:
    id -
    
    Returns:
    A List of all LocalParameter instances with the given name or identifier. This List can be empty, but never null.
  - findModifierSpeciesReference
```
public ModifierSpeciesReference findModifierSpeciesReference(java.lang.String id)
```
    Returns the ModifierSpeciesReference with all Reactions of this Model that has 'id' as id.
    
    Parameters:
    id - the identifier of the ModifierSpeciesReference of interest. Note that this is not the identifier of the Species instance referred to by the ModifierSpeciesReference.
    
    Returns:
    the ModifierSpeciesReference out of all Reactions which has 'id' as id (or name depending on level and version). null if it doesn't exist.
  - findNamedSBase
```
public NamedSBase findNamedSBase(java.lang.String id)
```
    Returns a NamedSBase element of the model that has the given 'id' as id or null if no element is found.
    
    Parameters:
    id - an id indicating an element of the model.
    
    Returns:
    a NamedSBase element of the model that has the given 'id' as id or null if no element is found.
  - findNamedSBaseWithDerivedUnit
```
public NamedSBaseWithDerivedUnit findNamedSBaseWithDerivedUnit(java.lang.String id)
```
    Returns a NamedSBaseWithDerivedUnit element of the Model that has the given 'id' as id or null if no element is found. It first tries to find a CallableSBase with the given identifier and, if this is not successful, it searches for an instance of Event with the given id.
    
    Parameters:
    id - an id indicating an element of the Model.
    
    Returns:
    a NamedSBaseWithDerivedUnit element of the Model that has the given 'id' as id or null if no element is found.
    See Also:
    findCallableSBase(String)
  - findQuantity
```
public Quantity findQuantity(java.lang.String id)
```
    Searches for an instance of Quantity within all of this Model's components that has the given identifier or name attribute and returns it. There might be multiple instances of LocalParameter with the same identifier or name, each located in different Reactions. In this case, the first match will be returned. Note that also global Parameter instances have a higher priority and are returned first.
    
    Parameters:
    id -
    
    Returns:
    the Compartment, Species, SpeciesReference or Parameter, or the first LocalParameter which has 'id' as id.
    See Also:
    findLocalParameters(String)
  - findQuantityWithUnit
```
public QuantityWithUnit findQuantityWithUnit(java.lang.String idOrName)
```
    Searches for an instance of QuantityWithUnit within all of this Model's components that has the given identifier or name attribute and returns it. There might be multiple instances of LocalParameter with the same identifier or name, each located in different Reactions. In this case, the first match will be returned. Note that also global Parameter instances have a higher priority and are returned first.
    
    Parameters:
    idOrName -
    
    Returns:
    See Also:
    findLocalParameters(String)
  - findReactionsForLocalParameter
```
public java.util.SortedSet<java.lang.String> findReactionsForLocalParameter(java.lang.String id)
```
    Returns a SortedSet of identifiers of all Reaction elements within this Model whose KineticLaws contain a LocalParameter that has the given 'id' or null if no element cannot be found.
    
    Parameters:
    id - an id indicating an LocalParameter element of the Model.
    
    Returns:
    a SortedSet of the identifiers of all Reaction elements within this Model whose KineticLaw contains a LocalParameter that has the given 'id' as id or null if no such element with this 'id' can be found.
  - findSimpleSpeciesReference
```
public SimpleSpeciesReference findSimpleSpeciesReference(java.lang.String id)
```
    Returns the SimpleSpeciesReference within all Reactions of this Model that has 'id' as id.
    
    Parameters:
    id - the identifier of the SimpleSpeciesReference of interest. Note that this is not the identifier of the Species instance referred to by the SimpleSpeciesReference.
    
    Returns:
    the SimpleSpeciesReference out of all Reactions which has 'id' as id (or name depending on level and version). null if it doesn't exist.
  - findSpeciesReference
```
public SpeciesReference findSpeciesReference(java.lang.String id)
```
    Returns the SpeciesReference with all Reactions of this Model that has 'id' as id.
    
    Parameters:
    id - the identifier of the SpeciesReference of interest. Note that this is not the identifier of the Species instance referred to by the SpeciesReference.
    
    Returns:
    the SpeciesReference out of all Reactions which has 'id' as id (or name depending on level and version). null if it doesn't exist.
  - findSymbol
```
public Symbol findSymbol(java.lang.String id)
```
    Searches in the list of Compartments, Species, and Parameters for the element with the given identifier.
    
    Parameters:
    id -
    
    Returns:
    a Symbol element with the given identifier or null if there is no such element.
  - findUniqueNamedSBase
```
public UniqueNamedSBase findUniqueNamedSBase(java.lang.String id)
```
    Returns a UniqueNamedSBase element that has the given 'id' within this Model or null if no such element can be found.
    
    Parameters:
    id - an id indicating an UniqueNamedSBase element of the Model.
    
    Returns:
    a UniqueNamedSBase element of the Model that has the given 'id' as id or null if no element with this 'id' can be found.
  - findUnitDefinition
```
public UnitDefinition findUnitDefinition(java.lang.String id)
```
    Returns a UnitDefinition element that has the given 'id' within this Model or null if no such element can be found.
    
    Parameters:
    id - an id indicating an UnitDefinition element of the Model.
    
    Returns:
    a UniqueNamedSBase element of the Model that has the given 'id' as id or null if no such element with this 'id' can be found.
  - findVariable
```
public Variable findVariable(java.lang.String id)
```
    Searches the Variable with the given identifier in this model.
    
    Parameters:
    id - The identifier of the Variable of interest.
    
    Returns:
    the Compartment, Species, SpeciesReference, or Parameter, which has 'variable' as id.
  - getAllowsChildren
```
public boolean getAllowsChildren()
```
    Specified by:
    
    getAllowsChildren in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getAllowsChildren in class AbstractSBase
  - getAreaUnits
```
public java.lang.String getAreaUnits()
```
    Returns the area units ID of this Model.
    
    Returns:
    the area units ID of this Model. Returns an empty String if it is not set.
  - getAreaUnitsInstance
```
public UnitDefinition getAreaUnitsInstance()
```
    Returns the UnitDefinition instance which has the areaUnitsID of this Model as id.
    
    Returns:
    the UnitDefinition instance which has the areaUnitsID of this Model as id. null if it doesn't exist.
  - getChildAt
```
public javax.swing.tree.TreeNode getChildAt(int index)
```
    Specified by:
    
    getChildAt in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getChildAt in class AbstractSBase
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getChildCount in class AbstractSBase
  - getCompartment
```
public Compartment getCompartment(int n)
```
    Gets the n^th Compartment instance of the listOfCompartments.
    
    Parameters:
    n -
    
    Returns:
    the n^th Compartment instance of the listOfCompartments. null if the listOfCompartments is not set.
  - getCompartment
```
public Compartment getCompartment(java.lang.String id)
```
    Gets the Compartment of the listOfCompartments which has 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the Compartment of the listOfCompartments which has 'id' as id (or name depending on the version and level). null if the listOfCompartments is not set.
  - getCompartmentCount
```
public int getCompartmentCount()
```
    Returns the number of Compartments of this Model.
    
    Returns:
    the number of Compartments of this Model.
  - getCompartmentType
```
@Deprecated
public CompartmentType getCompartmentType(int n)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Gets the n^th CompartmentType object in this Model.
    
    Parameters:
    n - index
    
    Returns:
    the n^th CompartmentType of this Model. Returns null if there are no compartmentType defined or if the index n is too big or lower than zero.
  - getCompartmentType
```
@Deprecated
public CompartmentType getCompartmentType(java.lang.String id)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Gets the CompartmentType with the given id.
    
