Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.arrays | |
org.sbml.jsbml.ext.comp |
Provides classes for the
Hierarchical Model Composition package.
|
org.sbml.jsbml.ext.distrib | |
org.sbml.jsbml.ext.dyn |
Provides classes for the
Dynamic Structures package.
|
org.sbml.jsbml.ext.fbc |
Provides classes for the
Flux Balance Constraints package (FBC).
|
org.sbml.jsbml.ext.groups |
Provides classes for the Groups
package.
|
org.sbml.jsbml.ext.layout |
Provides classes for the Layout
package.
|
org.sbml.jsbml.ext.multi |
Provides classes for the Multi package.
|
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.ext.render |
Provides classes for the render package, see the specification at sbml.org.
|
org.sbml.jsbml.ext.req | |
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.util |
A collection of handy utilities when working with JSBML classes,
such as classes for String manipulation or mathematical operations.
|
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 |
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 |
---|---|---|
abstract AbstractSBase |
AbstractSBase.clone() |
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 | 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 | 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. |
Modifier and Type | Class | Description |
---|---|---|
class |
DynElement |
|
class |
SpatialComponent |
Modifier and Type | Method | Description |
---|---|---|
AbstractSBase |
DynElement.clone() |
|
AbstractSBase |
SpatialComponent.clone() |
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.
|
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 | 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 | 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 |
---|---|---|
AbstractSBase |
PossibleSpeciesFeatureValue.clone() |
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 | 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 | Class | Description |
---|---|---|
class |
ChangedMath |
Declares which package has modified the value or the mathematical meaning of
an
SBase and in which way. |
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. |