Package org.sbml.libsbml

Interface Summary

Interface	Description
libsbmlConstants

Class Summary

Class	Description
AlgebraicRule	Implementation of SBML's AlgebraicRule construct.
AssignmentRule	Implementation of SBML's AssignmentRule construct.
Association	fbc Implementation of the 'fbc' proposed package Association construct.
ASTNode	Abstract Syntax Tree (AST) representation of a mathematical expression.
ASTNodeList
BoundingBox	layout Representation of a bounding box.
ColorDefinition	LibSBML implementation for the ColorDefinition construct from the SBML render extension.
Compartment	Implementation of SBML's Compartment construct.
CompartmentGlyph	layout Representation of a compartment glyph.
CompartmentType	Implementation of SBML's Level 2's CompartmentType construct.
CompBase	comp A convenience subclass of &ldquocomp&rdquo package SBase-derived classes
CompExtension	comp The core module of the &ldquocomp&rdquo package extension.
CompModelPlugin	comp Implementation of the &ldquocomp&rdquo package extention to the Model construct.
CompPkgNamespaces	Class to store the Level, Version and XML namespace information of an SBML extension package.
CompSBasePlugin	comp Implementation of the &ldquocomp&rdquo package extention to the SBase construct.
CompSBMLDocumentPlugin	comp Implementation of the &ldquocomp&rdquo package extention to the SBMLDocument construct.
Constraint	Implementation of SBML's Constraint construct.
ConversionOption	Class of object that encapsulates a conversion option.
ConversionProperties	Class of object that encapsulates the properties of an SBML converter.
CubicBezier	layout A CubicBezier represents a smooth curve in the &ldquolayout&rdquo package.
Curve	layout The Curve class describes how to connect elements in a diagram defined with the use of the &ldquolayout&rdquo package.
CVTerm	Representation of MIRIAM-compliant controlled vocabulary annotation.
CVTermList
Date	Representation of MIRIAM-compliant dates used in ModelHistory.
DateList
DefaultTerm	qual The DefaultTerm class for the Qualitative Models package.
Delay	Implementation of SBML's Delay construct for Event.
Deletion	comp Implementation of the Deletion construct from the &ldquocomp&rdquo package.
Dimensions	layout The Dimensions class describes the overall 2D or 3D shape of a &ldquolayout&rdquo package object.
double_array
Ellipse	graphical representation of an ellipse from the SBML render extension
Event	Implementation of SBML's Event construct.
EventAssignment	Implementation of SBML's EventAssignment construct for Event.
ExternalModelDefinition	comp Implementation of the ExternalModelDefinition construct from the &ldquocomp&rdquo package.
FbcExtension	fbc The core module of the 'fbc' package extension.
FbcModelPlugin	fbc Implementation of the 'fbc' package extention to the Model construct.
FbcPkgNamespaces	Class to store the Level, Version and XML namespace information of an SBML extension package.
FbcSpeciesPlugin	fbc Implementation of the 'fbc' package extention to the Species construct.
FluxBound	fbc Implementation of the 'fbc' package FluxBound construct.
FluxObjective	fbc Implementation of the 'fbc' package FluxObjective construct.
FunctionDefinition	Implementation of SBML's FunctionDefinition construct.
FunctionTerm	qual The FunctionTerm class for the Qualitative Models package.
GeneAssociation	fbc Implementation of the 'fbc' package GeneAssociation construct.
GeneralGlyph	layout The GeneralGlyph is used by the &ldquolayout&rdquo package to represent any SBML object.
GlobalRenderInformation	GlobalRenderInformation is the render information stored in the ListOfLayouts.
GlobalStyle	implementation of the GlobalStyle concept of the SBML render extension.
GradientBase	abstract base class for linear and radial gradients
GradientStop	LibSBML implementation of the gradient stop concept from the
GraphicalObject	layout The basic &ldquolayout&rdquo package element for storing layout information.
GraphicalPrimitive1D	base class for all graphical primitives which implements all 1D attributes
GraphicalPrimitive2D	base class for all graphical primitives which implements all 2D attributes
Group
GroupsExtension
GroupsModelPlugin
GroupsPkgNamespaces	Class to store the Level, Version and XML namespace information of an SBML extension package.
Image	implementation of the Image concept from the SBML render extension
InitialAssignment	Implementation of SBML's InitialAssignment construct.
Input	qual The Input class for the Qualitative Models package.
int_array
KineticLaw	Implementation of SBML's KineticLaw construct.