    Parameters:
    id -
    
    Returns:
    the CompartmentType of the listOfCompartmentTypes which has 'id' as id (or name depending on the level and version). null if the listOfCompartmentTypes is not set or the id is not found.
  - getCompartmentTypeCount
```
@Deprecated
public int getCompartmentTypeCount()
```
    Deprecated. using CompartmentType is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns the number of CompartmentTypes of this Model.
    
    Returns:
    the number of CompartmentTypes of this Model.
  - getConstraint
```
public Constraint getConstraint(int n)
```
    Gets the n^th Constraint object in this Model.
    
    Parameters:
    n -
    
    Returns:
    the n^th Constraint of this Model. Returns null if there are no constraint defined or if the index n is too big or lower than zero.
  - getConstraintCount
```
public int getConstraintCount()
```
    Returns the number of Constraints of this Model.
    
    Returns:
    the number of Constraints of this Model.
  - getConversionFactor
```
public java.lang.String getConversionFactor()
```
    Returns the conversionFactor ID of this Model.
    
    Returns:
    the conversionFactorID of this Model. Returns an empty String if it is not set.
  - getConversionFactorInstance
```
public Parameter getConversionFactorInstance()
```
    Returns the Parameter instance which has the conversionFactorID of this Model as id.
    
    Returns:
    the Parameter instance which has the conversionFactorID of this Model as id. null if it doesn't exist
  - getDelayCount
```
public int getDelayCount()
```
    Returns the number of Delays of this Model.
    
    Returns:
    the number of Delays of this Model.
  - getEvent
```
public Event getEvent(int n)
```
    Gets the n^th Event object in this Model.
    
    Parameters:
    n -
    
    Returns:
    the n^th Event of this Model. Returns null if there are no event defined or if the index n is too big or lower than zero.
  - getEvent
```
public Event getEvent(java.lang.String id)
```
    Gets the Event which as the given id as id.
    
    Parameters:
    id -
    
    Returns:
    the Event of the listOfEvents which has 'id' as id (or name depending on the level and version). null if the listOfEvents is not set.
  - getEventAssignmentCount
```
public int getEventAssignmentCount()
```
    Returns the number of EventAssignments of this Model.
    
    Returns:
    return the number of EventAssignments of this Model.
  - getEventCount
```
public int getEventCount()
```
    Returns the number of Events of this Model.
    
    Returns:
    the number of Events of this Model.
  - getExtentUnits
```
public java.lang.String getExtentUnits()
```
    Returns the extent units ID of this Model.
    
    Returns:
    the extent units ID of this Model. Returns an empty String if it is not set.
  - getExtentUnitsInstance
```
public UnitDefinition getExtentUnitsInstance()
```
    Returns the UnitDefinition instance which has the extent units ID of this Model as id.
    
    Returns:
    the UnitDefinition instance which has the extent units ID of this Model as id. null if it doesn't exist
  - getFunctionDefinition
```
public FunctionDefinition getFunctionDefinition(int n)
```
    Gets the n^th FunctionDefinition instance of the listOfFunstionDefinitions.
    
    Parameters:
    n -
    
    Returns:
    the n^th FunctionDefinition instance of the listOfFunstionDefinitions. null if the listOfFunctionDefinitions is not set.
  - getFunctionDefinition
```
public FunctionDefinition getFunctionDefinition(java.lang.String id)
```
    Returns the FunctionDefinition of the listOfFunctionDefinitions which has 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the FunctionDefinition of the listOfFunctionDefinitions which has 'id' as id (or name depending on the level and version). null if the listOfFunctionDefinitions is not set.
  - getFunctionDefinitionCount
```
public int getFunctionDefinitionCount()
```
    Returns the number of FunctionDefinitions of this Model.
    
    Returns:
    the number of FunctionDefinitions of this Model.
  - getInitialAssignment
```
public InitialAssignment getInitialAssignment(int n)
```
    Gets the n^th InitialAssignment object in this Model.
    
    Parameters:
    n -
    
    Returns:
    the n^th InitialAssignment of this Model. null if the listOfInitialAssignments is not set.
  - getInitialAssignment
```
public InitialAssignment getInitialAssignment(java.lang.String variable)
```
    Returns the InitialAssignment of the listOfInitialAssignments whose symbol attribute, i.e., whose Variable has the given variable as identifier.
    
    Parameters:
    variable - The identifier of a variable, for which a corresponding InitialAssignment is requested.
    
    Returns:
    the first InitialAssignment of the listOfInitialAssignments, whose Variable has the variable as identifier (or name depending on the level and version). null if it doesn't exist.
  - getInitialAssignmentCount
```
public int getInitialAssignmentCount()
```
    Returns the number of InitialAssignments of this Model.
    
    Returns:
    the number of InitialAssignments of this Model.
  - getKineticLawCount
```
public int getKineticLawCount()
```
    Returns the number of KineticLaws of this Model.
    
    Returns:
    the number of KineticLaws of this Model.
  - getLastElementOf
```
private <T> T getLastElementOf(ListOf<? extends T> listOf)
```
    Returns the last element added in the given list.
    
    Returns:
    the last element added in the model, corresponding to the last element of the list of these elements, or null is no element exist for this type.
  - getLengthUnits
```
public java.lang.String getLengthUnits()
```
    Returns the length units ID of this Model.
    
    Returns:
    the length units ID of this Model. Returns an empty String if it is not set.
  - getLengthUnitsInstance
```
public UnitDefinition getLengthUnitsInstance()
```
    Returns the length units of this Model as a UnitDefinition.
    
    Returns:
    the UnitDefinition instance which has the lengthUnitsID of this Model as id. null if it doesn't exist.
  - getListOfCompartments
```
public ListOf<Compartment> getListOfCompartments()
```
    Returns the listOfCompartments of this Model.
    
    Returns:
    the listOfCompartments of this Model.
  - getListOfCompartmentTypes
```
@Deprecated
public ListOf<CompartmentType> getListOfCompartmentTypes()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns the listOfCompartmentTypes of this Model.
    
    Returns:
    the listOfCompartmentTypes of this Model.
  - getListOfConstraints
```
public ListOf<Constraint> getListOfConstraints()
```
    Returns the listOfConstraints of this Model.
    
    Returns:
    the listOfConstraints of this Model. set.
  - getListOfCount
```
public int getListOfCount()
```
    Returns the number of ListOfs of this Model.
    
    Returns:
    the number of ListOfs of this Model.
  - getListOfEvents
```
public ListOf<Event> getListOfEvents()
```
    Returns the listOfEvents of this Model.
    
    Returns:
    the listOfEvents of this Model.
  - getListOfFunctionDefinitions
```
public ListOf<FunctionDefinition> getListOfFunctionDefinitions()
```
    Returns the listOfFunctionDefinitions of this Model.
    
    Returns:
    the listOfFunctionDefinitions of this Model.
  - getListOfInitialAssignments
```
public ListOf<InitialAssignment> getListOfInitialAssignments()
```
    Returns the listOfInitialAssignments of this Model.
    
    Returns:
    the listOfInitialAssignments of this Model.
  - getListOfParameters
```
public ListOf<Parameter> getListOfParameters()
```
    Returns the listOfParameters of this Model.
    
    Returns:
    the listOfParameters of this Model.
  - getListOfPredefinedUnitDefinitions
```
public java.util.List<UnitDefinition> getListOfPredefinedUnitDefinitions()
```
    Returns:
  - getListOfReactions
```
public ListOf<Reaction> getListOfReactions()
```
    Returns the listOfReactions of this Model.
    
    Returns:
    the listOfReactions of this Model.
  - getListOfRules
```
public ListOf<Rule> getListOfRules()
```
    Returns the listOfRules of this Model.
    
    Returns:
    the listOfRules of this Model.
  - getListOfSpecies
```
public ListOf<Species> getListOfSpecies()
```
    Returns the listOfSpecies of this Model.
    
    Returns:
    the listOfSpecies of this Model.
  - getListOfSpeciesTypes
```
@Deprecated
public ListOf<SpeciesType> getListOfSpeciesTypes()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns the listOfSpeciesTypes of this Model.
    
