libsbmlcs Namespace Reference

Classes
class	AlgebraicRule
	An SBML algebraic rule representing 0 = f(W). More...
class	AssignmentRule
	An SBML assignment rule representing x = f(Y). More...
class	Association
	fbc Annotation helper class for “fbc” Version 1. More...
class	ASTBasePlugin
	Base class for extensions that plug into AST classes. More...
class	ASTNode
	Abstract Syntax Tree (AST) representation of a mathematical expression. More...
class	ASTNodeList
class	ASTNodeValues_t
class	BindingSiteSpeciesType
	multi Extension of MultiSpeciesType to define a binding site. More...
class	BoundingBox
	layout A bounding box for an item in a diagram. More...
class	Callback
class	CallbackRegistry
	More...
class	CobraToFbcConverter
	fbc COBRA to SBML Level 3 “fbc” converter. More...
class	ColorDefinition
	render Definition of an identifier for an RGBA color value. More...
class	Compartment
	An SBML compartment, where species are located. More...
class	CompartmentGlyph
	layout A glyph for an SBML compartment. More...
class	CompartmentReference
	multi Child of a Compartment that references a different Compartment. More...
class	CompartmentType
	A compartment type in SBML Level 2. More...
class	CompBase
	comp Convenience class for SBase-derived classes. More...
class	CompExtension
	comp Base extension class for the package. More...
class	CompFlatteningConverter
	comp 'Flattens' a model, removing composition. More...
class	CompModelPlugin
	comp Extension of Model. More...
class	CompPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	CompSBasePlugin
	comp Extension of SBase. More...
class	CompSBMLDocumentPlugin
	comp Extension of SBMLDocument. More...
class	Constraint
	An SBML constraint, for stating validity assumptions. More...
class	ConversionOption
	A single configuration setting for an SBML converter. More...
class	ConversionProperties
	Set of configuration option values for a converter. More...
class	CubicBezier
	layout A Cubic Bézier smooth curve. More...
class	Curve
	layout A curve connecting elements in a diagram. More...
class	CVTerm
	A MIRIAM-compliant controlled vocabulary term. More...
class	CVTermList
class	Date
	A MIRIAM-compliant date representation. More...
class	DateList
class	DefaultTerm
	qual The default result of a Transition. More...
class	DefaultValues
	render Encoding of default values. More...
class	DefinitionURLRegistry
	Registry of all libSBML SBML DefinitionURLs. More...
class	Delay
	A delay on the time of execution of an SBML event. More...
class	Deletion
	comp Deletion of an object from a submodel. More...
class	Dimensions
	layout Spatial dimensions of a 2D or 3D shape. More...
class	double_array
class	ElementFilter
	Base class for filter functions.
class	Ellipse
	render Graphical representation of an ellipse. More...
class	Event
	A discontinuous SBML event. More...
class	EventAssignment
	An assignment to a variable by an SBML event. More...
class	ExternalModelDefinition
	comp A reference to an externally-defined model. More...
class	FbcAnd
	fbc An “and” relationship for gene products More...
class	FbcAssociation
	fbc Base class for FbcAnd, FbcOr, and GeneProductRef More...
class	FbcExtension
	fbc Base extension class for the “fbc” package. More...
class	FbcModelPlugin
	fbc Extension of Model. More...
class	FbcOr
	fbc An “or” relationship for gene products More...
class	FbcPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	FbcReactionPlugin
	fbc Extension of Reaction by the “fbc” package. More...
class	FbcSBMLDocumentPlugin
	fbc Extension of SBMLDocument for the “fbc” package. More...
class	FbcSpeciesPlugin
	fbc Extension of Species. More...
class	FbcToCobraConverter
	fbc SBML Level 3 “fbc” to COBRA converter. More...
class	FbcV1ToV2Converter
	fbc Convert “fbc” Version 1 models to Version 2 More...
class	FbcV2ToV1Converter
	fbc Convert “fbc” Version 2 models to Version 1 More...
class	FluxBound
	fbc Max or min value for a reaction flux. More...
class	FluxObjective
	fbc An objective function for a flux. More...
class	FunctionDefinition
	A user-defined function in an SBML model. More...
