org.sbml.jsbml
public class Model extends AbstractNamedSBase implements UniqueNamedSBase
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.
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 subnode of a model element.
|
private static org.apache.log4j.Logger |
logger |
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 themself: |
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.
|
lv
listOfListeners, parent
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.
|
Modifier and Type | Method and Description |
---|---|
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 copy of this object, i.e., e new
SBase with the same properties
like this one and returns a pointer to it. |
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)
|
boolean |
containsSpecies(java.lang.String id)
|
boolean |
containsUniqueNamedSBase(java.lang.String id)
|
boolean |
containsUnitDefinition(java.lang.String units)
|
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. |
CompartmentType |
createCompartmentType(java.lang.String id)
Deprecated.
CompartmentType s should no longer be used. |
Constraint |
createConstraint()
Creates a new
Constraint inside this Model and returns it. |
Delay |
createDelay()
|
Event |
createEvent()
|
Event |
createEvent(java.lang.String id)
|
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()
|
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) |
RateRule |
createRateRule()
|
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()
|
Reaction |
createReaction(java.lang.String id)
|
Species |
createSpecies()
|
Species |
createSpecies(java.lang.String id)
|
Species |
createSpecies(java.lang.String id,
Compartment c)
|
SpeciesType |
createSpeciesType()
Deprecated.
|
SpeciesType |
createSpeciesType(java.lang.String id)
Deprecated.
|
Trigger |
createTrigger()
|
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)
|
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. |
java.util.List<LocalParameter> |
findLocalParameters(java.lang.String id)
|
ModifierSpeciesReference |
findModifierSpeciesReference(java.lang.String 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)
|
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)
|
SpeciesReference |
findSpeciesReference(java.lang.String 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 area units ID of
this Model as id. |
javax.swing.tree.TreeNode |
getChildAt(int index) |
int |
getChildCount() |
Compartment |
getCompartment(int n)
Gets the nth
Compartment instance of the listOfCompartments. |
Compartment |
getCompartment(java.lang.String id)
Gets the
Compartment of the listOfCompartments which has 'id' as
id. |
CompartmentType |
getCompartmentType(int n)
Deprecated.
|
CompartmentType |
getCompartmentType(java.lang.String id)
Deprecated.
|
Constraint |
getConstraint(int n)
Gets the nth Constraint object in 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.
|
Event |
getEvent(int n)
Gets the nth Event object in this Model.
|
Event |
getEvent(java.lang.String id)
Gets the
Event which as the given id as id. |
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 nth
FunctionDefinition instance of the
listOfFunstionDefinitions. |
FunctionDefinition |
getFunctionDefinition(java.lang.String id)
Returns the
FunctionDefinition of the listOfFunctionDefinitions
which has 'id' as id. |
InitialAssignment |
getInitialAssignment(int n)
Gets the nth
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. |
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.
|
ListOf<Constraint> |
getListOfConstraints()
Returns the listOfConstraints 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.
|
ListOf<UnitDefinition> |
getListOfUnitDefinitions()
Returns the listOfUnitDefinitions of this
Model . |
History |
getModelHistory()
Deprecated.
|
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
SpeciesReferences 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)
|
Parameter |
getParameter(java.lang.String id)
Returns the
Parameter of the listOfParameters which has 'id' as id |
SBMLDocument |
getParent()
This is equivalent to calling
AbstractSBase.getParentSBMLObject() , but this
method is needed for TreeNode . |
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 . |
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. |
Rule |
getRule(int n)
Gets the nth
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. |
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. |
SpeciesType |
getSpeciesType(int n)
Deprecated.
|
SpeciesType |
getSpeciesType(java.lang.String id)
Deprecated.
|
java.lang.String |
getSubstanceUnits()
Returns the substance units ID of this model.
|
UnitDefinition |
getSubstanceUnitsInstance()
Returns the
UnitDefinition which has the substance units ID of this
Model as id. |
java.lang.String |
getTimeUnits()
Returns the time units ID of this
Model . |
UnitDefinition |
getTimeUnitsInstance()
Gets the
UnitDefinition representing the time units of this
Model . |
UnitDefinition |
getUnitDefinition(int n)
Gets the nth
UnitDefinition object in this Model . |
UnitDefinition |
getUnitDefinition(java.lang.String id)
Returns the UnitDefinition of the listOfUnitDefinitions which has 'id' as
id.
|
java.lang.String |
getVolumeUnits()
Returns the volume units ID of this
Model . |
UnitDefinition |
getVolumeUnitsInstance()
Returns the
UnitDefinition instance which has the volume units ID
of this Model as id. |
int |
hashCode() |
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.
|
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.
|
boolean |
isSetListOfUnitDefinitions()
Returns true if the listOfUnitDefinitions of this Model is not null and not
empty.
|
boolean |
isSetModelHistory()
Deprecated.
|
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)
If the attribute is an id or name attribute, it will set the id or name
of this object with the value of the XML attribute ('value').
|
private boolean |
registerId(KineticLaw kl,
LocalParameter lp,
boolean delete,
boolean alreadyRegisteredInKL)
Registration of
LocalParameter instances in the Model . |
(package private) boolean |
registerId(NamedSBase nsb,
boolean add)
Registers the identifier of a
NamedSBase and its associated object
in this 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 . |
(package private) boolean |
registerIds(SBase parent,
SBase newElem,
boolean recursively,
boolean delete)
Registers the given element in this
Model . |
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.
|
CompartmentType |
removeCompartmentType(java.lang.String id)
Deprecated.
|
Constraint |
removeConstraint(int n)
Removes the n-th
Constraint of the Model . |
Event |
removeEvent(int n)
|
Event |
removeEvent(java.lang.String 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)
|
boolean |
removeParameter(Parameter parameter)
Removes the Parameter 'parameter' from this Model.
