Uses of Package org.sbml.libsbml (LibSBML Java API)

Classes in org.sbml.libsbml used by org.sbml.libsbml
Class and 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 &ldquofbc&rdquo 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.
CompBase comp Convenience class for `SBase`-derived classes.
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`.
DefaultValues TODO:Definition of the `DefaultValues` class.
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.
FbcSBMLDocumentPlugin fbc Extension of `SBMLDocument` for the &ldquofbc&rdquo package.
FbcSpeciesPlugin fbc Extension of `Species`.
FbcToCobraConverter fbc SBML Level 3 &ldquofbc&rdquo 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 groups Representation of a group of SBML components.
GroupsExtension groups Base extension class for the package.
GroupsModelPlugin groups Extension of `Model`.
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`.
libsbmlConstants
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 groups A list of `Group` objects.
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.
ListOfMembers groups A list of `Member` objects.
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.
Member groups TODO:Definition of the `Member` class.
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.
OStream
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).
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.
SBMLConstructorException Exceptions thrown by some libSBML constructors.
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.
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.
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.
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.
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.
XMLConstructorException Exceptions thrown by some libSBML constructors.
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.
XMLToken A token in an XML stream.
XMLTriple A qualified XML name.

Uses of Packageorg.sbml.libsbml

Uses of Package
org.sbml.libsbml