class	FunctionTerm
	qual A function term. More...
class	GeneAssociation
	fbc Annotation helper class for “fbc” Version 1. More...
class	GeneProduct
	fbc Association of a gene product with a Reaction More...
class	GeneProductAssociation
	fbc Association between gene products and reactions More...
class	GeneProductRef
	fbc Reference to a gene product of a reaction More...
class	GeneralGlyph
	layout A glyph for miscellaneous items. More...
class	GlobalRenderInformation
	render Render information stored in a ListOfLayouts. More...
class	GlobalStyle
	render A style that can be associated with a layout. More...
class	GradientBase
	render Abstract base class for linear and radial gradients. More...
class	GradientStop
	render A color at a certain location in a color gradient. More...
class	GraphicalObject
	layout Base class of objects that store layouts. More...
class	GraphicalPrimitive1D
	render Base class for graphical primitives implementing 1D attributes. More...
class	GraphicalPrimitive2D
	render Base class for graphical primitives implementing 2D attributes. More...
class	Group
	groups Representation of a group of SBML components. More...
class	GroupsExtension
	groups Base extension class for the package. More...
class	GroupsModelPlugin
	groups Extension of Model. More...
class	GroupsPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	IdentifierTransformer
	Base class for identifier transformers. More...
class	IdList
	Maintains a list of SIds. More...
class	Image
	render Representation of images. More...
class	InitialAssignment
	An SBML initial assignment, evaluated once only. More...
class	Input
	qual The input to a QualitativeSpecies. More...
class	InSpeciesTypeBond
	multi Defines a bond within a MultiSpeciesType. More...
class	int_array
class	IntraSpeciesReaction
	multi A subclass of Reaction for changes of an internal species bond. More...
class	ISBMLExtensionNamespaces
class	KineticLaw
	The rate expression for an SBML reaction. More...
class	L3ParserSettings
	Controls the behavior of the Level 3 formula parser. More...
class	Layout
	layout The layout of a diagram of an SBML model. More...
class	LayoutExtension
	layout Base extension class for the package. More...
class	LayoutModelPlugin
	layout Extension of Model. More...
class	LayoutPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	LayoutSpeciesReferencePlugin
	layout Extension of SpeciesReference. More...
class	libsbml
class	LinearGradient
	render Representation of a linear gradient. More...
class	LineEnding
	render Decoration element for the start and/or end of curves. More...
class	LineSegment
	layout Representation of a line. More...
class	ListOf
	Parent class for libSBML's 'ListOfXYZ' classes. More...
class	ListOfColorDefinitions
	render A list of ColorDefinition objects. More...
class	ListOfCompartmentGlyphs
	layout A list of CompartmentGlyph objects. More...
class	ListOfCompartmentReferences
	multi A list of CompartmentReference objects. More...
class	ListOfCompartments
	A list of Compartment objects. More...
class	ListOfCompartmentTypes
	A list of CompartmentType objects. More...
class	ListOfConstraints
	A list of Constraint objects. More...
class	ListOfCurveElements
	render A list of curve elements. More...
class	ListOfDeletions
	comp A list of Deletion objects. More...
class	ListOfDrawables
	render A list of Transformation2D objects. More...
class	ListOfEventAssignments
	A list of EventAssignment objects. More...
class	ListOfEvents
	A list of Event objects. More...
class	ListOfExternalModelDefinitions
	comp A list of ExternalModelDefinition objects. More...
class	ListOfFbcAssociations
	fbc A list of FbcAssociation objects. More...
class	ListOfFluxBounds
	fbc A list of FluxBound objects. More...
class	ListOfFluxObjectives
	fbc A list of FluxObjective objects. More...
class	ListOfFunctionDefinitions
	A list of FunctionDefinition objects. More...
class	ListOfFunctionTerms
	qual A list of FunctionTerm objects. More...
class	ListOfGeneAssociations
	fbc A list of GeneAssociation objects. More...
class	ListOfGeneProducts
	fbc A list of GeneProduct objects. More...
class	ListOfGlobalRenderInformation
	render A list of GlobalRenderInformation objects. More...
class	ListOfGlobalStyles
	render A list of GlobalStyle objects. More...