    Returns:
    the listOfSpeciesTypes of this Model.
  - getListOfUnitDefinitions
```
public ListOf<UnitDefinition> getListOfUnitDefinitions()
```
    Returns the listOfUnitDefinitions of this Model.
    
    Returns:
    the listOfUnitDefinitions of this Model.
  - getLocalParameterCount
```
public int getLocalParameterCount()
```
    Returns the number of parameters that are contained within kineticLaws in the reactions of this model.
    
    Returns:
    the number of parameters that are contained within kineticLaws in the reactions of this model.
  - getMathContainerCount
```
public int getMathContainerCount()
```
    Returns the number of elements that can contain math in the Model .
    
    Returns:
    the number of elements that can contain math in the Model .
    See Also:
    MathContainer
  - getModelHistory
```
@Deprecated
public History getModelHistory()
```
    Deprecated. use SBase.getHistory()
    
    Returns History of this model.
    
    Returns:
    the History of this model.
    See Also:
    SBase.getHistory()
  - getModifierSpeciesReferenceCount
```
public int getModifierSpeciesReferenceCount()
```
    Returns the number of ModifierSpeciesReferences in the Model.
    
    Returns:
    the number of ModifierSpeciesReferences in the Model.
  - getModifierSpeciesReferences
```
public java.util.Set<ModifierSpeciesReference> getModifierSpeciesReferences()
```
    Returns all ModifierSpeciesReferences, registered in any Reaction.
    
    Returns:
  - getNamedSBaseCount
```
public int getNamedSBaseCount()
```
    Returns the number of NamedSBases in the Model, so elements that can have a name.
    
    Returns:
    the number of NamedSBases in the Model, so elements that can have a name.
  - getNamedSBaseWithDerivedUnitCount
```
public int getNamedSBaseWithDerivedUnitCount()
```
  - getNumCompartments
```
public int getNumCompartments()
```
    Returns the number of Compartments of this Model.
    
    Returns:
    the number of Compartments of this Model.
  - getNumCompartmentTypes
```
@Deprecated
public int getNumCompartmentTypes()
```
    Deprecated.
    
    Returns the number of CompartmentTypes of this Model.
    
    Returns:
    the number of CompartmentTypes of this Model.
  - getNumConstraints
```
public int getNumConstraints()
```
    Returns the number of Constraints of this Model.
    
    Returns:
    the number of Constraints of this Model.
  - getNumDelays
```
public int getNumDelays()
```
    Returns the number of Delays of this Model.
    
    Returns:
    the number of Delays of this Model.
  - getNumEventAssignments
```
public int getNumEventAssignments()
```
    Returns the number of EventAssignments of this Model.
    
    Returns:
    return the number of EventAssignments of this Model.
  - getNumEvents
```
public int getNumEvents()
```
    Returns the number of Events of this Model.
    
    Returns:
    the number of Events of this Model.
  - getNumFunctionDefinitions
```
public int getNumFunctionDefinitions()
```
    Returns the number of FunctionDefinitions of this Model.
    
    Returns:
    the number of FunctionDefinitions of this Model.
  - getNumInitialAssignments
```
public int getNumInitialAssignments()
```
    Returns the number of InitialAssignments of this Model.
    
    Returns:
    the number of InitialAssignments of this Model.
  - getNumKineticLaws
```
public int getNumKineticLaws()
```
    Returns the number of KineticLaws of this Model.
    
    Returns:
    the number of KineticLaws of this Model.
  - getNumListsOf
```
public int getNumListsOf()
```
    Returns the number of ListOfs of this Model.
    
    Returns:
    the number of ListOfs of this Model.
  - getNumLocalParameters
```
public int getNumLocalParameters()
```
    Returns the number of parameters that are contained within kineticLaws in the reactions of this model.
    
    Returns:
    the number of parameters that are contained within kineticLaws in the reactions of this model.
  - getNumMathContainers
```
public int getNumMathContainers()
```
    Returns the number of elements that can contain math in the Model .
    
    Returns:
    the number of elements that can contain math in the Model .
    See Also:
    MathContainer
  - getNumModifierSpeciesReferences
```
public int getNumModifierSpeciesReferences()
```
    Returns the number of ModifierSpeciesReferences in the Model.
    
    Returns:
    the number of ModifierSpeciesReferences in the Model.
  - getNumNamedSBases
```
public int getNumNamedSBases()
```
    Returns the number of NamedSBases in the Model, so elements that can have a name.
    
    Returns:
    the number of NamedSBases in the Model, so elements that can have a name.
  - getNumNamedSBasesWithDerivedUnit
```
public int getNumNamedSBasesWithDerivedUnit()
```
    Returns the number of NamedSBaseWithDerivedUnits in the Model, so elements that can have a name and a unit that can be derived.
    
    Returns:
    the number of NamedSBaseWithDerivedUnits in the Model, so elements that can have a name and a unit that can be derived.
  - getNumParameters
```
public int getNumParameters()
```
    Returns the number of Parameters of this Model.
    
    Returns:
    the number of Parameters of this Model.
  - getNumQuantities
```
public int getNumQuantities()
```
    Returns the number of Quantitys of this Model.
    
    Returns:
    the number of Quantitys of this Model.
  - getNumQuantitiesWithUnit
```
public int getNumQuantitiesWithUnit()
```
    Returns the number of QuantityWithUnits of this Model.
    
    Returns:
    the number of QuantityWithUnits of this Model.
  - getNumReactions
```
public int getNumReactions()
```
    Returns the number of Reactions of this Model.
    
    Returns:
    the number of Reactions of this Model.
  - getNumRules
```
public int getNumRules()
```
    Returns the number of Rules of this Model.
    
    Returns:
    the number of Rules of this Model.
  - getNumSBases
```
public int getNumSBases()
```
    Returns the number of SBases of this Model.
    
    Returns:
    the number of SBases of this Model.
  - getNumSBasesWithDerivedUnit
```
public int getNumSBasesWithDerivedUnit()
```
    Returns the number of SBaseWithDerivedUnits of this Model.
    
    Returns:
    the number of SBaseWithDerivedUnits of this Model.
  - getNumSpecies
```
public int getNumSpecies()
```
    Returns the number of Species of this Model.
    
    Returns:
    the number of Species of this Model.
  - getNumSpeciesReferences
```
public int getNumSpeciesReferences()
```
    Returns the number of SpeciesReferences of this Model.
    
    Returns:
    the number of SpeciesReferences of this Model.
  - getNumSpeciesTypes
```
@Deprecated
public int getNumSpeciesTypes()
```
    Deprecated.
    
    Returns the number of SpeciesTypes of this Model.
    
    Returns:
    the number of SpeciesTypes of this Model.
  - getNumSpeciesWithBoundaryCondition
```
public int getNumSpeciesWithBoundaryCondition()
```
    Returns the number of Species whose boundary condition is set to true.
    
