Modifier and Type | Class | Description |
---|---|---|
class |
ListOf<T extends SBase> |
This list implementation is a Java
List that extends
AbstractSBase . |
Modifier and Type | Interface | Description |
---|---|---|
interface |
Assignment |
An
Assignment can be seen as a mathematical equation with a
Variable on the left hand side and an equation on the right hand side
that assigns a value to the Variable . |
interface |
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
interface |
CompartmentalizedSBase |
|
interface |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
interface |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
interface |
NamedSBaseWithDerivedUnit |
All objects that implement this interface can be referenced in abstract
syntax trees as implemented in
ASTNode . |
interface |
Quantity |
A quantity is an element that represents a value with an associated unit that
can be addressed through the identifier or name attribute of this element.
|
interface |
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
interface |
SBaseWithUnit |
Defines a kind of
SBase that is equipped with a defined unit. |
interface |
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
interface |
Variable |
A variable of the system is a
Quantity whose value may change during
a simulation. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
class |
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
class |
AbstractNamedSBaseWithUnit |
This simple implementation of the interfaces
NamedSBaseWithDerivedUnit and SBaseWithUnit defines elements
that can be addressed by their identifier and are or can be associated with a
defined Unit or UnitDefinition . |
class |
AbstractSBase |
The base class for each
SBase component. |
class |
AlgebraicRule |
Represents the algebraicRule XML element of a SBML file.
|
class |
AssignmentRule |
Represents the assignmentRule XML element of a SBML file.
|
class |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
class |
CompartmentType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
class |
Constraint |
Represents the constraint XML element of a SBML file.
|
class |
Delay |
Represents the delay subnode of an event element.
|
class |
Event |
Represents the event XML element of a SBML file.
|
class |
EventAssignment |
Represents the eventAssignment XML element of a SBML file.
|
class |
ExplicitRule |
An explicit
Rule is a rule that explicitly declares its variable
element. |
class |
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
class |
InitialAssignment |
Represents the initialAssignment XML element of a SBML file.
|
class |
KineticLaw |
Represents the kineticLaw XML element of a SBML file.
|
class |
ListOf<T extends SBase> |
This list implementation is a Java
List that extends
AbstractSBase . |
class |
LocalParameter |
A local parameter can only be used to specify a constant within a
KineticLaw . |
class |
Model |
JSBML implementation of SBML's
Model construct. |
class |
ModifierSpeciesReference |
Represents the modifierSpeciesReference XML element of a SBML file.
|
class |
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
class |
Priority |
This class represents the priority element in SBML.
|
class |
QuantityWithUnit |
This object represents an element with identifier and name, a value, and a
defined unit.
|
class |
RateRule |
Represents the rateRule XML element of a SBML file.
|
class |
Reaction |
Represents the reaction XML element of a SBML file.
|
class |
Rule |
|
class |
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
class |
SimpleSpeciesReference |
The base class of
SpeciesReference and
ModifierSpeciesReference . |
class |
Species |
Represents the species XML element of a SBML file.
|
class |
SpeciesReference |
Represents the speciesReference XML element of a SBML file.
|
class |
SpeciesType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
class |
StoichiometryMath |
Deprecated.
Since SBML Level 3 Version 1 use
AssignmentRule with
instances of SpeciesReference as Variable
instead. |
class |
Symbol |
|
class |
Trigger |
Represents the trigger XML element of a SBML file.
|
class |
Unit |
Represents the unit XML element of a SBML file.
|
class |
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Modifier and Type | Method | Description |
---|---|---|
static <T extends SBase> |
ListOf.initListOf(SBase parent,
ListOf<T> list,
ListOf.Type type) |
Initializes newly created lists.
|
static <T extends SBase> |
ListOf.newInstance(SBase parent,
java.lang.Class<T> clazz) |
Initializes a new
ListOf object for the given
parent SBML object and with the given Class as the type of the
list. |
<T extends SBase> |
Model.remove(java.lang.String id) |
Removes any
UniqueNamedSBase with the given identifier from this
Model and returns the removed element if the operation was
successful. |
Modifier and Type | Method | Description |
---|---|---|
SBase |
SBase.clone() |
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
SBase |
SBMLDocument.findSBase(java.lang.String metaId) |
Looks up the
SBase registered in this SBMLDocument for the
given metaId. |
SBase |
Model.findUniqueSBase(java.lang.String id) |
|
SBase |
AbstractSBase.getElementByMetaId(java.lang.String id) |
|
SBase |
SBase.getElementByMetaId(java.lang.String metaid) |
Returns the first child element found that has the given metaid.