class	ListOfGradientDefinitions
	render A list of GradientBase objects. More...
class	ListOfGradientStops
	render A list of one or more GradientStop objects. More...
class	ListOfGraphicalObjects
	layout A list of GraphicalObject objects. More...
class	ListOfGroups
	groups A list of Group objects. More...
class	ListOfInitialAssignments
	A list of InitialAssignment objects. More...
class	ListOfInputs
	qual A list of Input objects. More...
class	ListOfInSpeciesTypeBonds
	multi A list of InSpeciesTypeBond objects. More...
class	ListOfLayouts
	layout A list of Layout objects. More...
class	ListOfLineEndings
	render A list of LineEnding objects. More...
class	ListOfLineSegments
	layout A list of LineSegment objects. More...
class	ListOfLocalParameters
	A list of LocalParameter objects. More...
class	ListOfLocalRenderInformation
	render A list of LocalRenderInformation objects. More...
class	ListOfLocalStyles
	render A list of LocalStyle objects. More...
class	ListOfMembers
	groups A list of Member objects. More...
class	ListOfModelDefinitions
	comp A list of ModelDefinition objects. More...
class	ListOfMultiSpeciesTypes
	multi A list of MultiSpeciesType objects. More...
class	ListOfObjectives
	fbc A list of Objective objects. More...
class	ListOfOutputs
	qual A list of Output objects. More...
class	ListOfOutwardBindingSites
	multi A list of OutwardBindingSite objects. More...
class	ListOfParameters
	A list of Parameter objects. More...
class	ListOfPorts
	comp A list of Port objects. More...
class	ListOfPossibleSpeciesFeatureValues
	multi A list of PossibleSpeciesFeatureValue objects. More...
class	ListOfQualitativeSpecies
	qual A list of QualitativeSpecies objects. More...
class	ListOfReactionGlyphs
	layout A list of ReactionGlyph objects. More...
class	ListOfReactions
	A list of Reaction objects. More...
class	ListOfReferenceGlyphs
	layout A list of ReferenceGlyph objects. More...
class	ListOfReplacedElements
	comp A list of ReplacedElement objects. More...
class	ListOfRules
	A list of Rule objects. More...
class	ListOfSpecies
	A list of Species objects. More...
class	ListOfSpeciesFeatures
	multi A list of SpeciesFeature objects. More...
class	ListOfSpeciesFeatureTypes
	multi A list of SpeciesFeatureType objects. More...
class	ListOfSpeciesFeatureValues
	multi A list of SpeciesFeatureValue objects. More...
class	ListOfSpeciesGlyphs
	layout A list of SpeciesGlyph objects. More...
class	ListOfSpeciesReferenceGlyphs
	layout A list of SpeciesReferenceGlyph objects. More...
class	ListOfSpeciesReferences
	A list of SpeciesReference objects. More...
class	ListOfSpeciesTypeComponentIndexes
	multi A list of SpeciesTypeComponentIndex objects. More...
class	ListOfSpeciesTypeComponentMapInProducts
	multi A list of SpeciesTypeComponentMapInProduct objects. More...
class	ListOfSpeciesTypeInstances
	multi A list of SpeciesTypeInstance objects. More...
class	ListOfSpeciesTypes
	A list of SpeciesType objects. More...
class	ListOfSubmodels
	comp A list of Submodel objects. More...
class	ListOfTextGlyphs
	layout A list of TextGlyph objects. More...
class	ListOfTransitions
	qual A list of Transition objects. More...
class	ListOfUnitDefinitions
	A list of UnitDefinition objects. More...
class	ListOfUnits
	A list of Unit objects. More...
class	LocalParameter
	A parameter inside an SBML reaction definition. More...
class	LocalRenderInformation
	render Rendering information stored in Layouts. More...
class	LocalStyle
	render Style information object used in LocalRenderInformation. More...
class	Member
	groups The Member class defines what objects are parts of a Group. More...
class	Model
	An SBML model. More...
class	ModelCreator
	MIRIAM-compliant data about a model's creator. More...
class	ModelCreatorList
class	ModelDefinition
	comp A model used in model composition. More...
class	ModelHistory
	MIRIAM-compliant data about a model's history. More...