    Returns:
    the number of Species whose boundary condition is set to true.
  - getNumStoichiometryMath
```
public int getNumStoichiometryMath()
```
    Returns the number of StoichiometryMath in the Model.
    
    Returns:
    the number of StoichiometryMath in the Model.
  - getNumSymbols
```
public int getNumSymbols()
```
    Returns the number of all instances of Symbol referenced within the model. There is no dedicated list for Symbols. This is a convenient method to support working with the model data structure.
    
    Returns:
    The number of Compartments, Species, and Parameters in the model.
  - getNumTriggers
```
public int getNumTriggers()
```
    Returns the number of Trigger of this Model.
    
    Returns:
    the number of Trigger of this Model.
  - getNumUnitDefinitions
```
public int getNumUnitDefinitions()
```
    Returns the number of UnitDefinitions of this Model.
    
    Returns:
    the number of UnitDefinitions of this Model.
  - getNumUnits
```
public int getNumUnits()
```
    Returns the number of Units of this Model.
    
    Returns:
    the number of Units of this Model.
  - getNumVariables
```
public int getNumVariables()
```
    Returns the number of Variables of this Model.
    
    Returns:
    the number of Variables of this Model.
  - getParameter
```
public Parameter getParameter(int n)
```
    Gets the n^th Parameter object in this Model.
    
    Parameters:
    n - index
    
    Returns:
    the n^th Parameter of this Model.
  - getParameter
```
public Parameter getParameter(java.lang.String id)
```
    Returns the Parameter of the listOfParameters which has 'id' as id
    
    Parameters:
    id -
    
    Returns:
    the Parameter of the listOfParameters which has 'id' as id (or name depending on the level and version). null if it doesn't exist.
  - getParameterCount
```
public int getParameterCount()
```
    Returns the number of Parameters of this Model.
    
    Returns:
    the number of Parameters of this Model.
  - getPredefinedUnitDefinition
```
public UnitDefinition getPredefinedUnitDefinition(java.lang.String unitKind)
```
    Returns a UnitDefinition representing one of the predefined units of SBML, returns null if the given unit kind is not a valid one for the SBML level and version of this Model.
    
    Parameters:
    unitKind - a unit kind for one of the predefined units from the SBML Specifications
    
    Returns:
    a UnitDefinition representing one of the predefined units of SBML, null if the unitKind is invalid.
  - getQuantityCount
```
public int getQuantityCount()
```
    Returns the number of Quantitys of this Model.
    
    Returns:
    the number of Quantitys of this Model.
  - getQuantityWithUnitCount
```
public int getQuantityWithUnitCount()
```
    Returns the number of QuantityWithUnits of this Model.
    
    Returns:
    the number of QuantityWithUnits of this Model.
  - getReaction
```
public Reaction getReaction(int n)
```
    Gets the n-th Reaction object in this Model.
    
    Parameters:
    n - the reaction index
    
    Returns:
    the n-th Reaction of this Model.
  - getReaction
```
public Reaction getReaction(java.lang.String id)
```
    Returns the Reaction of the listOfReactions which has 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the Reaction of the listOfReactions which has 'id' as id (or name depending on the level and version). null if it doesn't exist.
  - getReactionCount
```
public int getReactionCount()
```
    Returns the number of Reactions of this Model.
    
    Returns:
    the number of Reactions of this Model.
  - getRule
```
public Rule getRule(int n)
```
    Gets the n^th Rule of the listOfRules.
    
    Parameters:
    n - an index
    
    Returns:
    the n^th Rule of the listOfRules. null if it doesn't exist.
  - getRule
```
public ExplicitRule getRule(java.lang.String variable)
```
    Searches for the first instance of ExplicitRule within this Model's listOfRules, whose variable attribute is set to the value passed to this method.
    
    Parameters:
    variable -
    
    Returns:
    null if no element with the required property exists.
  - getRuleCount
```
public int getRuleCount()
```
    Returns the number of Rules of this Model.
    
    Returns:
    the number of Rules of this Model.
  - getSBaseCount
```
public int getSBaseCount()
```
    Returns the number of SBases of this Model.
    
    Returns:
    the number of SBases of this Model.
  - getSBaseWithDerivedUnitCount
```
public int getSBaseWithDerivedUnitCount()
```
    Returns the number of SBaseWithDerivedUnits of this Model.
    
    Returns:
    the number of SBaseWithDerivedUnits of this Model.
  - getSpecies
```
public Species getSpecies(int n)
```
    Gets the n-th Species object in this Model.
    
    Parameters:
    n - an index
    
    Returns:
    the Species with the given index if it exists, null otherwise.
  - getSpecies
```
public Species getSpecies(java.lang.String id)
```
    Gets the Species of the listOfSpecies which has 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the Species of the listOfSpecies which has 'id' as id (or name depending on the level and version). null if it doesn't exist.
  - getSpeciesCount
```
public int getSpeciesCount()
```
    Returns the number of Species of this Model.
    
    Returns:
    the number of Species of this Model.
  - getSpeciesReferenceCount
```
public int getSpeciesReferenceCount()
```
    Returns the number of SpeciesReferences of this Model.
    
    Returns:
    the number of SpeciesReferences of this Model.
  - getSpeciesType
```
@Deprecated
public SpeciesType getSpeciesType(int n)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Gets the n^th SpeciesType object in this Model.
    
    Parameters:
    n - index
    
    Returns:
    the n^th SpeciesType of this Model. Returns null if there are no speciesType defined or if the index n is too big or lower than zero.
  - getSpeciesType
```
@Deprecated
public SpeciesType getSpeciesType(java.lang.String id)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns the SpeciesType of the listOfSpeciesTypes which has 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the SpeciesType of the listOfSpeciesTypes which has 'id' as id (or name depending on the level and version). null if it doesn't exist.
  - getSpeciesTypeCount
```
@Deprecated
public int getSpeciesTypeCount()
```
    Deprecated. the use of SpeciesType is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns the number of SpeciesTypes of this Model.
    
    Returns:
    the number of SpeciesTypes of this Model.
  - getSpeciesWithBoundaryConditionCount
```
public int getSpeciesWithBoundaryConditionCount()
```
    Returns the number of Species whose boundary condition is set to true.
    
    Returns:
    the number of Species whose boundary condition is set to true.
  - getStoichiometryMathCount
```
public int getStoichiometryMathCount()
```
    Returns the number of StoichiometryMath in the Model.
    
    Returns:
    the number of StoichiometryMath in the Model.
  - getSubstanceUnits
```
public java.lang.String getSubstanceUnits()
```
    Returns the substance units ID of this model.
    
    Returns:
    the substance units ID of this model. Returns the empty String if it is not set.
  - getSubstanceUnitsInstance
```
public UnitDefinition getSubstanceUnitsInstance()
```
    Returns the UnitDefinition which has the substanceUnitsID of this Model as id.
    
    Returns:
    the UnitDefinition which has the substanceUnitsID of this Model as id. null if it doesn't exist.
  - getSymbolCount
```
public int getSymbolCount()
```
    Returns the number of all instances of Symbol referenced within the model. There is no dedicated list for Symbols. This is a convenient method to support working with the model data structure.
    
    Returns:
    The number of Compartments, Species, and Parameters in the model.
  - getTimeUnits
```
public java.lang.String getTimeUnits()
```
    Returns the time units ID of this Model.
    