|
Parameter |
removeParameter(java.lang.String id)
|
Reaction |
removeReaction(int n)
|
boolean |
removeReaction(Reaction reac)
Removes a reaction from the model.
|
Reaction |
removeReaction(java.lang.String id)
|
Rule |
removeRule(int i)
|
Rule |
removeRule(java.lang.String variableId)
|
Species |
removeSpecies(int i)
|
boolean |
removeSpecies(Species spec)
Removes a species from the model.
|
Species |
removeSpecies(java.lang.String id)
|
SpeciesType |
removeSpeciesType(int n)
Deprecated.
|
SpeciesType |
removeSpeciesType(java.lang.String id)
Deprecated.
|
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(UnitDefinition areaUnits)
Sets the areaUnitsID of this
Model to the id of the
UnitDefinition 'areaUnits'. |
void |
setConversionFactor(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(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(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.
|
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.
|
void |
setListOfUnitDefinitions(ListOf<UnitDefinition> listOfUnitDefinitions)
Sets the listOfUnitDefinitions of this
Model to
'listOfUnitDefinitions'. |
void |
setModelHistory(History history)
Deprecated.
|
void |
setSubstanceUnits(java.lang.String substanceUnitsID)
Sets the substanceUnitsID of this
Model to 'substanceUnitsID' |
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(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(UnitDefinition volumeUnits)
Sets the volumeUnitsID of this
Model to the id of the
UnitDefinition 'volumeUnits'. |
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.
|
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.
|
boolean |
unsetListOfUnitDefinitions()
Removes the
listOfUnitDefinitions from this Model and
notifies all registered instances of TreeNodeChangeListener . |
void |
unsetModelHistory()
Deprecated.
|
void |
unsetSubstanceUnits()
|
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() |
checkIdentifier, getId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addNamespace, appendNotes, appendNotes, checkLevelAndVersionCompatibility, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, getAnnotation, getAnnotationString, getCVTerm, getCVTerms, getDeclaredNamespaces, getElementName, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespaces, getNotes, getNotesString, getNumCVTerms, getParentSBMLObject, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, notifyChildChange, registerChild, removeNamespace, setAnnotation, setHistory, setLevel, setLevelAndVersion, setMetaId, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregister, unsetAnnotation, unsetCVTerms, unsetHistory, unsetMetaId, unsetNotes, unsetSBOTerm
addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, fireNodeAddedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getTreeNodeChangeListenerCount, indexOf, isLeaf, isRoot, isSetParent, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, setParent
finalize, getClass, notify, notifyAll, wait, wait, wait
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addNamespace, appendNotes, appendNotes, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTerms, getDeclaredNamespaces, getElementName, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespaces, getNotes, getNotesString, getNumCVTerms, getParentSBMLObject, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetSBOTerm, isSetVersion, registerChild, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregister, unsetAnnotation, unsetCVTerms, unsetHistory, unsetMetaId, unsetNotes, unsetSBOTerm
addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getTreeNodeChangeListenerCount, isRoot, isSetParent, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener
private static final java.lang.String COULD_NOT_CREATE_ELEMENT_MSG
private static final transient org.apache.log4j.Logger logger
private static final long serialVersionUID
private java.lang.String areaUnitsID
private java.lang.String conversionFactorID
private java.lang.String extentUnitsID
private java.lang.String lengthUnitsID
private ListOf<Compartment> listOfCompartments
@Deprecated private ListOf<CompartmentType> listOfCompartmentTypes
private ListOf<Constraint> listOfConstraints
private ListOf<Event> listOfEvents
private ListOf<FunctionDefinition> listOfFunctionDefinitions
private ListOf<InitialAssignment> listOfInitialAssignments
private ListOf<Parameter> listOfParameters
private java.util.List<UnitDefinition> listOfPredefinedUnitDefinitions
private ListOf<Reaction> listOfReactions
private ListOf<Species> listOfSpecies
@Deprecated private ListOf<SpeciesType> listOfSpeciesTypes
private ListOf<UnitDefinition> listOfUnitDefinitions
private java.util.Map<java.lang.String,java.util.List<Reaction>> mapOfLocalParameters
LocalParameter
s and the
containing Reaction
objects.private java.util.Map<java.lang.String,UniqueNamedSBase> mapOfUniqueNamedSBases
UniqueNamedSBase
s in Model
s themself:private java.util.Map<java.lang.String,UnitDefinition> mapOfUnitDefinitions
UnitDefinition
objects.private java.lang.String substanceUnitsID
private java.lang.String timeUnitsID
private java.lang.String volumeUnitsID
public Model()
public Model(int level, int version)
level
- version
- public Model(Model model)
model
- public Model(java.lang.String id)
id
- public Model(java.lang.String id, int level, int version)
id
- level
- version
- public boolean addCompartment(Compartment compartment)
compartment
- true
if the listOfCompartments
was changed as
a result of this call.@Deprecated public boolean addCompartmentType(CompartmentType compartmentType)
compartmentType
- true
if the listOfCompartmentTypes
was
changed as a result of this call.public boolean addConstraint(Constraint constraint)
Constraint
instance to the listOfConstraints of this
Model
.constraint
- true
if the listOfConstraints
was changed as
a result of this call.public boolean addEvent(Event event)
Event
instance to the listOfEvents of this Model.event
- true
if the listOfEvents
was changed as a
result of this call.PropertyNotAvailableException
- for inappropriate Level/Version combinations.public boolean addFunctionDefinition(FunctionDefinition functionDefinition)
FunctionDefinition
instance to the listOfFunctionDefinitions
of this Model
.functionDefinition
- true
if the listOfFunctionDefinitions
was
changed as a result of this call.public boolean addInitialAssignment(InitialAssignment initialAssignment)
initialAssignment
- true
