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Package org.sbml.jsbml

Added Classes
SBMLTypeUndefinedException This error can be thrown whenever a data type is being initialized that is undefined for a certain SBML Level/Version combination.

Changed Classes and Interfaces
ASTNode A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.
AbstractSBase The base class for each SBase component.
AbstractTreeNode A basic implementation of the TreeNode interface.
Annotation An Annotation represents the annotations of an SBase element.
CVTerm Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element of a SBML component.
CVTerm.Qualifier This {@code enum} list all the possible MIRIAM qualifiers.
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).
Event Represents the event XML element of a SBML file.
FunctionDefinition Represents the functionDefinition XML element of a SBML file.
History Contains all the history information about a Model (or other SBase if level >= 3).
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.
LocalParameter A local parameter can only be used to specify a constant within a KineticLaw.

JSBML implementation of SBML's Model construct.

PropertyUndefinedError This PropertyException indicates that the value belonging to a mandatory property, for which there is no default value, has not been declared by the user.
Reaction Represents the reaction XML element of a SBML file.
SBMLDocument Represents the 'sbml' root node of a SBML file.
SBMLError Representation of errors, warnings and other diagnostics.
SBMLErrorLog Log of errors and other events encountered during SBML processing.
SBMLInputConverter This interface allows the implementing class to create a JSBML model based on some other data structure.
SBMLOutputConverter This interface allows the implementing class to convert a JSBML model into another data structure.
SBO Methods for interacting with Systems Biology Ontology (SBO) terms.
SBO.Term This is a convenient wrapper class for the corresponding implementation of org.biojava.ontology.Term in BioJava as it provides specialized methods to obtain the information from the SBO OBO file directly and under the same name as the keys are given in that file.
SBO.Triple This is a wrapper class for the corresponding BioJava class org.biojava.ontology.Triple, to allow for simplified access to the properties of a subject-predicate-object triple in this ontology.
SBase The interface to implement for each SBML element.
Species Represents the species XML element of a SBML file.
SpeciesReference Represents the speciesReference XML element of a SBML file.
Unit Represents the unit XML element of a SBML file.
UnitDefinition Represents the unitDefinition XML element of a SBML file.