    Returns:
    the time units ID of this Model or an empty String if it is not set.
  - getTimeUnitsInstance
```
public UnitDefinition getTimeUnitsInstance()
```
    Gets the UnitDefinition representing the time units of this Model.
    
    Returns:
    the UnitDefinition representing the time units of this Model, null if it is not defined in this Model
  - getTriggerCount
```
public int getTriggerCount()
```
    Returns the number of Trigger of this Model.
    
    Returns:
    the number of Trigger of this Model.
  - getUnitCount
```
public int getUnitCount()
```
    Returns the number of Units of this Model.
    
    Returns:
    the number of Units of this Model.
  - getUnitDefinition
```
public UnitDefinition getUnitDefinition(int n)
```
    Gets the n^th UnitDefinition object in this Model.
    
    Parameters:
    n -
    
    Returns:
    the n^th UnitDefinition of this Model. Returns null if there are no UnitDefinitions defined or if the index n is too big or lower than zero.
  - getUnitDefinition
```
public UnitDefinition getUnitDefinition(java.lang.String id)
```
    Returns the UnitDefinition of the listOfUnitDefinitions which has 'id' as id. If no UnitDefinition are found, we check in the listOfPredefinedUnitDefinitions. If we still did not find a UnitDefinition, null is returned.
    
    Parameters:
    id -
    
    Returns:
    the UnitDefinition of the listOfUnitDefinitionss which has 'id' as id (or name depending on the level and version). null if it doesn't exist.
  - getUnitDefinitionCount
```
public int getUnitDefinitionCount()
```
    Returns the number of UnitDefinitions of this Model.
    
    Returns:
    the number of UnitDefinitions of this Model.
  - getVariableCount
```
public int getVariableCount()
```
    Returns the number of Variables of this Model.
    
    Returns:
    the number of Variables of this Model.
  - getVolumeUnits
```
public java.lang.String getVolumeUnits()
```
    Returns the volume units ID of this Model.
    
    Returns:
    the volume units ID of this Model. Returns an empty String if it is not set.
  - getVolumeUnitsInstance
```
public UnitDefinition getVolumeUnitsInstance()
```
    Returns the UnitDefinition instance which has the volumeUnitsID of this Model as id.
    
    Returns:
    the UnitDefinition instance which has the volumeUnitsID of this Model as id. null if it doesn't exist.
  - hashCode
```
public int hashCode()
```
    Description copied from interface: SBase
    
    Returns a hash code value for this SBase instance.
    
    Specified by:
    
    hashCode in interface SBase
    
    Overrides:
    
    hashCode in class AbstractNamedSBase
    
    Returns:
    a hash code value for this SBase instance.
    See Also:
    Object.hashCode()
  - hasUnit
```
public boolean hasUnit(java.lang.String id)
```
    Returns true if this model has a reference to the unit with the given identifier.
    
    Parameters:
    id -
    
    Returns:
    true if this model has a reference to the unit with the given identifier, false otherwise.
  - initDefaults
```
public void initDefaults()
```
    Initializes the default values using the current Level/Version configuration.
  - initDefaults
```
public void initDefaults(int level,
                int version)
```
    Initializes the default values of the attributes of the Model
  - isIdMandatory
```
public boolean isIdMandatory()
```
    Description copied from interface: NamedSBase
    
    This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
    
    Specified by:
    
    isIdMandatory in interface NamedSBase
    
    Returns:
    true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.
  - isSetAreaUnits
```
public boolean isSetAreaUnits()
```
    Returns true if the area units ID of this Model is not null.
    
    Returns:
    true if the area units ID of this Model is not null.
  - isSetAreaUnitsInstance
```
public boolean isSetAreaUnitsInstance()
```
    Returns true if the UnitDefinition which has the area units ID of this Model as id is not null.
    
    Returns:
    true if the UnitDefinition which has the area units ID of this Model as id is not null.
  - isSetConversionFactor
```
public boolean isSetConversionFactor()
```
    Returns true if the conversionFactorID of this Model is not null.
    
    Returns:
    true if the conversionFactorID of this Model is not null.
  - isSetConversionFactorInstance
```
public boolean isSetConversionFactorInstance()
```
    Returns true if the Parameter which has the conversionFactorID of this Model as id is not null.
    
    Returns:
    true if the Parameter which has the conversionFactorID of this Model as id is not null.
  - isSetExtentUnits
```
public boolean isSetExtentUnits()
```
    Returns true if the extentUnitsID of this Model is not null.
    
    Returns:
    true if the extentUnitsID of this Model is not null.
  - isSetExtentUnitsInstance
```
public boolean isSetExtentUnitsInstance()
```
    Returns true if the UnitDefinition which has the extentUnitsID of this Model as id is not null.
    
    Returns:
    true if the UnitDefinition which has the extentUnitsID of this Model as id is not null.
  - isSetLengthUnits
```
public boolean isSetLengthUnits()
```
    Returns true if the lengthUnitsID of this Model is not null.
    
    Returns:
    true if the lengthUnitsID of this Model is not null.
  - isSetLengthUnitsInstance
```
public boolean isSetLengthUnitsInstance()
```
    Returns true if the UnitDefinition which has the lengthUnitsID of this Model as id is not null.
    
    Returns:
    true if the UnitDefinition which has the lengthUnitsID of this Model as id is not null.
  - isSetListOfCompartments
```
public boolean isSetListOfCompartments()
```
    Returns true if the listOfCompartments of this Model is not null and not empty.
    
    Returns:
    true if the listOfCompartments of this Model is not null and not empty.
  - isSetListOfCompartmentTypes
```
@Deprecated
public boolean isSetListOfCompartmentTypes()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns true if the listOfCompartmentTypes of this Model is not null and not empty.
    
    Returns:
    true if the listOfCompartmentTypes of this Model is not null and not empty.
  - isSetListOfConstraints
```
public boolean isSetListOfConstraints()
```
    Returns true if the listOfConstraints of this Model is not null and not empty.
    
    Returns:
    true if the listOfConstraints of this Model is not null and not empty.
  - isSetListOfEvents
```
public boolean isSetListOfEvents()
```
    Returns true if the listOfEvents of this Model is not null and not empty.
    
    Returns:
    true if the listOfEvents of this Model is not null and not empty.
  - isSetListOfFunctionDefinitions
```
public boolean isSetListOfFunctionDefinitions()
```
    Returns true if the listOfFunctionDefinitions of this Model is not null and not empty.
    
    Returns:
    true if the listOfFunctionDefinitions of this Model is not null and not empty.
  - isSetListOfInitialAssignments
```
public boolean isSetListOfInitialAssignments()
```
    Returns true if the listOfInitialAssignments of this Model is not null and not empty.
    
    Returns:
    true if the listOfInitialAssignments of this Model is not null and not empty.
  - isSetListOfParameters
```
public boolean isSetListOfParameters()
```
    Returns true if the listOfParameters of this Model is not null and not empty.
    
    Returns:
    true if the listOfParameters of this Model is not null and not empty.
  - isSetListOfReactions
```
public boolean isSetListOfReactions()
```
    Returns true if the listOfReactions of this Model is not null and not empty.
    
    Returns:
    true if the listOfReactions of this Model is not null and not empty.
  - isSetListOfRules
```
public boolean isSetListOfRules()
```
    Returns true if the listOfRules of this Model is not null and not empty.
    
    Returns:
    true if the listOfRules of this Model is not null and not empty.
  - isSetListOfSpecies
```
public boolean isSetListOfSpecies()
```
    Returns true if the listOfSpecies of this Model is not null and not empty.
    
    Returns:
    true if the listOfSpecies of this Model is not null and not empty.
  - isSetListOfSpeciesTypes
```
@Deprecated
public boolean isSetListOfSpeciesTypes()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Returns true if the listOfSpeciesTypes of this Model is not null and not empty.
    