L3ParserSettings	A helper class for controlling the behavior of the text-string formula parser.
Layout	layout Each Layout object stores a set of layout information for objects in the Model.
LayoutExtension	layout The core module of the 'layout' package extension.
LayoutModelPlugin	layout Implementation of the 'layout' package extention to the Model construct.
LayoutPkgNamespaces	Class to store the Level, Version and XML namespace information of an SBML extension package.
LayoutSpeciesReferencePlugin	layout Implementation of the 'layout' package extention to the SpeciesReference construct.
libsbml	Wrapper class for global methods and constants defined by libSBML.
LinearGradient	Representation of a linear gradient object from the SBML render extension.
LineEnding	a LineEnding is a decoration element for the start and/or end of curves in the SBML render extension, e.g.
LineSegment	layout The representation of a line in the &ldquolayout&rdquo package.
ListOf	Parent class for libSBML's 'ListOfXYZ' classes.
ListOfColorDefinitions	LibSBML implementation for a container which holds zero or more ColorDefinition objects.
ListOfCompartmentGlyphs	layout Implementation of the ListOfCompartmentGlyphs construct from the &ldquolayout&rdquo package.
ListOfCompartments	Implementation of SBML Level 2's ListOfCompartments construct.
ListOfCompartmentTypes	Implementation of SBML's ListOfCompartmentTypes construct.
ListOfConstraints	Implementation of SBML's ListOfConstraints construct.
ListOfCurveElements	A container to store curve elements (RenderPoint and RenderCubicBezier).
ListOfDeletions	comp Implementation of the ListOfDeletions construct from the &ldquocomp&rdquo package.
ListOfDrawables	container class that stores objects derived from Transformation2D.
ListOfEventAssignments	Implementation of SBML's ListOfEventAssignments construct.
ListOfEvents	Implementation of SBML's ListOfEvents construct.
ListOfExternalModelDefinitions	comp Implementation of the ListOfExternalModelDefinitions construct from the &ldquocomp&rdquo package.
ListOfFluxBounds	fbc Implementation of the ListOfFluxBounds construct from the 'fbc' package.
ListOfFluxObjectives	fbc Implementation of the 'fbc' package ListOfFluxObjectives construct.
ListOfFunctionDefinitions	Implementation of SBML's ListOfFunctionDefinitions construct.
ListOfFunctionTerms	qual Implementation of the ListOfFunctionTerms construct from the 'qual' package.
ListOfGeneAssociations	fbc Implementation of the 'fbc' package suggested ListOfGeneAssociations annotation construct.
ListOfGlobalRenderInformation	container class that stores GlobalRenderInformation objects.
ListOfGlobalStyles	ListOfGlobalStyles is the container class that stores GlobalStyles in GlobalRenderInformation objects.
ListOfGradientDefinitions	a container class that holds a list of gradient definitions.
ListOfGradientStops	a container that holds zero or more GradientStop objects.
ListOfGraphicalObjects	layout Implementation of the ListOfAdditionalGraphicalObjects construct from the &ldquolayout&rdquo package.
ListOfGroups
ListOfInitialAssignments	Implementation of SBML's ListOfInitialAssignments construct.
ListOfInputs	qual Implementation of the ListOfInputs construct from the 'qual' package.
ListOfLayouts	layout Implementation of the * ListOfLayouts construct from the &ldquolayout&rdquo package.
ListOfLineEndings	container class to store LineEnding objects
ListOfLineSegments	layout Implementation of the ListOfLineSegments construct from the 'layout' package.
ListOfLocalParameters	Implementation of SBML Level 3's ListOfLocalParameters construct.
ListOfLocalRenderInformation	container class that stores LocalRenderInformation objects.
ListOfLocalStyles	ListOfLocalStyles is the container class that stores LocalStyles in LocalRenderInformation objects.
ListOfMemberConstraints
ListOfMembers
ListOfModelDefinitions	comp Implementation of the ListOfModelDefinitions construct from the &ldquocomp&rdquo package.
ListOfObjectives	fbc Implementation of the ListOfObjectives construct from the 'fbc' package.
ListOfOutputs	qual Implementation of the ListOfOutputs construct from the 'qual' package.
ListOfParameters	Implementation of SBML's ListOfParameters construct.
ListOfPorts	comp Implementation of the ListOfPorts construct from the &ldquocomp&rdquo package.