if the listOfInitialAssignments
was
changed as a result of this call.public boolean addParameter(Parameter parameter)
parameter
- true
if the listOfParameters
was changed as a
result of this call.private void addPredefinedUnits()
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.public boolean addReaction(Reaction reaction)
reaction
- true
if the listOfReactions
was changed as a
result of this call.public boolean addRule(Rule rule)
rule
- true
if the listOfRules
was changed as a
result of this call.public boolean addSpecies(Species spec)
spec
- true
if the listOfSpecies
was changed as a
result of this call.@Deprecated public boolean addSpeciesType(SpeciesType speciesType)
speciesType
- true
if the listOfSpeciesTypes
was changed as
a result of this call.public boolean addUnitDefinition(UnitDefinition unitDefinition)
unitDefinition
- true
if the listOfUnitDefinitions
was changed
as a result of this call.public java.lang.String addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition units)
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.units
- The unit to be checked and added if no identical
UnitDefinition
can be found.public Model clone()
SBase
SBase
with the same properties
like this one and returns a pointer to it.clone
in interface SBase
clone
in class AbstractSBase
public boolean containsCompartment(java.lang.String id)
Compartment
with the given identifier.id
- Compartment
with the given identifier.public boolean containsFunctionDefinition(java.lang.String id)
FunctionDefinition
with the given identifier.id
- FunctionDefinition
with the given identifier.public boolean containsParameter(java.lang.String id)
Parameter
with
the given identifier.id
- Parameter
with
the given identifier.public boolean containsQuantity(Quantity quantity)
public boolean containsSpecies(java.lang.String id)
public boolean containsUniqueNamedSBase(java.lang.String id)
units
- true
if this Model
contains a reference to the given
UniqueNamedSBase
.public boolean containsUnitDefinition(java.lang.String units)
units
- true
if this Model
contains a reference to the given
UnitDefinition
.public AlgebraicRule createAlgebraicRule()
AlgebraicRule
inside this Model
and returns
it.
AlgebraicRule
object created
addRule(Rule r)
public AssignmentRule createAssignmentRule()
AssignmentRule
inside this Model
and returns
it.
AssignmentRule
object created
addRule(Rule r)
public Compartment createCompartment()
Compartment
inside this Model
and returns it.
Compartment
object created
addCompartment(Compartment c)
public Compartment createCompartment(java.lang.String id)
Compartment
inside this Model
and returns it.id
- the id of the new element to createCompartment
object created@Deprecated public CompartmentType createCompartmentType()
CompartmentType
s should no longer be used.CompartmentType
inside this Model
and returns
it.
CompartmentType
object created
addCompartmentType(CompartmentType ct)
@Deprecated public CompartmentType createCompartmentType(java.lang.String id)
CompartmentType
s should no longer be used.CompartmentType
inside this Model
and returns
it.id
- the id of the new element to createCompartmentType
object createdpublic Constraint createConstraint()
Constraint
inside this Model
and returns it.
Constraint
object created
addConstraint(Constraint c)
public Delay createDelay()
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.
Delay
object createdpublic Event createEvent(java.lang.String id)
id
- the id of the new element to createEvent
object createdpublic EventAssignment createEventAssignment()
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.
EventAssignment
object createdpublic FunctionDefinition createFunctionDefinition()
FunctionDefinition
inside this Model
and
returns it.
FunctionDefinition
object created
addFunctionDefinition(FunctionDefinition fd)
public FunctionDefinition createFunctionDefinition(java.lang.String id)
FunctionDefinition
inside this Model
and
returns it.id
- the id of the new element to createFunctionDefinition
object createdpublic InitialAssignment createInitialAssignment()
InitialAssignment
inside this Model
and
returns it.
InitialAssignment
object created
addInitialAssignment(InitialAssignment ia)
public KineticLaw createKineticLaw()
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.
KineticLaw
object createdpublic LocalParameter createKineticLawParameter()
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.
LocalParameter
object createdpublic LocalParameter createKineticParameter(java.lang.String id)
LocalParameter
inside the KineticLaw
object of the last Reaction
created inside this Model
, and
returns a pointer to it.id
- the id of the new element to createLocalParameter
object createdpublic ModifierSpeciesReference createModifier()
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.
SpeciesReference
object createdpublic ModifierSpeciesReference createModifier(java.lang.String id)
ModifierSpeciesReference
with the specified 'id'.id
- the id of the new element to createSpeciesReference
object createdpublic Parameter createParameter()
Parameter
object created
addParameter(Parameter p)
public Parameter createParameter(java.lang.String id)
Parameter
.id
- the id of the new element to createParameter
object createdpublic SpeciesReference createProduct()
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.
SpeciesReference
object createdpublic SpeciesReference createProduct(java.lang.String id)
id
- public RateRule createRateRule()
RateRule
object created
addRule(Rule r)
public SpeciesReference createReactant()
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.
SpeciesReference
object createdpublic SpeciesReference createReactant(java.lang.String id)
SpeciesReference
object, with the specified 'id', for
a reactant inside the last Reaction
object in this Model
,
and returns a pointer to it.id
- the id of the new element to createSpeciesReference
object created.public Reaction createReaction()
Reaction
object created
addReaction(Reaction r)
public Reaction createReaction(java.lang.String id)
id
- the id of the new element to createReaction
object createdpublic Species createSpecies()
Species
object created
addSpecies(Species s)
public Species createSpecies(java.lang.String id)
id
- the id of the new element to createSpecies
object createdpublic Species createSpecies(java.lang.String id, Compartment c)
@Deprecated public SpeciesType createSpeciesType()
SpeciesType
inside this Model
and returns it.
