Interface | Description |
---|---|
libsbmlConstants |   |
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 | |
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 | |
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 | |
int_array |   |
KineticLaw |
Implementation of SBML's KineticLaw construct.
|
L3ParserSettings |
A helper class for controlling the behavior of the
text-string formula parser.
|
Layout | |
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 | |
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 | |
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 | |
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 | |
SpeciesReference |
Implementation of SBML's SpeciesReference construct.
|
SpeciesReferenceGlyph | |
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 | Description |
---|---|
SBMLConstructorException |
Class of exceptions thrown by constructors of some
libSBML objects.
|
XMLConstructorException |
Class of exceptions thrown by constructors of some
libSBML objects.
|