    Returns:
    true if the listOfSpeciesTypes of this Model is not null and not empty.
  - isSetListOfUnitDefinitions
```
public boolean isSetListOfUnitDefinitions()
```
    Returns true if the listOfUnitDefinitions of this Model is not null and not empty.
    
    Returns:
    true if the listOfUnitDefinitions of this Model is not null and not empty.
  - isSetModelHistory
```
@Deprecated
public boolean isSetModelHistory()
```
    Deprecated. use SBase.isSetHistory()
    
    Returns the History of the Model. This is equivalent to the call SBase.isSetHistory().
    
    Returns:
    the History of the Model.
  - isSetSubstanceUnits
```
public boolean isSetSubstanceUnits()
```
    Returns true if the substanceUnitsID of this Model is not null.
    
    Returns:
    true if the substanceUnitsID of this Model is not null.
  - isSetSubstanceUnitsInstance
```
public boolean isSetSubstanceUnitsInstance()
```
    Returns true if the UnitDefinition which has the substanceUnitsID of this Model as id is not null.
    
    Returns:
    true if the UnitDefinition which has the substanceUnitsID of this Model as id is not null.
  - isSetTimeUnits
```
public boolean isSetTimeUnits()
```
    Returns true if the timeUnitsID of this Model is not null.
    
    Returns:
    true if the timeUnitsID of this Model is not null.
  - isSetTimeUnitsInstance
```
public boolean isSetTimeUnitsInstance()
```
    Returns true if the UnitsDefinition which has the timeUnistID of this Model as id is not null.
    
    Returns:
    true if the UnitsDefinition which has the timeUnistID of this Model as id is not null.
  - isSetVolumeUnits
```
public boolean isSetVolumeUnits()
```
    Returns true if the volumeUnitsID of this Model is not null.
    
    Returns:
    true if the volumeUnitsID of this Model is not null.
  - isSetVolumeUnitsInstance
```
public boolean isSetVolumeUnitsInstance()
```
    Returns true if the UnitDefinition which has the volumeUnitsID of this Model as id is not null.
    
    Returns:
    true if the UnitDefinition which has the volumeUnitsID of this Model as id is not null.
  - readAttribute
```
public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)
```
    Description copied from interface: SBase
    
    Sets the given attribute in this SBase.
    If the given attribute name is not recognized, nothing is done and false is returned.
    
    Specified by:
    
    readAttribute in interface SBase
    
    Overrides:
    
    readAttribute in class AbstractNamedSBase
    
    Parameters:
    attributeName - localName of the XML attribute
    prefix - prefix of the XML attribute
    value - value of the XML attribute
    
    Returns:
    true if the attribute has been successfully read.
  - register
```
public boolean register(SBase sbase)
```
    Description copied from interface: IdManager
    
    Registers the given SBase element and all of it's children in this IdManager.
    
    Specified by:
    
    register in interface IdManager
    
    Returns:
    true if this operation was successfully performed, false otherwise.
  - registerId
```
private boolean registerId(KineticLaw kl,
                 LocalParameter lp,
                 boolean delete,
                 boolean alreadyRegisteredInKL)
```
    Registration of LocalParameter instances in the Model.
    
    Parameters:
    kl - the KineticLaw that contains the given LocalParameter
    lp - the LocalParameter whose identifier is to be registered.
    delete -
    
    Returns:
    true in case of success, otherwise false.
  - registerId
```
private boolean registerId(UniqueNamedSBase unsb,
                 boolean delete)
```
    Parameters:
    unsb -
    recursively -
    delete -
    
    Returns:
  - registerId
```
private boolean registerId(UnitDefinition ud,
                 boolean add)
```
    Registers the identifier and the corresponding UnitDefinition itself in this Model.
    
    Parameters:
    ud - the UnitDefinition to be registered.
    add -
    
    Returns:
    true if the operation was a success, false otherwise.
  - registerIds
```
private boolean registerIds(SBase parent,
                  SBase newElem,
                  boolean recursively,
                  boolean delete,
                  java.util.List<IdManager> idManagerList)
```
    Registers the given element in this Model.
    
    Parameters:
    parent -
    newElem -
    recursively -
    delete -
    idManagerList -
    
    Returns:
    true if this operation was successfully performed, false otherwise.
  - remove
```
private <T extends UniqueNamedSBase> T remove(java.lang.Class<T> clazz,
                                    java.lang.String id)
```
    Removes the element with the given id from this model if such an element can be found. The type attribute is used to assess if the element with this id has the required type.
    
    Parameters:
    clazz - The desired type of the element to be removed, can be null.
    id - the identifier of the NamedSBase to be removed.
    
    Returns:
    the removed element in case of success, or null if no such element could be found or the action was not successful.
  - remove
```
public <T extends UniqueNamedSBase> T remove(java.lang.String id)
```
    Removes any UniqueNamedSBase with the given identifier from this Model and returns the removed element if the operation was successfull. Note that this method cannot be used to remove UnitDefinitions from this Model because UnitDefinitions exist in a separate namespace that might have overlapping identifiers. It would therefore not be clear, which element to remove in case of a identifier clash.
    
    Parameters:
    id - the identifier of the element that is to be removed from this model.
    
    Returns:
    the removed element or null if the operation was not successful.
  - removeCompartment
```
public Compartment removeCompartment(int i)
```
    Removes the i-th Compartment of the Model.
    
    Parameters:
    i - the index of the Compartment to remove
    
    Returns:
    the removed Compartment.
  - removeCompartment
```
public Compartment removeCompartment(java.lang.String id)
```
    Removes the Compartment of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed Compartment.
  - removeCompartmentType
```
@Deprecated
public CompartmentType removeCompartmentType(int n)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Removes the n-th CompartmentType of the Model.
    
    Parameters:
    n - the index of the Compartment to remove
    
    Returns:
    the removed CompartmentType.
  - removeCompartmentType
```
@Deprecated
public CompartmentType removeCompartmentType(java.lang.String id)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Removes the CompartmentType of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeConstraint
```
public Constraint removeConstraint(int n)
```
    Removes the n-th Constraint of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeEvent
```
public Event removeEvent(int n)
```
    Removes the n-th Event of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeEvent
```
public Event removeEvent(java.lang.String id)
```
    Removes the Event of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeFunctionDefinition
```
public FunctionDefinition removeFunctionDefinition(int n)
```
    Removes the n-th FunctionDefinition of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeFunctionDefinition
```
public FunctionDefinition removeFunctionDefinition(java.lang.String id)
```
    Removes the FunctionDefinition of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeInitialAssignment
```
public InitialAssignment removeInitialAssignment(int n)
```
    Removes the n-th InitialAssignment of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeParameter
```
public Parameter removeParameter(int n)
```
    Removes the n-th Parameter of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeParameter
```
public boolean removeParameter(Parameter parameter)
```
    Removes the Parameter 'parameter' from this Model.
    
    Parameters:
    parameter -
    
    Returns:
    true if the Parameter was found and removed.
  - removeParameter
```
public Parameter removeParameter(java.lang.String id)
```
    Removes the Parameter of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeReaction
```
public Reaction removeReaction(int n)
```
    Removes the n-th Reaction of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeReaction
```
public boolean removeReaction(Reaction reac)
```
    Removes a reaction from the model.
    
