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Package org.sbml.jsbml

Added Interfaces
UniqueSId This interface is used to tag all those elements whose identifier must be unique within an SBML Model.
 

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.