|
SBase |
SBMLDocument.getElementByMetaId(java.lang.String metaid) |
|
SBase |
AbstractSBase.getElementBySId(java.lang.String id) |
|
SBase |
Model.getElementBySId(java.lang.String id) |
Returns an
SBase element of the model that has the given 'id'
as id or null if no element is found. |
SBase |
SBase.getElementBySId(java.lang.String id) |
Returns the first child element found that has the given id.
|
SBase |
AbstractSBase.getParent() |
This is equivalent to calling
AbstractSBase.getParentSBMLObject() , but this
method is needed for TreeNode . |
SBase |
AbstractSBase.getParentSBMLObject() |
|
SBase |
SBase.getParentSBMLObject() |
Returns the parent of this
SBase . |
SBase |
Model.getSBaseById(java.lang.String id) |
Returns an
SBase element of the model that has the given 'id'
as id or null if no element is found. |
SBase |
SBMLError.getSource() |
Returns the source for this
SBMLError . |
Modifier and Type | Method | Description |
---|---|---|
java.util.Set<SBase> |
ASTNode.getReferencedNamedSBases() |
Returns a set of all the
NamedSBase referenced on this node and
all his descendant. |
java.lang.Class<? extends SBase> |
ListOf.Type.toClass() |
Gives the corresponding
Class object for this ListOf.Type . |
Modifier and Type | Method | Description |
---|---|---|
boolean |
KineticLaw.accept(SBase sbase) |
|
boolean |
Model.accept(SBase sbase) |
|
static IdentifierException |
IdentifierException.createIdentifierExceptionForId(SBase sb,
java.lang.String id) |
Creates a new
IdentifierException instance for id. |
static IdentifierException |
IdentifierException.createIdentifierExceptionForMetaId(SBase sb,
java.lang.String metaId) |
Creates a new
IdentifierException instance for metaid. |
static java.util.HashMap<java.lang.String,java.lang.String> |
AbstractSBase.getAllDeclaredNamespaces(SBase sb) |
Returns a map of all the declared namespaces in the SBML tree, visible to the given
SBase . |
static <T extends SBase> |
ListOf.initListOf(SBase parent,
ListOf<T> list,
ListOf.Type type) |
Initializes newly created lists.
|
static java.lang.String |
LevelVersionError.levelMismatchMessage(SBase element1,
SBase element2) |
Creates an error message if the level fields of both elements are not
identical, or an empty
String otherwise. |
static <T extends SBase> |
ListOf.newInstance(SBase parent,
java.lang.Class<T> clazz) |
Initializes a new
ListOf object for the given
parent SBML object and with the given Class as the type of the
list. |
static java.lang.String |
LevelVersionError.packageVersionMismatchMessage(SBasePlugin element1,
SBase element2) |
Creates an error message showing the different package versions of the given SBase elements.
|
static java.lang.String |
LevelVersionError.packageVersionMismatchMessage(SBase element1,
SBase element2) |
Creates an error message showing the different package versions of the given SBase elements.
|
boolean |
KineticLaw.register(SBase sbase) |
|
boolean |
Model.register(SBase sbase) |
|
boolean |
AbstractSBase.registerChild(SBase sbase) |
|
boolean |
SBase.registerChild(SBase sbase) |
Sets this object as SBML parent of 'sbase'.
|
boolean |
ListOf.remove(SBase nsb) |
Removes a
SBase according to its unique id. |
void |
SBMLError.setSource(SBase source) |
Sets the source of this
SBMLError . |
void |
AbstractSBase.setThisAsParentSBMLObject(SBase sbase) |
Deprecated.
|
void |
SBase.setThisAsParentSBMLObject(SBase sbase) |
Deprecated.