SpeciesType
object created
addSpeciesType(SpeciesType st)
@Deprecated public SpeciesType createSpeciesType(java.lang.String id)
SpeciesType
inside this Model
and returns it.id
- the id of the new element to createSpeciesType
object createdpublic Trigger createTrigger()
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.
Trigger
object createdpublic Unit createUnit()
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.
Unit
object created
addUnitDefinition(UnitDefinition ud)
public Unit createUnit(Unit.Kind kind)
Unit
object within the last UnitDefinition
object created in this model and returns a pointer to it.kind
- the kind of the new unit.Unit
object createdpublic UnitDefinition createUnitDefinition()
UnitDefinition
inside this Model
and returns
it.
UnitDefinition
object created
addUnitDefinition(UnitDefinition ud)
public UnitDefinition createUnitDefinition(java.lang.String id)
UnitDefinition
inside this Model
and returns
it.id
- the id of the new element to createUnitDefinition
object createdpublic boolean equals(java.lang.Object object)
SBase
SBase
has exactly the same
properties like this SBase
instance.equals
in interface SBase
equals
in class AbstractNamedSBase
Object
is an instance of
SBase
that has exactly the same properties like this
SBase instance.public CallableSBase findCallableSBase(java.lang.String id)
CallableSBase
element of the Model
that has the
given 'id' as identifier or null if no element is found.id
- an identifier indicating an element of the Model
.CallableSBase
element of the Model
that has the
given 'id' as id or null if no element is found.public java.util.List<LocalParameter> findLocalParameters(java.lang.String id)
id
- List
of all LocalParameter
instances with the
given name or identifier. This List
can be empty, but never
null.public ModifierSpeciesReference findModifierSpeciesReference(java.lang.String id)
id
- the identifier of the ModifierSpeciesReference
of interest.
Note that this is not the identifier of the Species
instance
referred to by the ModifierSpeciesReference
.ModifierSpeciesReference
out of all Reaction
s
which has 'id' as id (or name depending on level and version).
null
if it doesn't exist.public NamedSBase findNamedSBase(java.lang.String id)
NamedSBase
element of the model that has the given 'id'
as id or null if no element is found.id
- an id indicating an element of the model.NamedSBase
element of the model that has the given 'id'
as id or null
if no element is found.public NamedSBaseWithDerivedUnit findNamedSBaseWithDerivedUnit(java.lang.String id)
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.id
- an id indicating an element of the Model
.NamedSBaseWithDerivedUnit
element of the Model
that has the given 'id' as id or null if no element is found.findCallableSBase(String)
public Quantity findQuantity(java.lang.String id)
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
Reaction
s. In this case, the first match will be returned. Note
that also global Parameter
instances have a higher priority and are
returned first.id
- Compartment
, Species
, SpeciesReference
or Parameter
, or the first LocalParameter
which has
'id' as id.findLocalParameters(String)
public QuantityWithUnit findQuantityWithUnit(java.lang.String idOrName)
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
Reaction
s. In this case, the first match will be returned. Note
that also global Parameter
instances have a higher priority and are
returned first.idOrName
- findLocalParameters(String)
public java.util.SortedSet<java.lang.String> findReactionsForLocalParameter(java.lang.String id)
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.id
- an id indicating an LocalParameter
element of the
Model
.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.public SimpleSpeciesReference findSimpleSpeciesReference(java.lang.String id)
id
- the identifier of the SimpleSpeciesReference
of interest.
Note that this is not the identifier of the Species
instance
referred to by the SimpleSpeciesReference
.SimpleSpeciesReference
out of all Reaction
s
which has 'id' as id (or name depending on level and version).
null
if it doesn't exist.public SpeciesReference findSpeciesReference(java.lang.String id)
id
- the identifier of the SpeciesReference
of interest.
Note that this is not the identifier of the Species
instance
referred to by the SpeciesReference
.SpeciesReference
out of all Reaction
s
which has 'id' as id (or name depending on level and version).
null
if it doesn't exist.public Symbol findSymbol(java.lang.String id)
Compartment
s, Species
, and
Parameter
s for the element with the given identifier.id
- Symbol
element with the given identifier or null if there
is no such element.public UniqueNamedSBase findUniqueNamedSBase(java.lang.String id)
UniqueNamedSBase
element that has the given 'id' within
this Model
or null
if no such element can be found.id
- an id indicating an UniqueNamedSBase
element of the
Model
.UniqueNamedSBase
element of the Model
that has
the given 'id' as id or null
if no element with this
'id' can be found.public UnitDefinition findUnitDefinition(java.lang.String id)
UnitDefinition
element that has the given 'id' within
this Model
or null
if no such element can be found.id
- an id indicating an UnitDefinition
element of the
Model
.UniqueNamedSBase
element of the Model
that has
the given 'id' as id or null
if no such element with
this 'id' can be found.public Variable findVariable(java.lang.String id)
Variable
with the given identifier in this model.id
- The identifier of the Variable
of interest.Compartment
, Species
, SpeciesReference
,
or Parameter
, which has 'variable' as id.public boolean getAllowsChildren()
getAllowsChildren
in interface javax.swing.tree.TreeNode
getAllowsChildren
in class AbstractSBase
public java.lang.String getAreaUnits()
Model
.Model
. Returns an empty
String
if it is not set.public UnitDefinition getAreaUnitsInstance()
UnitDefinition
instance which has the area units ID of
this Model as id.UnitDefinition
instance which has the area Units ID of
this Model as id. Null if it doesn't existpublic javax.swing.tree.TreeNode getChildAt(int index)
getChildAt
in interface javax.swing.tree.TreeNode
getChildAt
in class AbstractSBase
public int getChildCount()
getChildCount
in interface javax.swing.tree.TreeNode
getChildCount
in class AbstractSBase
public Compartment getCompartment(int n)
Compartment
instance of the listOfCompartments.n
- Compartment
instance of the listOfCompartments.