    Parameters:
    reac -
    
    Returns:
    true if the Reaction was found and removed.
  - removeReaction
```
public Reaction removeReaction(java.lang.String id)
```
    Removes the Reaction of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeRule
```
public Rule removeRule(int i)
```
    Removes the i-th Rule of the Model.
    
    Parameters:
    i -
    
    Returns:
    the removed element.
  - removeRule
```
public Rule removeRule(java.lang.String variableId)
```
    Removes the Rule of the Model with 'variableId' as variable.
    
    Parameters:
    variableId -
    
    Returns:
    the removed element.
  - removeRule
```
public boolean removeRule(Rule rule)
```
    Removes a Rule from the Model.
    
    Parameters:
    rule - the Rule to be removed.
    
    Returns:
    true if the Rule was found and removed.
  - removeSpecies
```
public Species removeSpecies(int i)
```
    Removes the i-th Species of the Model.
    
    Parameters:
    i -
    
    Returns:
    the removed element.
  - removeSpecies
```
public boolean removeSpecies(Species spec)
```
    Removes a species from the model.
    
    Parameters:
    spec -
    
    Returns:
    true if the Species was found and removed.
  - removeSpecies
```
public Species removeSpecies(java.lang.String id)
```
    Removes the Species of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeSpeciesType
```
@Deprecated
public SpeciesType removeSpeciesType(int n)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Removes the n-th SpeciesType of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeSpeciesType
```
@Deprecated
public SpeciesType removeSpeciesType(java.lang.String id)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Removes the SpeciesType of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeUnitDefinition
```
public UnitDefinition removeUnitDefinition(int n)
```
    Removes the n-th UnitDefinition of the Model.
    
    Parameters:
    n -
    
    Returns:
    the removed element.
  - removeUnitDefinition
```
public UnitDefinition removeUnitDefinition(java.lang.String id)
```
    Removes the UnitDefinition of the Model with 'id' as id.
    
    Parameters:
    id -
    
    Returns:
    the removed element.
  - removeUnitDefinition
```
public boolean removeUnitDefinition(UnitDefinition unitDefininition)
```
    Removes a UnitDefinition of the Model.
    
    Parameters:
    unitDefininition -
    
    Returns:
    true if the UnitDefinition 'unitDefinition' has been removed from the Model.
  - setAreaUnits
```
public void setAreaUnits(java.lang.String areaUnitsID)
```
    Sets the areaUnitsID of this Model to 'areaUnitsID'
    
    Parameters:
    areaUnitsID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setAreaUnits
```
public void setAreaUnits(Unit.Kind kind)
```
    Parameters:
    kind -
  - setAreaUnits
```
public void setAreaUnits(UnitDefinition areaUnits)
```
    Sets the areaUnitsID of this Model to the id of the UnitDefinition 'areaUnits'.
    
    Parameters:
    areaUnits -
  - setConversionFactor
```
public void setConversionFactor(Parameter conversionFactor)
```
    Sets the conversionFactorID of this Model to the id of the Parameter 'conversionFactor'.
    
    Parameters:
    conversionFactor -
  - setConversionFactor
```
public void setConversionFactor(java.lang.String conversionFactorID)
```
    Sets the conversionFactorID of this Model to 'conversionFactorID'.
    
    Parameters:
    conversionFactorID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setExtentUnits
```
public void setExtentUnits(java.lang.String extentUnitsID)
```
    Sets the extendUnitsID of this Model to 'extentUnitsID'.
    
    Parameters:
    extentUnitsID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setExtentUnits
```
public void setExtentUnits(Unit.Kind kind)
```
    Parameters:
    kind -
  - setExtentUnits
```
public void setExtentUnits(UnitDefinition extentUnits)
```
    Sets the extentUnitsID of this Model to the id of the UnitDefinition 'extentUnits'.
    
    Parameters:
    extentUnits -
  - setLengthUnits
```
public void setLengthUnits(java.lang.String lengthUnitsID)
```
    Sets the lengthUnitsID of this Model to 'lengthUnitsID'.
    
    Parameters:
    lengthUnitsID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setLengthUnits
```
public void setLengthUnits(Unit.Kind kind)
```
    Parameters:
    kind -
  - setLengthUnits
```
public void setLengthUnits(UnitDefinition lengthUnits)
```
    Sets the lengthUnitsID of this Model to the id of the UnitDefinition 'lengthUnits'.
    
    Parameters:
    lengthUnits -
  - setListOfCompartments
```
public void setListOfCompartments(ListOf<Compartment> listOfCompartments)
```
    Sets the listOfCompartments of this Model to 'listOfCompartments'. Automatically sets the parentSBML objects of 'listOfCompartments' to this Model.
    
    Parameters:
    listOfCompartments -
  - setListOfCompartmentTypes
```
@Deprecated
public void setListOfCompartmentTypes(ListOf<CompartmentType> listOfCompartmentTypes)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Sets the listOfCompartmentTypes of this Model to 'listOfCompartmentTypes'. Automatically sets the parentSBML objects of 'listOfCompartmentTypes' to this Model.
    
    Parameters:
    listOfCompartmentTypes - the listOfCompartmentTypes to set
  - setListOfConstraints
```
public void setListOfConstraints(ListOf<Constraint> listOfConstraints)
```
    Sets the listOfConstraints of this Model to 'listOfConstraints'. Automatically sets the parentSBML objects of 'listOfCanstraints' to this Model.
    
    Parameters:
    listOfConstraints - the listOfConstraints to set
  - setListOfEvents
```
public void setListOfEvents(ListOf<Event> listOfEvents)
```
    Sets the listOfEvents of this Model to 'listOfEvents'. Automatically sets the parentSBML objects of 'listOfEvents' to this Model.
    
    Parameters:
    listOfEvents -
  - setListOfFunctionDefinitions
```
public void setListOfFunctionDefinitions(ListOf<FunctionDefinition> listOfFunctionDefinitions)
```
    Sets the listOfFunctionDefinitions of this Model to 'listOfFunctionDefinitions'. Automatically sets the parentSBML objects of 'listOfFunctionDefinitions' to this Model.
    
    Parameters:
    listOfFunctionDefinitions - the listOfFunctionDefinitions to set
  - setListOfInitialAssignments
```
public void setListOfInitialAssignments(ListOf<InitialAssignment> listOfInitialAssignments)
```
    Sets the listOfInitialAssignments of this Model to 'listOfInitialAssignments'. Automatically sets the parentSBML objects of 'listOfInitialAssignments' to this Model.
    
    Parameters:
    listOfInitialAssignments - the listOfInitialAssignments to set
  - setListOfParameters
```
public void setListOfParameters(ListOf<Parameter> listOfParameters)
```
    Sets the listOfParameters of this Model to 'listOfParameters'. Automatically sets the parentSBML objects of 'listOfParameters' to this Model.
    
    Parameters:
    listOfParameters -
  - setListOfReactions
```
public void setListOfReactions(ListOf<Reaction> listOfReactions)
```
    Sets the listOfReactions of this Model to 'listOfReactions'. Automatically sets the parentSBML objects of 'listOfReactions' to this Model.
    
    Parameters:
    listOfReactions -
  - setListOfRules
```
public void setListOfRules(ListOf<Rule> listOfRules)
```
    Sets the listOfRules of this Model to 'listOfRules'. Automatically sets the parentSBML objects of 'listOfRules' to this Model.
    
    Parameters:
    listOfRules -
  - setListOfSpecies
```
public void setListOfSpecies(ListOf<Species> listOfSpecies)
```
    Sets the listOfSpecies of this Model to 'listOfSpecies'. Automatically sets the parentSBML objects of 'listOfSpecies' to this Model.
    
    Parameters:
    listOfSpecies -
  - setListOfSpeciesTypes
```
@Deprecated
public void setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes)
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Sets the listOfSpeciesTypes of this Model to 'listOfSpeciesTypes'. Automatically sets the parentSBML objects of 'listOfSpeciesTypes' to this Model.
    