|
boolean |
KineticLaw.unregister(SBase sbase) |
|
boolean |
Model.unregister(SBase sbase) |
|
void |
AbstractSBase.unregisterChild(SBase sbase) |
|
void |
SBase.unregisterChild(SBase sbase) |
Unregisters recursively the given SBase from the
Model
and SBMLDocument . |
static java.lang.String |
LevelVersionError.versionMismatchMessage(SBase element1,
SBase element2) |
Creates an error message if the version fields of both elements are not
identical, or an empty
String otherwise. |
Modifier and Type | Method | Description |
---|---|---|
static ListOf.Type |
ListOf.Type.valueOf(java.lang.Class<? extends SBase> type) |
Gives the corresponding
ListOf.Type for the given Class
object. |
Constructor | Description |
---|---|
AbstractSBase(SBase sb) |
Creates an
AbstractSBase instance from a given
AbstractSBase . |
IdentifierException(SBase sb,
java.lang.String identifier,
java.lang.String message,
java.lang.String preIdentifierName) |
Creates a new
IdentifierException instance. |
LevelVersionError(SBasePlugin element1,
SBase element2) |
|
LevelVersionError(SBase sbase) |
|
LevelVersionError(SBase element1,
SBase element2) |
|
PropertyNotAvailableException(java.lang.String property,
SBase sbase) |
|
PropertyUndefinedError(java.lang.String property,
SBase sbase) |
Constructor | Description |
---|---|
ListOf(ListOf<? extends SBase> listOf) |
Creates a ListOf instance from a given ListOf.
|
Modifier and Type | Method | Description |
---|---|---|
SBase |
AbstractSBasePlugin.getExtendedSBase() |
|
SBase |
SBasePlugin.getExtendedSBase() |
Returns the SBase object that is extended by this plug-in.
|
SBase |
AbstractASTNodePlugin.getParentSBMLObject() |
|
SBase |
AbstractSBasePlugin.getParentSBMLObject() |
|
SBase |
ASTNodePlugin.getParentSBMLObject() |
Returns the parent
SBase object to which this plugin object is connected. |
SBase |
SBasePlugin.getParentSBMLObject() |
Returns the parent
SBase object to which this plugin object connected. |
Modifier and Type | Method | Description |
---|---|---|
void |
AbstractSBasePlugin.setExtendedSBase(SBase extendedSBase) |
Sets the extended
SBase . |
Constructor | Description |
---|---|
AbstractSBasePlugin(SBase extendedSBase) |
Modifier and Type | Class | Description |
---|---|---|
class |
Dimension |
|
class |
Index |
The
Index is used to referenced an arrayed element specified in
an attribute. |
Modifier and Type | Method | Description |
---|---|---|
boolean |
ArraysSBasePlugin.accept(SBase sbase) |
|
boolean |
ArraysSBasePlugin.register(SBase sbase) |
|
boolean |
ArraysSBasePlugin.unregister(SBase sbase) |
Constructor | Description |
---|---|
ArraysSBasePlugin(SBase extendedSBase) |
Creates an new
ArraysSBasePlugin instance. |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
ArraysMath.evaluateIndexBounds(Model model,
SBase reference,
int arrayDim,
ASTNode math,
java.util.Map<java.lang.String,java.lang.Double> dimSizes) |
|
static boolean |
ArraysMath.evaluateIndexBounds(Model model,
SBase parent,
java.lang.String refAttribute,
ASTNode math,
int arrayDim) |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
ExtendedSBaseValidator.canHaveDimension(SBase sbase) |
|
static java.util.List<SBMLError> |
ExtendedSBaseValidator.validate(Model model,
SBase sbase) |
Validates the given
SBase object. |
Constructor | Description |
---|---|
DimensionArrayDimCheck(Model model,
SBase sbase) |
Creates a DimensionArrayDimCheck with a model and sbase.
|
DimensionIDCheck(Model model,
SBase sbase) |
|
IndexArrayDimCheck(Model model,
SBase sbase) |
Creates a new
IndexArrayDimCheck instance with a model and sbase |
SBaseWithDimensionCheck(Model model,
SBase sbase) |
Creates a new SBaseWithDimensionCheck with a model and sbase.
|
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractNamedSBaseRef |
This abstract class is used by Deletion and Port classes.
|
class |
Deletion |
Defines a deletion operation to
be applied when a submodel instantiates a model definition.
|
class |
ExternalModelDefinition |
The
ExternalModelDefinition objects are model definitions - in and of
themselves, they are definitions of the models but not uses of those models. |
class |
ModelDefinition |
Holder class for model definitions, which are
Model s. |
class |
Port |
|
class |
ReplacedBy |
Indicates when the parent object is to be replaced by another object.
|
class |
ReplacedElement |
Points to a submodel object that should be considered "replaced".