Null if if the listOfCompartments is not set.public Compartment getCompartment(java.lang.String id)
Compartment
of the listOfCompartments which has 'id' as
id.id
- Compartment
of the listOfCompartments which has 'id' as
id (or name depending on the version and level). Null if if the
listOfCompartments is not set.@Deprecated public CompartmentType getCompartmentType(int n)
n
- index@Deprecated public CompartmentType getCompartmentType(java.lang.String id)
CompartmentType
with the given id
.id
- 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.public Constraint getConstraint(int n)
n
- public java.lang.String getConversionFactor()
Model
.Model
. Returns an empty
String
if it is not set.public Parameter getConversionFactorInstance()
public Event getEvent(int n)
n
- public Event getEvent(java.lang.String id)
Event
which as the given id
as id.id
- Event
of the listOfEvents
which has 'id' as id
(or name depending on the level and version). Null if if the
listOfEvents
is not set.public java.lang.String getExtentUnits()
Model
.Model
. Returns an empty
String
if it is not set.public UnitDefinition getExtentUnitsInstance()
UnitDefinition
instance which has the extent units ID
of this Model as id.UnitDefinition
instance which has the extent units ID
of this Model as id. Null if it doesn't existpublic FunctionDefinition getFunctionDefinition(int n)
FunctionDefinition
instance of the
listOfFunstionDefinitions.n
- FunctionDefinition
instance of the
listOfFunstionDefinitions. Null if if the listOfFunctionDefinitions
is not set.public FunctionDefinition getFunctionDefinition(java.lang.String id)
FunctionDefinition
of the listOfFunctionDefinitions
which has 'id' as id.id
- FunctionDefinition
of the listOfFunctionDefinitions
which has 'id' as id (or name depending on the level and version).
Null if if the listOfFunctionDefinitions
is not set.public InitialAssignment getInitialAssignment(int n)
InitialAssignment
object in this Model
.n
- InitialAssignment
of this Model
. Null if
the listOfInitialAssignments is not set.public InitialAssignment getInitialAssignment(java.lang.String variable)
InitialAssignment
of the
listOfInitialAssignments
whose symbol
attribute,
i.e., whose Variable
has the given variable
as
identifier.variable
- The identifier of a variable, for which a corresponding
InitialAssignment
is requested.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.private <T> T getLastElementOf(ListOf<? extends T> listOf)
public java.lang.String getLengthUnits()
Model
.Model
. Returns an empty
String
if it is not set.public UnitDefinition getLengthUnitsInstance()
Model
as a UnitDefinition
.public ListOf<Compartment> getListOfCompartments()
Model
.Model
.@Deprecated public ListOf<CompartmentType> getListOfCompartmentTypes()
Model
.Model
.public ListOf<Constraint> getListOfConstraints()
Model
.Model
. set.public ListOf<Event> getListOfEvents()
Model
.Model
.public ListOf<FunctionDefinition> getListOfFunctionDefinitions()
Model
.Model
.public ListOf<InitialAssignment> getListOfInitialAssignments()
Model
.Model
.public ListOf<Parameter> getListOfParameters()
Model
.Model
.public java.util.List<UnitDefinition> getListOfPredefinedUnitDefinitions()
public ListOf<Reaction> getListOfReactions()
Model
.Model
.public ListOf<Rule> getListOfRules()
Model
.Model
.public ListOf<Species> getListOfSpecies()
Model
.Model
.@Deprecated public ListOf<SpeciesType> getListOfSpeciesTypes()
Model
.Model
.public ListOf<UnitDefinition> getListOfUnitDefinitions()
Model
.Model
.@Deprecated public History getModelHistory()
SBase.getHistory()
History
of this model.History
of this model.SBase.getHistory()
public int getNumCompartments()
Compartment
s of this Model.Compartment
s of this Model.@Deprecated public int getNumCompartmentTypes()
CompartmentType
s of this Model.CompartmentType
s of this Model.public int getNumConstraints()
Constraint
s of this Model.Constraint
s of this Model.public int getNumDelays()
Delay
s of this Model.Delay
s of this Model.public int getNumEventAssignments()
EventAssignment
s of this Model.EventAssignment
s of this Model.public int getNumEvents()
Event
s of this Model.Event
s of this Model.public int getNumFunctionDefinitions()
FunctionDefinition
s of this Model.FunctionDefinition
s of this Model.public int getNumInitialAssignments()
InitialAssignment
s of this Model.InitialAssignment
s of this Model.public int getNumKineticLaws()
KineticLaw
s of this Model.KineticLaw
s of this Model.public int getNumListsOf()
ListOf
s of this Model.ListOf
s of this Model.public int getNumLocalParameters()
public int getNumMathContainers()
Model
.Model
.MathContainer
public int getNumModifierSpeciesReferences()
ModifierSpeciesReference
s in the
Model
.ModifierSpeciesReference
s in the
Model
.public int getNumNamedSBases()
NamedSBase
s in the Model
, so elements
that can have a name.NamedSBase
s in the Model
, so elements
that can have a name.public int getNumNamedSBasesWithDerivedUnit()
NamedSBaseWithDerivedUnit
s in the
Model
, so elements that can have a name and a unit that can be
derived.NamedSBaseWithDerivedUnit
s in the
Model
, so elements that can have a name and a unit that can
be derived.public int getNumParameters()
Parameter
s of this Model.Parameter
s of this Model.public int getNumQuantities()
Quantity
s of this Model.Quantity
s of this Model.public int getNumQuantitiesWithUnit()
QuantityWithUnit
s of this Model.QuantityWithUnit
s of this Model.public int getNumReactions()
Reaction
s of this Model.Reaction