    Parameters:
    listOfSpeciesTypes - the listOfSpeciesTypes to set
  - setListOfUnitDefinitions
```
public void setListOfUnitDefinitions(ListOf<UnitDefinition> listOfUnitDefinitions)
```
    Sets the listOfUnitDefinitions of this Model to 'listOfUnitDefinitions'. Automatically sets the parentSBML objects of 'listOfUnitDefinitions' to this Model.
    
    Parameters:
    listOfUnitDefinitions -
  - setModelHistory
```
@Deprecated
public void setModelHistory(History history)
```
    Deprecated. use AbstractSBase.setHistory(History)
    
    Parameters:
    history -
    See Also:
    AbstractSBase.setHistory(History history)
  - setSubstanceUnits
```
public void setSubstanceUnits(java.lang.String substanceUnitsID)
```
    Sets the substanceUnitsID of this Model to 'substanceUnitsID'
    
    Parameters:
    substanceUnitsID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setSubstanceUnits
```
public void setSubstanceUnits(UnitDefinition substanceUnits)
```
    Sets the substanceUnitsID of this Model to the id of 'substanceUnits'.
    
    Parameters:
    substanceUnits -
  - setSubstanceUnits
```
public void setSubstanceUnits(Unit.Kind kind)
```
    Parameters:
    kind -
  - setTimeUnits
```
public void setTimeUnits(java.lang.String timeUnitsID)
```
    Sets the timeUnits of this Model to 'timeUnistID'
    
    Parameters:
    timeUnitsID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setTimeUnits
```
public void setTimeUnits(UnitDefinition timeUnits)
```
    Sets the timeUnitsID of this Model to the id of the UnitDefinition 'timeUnits'.
    
    Parameters:
    timeUnits -
  - setTimeUnits
```
public void setTimeUnits(Unit.Kind kind)
```
    Sets the timeUnitsID of this Model to the given unit kind.
    
    Parameters:
    kind -
  - setVolumeUnits
```
public void setVolumeUnits(java.lang.String volumeUnitsID)
```
    Sets the volumeUnitsID of this Model to 'volumeUnitsID'
    
    Parameters:
    volumeUnitsID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setVolumeUnits
```
public void setVolumeUnits(Unit.Kind kind)
```
    Parameters:
    kind -
  - setVolumeUnits
```
public void setVolumeUnits(UnitDefinition volumeUnits)
```
    Sets the volumeUnitsID of this Model to the id of the UnitDefinition 'volumeUnits'.
    
    Parameters:
    volumeUnits -
  - unregister
```
public boolean unregister(SBase sbase)
```
    Description copied from interface: IdManager
    
    Unregisters the given SBase element and all of it's children in this IdManager.
    
    Specified by:
    
    unregister in interface IdManager
    
    Returns:
    true if this operation was successfully performed, false otherwise.
  - unsetAreaUnits
```
public void unsetAreaUnits()
```
    Sets the areaUnitsID of this Model to null.
  - unsetConversionFactor
```
public void unsetConversionFactor()
```
    Sets the conversionFactorID of this Model to null.
  - unsetExtentUnits
```
public void unsetExtentUnits()
```
    Sets the extentUnitsID of this Model to null.
  - unsetLengthUnits
```
public void unsetLengthUnits()
```
    Sets the lengthUnitsID of this Model to null.
  - unsetListOfCompartments
```
public boolean unsetListOfCompartments()
```
    Removes the listOfCompartments from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfCompartmentTypes
```
@Deprecated
public boolean unsetListOfCompartmentTypes()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Removes the listOfCompartmentTypes from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfConstraints
```
public boolean unsetListOfConstraints()
```
    Removes the listOfConstraints from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfEvents
```
public boolean unsetListOfEvents()
```
    Removes the listOfEvents from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfFunctionDefinitions
```
public boolean unsetListOfFunctionDefinitions()
```
    Removes the listOfFunctionDefinitions from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfInitialAssignments
```
public boolean unsetListOfInitialAssignments()
```
    Removes the listOfInitialAssignments from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfParameters
```
public boolean unsetListOfParameters()
```
    Removes the listOfParameters from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfReactions
```
public boolean unsetListOfReactions()
```
    Removes the listOfReactions from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfRules
```
public boolean unsetListOfRules()
```
    Removes the listOfRules from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfSpecies
```
public boolean unsetListOfSpecies()
```
    Removes the listOfSpecies from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfSpeciesTypes
```
@Deprecated
public boolean unsetListOfSpeciesTypes()
```
    Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
    
    Removes the listOfSpeciesTypes from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfUnitDefinitions
```
public boolean unsetListOfUnitDefinitions()
```
    Removes the listOfUnitDefinitions from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetModelHistory
```
@Deprecated
public void unsetModelHistory()
```
    Deprecated. use AbstractSBase.unsetHistory().
    
    See Also:
    AbstractSBase.unsetHistory()
  - unsetSubstanceUnits
```
public void unsetSubstanceUnits()
```
    Sets the substanceUnitsID of this Model to null.
  - unsetTimeUnits
```
public void unsetTimeUnits()
```
    Sets the timeUnitsID of this Model to null.
  - unsetVolumeUnits
```
public void unsetVolumeUnits()
```
    Sets the volumeUnitsID of this Model to null.
  - writeXMLAttributes
```
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
```
    Description copied from interface: SBase
    
    Returns a map with all the attributes of this SBase that need to be written out in XML.
    The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.
    
    Specified by:
    
    writeXMLAttributes in interface SBase
    
    Overrides:
    
    writeXMLAttributes in class AbstractNamedSBase
    
    Returns:
    a Map containing the XML attributes of this object.

Class Model

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.NamedSBase

Methods inherited from interface org.sbml.jsbml.SBase

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Methods inherited from interface javax.swing.tree.TreeNode

Field Detail

COULD_NOT_CREATE_ELEMENT_MSG

logger

serialVersionUID

areaUnitsID

conversionFactorID

extentUnitsID

lengthUnitsID

listOfCompartments

listOfCompartmentTypes

listOfConstraints

listOfEvents

listOfFunctionDefinitions

listOfInitialAssignments

listOfParameters

listOfPredefinedUnitDefinitions

listOfReactions

listOfRules

listOfSpecies

listOfSpeciesTypes

listOfUnitDefinitions

mapOfLocalParameters

mapOfUniqueNamedSBases

mapOfUnitDefinitions

substanceUnitsID

timeUnitsID

volumeUnitsID

Constructor Detail

Model

Model

Model

Model

Model

Method Detail

accept

addCompartment

addCompartmentType

addConstraint

addEvent

addFunctionDefinition

addInitialAssignment

addParameter

addPredefinedUnits

addReaction

addRule

addSpecies

addSpeciesType

addUnitDefinition

addUnitDefinitionOrReturnIdenticalUnit

clone

containsCompartment

containsFunctionDefinition

containsParameter

containsQuantity

containsReaction

containsSpecies

containsUniqueNamedSBase

containsUnitDefinition

createAlgebraicRule

createAssignmentRule

createCompartment

createCompartment

createCompartmentType

createCompartmentType

createConstraint

createDelay