|
class |
SBaseRef |
Contains the machinery for constructing references to specific components
within enclosed models or even within external models located in other files.
|
class |
Submodel |
Submodel s are instantiations of models contained within other models. |
Modifier and Type | Method | Description |
---|---|---|
SBase |
CompSBasePlugin.getParent() |
|
SBase |
CompSBasePlugin.getParentSBMLObject() |
Modifier and Type | Method | Description |
---|---|---|
boolean |
CompModelPlugin.accept(SBase sbase) |
|
boolean |
CompModelPlugin.register(SBase sbase) |
|
boolean |
CompModelPlugin.unregister(SBase sbase) |
Constructor | Description |
---|---|
CompSBasePlugin(SBase extendedSBase) |
Creates a CompSBasePlugin instance with a level and version.
|
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractDistribSBase |
|
class |
Uncertainty |
The
Uncertainty class is a collection of zero or more statistical measures related to the uncertainty of the parent
SBML element. |
class |
UncertParameter |
Defines one uncertainty statistic about the parent element.
|
class |
UncertSpan |
The
UncertSpan class defines a span of values that define an uncertainty statistic such as confidence interval or
range. |
Constructor | Description |
---|---|
DistribSBasePlugin(SBase sbase) |
Creates a new
DistribSBasePlugin instance. |
Modifier and Type | Method | Description |
---|---|---|
static void |
DistribModelBuilder.createRange(SBase sbase,
java.lang.String lower,
java.lang.String upper) |
Creates the constructs needed for a uncertml Range.
|
static void |
DistribModelBuilder.createStatisticsCollection(SBase sbase,
java.lang.String[] inputTypes,
java.lang.String[] inputs,
java.lang.String[] values) |
Creates the constructs needed for a StatisticsCollection.
|
static void |
DistribModelBuilder.createStatisticsCollection(SBase sbase,
java.lang.String[] inputTypes,
java.lang.String[] inputs,
java.lang.String[] values,
java.lang.String[] attributeNames,
java.lang.String[] attributeValues) |
Creates the constructs needed for a StatisticsCollection.
|
Modifier and Type | Class | Description |
---|---|---|
class |
DynElement |
|
class |
SpatialComponent |
Modifier and Type | Method | Description |
---|---|---|
SBase |
DynSBasePlugin.getParent() |
|
SBase |
DynSBasePlugin.getParentSBMLObject() |
Constructor | Description |
---|---|
DynSBasePlugin(SBase extendedSBase) |
Constructor
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
Association |
Represents either
a single gene, or a collection of genes in a logical expression and is only ever instantiated as one of its subclasses:
GeneProductRef , And and Or . |
Modifier and Type | Class | Description |
---|---|---|
class |
And |
This class represents a set of two or more associations that are related in an order independent ‘and’
relationship.
|
class |
FluxBound |
Deprecated.
Only defined in FBC Version 1.
|
class |
FluxObjective |
The
FluxObjective class is a relatively simple container for a model
variable weighted by a signed linear coefficient. |
class |
GeneProduct |
Defines a single gene product.
|
class |
GeneProductAssociation |
Contains a single
Association . |
class |
GeneProductRef |
References a
GeneProduct . |
class |
ListOfObjectives |
ListOfObjectives adds an additional required attribute: 'activeObjective'. |
class |
LogicalOperator |
Represents a collection of genes in a logical expression.
|
class |
Objective |
An integral component in a complete description of a steady-state model is the so-called
'objective function' which generally consists of a linear combination of model variables
(fluxes) and a sense (direction).
|
class |
Or |
This class represents a set of two or more associations that are related in an order independent ‘and’
relationship.
|
Constructor | Description |
---|---|
AbstractFBCSBasePlugin(SBase sbase) |
Modifier and Type | Class | Description |
---|---|---|
class |
Group |
|
class |
ListOfMemberConstraint |
Deprecated.
This class was removed from the specifications as of version 0.7
(2015-11-24) as no software wanted to implement support for it.
It might be added back in a future version of the specifications
if somebody want to implement it.
|
class |
ListOfMembers |
|
class |
Member |
|
class |
MemberConstraint |
Deprecated.
This class was removed from the specifications as of version 0.7
(2015-11-24) as no software wanted to implement support for it.
