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 |
CompExtension
comp
Base extension class for the package.
|
CompFlatteningConverter
comp
'Flattens' a model, removing composition.
|
CompModelPlugin |
CompPkgNamespaces
Set of SBML Level + Version + namespace triples.
|
CompSBasePlugin |
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 |
FbcExtension
fbc
Base extension class for the &ldquofbc&rdquo package.
|
FbcModelPlugin |
FbcOr
fbc
An &ldquoor&rdquo relationship for gene products
|
FbcPkgNamespaces
Set of SBML Level + Version + namespace triples.
|
FbcReactionPlugin |
FbcSpeciesPlugin |
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 |
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 |
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 |
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 |
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 |
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 |
ListOfLayouts |
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 |
ListOfModelDefinitions
comp
A list of
ModelDefinition objects. |
ListOfObjectives |
ListOfOutputs |
ListOfParameters
A list of
Parameter objects. |
ListOfPorts |
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 |
ListOfTextGlyphs |
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 |
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 |
QualModelPlugin |
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 |
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.
|