s of this Model.public int getNumRules()
Rule
s of this model.Rule
s of this model.public int getNumSBases()
SBase
s of this model.SBase
s of this model.public int getNumSBasesWithDerivedUnit()
SBaseWithDerivedUnit
s of this model.SBaseWithDerivedUnit
s of this model.public int getNumSpecies()
Species
of this Model.Species
of this Model.public int getNumSpeciesReferences()
SpeciesReferences
s of this Model.SpeciesReferences
s of this Model.@Deprecated public int getNumSpeciesTypes()
SpeciesType
s of this Model.SpeciesType
s of this Model.public int getNumSpeciesWithBoundaryCondition()
Species
whose boundary condition is set to
true.Species
whose boundary condition is set to
true.public int getNumStoichiometryMath()
StoichiometryMath
in the Model
.StoichiometryMath
in the Model
.public int getNumSymbols()
Symbol
referenced within the
model. There is no dedicated list for Symbol
s. This is a convenient
method to support working with the model data structure.Compartment
s, Species
, and
Parameter
s in the model.public int getNumTriggers()
Trigger
of this Model.Trigger
of this Model.public int getNumUnitDefinitions()
UnitDefinition
s of this Model.UnitDefinition
s of this Model.public int getNumUnits()
Unit
s of this Model.Unit
s of this Model.public int getNumVariables()
Variable
s of this Model.Variable
s of this Model.public Parameter getParameter(int n)
public Parameter getParameter(java.lang.String id)
Parameter
of the listOfParameters which has 'id' as idid
- Parameter
of the listOfParameters which has 'id' as id
(or name depending on the level and version). Null if it doesn't
exist.public SBMLDocument getParent()
AbstractSBase
AbstractSBase.getParentSBMLObject()
, but this
method is needed for TreeNode
.getParent
in interface javax.swing.tree.TreeNode
getParent
in class AbstractSBase
AbstractSBase.getParentSBMLObject()
public UnitDefinition getPredefinedUnitDefinition(java.lang.String unitKind)
Model
.unitKind
- a unit kind for one of the predefined units from the SBML
Specificationspublic Reaction getReaction(int n)
Reaction
object in this Model.reactionIndex
- Reaction
of this Model.public Reaction getReaction(java.lang.String id)
Reaction
of the listOfReactions
which has 'id' as id.id
- Reaction
of the listOfReactions
which has 'id' as id
(or name depending on the level and version). null
if it doesn't
exist.public Rule getRule(int n)
Rule
of the listOfRules.n
- an indexRule
of the listOfRules. Null if it doesn't exist.public ExplicitRule getRule(java.lang.String variable)
ExplicitRule
within this
Model
's listOfRules
, whose variable attribute is set to
the value passed to this method.variable
- public Species getSpecies(int n)
Species
object in this Model.n
- an indexSpecies
with the given index if it exists, null
otherwise.public Species getSpecies(java.lang.String id)
Species
of the listOfSpecies which has 'id' as id.id
- Species
of the listOfSpecies which has 'id' as id (or
name depending on the level and version). Null if it doesn't exist.@Deprecated public SpeciesType getSpeciesType(int n)
SpeciesType
object in this Model.n
- indexSpeciesType
of this Model. Returns null if there
are no speciesType defined or if the index n is too big or lower
than zero.@Deprecated public SpeciesType getSpeciesType(java.lang.String id)
SpeciesType
of the listOfSpeciesTypes
which has 'id' as
id.id
- SpeciesType
of the listOfSpeciesTypes
which has 'id' as
id (or name depending on the level and version). null
if it doesn't
exist.public java.lang.String getSubstanceUnits()
String
if it is not set.public UnitDefinition getSubstanceUnitsInstance()
UnitDefinition
which has the substance units ID of this
Model as id.UnitDefinition
which has the substanceUnitsID of this
Model as id. Null if it doesn't exist.public java.lang.String getTimeUnits()
Model
.Model
or an empty String
if it is not set.public UnitDefinition getTimeUnitsInstance()
UnitDefinition
representing the time units of this
Model
.UnitDefinition
representing the time units of this
Model
, null if it is not defined in this Model
public UnitDefinition getUnitDefinition(int n)
UnitDefinition
object in this Model
.n
- UnitDefinition
of this Model. Returns null if there
are no UnitDefinition defined or if the index n is too big or lower
than zero.public UnitDefinition getUnitDefinition(java.lang.String id)
id
- public java.lang.String getVolumeUnits()
Model
.Model
. Returns an empty String
if it is not set.public UnitDefinition getVolumeUnitsInstance()
UnitDefinition
instance which has the volume units ID
of this Model
as id.UnitDefinition
instance which has the volume units ID
of this Model
as id. Null if it doesn't existpublic int hashCode()
hashCode
in interface SBase
hashCode
in class AbstractNamedSBase
Object.hashCode()
public boolean hasUnit(java.lang.String id)
id
- public void initDefaults()
public void initDefaults(int level, int version)
Model
public boolean isIdMandatory()
NamedSBase
NamedSBase
is
required to be defined (i.e., not null) in the definition of SBML.isIdMandatory
in interface NamedSBase
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.public boolean isSetAreaUnits()
public boolean isSetAreaUnitsInstance()
public boolean isSetConversionFactor()
public boolean isSetConversionFactorInstance()
public boolean isSetExtentUnits()
public boolean isSetExtentUnitsInstance()
public boolean isSetLengthUnits()
public boolean isSetLengthUnitsInstance()
public boolean isSetListOfCompartments()
@Deprecated public boolean isSetListOfCompartmentTypes()