It might be added back in a future version of the specifications
if somebody want to implement it.
|
Modifier and Type | Method | Description |
---|---|---|
SBase |
GroupsModelPlugin.getChildAt(int childIndex) |
|
SBase |
GroupsModelPlugin.getGroup(java.lang.String sbmlID) |
Gets the
Group that has the given id. |
SBase |
Member.getSBaseInstance() |
Gets the actual SBase instance referred by the
idRef or metaIdRef , returns null
if nothing is found. |
Modifier and Type | Method | Description |
---|---|---|
Member |
Group.createMember(java.lang.String id,
SBase sbase) |
|
Member |
Group.creteMember(SBase sbase) |
|
void |
Member.setIdRef(SBase namedSbase) |
Sets the value of idRef, using the id defined in the given
SBase |
void |
Member.setMetaIdRef(SBase sbase) |
Sets the value of metaIdRef, using the metaid defined in the given
SBase |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractReferenceGlyph |
Abstract super class for all kinds of glyphs that graphically represent an
instance of
NamedSBase . |
class |
BoundingBox |
The
BoundingBox class specifies the required elements position and dimension. |
class |
CompartmentGlyph |
The
CompartmentGlyph class is derived from GraphicalObject
and inherits its attributes. |
class |
CubicBezier |
Represents smooth curves in the
Layout package. |
class |
Curve |
|
class |
CurveSegment |
Parent class to
LineSegment and CubicBezier . |
class |
Dimensions |
A
Dimensions is specified via the required attributes width,
height and an optional attribute depth, all of which are of type double. |
class |
GeneralGlyph |
The
GeneralGlyph is used to facilitate the representation of elements
other than Compartment , Species
and Reaction and thus
can be used for the display of relationships of Rule
or
elements defined by other SBML packages. |
class |
GraphicalObject |
All the more specific layout elements (
CompartmentGlyph , GeneralGlyph ,
SpeciesGlyph , ReactionGlyph , ReferenceGlyph , TextGlyph ,
and SpeciesReferenceGlyph ) are derived from the class GraphicalObject . |
class |
Layout |
|
class |
LineSegment |
The
LineSegment class consists of the mandatory attribute xsi:type and two child
elements of type Point . |
class |
Point |
The representation of a point in the "layout" package.
|
class |
ReactionGlyph |
Analogous to how a
Reaction object has to at least have one reactant
or product, the ReactionGlyph has to at least have one
SpeciesReferenceGlyph stored in the
ReactionGlyph.listOfSpeciesReferenceGlyphs . |
class |
ReferenceGlyph |
The
ReferenceGlyph element describes the graphical connection between
an arbitrary GraphicalObject (or derived element) and a
GeneralGlyph (which would be an arrow or some curve in most cases). |
class |
SpeciesGlyph |
The
SpeciesGlyph class has an optional species attribute, in
addition to to the attributes from GraphicalObject . |
class |
SpeciesReferenceGlyph |
The
SpeciesReferenceGlyph class describes the graphical connection
between a SpeciesGlyph and a ReactionGlyph (which would be
an arrow or some curve in most cases). |
class |
TextGlyph |
The
TextGlyph class describes the position and dimension of text labels. |
Modifier and Type | Method | Description |
---|---|---|
SBase |
LayoutModelPlugin.getChildAt(int index) |
|
SBase |
AbstractReferenceGlyph.getSBaseInstance() |
Gets the
SBase instance corresponding to the reference id. |
Modifier and Type | Method | Description |
---|---|---|
void |
AbstractReferenceGlyph.setSBase(SBase sbase) |
Sets the reference based on the id of the given
SBase . |
Modifier and Type | Class | Description |
---|---|---|
class |
BindingSiteSpeciesType |
A
BindingSiteSpeciesType object is a binding site, and therefore its instance can further define the bindingStatus
attribute and can participate a binding internally and explicitly in an InSpeciesTypeBond object, or externally and
implicitly defined by an OutwardBindingSite object. |
class |
CompartmentReference |
|
class |
InSpeciesTypeBond |
Defines a bond existing within a
MultiSpeciesType . |
class |
IntraSpeciesReaction |
|
class |
MultiSpeciesType |
The element MultiSpeciesType, which is part of SBML Level 2 Version 4 specification, is not part
of SBML Level 3 Version 1 Core any more.
