Changed Classes and Interfaces |
ASTNode
|
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression. |
AbstractMathContainer
|
Base class for all the SBML components which contain MathML nodes. |
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. |
AbstractSBase
|
The base class for each SBase component. |
AbstractTreeNode
|
A basic implementation of the TreeNode 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. |
CVTerm
|
Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
of a SBML component. |
Compartment
|
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation. |
Constraint
|
Represents the constraint XML element of a SBML file. |
Creator
|
Contains all the information about a creator of a Model (or other
SBase in level 3). |
Delay
|
Represents the delay subnode of an event element. |
Event
|
Represents the event XML element of a SBML file. |
EventAssignment
|
Represents the eventAssignment XML element of a SBML file. |
FunctionDefinition
|
Represents the functionDefinition XML element of a SBML file. |
JSBML
|
Wrapper class for global methods and constants defined by JSBML. |
KineticLaw
|
Represents the kineticLaw XML element of a SBML file. |
ListOf
|
This list implementation is a Java List that extends
AbstractSBase. |
Model
|
JSBML implementation of SBML's Model construct. |
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. |
Priority
|
This class represents the priority element in SBML. |
Reaction
|
Represents the reaction XML element of a SBML file. |
Rule
|
The base class for the AlgebraicRule, RateRule,
AssignmentRule. |
SBMLDocument
|
Represents the 'sbml' root node of a SBML file. |
SBMLErrorLog
|
Log of errors and other events encountered during SBML processing. |
SBO
|
Methods for interacting with Systems Biology Ontology (SBO) terms. |
SBase
|
The interface to implement for each SBML element. |
SimpleSpeciesReference
|
The base class of SpeciesReference and
ModifierSpeciesReference. |
Species
|
Represents the species XML element of a SBML file. |
SpeciesReference
|
Represents the speciesReference XML element of a SBML file. |
Trigger
|
Represents the trigger XML element of a SBML file. |
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. |
Unit
|
Represents the unit XML element of a SBML file. |
UnitDefinition
|
Represents the unitDefinition XML element of a SBML file. |