org.sbml.libsbml (LibSBML Java API)

Interface Summary
Interface Description

libsbmlConstants

Interface Summary
Interface	Description
libsbmlConstants

Class Summary
Class	Description
AlgebraicRule	An SBML algebraic rule representing 0 = f(W).
AssignmentRule	An SBML assignment rule representing x = f(Y).
Association	fbc Annotation helper class for &ldquofbc&rdquo Version 1.
ASTNode	Abstract Syntax Trees for mathematical expressions.
ASTNodeList
BoundingBox	layout A bounding box for an item in a diagram.
CobraToFbcConverter	fbc COBRA to SBML Level 3 'fbc' converter.
ColorDefinition	LibSBML implementation for the ColorDefinition construct from the SBML render extension.
Compartment	An SBML compartment, where species are located.
CompartmentGlyph	layout A glyph for an SBML compartment.
CompartmentType	A compartment type in SBML Level 2.
CompExtension	comp Base extension class for the package.
CompFlatteningConverter	comp 'Flattens' a model, removing composition.
CompModelPlugin	comp Extension of `Model`.
CompPkgNamespaces	Set of SBML Level + Version + namespace triples.
CompSBasePlugin	comp Extension of `SBase`.
CompSBMLDocumentPlugin	comp Extension of `SBMLDocument`.
Constraint	An SBML constraint, for stating validity assumptions.
ConversionOption	A single configuration setting for an SBML converter.
ConversionProperties	Set of configuration option values for a converter.
CubicBezier	layout A Cubic Bézier smooth curve.
Curve	layout A curve connecting elements in a diagram.
CVTerm	A MIRIAM-compliant controlled vocabulary term.
CVTermList
Date	A MIRIAM-compliant date representation.
DateList
DefaultTerm	qual The default result of a `Transition`.
Delay	A delay on the time of execution of an SBML event.
Deletion	comp Deletion of an object from a submodel.
Dimensions	layout Spatial dimensions of a 2D or 3D shape.
double_array
ElementFilter	Base class for filter functions.
Ellipse	graphical representation of an ellipse from the SBML render extension
Event	A discontinuous SBML event.
EventAssignment	An assignment to a variable by an SBML event.
ExternalModelDefinition	comp A reference to an externally-defined model.
FbcAnd	fbc An &ldquoand&rdquo relationship for gene products
FbcAssociation	fbc Base class for `FbcAnd`, `FbcOr`, and `GeneProductRef`
FbcExtension	fbc Base extension class for the &ldquofbc&rdquo package.
FbcModelPlugin	fbc Extension of `Model`.
FbcOr	fbc An &ldquoor&rdquo relationship for gene products
FbcPkgNamespaces	Set of SBML Level + Version + namespace triples.
FbcReactionPlugin	fbc Extension of `Reaction` by the &ldquofbc&rdquo package.
FbcSpeciesPlugin	fbc Extension of `Species`.
FbcToCobraConverter	fbc SBML Level 3 'fbc' to COBRA converter.
FbcV1ToV2Converter	fbc Convert &ldquofbc&rdquo Version 1 models to Version 2
FbcV2ToV1Converter	fbc Convert &ldquofbc&rdquo Version 2 models to Version 1
FluxBound	fbc Max or min value for a reaction flux.
FluxObjective	fbc An objective function for a flux.
FunctionDefinition	A user-defined function in an SBML model.
FunctionTerm	qual A function term.
GeneAssociation	fbc Annotation helper class for &ldquofbc&rdquo Version 1.
GeneProduct	fbc `Association` of a gene product with a `Reaction`
GeneProductAssociation	fbc `Association` between gene products and reactions
GeneProductRef	fbc Reference to a gene product of a reaction
GeneralGlyph	layout A glyph for miscellaneous items.
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 Base class of objects that store layouts.
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	Set of SBML Level + Version + namespace triples.
Image	implementation of the `Image` concept from the SBML render extension
InitialAssignment	An SBML initial assignment, evaluated once only.
Input	qual The input to a `QualitativeSpecies`.
int_array
KineticLaw	The rate expression for an SBML reaction.
L3ParserSettings	Controls the behavior of the Level 3 formula parser.
Layout	layout The layout of a diagram of an SBML model.
LayoutExtension	layout Base extension class for the package.
LayoutModelPlugin	layout Extension of `Model`.
LayoutPkgNamespaces	Set of SBML Level + Version + namespace triples.
LayoutSpeciesReferencePlugin	layout Extension of `SpeciesReference`.
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 Representation of a line.
ListOf	Parent class for libSBML's 'ListOfXYZ' classes.
ListOfColorDefinitions	LibSBML implementation for a container which holds zero or more `ColorDefinition` objects.