|
class |
OutwardBindingSite |
A binding site not involved in any
InSpeciesTypeBond object in the MultiSpeciesType referenced by a Species is
an outwardBindingSite. |
class |
PossibleSpeciesFeatureValue |
Each state feature (
SpeciesFeatureType ) also requires the definition of all
the possible values it can take. |
class |
SpeciesFeature |
Defines the state of a component in a species by selecting values from
the listOfPossibleSpeciesFeatureValues of the referenced
SpeciesFeatureType . |
class |
SpeciesFeatureType |
A species type (
MultiSpeciesType ) can carry any number of features
(SpeciesFeatureType ), which are characteristic properties specific
for this type of species (Species ). |
class |
SpeciesFeatureValue |
|
class |
SpeciesTypeComponentIndex |
Provides a way to identify or index a component within a
MultiSpeciesType . |
class |
SpeciesTypeComponentMapInProduct |
A speciesTypeComponentMapInProduct defines the mapping between a component in a reactant and a component
in a product.
|
class |
SpeciesTypeInstance |
Provides a way to construct
MultiSpeciesType s and Species with multiple components. |
class |
SubListOfSpeciesFeature |
Allows to regroup a set of
SpeciesFeature that have a specific Relation between them. |
Modifier and Type | Method | Description |
---|---|---|
SBase |
MultiModelPlugin.getChildAt(int childIndex) |
|
SBase |
MultiSpeciesPlugin.getChildAt(int childIndex) |
Modifier and Type | Interface | Description |
---|---|---|
interface |
ListOfSpeciesFeatureContent |
Represents elements that can go into the combined ListOfSpeciesFeatures, meaning
SpeciesFeature and SubListOfSpeciesFeature . |
Modifier and Type | Class | Description |
---|---|---|
class |
FunctionTerm |
Each
FunctionTerm is also associated with a result and in addition to a Boolean
function inside a Math element that can be used to set the conditions under which this term
is selected. |
class |
Input |
|
class |
Output |
Each
Output refers to a QualitativeSpecies that participates
in (is affected by) the corresponding Transition . |
class |
QualitativeSpecies |
Similarly to the
Species in SBML, the components of qualitative
models refer to pools of entities that are considered indistinguishable and
are each located in a specific Compartment . |
class |
Transition |
A
Transition defines the changes in level associated with the QualitativeSpecies
that occur when a Transition is enabled. |
Modifier and Type | Method | Description |
---|---|---|
SBase |
QualModelPlugin.getChildAt(int childIndex) |
Constructor | Description |
---|---|
QualConstants(SBase source,
java.lang.String propertyName,
java.lang.Object oldValue,
java.lang.Object newValue) |
Constructs a new
PropertyChangeEvent . |
Modifier and Type | Class | Description |
---|---|---|
class |
ColorDefinition |
|
class |
DefaultValues |
Encodes default values within the containing
ListOfGlobalRenderInformation or
ListOfLocalRenderInformation . |
class |
Ellipse |
Encodes an ellipse.
|
class |
GlobalRenderInformation |
|
class |
GradientBase |
|
class |
GradientStop |
|
class |
GraphicalPrimitive1D |
|
class |
GraphicalPrimitive2D |
|
class |
Image |
|
class |
LinearGradient |
|
class |
LineEnding |
|
class |
ListOfGlobalRenderInformation |
Derives from the
ListOf class and contains one or more objects of type GlobalRenderInformation . |
class |
ListOfLocalRenderInformation |
Derives from the
ListOf class and contains one or more objects of type LocalRenderInformation . |
class |
ListOfRenderInformation<T extends RenderInformationBase> |
Derives from the
ListOf class and contains one or more objects of type RenderInformationBase . |
class |
LocalRenderInformation |
|
class |
LocalStyle |
|
class |
Polygon |
|
class |
RadialGradient |
|
class |
Rectangle |
|
class |
RenderCubicBezier |
|
class |
RenderCurve |
Implements the curve concept from the SBML render extension.