ListOfQualitativeSpecies	qual Implementation of the ListOfQualitativeSpecies construct from the 'qual' package.
ListOfReactionGlyphs	layout Implementation of the ListOfReactionGlyphs construct from the &ldquolayout&rdquo package.
ListOfReactions	Implementation of SBML's ListOfReactions construct.
ListOfReferenceGlyphs	layout Implementation of the ListOfReferenceGlyphs construct from the &ldquolayout&rdquo package.
ListOfReplacedElements	comp Implementation of the ListOfReplacedElements construct from the &ldquocomp&rdquo package.
ListOfRules	Implementation of SBML's ListOfRules construct.
ListOfSpecies	Implementation of SBML Level 2's ListOfSpecies construct.
ListOfSpeciesGlyphs	layout Implementation of the ListOfSpeciesGlyphs construct from the &ldquolayout&rdquo package.
ListOfSpeciesReferenceGlyphs	layout Implementation of the ListOfSpeciesReferenceGlyphs construct from the &ldquolayout&rdquo package.
ListOfSpeciesReferences	Implementation of SBML's ListOfSpeciesReferences construct.
ListOfSpeciesTypes	Implementation of SBML's ListOfSpeciesTypes construct.
ListOfSubmodels	comp Implementation of the ListOfSubmodels construct from the &ldquocomp&rdquo package.
ListOfTextGlyphs	layout Implementation of the ListOfTextGlyphs construct from the &ldquolayout&rdquo package.
ListOfTransitions	qual Implementation of the ListOfTransitions construct from the 'qual' package.
ListOfUnitDefinitions	Implementation of SBML's ListOfUnitDefinitions construct.
ListOfUnits	Implementation of SBML's ListOfUnits construct.
LocalParameter	Implementation of SBML Level 3's LocalParameter construct.
LocalRenderInformation	LocalRenderInformation is the render information stored in Layouts.
LocalStyle	implementation of the LocalStyle concept of the SBML render extension.
Member
MemberConstraint
Model	Implementation of SBML's Model construct.
ModelCreator	Representation of MIRIAM-compliant model creator data used in ModelHistory.
ModelCreatorList
ModelDefinition	comp Implementation of the ModelDefinition construct from the &ldquocomp&rdquo package.
ModelHistory	Representation of MIRIAM-compliant model history data.
ModifierSpeciesReference	Implementation of SBML's ModifierSpeciesReference construct.
Objective	fbc Implementation of the 'fbc' package Objective construct.
OFStream
OStream
OStringStream
Output	qual The Output class for the Qualitative Models package.
Parameter	Implementation of SBML's Parameter construct.
Point	layout The representation of a point in the &ldquolayout&rdquo package.
Polygon	class representing a polygon from the SBML render extension
Port	comp Implementation of the Port construct from the &ldquocomp&rdquo package.
Priority	Implementation of SBML Level 3's Priority construct for Event.
QualExtension	qual The core module of the 'qual' package extension.
QualitativeSpecies	qual The QualitativeSpecies class for the Qualitative Models package.
QualModelPlugin	qual Implementation of the 'qual' package extention to the Model construct.
QualPkgNamespaces	Class to store the Level, Version and XML namespace information of an SBML extension package.
RadialGradient	Representation of a radial gradient object from the SBML render extension.
RateRule	Implementation of SBML's RateRule construct.
RDFAnnotationParser	Read/write/manipulate RDF annotations stored in SBML annotation elements.
Reaction	Implementation of SBML's Reaction construct.
ReactionGlyph	layout The ReactionGlyph is used to represent Reaction elements in the layout.
Rectangle
ReferenceGlyph	layout The ReferenceGlyph is used by the &ldquolayout&rdquo package to connect a GraphicalObject and a GeneralGlyph.
RelAbsVector	This class represents a pair of numerical values where one value represents an absolute value and the other value is a relative value in percent.
RenderCubicBezier	CubicBezier representation for RenderCurve objects and Polygon objects.
RenderCurve	implementation of the Curve concept from the SBML render extension
RenderExtension
RenderGraphicalObjectPlugin
RenderGroup	The RenderGroup concept from the SBML render extension is used to group graphical primitives together to create composite representations from simple primitives.
RenderInformationBase	abstract base class for local and global render information.
RenderLayoutPlugin
RenderListOfLayoutsPlugin
RenderPkgNamespaces	Class to store the Level, Version and XML namespace information of an SBML extension package.