ListOfCompartmentGlyphs	layout A list of `CompartmentGlyph` objects.
ListOfCompartments	A list of `Compartment` objects.
ListOfCompartmentTypes	A list of `CompartmentType` objects.
ListOfConstraints	A list of `Constraint` objects.
ListOfCurveElements	A container to store curve elements (RenderPoint and `RenderCubicBezier`).
ListOfDeletions	comp A list of `Deletion` objects.
ListOfDrawables	container class that stores objects derived from `Transformation2D`.
ListOfEventAssignments	A list of `EventAssignment` objects.
ListOfEvents	A list of `Event` objects.
ListOfExternalModelDefinitions	comp A list of `ExternalModelDefinition` objects.
ListOfFbcAssociations	fbc A list of `FbcAssociation` objects.
ListOfFluxBounds	fbc A list of `FluxBound` objects.
ListOfFluxObjectives	fbc A list of `FluxObjective` objects.
ListOfFunctionDefinitions	A list of `FunctionDefinition` objects.
ListOfFunctionTerms	qual A list of `FunctionTerm` objects.
ListOfGeneAssociations	fbc A list of `GeneAssociation` objects.
ListOfGeneProducts	fbc A list of `GeneProduct` objects.
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 A list of `GraphicalObject` objects.
ListOfGroups
ListOfInitialAssignments	A list of `InitialAssignment` objects.
ListOfInputs	qual A list of `Input` objects.
ListOfLayouts	layout A list of `Layout` objects.
ListOfLineEndings	container class to store `LineEnding` objects
ListOfLineSegments	layout A list of `LineSegment` objects.
ListOfLocalParameters	A list of `LocalParameter` objects.
ListOfLocalRenderInformation	container class that stores `LocalRenderInformation` objects.
ListOfLocalStyles	`ListOfLocalStyles` is the container class that stores LocalStyles in `LocalRenderInformation` objects.
ListOfMemberConstraints
ListOfMembers
ListOfModelDefinitions	comp A list of `ModelDefinition` objects.
ListOfObjectives	fbc A list of `Objective` objects.
ListOfOutputs	qual A list of `Output` objects.
ListOfParameters	A list of `Parameter` objects.
ListOfPorts	comp A list of `Port` objects.
ListOfQualitativeSpecies	qual A list of `QualitativeSpecies` objects.
ListOfReactionGlyphs	layout A list of `ReactionGlyph` objects.
ListOfReactions	A list of `Reaction` objects.
ListOfReferenceGlyphs	layout A list of `ReferenceGlyph` objects.
ListOfReplacedElements	comp A list of `ReplacedElement` objects.
ListOfRules	A list of `Rule` objects.
ListOfSpecies	A list of `Species` objects.
ListOfSpeciesGlyphs	layout A list of `SpeciesGlyph` objects.
ListOfSpeciesReferenceGlyphs	layout A list of `SpeciesReferenceGlyph` objects.
ListOfSpeciesReferences	A list of `SpeciesReference` objects.
ListOfSpeciesTypes	A list of `SpeciesType` objects.
ListOfSubmodels	comp A list of `Submodel` objects.
ListOfTextGlyphs	layout A list of `TextGlyph` objects.
ListOfTransitions	qual A list of `Transition` objects.
ListOfUnitDefinitions	A list of `UnitDefinition` objects.
ListOfUnits	A list of `Unit` objects.
LocalParameter	A parameter inside an SBML reaction definition.
LocalRenderInformation	`LocalRenderInformation` is the render information stored in Layouts.
LocalStyle	implementation of the `LocalStyle` concept of the SBML render extension.
MathML
Member
MemberConstraint
Model	An SBML model.
ModelCreator	MIRIAM-compliant data about a model's creator.
ModelCreatorList
ModelDefinition	comp A model used in model composition.
ModelHistory	MIRIAM-compliant data about a model's history.
ModifierSpeciesReference	A reference to an SBML modifier species.
Objective	fbc An objective function.
OFStream
OStream
OStringStream
Output	qual The output from a `QualitativeSpecies`.
Parameter	An SBML parameter: a named symbol with a value.
Point	layout Representation of a point.
Polygon	class representing a polygon from the SBML render extension
Port	comp An interface to be used in composition.
Priority	The priority of execution of an SBML event.
QualExtension	qual Base extension class for the package.
QualitativeSpecies	qual Extension of `Species`.
QualModelPlugin	qual Extension of `Model`.
QualPkgNamespaces	Set of SBML Level + Version + namespace triples.
RadialGradient	Representation of a radial gradient object from the SBML render extension.
RateRule	An SBML rate rule representing dx/dt = f(Y).
RDFAnnotationParser	MIRIAM-compliant RDF annotation reader/writer.
Reaction	An SBML reaction between species in an SBML model.
ReactionGlyph	layout A glyph for an SBML reaction.
Rectangle
