Interface | Description |
---|---|
libsbmlConstants |   |
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 &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 . |
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 | |
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 | |
FbcSBMLDocumentPlugin |
fbc
Extension of
SBMLDocument for the &ldquofbc&rdquo package. |
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 . |
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 | |
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. |
MathFilter |   |
MathML |   |
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.
|
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 | |
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).
|
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 | |
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 | Description |
---|---|
SBMLConstructorException |
Exceptions thrown by some libSBML constructors.
|
XMLConstructorException |
Exceptions thrown by some libSBML constructors.
|