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.distrib | |
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.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.validator.offline.constraints.helper |
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 |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
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 |
SBaseWithUnit |
Defines a kind of
SBase that is equipped with a defined unit. |
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 |
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 |
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 |
LocalParameter |
A local parameter can only be used to specify a constant within a
KineticLaw . |
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 |
Species |
Represents the species XML element of a SBML file.
|
class |
SpeciesReference |
Represents the speciesReference XML element of a SBML file.
|
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.
|
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 |
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 |
IntraSpeciesReaction |
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 . |
Modifier and Type | Class | Description |
---|---|---|
class |
AnalyticVolume |
|
class |
CoordinateComponent |
Modifier and Type | Field | Description |
---|---|---|
static ValidationFunction<SBaseWithDerivedUnit> |
ValidationTools.checkDerivedUnit |
Modifier and Type | Method | Description |
---|---|---|
static UnitDefinition |
ValidationTools.getDerivedUnitDefinition(ValidationContext ctx,
SBaseWithDerivedUnit sbase) |
Returns the derived
UnitDefinition for the given SBaseWithDerivedUnit . |