ReferenceGlyph	layout Connection between an object and a glyph.
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	Set of SBML Level + Version + namespace triples.
RenderPoint	Represents a point where the coordinates can be made up of absolute as well as relative values ( Render objects are often specified relative to the current viewport, i.e.
ReplacedBy	comp Indicates an object replaced by another.
ReplacedElement	comp Indicates an object replaces another.
Replacing	comp Convenience class.
Rule	Parent class for SBML rules in libSBML.
SBase	SBML's SBase class, base class of most SBML objects.
SBaseList
SBasePlugin	Base class for extending SBML objects in packages.
SBaseRef	comp Base class for references to objects.
SBMLConverter	Base class for SBML converters.
SBMLConverterRegistry	Registry of all libSBML SBML converters.
SBMLDocument	Overall SBML container object.
SBMLDocumentPlugin	Base class for extending `SBMLDocument` in packages.
SBMLError	An error, warning or other diagnostic.
SBMLErrorLog	Log of diagnostics reported during processing.
SBMLExtension	Base class for SBML Level 3 package plug-ins.
SBMLExtensionException	Exception used by package extensions
SBMLExtensionRegistry	Registry where package extensions are registered.
SBMLFileResolver	comp Resolves documents stored on a file system.
SBMLFunctionDefinitionConverter	Converter to expand user-defined functions in-line.
SBMLIdConverter	Converter for replacing object identifiers.
SBMLInferUnitsConverter	Converter for inferring and setting parameter units.
SBMLInitialAssignmentConverter	Converter that removes SBML initial assignments.
SBMLLevel1Version1Converter	Whole-document SBML Level/Version converter.
SBMLLevelVersionConverter	Whole-document SBML Level/Version converter.
SBMLLocalParameterConverter	Converter to turn local parameters into global ones.
SBMLNamespaces	Set of SBML Level + Version + namespace triples.
SBMLNamespacesList
SBMLReactionConverter	Converter to replace reactions with SBML rate rules.
SBMLReader	File and text-string SBML reader.
SBMLResolver	comp Base class for SBML resolvers.
SBMLResolverRegistry	comp Registry of all SBML resolvers.
SBMLRuleConverter	Converter that sorts SBML rules and assignments.
SBMLStripPackageConverter	Converter that removes SBML Level 3 packages.
SBMLUnitsConverter	Converts a model's existing units to SI units.
SBMLUri	comp Utility class for handling URIs.
SBMLValidator	Base class for SBML validators.
SBMLWriter	File and text-string SBML writer.
SBO	Facilities for using the Systems Biology Ontology.
SimpleSpeciesReference	Abstract class for references to species in reactions.
Species	An SBML species &ndash a pool of entities.
SpeciesGlyph	layout A glyph for an SBML species.
SpeciesReference	A reference to an SBML species in a reaction.
SpeciesReferenceGlyph	layout A glyph for an SBML species reference.
SpeciesType	A species type in SBML Level 2.
StoichiometryMath	Stochiometry expressions in SBML Level 2 reactions.
StringSet
Style	abstract base class for local and global styles
Submodel	comp A model instance inside another model.
SyntaxChecker	Methods for checking the validity of SBML identifiers.
Text	`Text` element from the SBML render extension.
TextGlyph	layout A glyph for a text label.
Transformation	implementation of a 3D transformation matrix.
Transformation2D	implementation of a 2D transformation matrix.
Transition	qual A transition of a `QualitativeSpecies`.
Trigger	The trigger expression for an SBML event.
Unit	A single unit referenced in an SBML unit definition.
UnitDefinition	A definition of a unit used in an SBML model.
XMLAttributes	A list of attributes on an XML element.
XMLError	XML-level errors, warnings and other diagnostics.
XMLErrorLog	Log of diagnostics reported during XML processing.
XMLInputStream	An interface to an XML input stream.
XMLNamespaces	An XML Namespace.
XMLNode	A node in libSBML's XML document tree.
XMLOutputStream	Interface to an XML output stream.
XMLOwningOutputFileStream
XMLOwningOutputStringStream
XMLToken	A token in an XML stream.
XMLTriple	A qualified XML name.

Exception Summary
Exception Description

SBMLConstructorException
Exceptions thrown by some libSBML constructors.

XMLConstructorException
Exceptions thrown by some libSBML constructors.

Exception	Description
SBMLConstructorException	Exceptions thrown by some libSBML constructors.
XMLConstructorException	Exceptions thrown by some libSBML constructors.

Package org.sbml.libsbml