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.
Model	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.