|
class |
RenderCurveSegment |
Parent class to
RenderPoint and RenderCubicBezier . |
class |
RenderGroup |
The
RenderGroup class from the SBML render extension is used to group graphical primitives together
to create composite representations from simple primitives. |
class |
RenderInformationBase |
|
class |
RenderPoint |
|
class |
Style |
|
class |
Text |
|
class |
Transformation |
|
class |
Transformation2D |
Modifier and Type | Method | Description |
---|---|---|
SBase |
GlobalRenderInformation.getChildAt(int childIndex) |
|
SBase |
GradientStop.getChildAt(int childIndex) |
|
SBase |
Image.getChildAt(int childIndex) |
|
SBase |
LocalRenderInformation.getChildAt(int childIndex) |
|
SBase |
Rectangle.getChildAt(int childIndex) |
|
SBase |
RenderCurve.getChildAt(int childIndex) |
|
SBase |
RenderInformationBase.getChildAt(int childIndex) |
|
SBase |
RenderLayoutPlugin.getChildAt(int childIndex) |
|
SBase |
RenderListOfLayoutsPlugin.getChildAt(int childIndex) |
Constructor | Description |
---|---|
AbstractRenderPlugin(SBase extendedElement) |
Creates an AbstractRenderPlugin instance
|
Modifier and Type | Class | Description |
---|---|---|
class |
ChangedMath |
Declares which package has modified the value or the mathematical meaning of
an
SBase and in which way. |
Constructor | Description |
---|---|
ReqSBasePlugin(SBase sbase) |
Creates a
ReqSBasePlugin instance associated with the given SBase . |
Modifier and Type | Interface | Description |
---|---|---|
interface |
SpatialNamedSBase |
Deprecated.
since id and name have been added to the spatial package classes, this interface is not needed any more and
NamedSBase can be used instead. |
Modifier and Type | Method | Description |
---|---|---|
SBase |
AbstractSpatialSBasePlugin.getParent() |
|
SBase |
AbstractSpatialSBasePlugin.getParentSBMLObject() |
|
SBase |
ParameterType.getVariableInstance() |
Modifier and Type | Method | Description |
---|---|---|
boolean |
SpatialModelPlugin.accept(SBase sbase) |
|
boolean |
SpatialModelPlugin.register(SBase sbase) |
|
boolean |
SpatialModelPlugin.unregister(SBase sbase) |
Constructor | Description |
---|---|
AbstractSpatialSBasePlugin(SBase extendedSBase) |
Modifier and Type | Class | Description |
---|---|---|
class |
ListOfWithName<T extends SBase> |
Deprecated.
since JSBML 1.2 and the introduction of
ListOf.setOtherListName(String) , this class is not necessary any more. |
Modifier and Type | Class | Description |
---|---|---|
class |
ListOfWithName<T extends SBase> |
Deprecated.
since JSBML 1.2 and the introduction of
ListOf.setOtherListName(String) , this class is not necessary any more. |
Modifier and Type | Method | Description |
---|---|---|
static <T extends SBase> |
SBMLtools.setLevelAndVersion(T sbase,
int level,
int version) |
Modifier and Type | Method | Description |
---|---|---|
boolean |
IdManager.accept(SBase sbase) |
|
static void |
CobraUtil.appendCobraNotes(SBase sbase,
java.util.Properties properties) |
|
static java.lang.String |
SBMLtools.getIdOrName(SBase nsb) |
|
static java.lang.String |
SBMLtools.getNameOrId(SBase nsb) |
|
static java.util.Properties |
CobraUtil.parseCobraNotes(SBase sbase) |
Parses the notes of the given
SBase element. |
boolean |
IdManager.register(SBase sbase) |
|
static void |
SBMLtools.setSBOTerm(SBase sbase,
int term) |
|
boolean |
IdManager.unregister(SBase sbase) |
|
static void |
CobraUtil.writeCobraNotes(SBase sbase,
java.util.Properties properties) |
Constructor | Description |
---|---|
ListOfWithName(ListOfWithName<? extends SBase> listOf) |
Deprecated.
|
Modifier and Type | Method | Description |
---|---|---|
abstract <T extends SBase> |
LevelVersionConverter.performAction(T sbase) |
Executes a conversion action on the given instance of
SBase . |
<T extends SBase> |
ToL3Converter.performAction(T sbase) |
|
<T extends SBase> |
ToL3V2Converter.performAction(T sbase) |
Modifier and Type | Method | Description |
---|---|---|
abstract boolean |
LevelVersionConverter.needsAction(SBase sbase) |
Test if a given instance of SBase requires an action during conversion.