public boolean isSetListOfConstraints()
public boolean isSetListOfEvents()
public boolean isSetListOfFunctionDefinitions()
public boolean isSetListOfInitialAssignments()
public boolean isSetListOfParameters()
public boolean isSetListOfReactions()
public boolean isSetListOfRules()
public boolean isSetListOfSpecies()
@Deprecated public boolean isSetListOfSpeciesTypes()
public boolean isSetListOfUnitDefinitions()
@Deprecated public boolean isSetModelHistory()
SBase.isSetHistory()
History
of the Model. This is equivalent to the call
SBase.isSetHistory()
.History
of the Model.public boolean isSetSubstanceUnits()
public boolean isSetSubstanceUnitsInstance()
public boolean isSetTimeUnits()
public boolean isSetTimeUnitsInstance()
public boolean isSetVolumeUnits()
public boolean isSetVolumeUnitsInstance()
public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBase
readAttribute
in interface SBase
readAttribute
in class AbstractNamedSBase
attributeName
- : localName of the XML attributeprefix
- : prefix of the XML attributevalue
- : value of the XML attributeprivate boolean registerId(KineticLaw kl, LocalParameter lp, boolean delete, boolean alreadyRegisteredInKL)
LocalParameter
instances in the Model
.kl
- the KineticLaw
that contains the given
LocalParameter
lp
- the LocalParameter
whose identifier is to be registered.delete
- true
in case of success, otherwise false
.boolean registerId(NamedSBase nsb, boolean add)
NamedSBase
and its associated object
in this Model
.nsb
- the element, whose identifier is to be registered.add
- If true
the identifier of the given NamedSBase
will be registered in this Model
Otherwise, the given
identifier will be removed from this Model
's hash.true
if this operation was successfully performed,
false
otherwise.private boolean registerId(UniqueNamedSBase unsb, boolean delete)
unsb
- recursively
- delete
- private boolean registerId(UnitDefinition ud, boolean add)
UnitDefinition
itself
in this Model
.ud
- the UnitDefinition
to be registered.add
- boolean registerIds(SBase parent, SBase newElem, boolean recursively, boolean delete)
Model
.parent
- newElem
- recursively
- delete
- true
if this operation was successfully performed,
false
otherwise.public Compartment removeCompartment(int i)
Compartment
of the Model
.i
- the index of the Compartment
to removeCompartment
.public Compartment removeCompartment(java.lang.String id)
Compartment
of the Model
with 'id' as id.id
- Compartment
.@Deprecated public CompartmentType removeCompartmentType(int n)
CompartmentType
of the Model
.n
- the index of the Compartment
to removeCompartmentType
.@Deprecated public CompartmentType removeCompartmentType(java.lang.String id)
CompartmentType
of the Model
with 'id' as id.id
- public Constraint removeConstraint(int n)
Constraint
of the Model
.n
- public Event removeEvent(int n)
n
- public Event removeEvent(java.lang.String id)
id
- public FunctionDefinition removeFunctionDefinition(int n)
FunctionDefinition
of the Model
.n
- public FunctionDefinition removeFunctionDefinition(java.lang.String id)
FunctionDefinition
of the Model
with 'id' as
id.id
- public InitialAssignment removeInitialAssignment(int n)
InitialAssignment
of the Model
.n
- public Parameter removeParameter(int n)
n
- public boolean removeParameter(Parameter parameter)
parameter
- Parameter
was found and removed.public Parameter removeParameter(java.lang.String id)
id
- public Reaction removeReaction(int n)
n
- public boolean removeReaction(Reaction reac)
reac
- Reaction
was found and removed.public Reaction removeReaction(java.lang.String id)
id
- public Rule removeRule(int i)
i
- public Rule removeRule(java.lang.String variableId)
variableId
- public Species removeSpecies(int i)
i
- public boolean removeSpecies(Species spec)
spec
- Species
was found and removed.public Species removeSpecies(java.lang.String id)
id
- @Deprecated public SpeciesType removeSpeciesType(int n)
SpeciesType
of the Model
.n
- @Deprecated public SpeciesType removeSpeciesType(java.lang.String id)
SpeciesType
of the Model
with 'id' as id.id
- public UnitDefinition removeUnitDefinition(int n)
UnitDefinition
of the Model
.n
- public UnitDefinition removeUnitDefinition(java.lang.String id)
UnitDefinition
of the Model
with 'id' as id.id
- public boolean removeUnitDefinition(UnitDefinition unitDefininition)
UnitDefinition
of the Model
.unitDefininition
- public void setAreaUnits(java.lang.String areaUnitsID)
Model
to 'areaUnitsID'areaUnitsID
- PropertyNotAvailableException
- if Level < 3.public void setAreaUnits(UnitDefinition areaUnits)
Model
to the id of the
UnitDefinition
'areaUnits'.areaUnits
- public void setConversionFactor(Parameter conversionFactor)
conversionFactor
- public void setConversionFactor(java.lang.String conversionFactorID)
Model
to
'conversionFactorID'.conversionFactorID
- PropertyNotAvailableException
- if Level < 3.public void setExtentUnits(java.lang.String extentUnitsID)
Model
to 'extentUnitsID'.extentUnitsID
- PropertyNotAvailableException
- if Level < 3.public void setExtentUnits(UnitDefinition extentUnits)
Model
to the id of the
UnitDefinition
'extentUnits'.extentUnits
- public void setLengthUnits(java.lang.String lengthUnitsID)
Model
to 'lengthUnitsID'.lengthUnitsID
- PropertyNotAvailableException
- if Level < 3.public void setLengthUnits(UnitDefinition lengthUnits)
Model
to the id of the
UnitDefinition 'lengthUnits'.lengthUnits
- public void setListOfCompartments(ListOf<Compartment> listOfCompartments)
Model
to 'listOfCompartments'.