RenderPoint	Represents a point where the coordinates can be made up of absolute as well as relative values (@see RelAbsVector)
ReplacedBy	comp Implementation of the ReplacedBy construct from the &ldquocomp&rdquo package.
ReplacedElement	comp Implementation of the ReplacedElement construct from the &ldquocomp&rdquo package.
Replacing	comp A convenience subclass of the ReplacedElement and ReplacedBy constructs from the &ldquocomp&rdquo package.
Rule	Implementation of SBML's Rule construct.
SBase	Implementation of SBase, the base class of most SBML objects.
SBaseList
SBasePlugin	Representation of a plug-in object of SBML's package extension.
SBaseRef	comp Implementation of the SBaseRef construct from the &ldquocomp&rdquo package.
SBMLConverter	Base class for SBML converters.
SBMLConverterRegistry	Registry of all SBML converters.
SBMLDocument	Container for an SBML document and interface for global operations on SBML documents.
SBMLDocumentPlugin	Template class for the SBMLDocument Plugin class needed by all packages.
SBMLError	Representation of errors, warnings and other diagnostics
SBMLErrorLog	Log of errors and other events encountered during SBML processing.
SBMLExtensionException	Exceptions for libSBML extensions for SBML Level 3 packages.
SBMLExtensionRegistry	Registry class in which extension packages are registered.
SBMLFileResolver	comp A resolver for documents stored on a file system.
SBMLFunctionDefinitionConverter	SBML converter for replacing function definitions.
SBMLInitialAssignmentConverter	SBML converter for replacing initial assignments.
SBMLLevelVersionConverter	SBML converter for transforming documents from one Level+Version to another.
SBMLNamespaces	Class to store SBML Level, Version and namespace information.
SBMLNamespacesList
SBMLReader	Methods for reading SBML from files and text strings.
SBMLResolver	comp Base class for SBML resolvers.
SBMLResolverRegistry	comp Registry of all SBML resolvers.
SBMLRuleConverter	SBML converter for reordering rules and assignments in a model.
SBMLStripPackageConverter	SBML converter for removing packages.
SBMLUnitsConverter	SBML converter to convert a model's units to SI units.
SBMLUri	comp utility class for handling URIs.
SBMLValidator	Base class for SBML validators
SBMLWriter	Methods for writing SBML to files and text strings.
SBO	Methods for interacting with Systems Biology Ontology terms.
SimpleSpeciesReference	Implementation of SBML's SimpleSpeciesReference construct.
Species	Implementation of SBML's Species construct.
SpeciesGlyph	layout The SpeciesGlyph represents a Species in the &ldquolayout&rdquo package.
SpeciesReference	Implementation of SBML's SpeciesReference construct.
SpeciesReferenceGlyph	layout A SpeciesReferenceGlyph represents a reactant or product from a Reaction in the &ldquolayout&rdquo package.
SpeciesType	Implementation of SBML Level 2's SpeciesType construct.
StoichiometryMath	Implementation of SBML Level 2's StoichiometryMath construct.
StringSet
Style	abstract base class for local and global styles
Submodel	comp Implementation of the Submodel construct from the &ldquocomp&rdquo package.
SyntaxChecker	Methods for checking syntax of SBML identifiers and other strings.
Text	Text element from the SBML render extension.
TextGlyph	layout The TextGlyph class describes the position and dimension of text labels in the &ldquolayout&rdquo package.
Transformation	implementation of a 3D transformation matrix.
Transformation2D	implementation of a 2D transformation matrix.
Transition	qual The Transition class for the Qualitative Models package.
Trigger	Implementation of SBML's Trigger construct for Event.
Unit	Implementation of SBML's Unit construct.
UnitDefinition	Implementation of SBML's UnitDefinition construct.
XMLAttributes	Representation of attributes on an XML node.
XMLError	Representation of errors, warnings and other diagnostics
XMLErrorLog	Log of errors and other events encountered while processing an XML file or data stream.
XMLInputStream	An interface to an XML input stream.
XMLNamespaces	Representation of XML Namespaces.
XMLNode	Representation of a node in an XML document tree.
XMLOutputStream	Interface to an XML output stream.
XMLToken	Representation of a token in an XML stream.
XMLTriple	Representation of a qualified XML name.

Exception Summary

Exception	Description
SBMLConstructorException	Class of exceptions thrown by constructors of some libSBML objects.
XMLConstructorException	Class of exceptions thrown by constructors of some libSBML objects.