|
boolean |
ToL3Converter.needsAction(SBase sbase) |
|
boolean |
ToL3V2Converter.needsAction(SBase sbase) |
Modifier and Type | Method | Description |
---|---|---|
java.util.Map<SBase,SBase> |
OverdeterminationValidator.getMatching() |
Returns the determined matching
|
java.util.Map<SBase,SBase> |
OverdeterminationValidator.getMatching() |
Returns the determined matching
|
Modifier and Type | Method | Description |
---|---|---|
static SBase |
LoggingValidationContext.getParentSBase(TreeNodeWithChangeSupport o) |
Modifier and Type | Method | Description |
---|---|---|
SBase |
SBaseRefConstraints.getModelOrSubmodel(SBase sbase) |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
SBaseConstraints.checkHtmlBodyContent(ValidationContext ctx,
SBase sb,
XMLNode topLevelNode) |
Checks that each sub elements of the given
XMLNode are allowed inside a body element. |
static boolean |
SBaseConstraints.checkHtmlHeadContent(ValidationContext ctx,
SBase sb,
XMLNode topLevelNode) |
Checks that each sub elements of the given
XMLNode are allowed inside a head element. |
SBase |
SBaseRefConstraints.getModelOrSubmodel(SBase sbase) |
|
static void |
ValidationConstraint.logError(ValidationContext ctx,
int errorCode,
SBase source,
java.lang.String... args) |
Logs a new
SBMLError into a LoggingValidationContext . |
static void |
ValidationConstraint.logErrorWithPostmessageCode(ValidationContext ctx,
int errorCode,
java.lang.String postErrorMessageKey,
SBase source,
java.lang.String... args) |
Logs a new
SBMLError into a LoggingValidationContext . |
Modifier and Type | Class | Description |
---|---|---|
class |
ElementOrderValidationFunction<T extends SBase> |
Class used to validate the order of the XML elements.
|
Modifier and Type | Field | Description |
---|---|---|
static ValidationFunction<SBase> |
SBOValidationConstraints.isInteraction |
Checks if the SBO of the SBase is part of the branch 'Interaction'.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isMaterialEntity |
Checks if the SBO of the SBase is part of the branch 'Material Entity'.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isMathematicalExpression |
Checks if the SBO of the SBase is part of the branch 'Mathematical Expression'.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isModellingFramework |
Checks if the SBO of the SBase is part of the branch 'Modelling Framework'.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isObsolete |
Checks if the SBO of the SBase is obsolete.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isParticipantRole |
Checks if the SBO of the SBase is part of the branch 'Participant Role'.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isQuantitativeParameter |
Checks if the SBO of the SBase is part of the branch 'Quantitative Parameter'.
|
static ValidationFunction<SBase> |
SBOValidationConstraints.isRateLaw |
Checks if the SBO of the SBase is part of the branch 'Rate Law'.
|
Modifier and Type | Method | Description |
---|---|---|
boolean |
AssignmentCycleValidation.check(ValidationContext ctx,
SBase sb) |
|
static java.lang.String |
ValidationTools.checkUnknownUnitSyntax(ValidationContext ctx,
SBase sbase,
java.lang.String attributeName) |
Checks if the given
SBase contains an attribute in the unknown XML user object. |
Modifier and Type | Method | Description |
---|---|---|
static SBMLError |
SBMLErrorFactory.createError(int id,
int level,
int version,
boolean customMessage,
SBase sbase) |
Creates a new
SBMLError instance. |
Modifier and Type | Method | Description |
---|---|---|
static void |
PackageUtil.checkPackages(SBase sbase,
java.util.List<java.lang.String> packageNamespaces,
boolean silent,
boolean fix) |
Checks the given
SBase , including all it's siblings, to make sure
that the package version and namespace is set properly. |
SBasePlugin |
ArraysParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
CompParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
DistribParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
DynParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
FBCParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
GroupsParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
L3LayoutParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
LayoutParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
MultiParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
PackageParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
QualParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
RenderParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
ReqParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
SpatialParser.createPluginFor(SBase sbase) |
|
void |
AnnotationReader.processAnnotation(SBase contextObject) |
Process the annotation of the given
SBase object. |
void |
SBMLRDFAnnotationParser.processAnnotation(SBase contextObject) |
|
XMLNode |
AnnotationWriter.writeAnnotation(SBase contextObject,
XMLNode xmlNode) |
|
XMLNode |
SBMLRDFAnnotationParser.writeAnnotation(SBase contextObject,
XMLNode xmlNode) |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
SBMLWriter.writeAnnotation(SBase sbase) |