Automatically sets the parentSBML objects of 'listOfCompartments' to this
Model.listOfCompartments
- @Deprecated public void setListOfCompartmentTypes(ListOf<CompartmentType> listOfCompartmentTypes)
Model
.listOfCompartmentTypes
- the listOfCompartmentTypes to setpublic void setListOfConstraints(ListOf<Constraint> listOfConstraints)
Model
to 'listOfConstraints'.
Automatically sets the parentSBML objects of 'listOfCanstraints' to this
Model.listOfConstraints
- the listOfConstraints to setpublic void setListOfEvents(ListOf<Event> listOfEvents)
Model
to 'listOfEvents'.
Automatically sets the parentSBML objects of 'listOfEvents' to this
Model
.listOfEvents
- public void setListOfFunctionDefinitions(ListOf<FunctionDefinition> listOfFunctionDefinitions)
Model
to
'listOfFunctionDefinitions'. Automatically sets the parentSBML objects of
'listOfFunctionDefinitions' to this Model.listOfFunctionDefinitions
- the listOfFunctionDefinitions to setpublic void setListOfInitialAssignments(ListOf<InitialAssignment> listOfInitialAssignments)
listOfInitialAssignments
of this Model
to
'listOfInitialAssignments'. Automatically sets the parentSBML objects of
'listOfInitialAssignments' to this Model.listOfInitialAssignments
- the listOfInitialAssignments to setpublic void setListOfParameters(ListOf<Parameter> listOfParameters)
listOfParameters
of this Model
to
'listOfParameters'. Automatically sets the parentSBML objects of
'listOfParameters' to this Model.listOfParameters
- public void setListOfReactions(ListOf<Reaction> listOfReactions)
listOfReactions
of this Model
to
'listOfReactions'. Automatically sets the parentSBML objects of
'listOfReactions' to this Model.listOfReactions
- public void setListOfRules(ListOf<Rule> listOfRules)
listOfRules
of this Model
to 'listOfRules'.
Automatically sets the parentSBML objects of 'listOfRules' to this Model.listOfRules
- public void setListOfSpecies(ListOf<Species> listOfSpecies)
Model
to 'listOfSpecies'.
Automatically sets the parentSBML objects of 'listOfSpecies' to this Model.listOfSpecies
- @Deprecated public void setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes)
listOfSpeciesTypes
- the listOfSpeciesTypes to setpublic void setListOfUnitDefinitions(ListOf<UnitDefinition> listOfUnitDefinitions)
Model
to
'listOfUnitDefinitions'. Automatically sets the parentSBML objects of
'listOfUnitDefinitions' to this Model.listOfUnitDefinitions
- @Deprecated public void setModelHistory(History history)
AbstractSBase.setHistory(History)
history
- AbstractSBase.setHistory(History history)
public void setSubstanceUnits(java.lang.String substanceUnitsID)
Model
to 'substanceUnitsID'substanceUnitsID
- PropertyNotAvailableException
- if Level < 3.public void setSubstanceUnits(UnitDefinition substanceUnits)
Model
to the id of
'substanceUnits'.substanceUnits
- public void setTimeUnits(java.lang.String timeUnitsID)
Model
to 'timeUnistID'timeUnitsID
- PropertyNotAvailableException
- if Level < 3.public void setTimeUnits(UnitDefinition timeUnits)
Model
to the id of the
UnitDefinition
'timeUnits'.timeUnits
- public void setVolumeUnits(java.lang.String volumeUnitsID)
Model
to 'volumeUnitsID'volumeUnitsID
- PropertyNotAvailableException
- if Level < 3.public void setVolumeUnits(UnitDefinition volumeUnits)
Model
to the id of the
UnitDefinition
'volumeUnits'.volumeUnits
- public void unsetAreaUnits()
Model
to null.public void unsetConversionFactor()
Model
to null.public void unsetExtentUnits()
Model
to null.public void unsetLengthUnits()
Model
to null.public boolean unsetListOfCompartments()
listOfCompartments
from this Model
and
notifies all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.@Deprecated public boolean unsetListOfCompartmentTypes()
listOfCompartmentTypes
from this Model
and
notifies all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfConstraints()
listOfConstraints
from this Model
and notifies
all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfEvents()
listOfEvents
from this Model
and notifies all
registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfFunctionDefinitions()
listOfFunctionDefinitions
from this Model
and
notifies all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfInitialAssignments()
listOfInitialAssignments
from this Model
and
notifies all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfParameters()
listOfParameters
from this Model
and notifies
all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfReactions()
listOfReactions
from this Model
and notifies
all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfRules()
listOfRules
from this Model
and notifies all
registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfSpecies()
listOfSpecies
from this Model
and notifies all
registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.@Deprecated public boolean unsetListOfSpeciesTypes()
listOfSpeciesTypes
from this Model
and
notifies all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.public boolean unsetListOfUnitDefinitions()
listOfUnitDefinitions
from this Model
and
notifies all registered instances of TreeNodeChangeListener
.true
if calling this method lead to a change in this
data structure.@Deprecated public void unsetModelHistory()
AbstractSBase.unsetHistory()
.AbstractSBase.unsetHistory()
public void unsetSubstanceUnits()
public void unsetTimeUnits()
Model
to null.public void unsetVolumeUnits()
Model
to null.public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
writeXMLAttributes
in interface SBase
writeXMLAttributes
in class AbstractNamedSBase
Map
containing the XML attributes of this object.