Package org.sbml.jsbml

Pure Java™ implementation of the data structures to represent all SBML constructs.

Author:

Nicolas Rodriguez, Andreas Dräger, Clemens Wrzodek

Interface Summary

Interface	Description
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.
CallableSBase	The interface CallableSBase represents an SBase that can be called in mathematical expressions, i.e., ASTNode, via its identifier.
CompartmentalizedSBase
MathContainer	Base interface for all the SBML components which contain MathML nodes.
NamedSBase	Base class for all the SBML components with an id and a name (optional or not) in SBML Level 3 Version 1 or lower.
NamedSBaseWithDerivedUnit	All objects that implement this interface can be referenced in abstract syntax trees as implemented in ASTNode.
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.
SBase	The interface to implement for each SBML element.
SBaseWithDerivedUnit	This type represents an SBase object that is associated to a unit.
SBaseWithUnit	Defines a kind of SBase that is equipped with a defined unit.
SBMLInputConverter<T>	This interface allows the implementing class to create a JSBML model based on some other data structure.
SBMLOutputConverter<T>	This interface allows the implementing class to convert a JSBML model into another data structure.
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.
UniqueSId	This interface is used to tag all those elements whose identifier must be unique within an SBML Model.
Variable	A variable of the system is a Quantity whose value may change during a simulation.

Class Summary

Class	Description
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.
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.
AbstractSBase	The base class for each SBase component.
AbstractTreeNode	A basic implementation of the TreeNode interface.
AlgebraicRule	Represents the algebraicRule XML element of a SBML file.
Annotation	An Annotation represents the annotations of an SBase element.
AnnotationElement	A common super class for all those elements that can be part of an Annotation.
AssignmentRule	Represents the assignmentRule XML element of a SBML file.
ASTNode	A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.
Compartment	Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation.
CompartmentType	Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
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).
CVTerm	Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element of a SBML component.
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.
ExplicitRule	An explicit Rule is a rule that explicitly declares its variable element.
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).
InitialAssignment	Represents the initialAssignment 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<T extends SBase>	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.
ModifierSpeciesReference	Represents the modifierSpeciesReference XML element of a SBML file.
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.
QuantityWithUnit	This object represents an element with identifier and name, a value, and a defined unit.
RateRule	Represents the rateRule XML element of a SBML file.
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.
SBMLReader	Provides methods for reading SBML from files, text strings or streams.
SBMLWriter	Provides methods for writing SBML to files, text strings or streams.
SBO	Methods for interacting with Systems Biology Ontology (SBO) terms.
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.
SpeciesType	Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
StoichiometryMath	Deprecated. Since SBML Level 3 Version 1 use AssignmentRule with instances of SpeciesReference as Variable instead.
Symbol	The base class for Compartment, Species, Parameter.
TidySBMLWriter	Provides methods for writing SBML to files, text strings or streams.
Trigger	Represents the trigger 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.

Enum Summary

Enum	Description
ASTNode.Type	An enumeration of all possible types that can be represented by an abstract syntax tree node.
CVTerm.Qualifier	This enum list all the possible MIRIAM qualifiers.
CVTerm.Type	This enum list all the possible MIRIAM qualifiers type.
ListOf.Type	This enum lists all the possible names of the listXXX components.
SBMLError.SEVERITY
SBMLException.Category	Category of this exception.
SBMLException.Code	Error codes.
SBMLException.Type
Unit.Kind	This enumeration contains an exhaustive list of all available unit kinds within all Levels and Versions of SBML.

Exception Summary

Exception	Description
IdentifierException	This exception is thrown when trying to set or add an identifier to an instance of NamedSBase but if the given identifier is already registered in the containing Model.
LevelVersionError	An SBMLError that indicates that associated instances of SBase cannot be combined within the same model due to their differently set Level or Version attribute.
PropertyException	This is an error of an undefined property or value for a property in some instance of SBase.
PropertyNotAvailableException	An error that indicates that a property of an SBase is not available for the current SBML Level/Version combination.
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.
SBMLError	Representation of errors, warnings and other diagnostics.
SBMLException	This class roughly corresponds to libSBML's SBMLError class.
SBMLTypeUndefinedException	This error can be thrown whenever a data type is being initialized that is undefined for a certain SBML Level/Version combination.