class	ModifierSpeciesReference
	A reference to an SBML modifier species. More...
class	MultiASTPlugin
	multi Extension of ASTBasePlugin. More...
class	MultiCompartmentPlugin
	multi Extension of Compartment for the 'multi' package. More...
class	MultiExtension
	multi Base extension class for the package. More...
class	MultiListOfReactionsPlugin
	multi Extension of ListOfReactions for the 'multi' package. More...
class	MultiModelPlugin
	multi Extension of Model. More...
class	MultiPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	MultiSBMLDocumentPlugin
	multi Extension of SBMLDocument for the 'multi' package. More...
class	MultiSimpleSpeciesReferencePlugin
	multi Extension of SimpleSpeciesReference for the 'multi' package. More...
class	MultiSpeciesPlugin
	multi Extension of Species for the 'multi' package. More...
class	MultiSpeciesReferencePlugin
	multi Extension of SpeciesReference for the 'multi' package. More...
class	MultiSpeciesType
	multi A type of Species in SBML Level 3 'multi' More...
class	Objective
	fbc An objective function. More...
class	OFStream
class	OStream
class	OStringStream
class	Output
	qual The output from a QualitativeSpecies. More...
class	OutwardBindingSite
	multi Defines a outward-facing binding site for a MultiSpeciesType. More...
class	Parameter
	An SBML parameter: a named symbol with a value. More...
class	Point
	layout Representation of a point. More...
class	Polygon
	render Representation of a Polygon More...
class	Port
	comp An interface to be used in composition. More...
class	PossibleSpeciesFeatureValue
	multi Defines one value of a SpeciesFeature. More...
class	Priority
	The priority of execution of an SBML event. More...
class	QualExtension
	qual Base extension class for the package. More...
class	QualitativeSpecies
	qual Extension of Species. More...
class	QualModelPlugin
	qual Extension of Model. More...
class	QualPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	RadialGradient
	render Representation of a radial gradient. More...
class	RateRule
	An SBML rate rule representing dx/dt = f(Y). More...
class	RDFAnnotationParser
	MIRIAM-compliant RDF annotation reader/writer. More...
class	Reaction
	An SBML reaction between species in an SBML model. More...
class	ReactionGlyph
	layout A glyph for an SBML reaction. More...
class	Rectangle
	render Representation of a rectangle. More...
class	ReferenceGlyph
	layout Connection between an object and a glyph. More...
class	RelAbsVector
	render Vectors with an absolute value and a relative value. More...
class	RenderCubicBezier
	render Representation of cubic Bezier curves. More...
class	RenderCurve
	render Representation of curves. More...
class	RenderExtension
	render Base extension class for the package. More...
class	RenderGraphicalObjectPlugin
	render The Render extension of the layout GraphicalObject class. More...
class	RenderGroup
	render A group of graphical primitives creating a composite. More...
class	RenderInformationBase
	render Abstract base class for local and global rendering information. More...
class	RenderLayoutPlugin
	render LibSBML implementation for the extension to the Layout class by the Render extension. More...
class	RenderListOfLayoutsPlugin
	render A list of layout objects used by the 'render' extension. More...
class	RenderPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	RenderPoint
	render A point with both absolute and relative values More...
class	ReplacedBy
	comp Indicates an object replaced by another. More...
class	ReplacedElement
	comp Indicates an object replaces another. More...
class	Replacing
	comp Convenience class. More...
class	Rule
	Parent class for SBML rules in libSBML. More...
class	SBase
	SBML's SBase class, base class of most SBML objects. More...
class	SBaseExtensionPoint
	Base class for extending SBML components
class	SBaseList
class	SBasePlugin
	Base class for extending SBML objects in packages. More...
class	SBaseRef
	comp Base class for references to objects. More...
class	SBMLConstructorException
	Exceptions thrown by some libSBML constructors. More...
class	SBMLConverter
	Base class for SBML converters. More...
class	SBMLConverterRegistry
	Registry of all libSBML SBML converters. More...
class	SBMLDocumentPlugin
	Base class for extending SBMLDocument in packages. More...
class	SBMLError
	An error, warning or other diagnostic. More...
class	SBMLErrorLog
	Log of diagnostics reported during processing. More...
class	SBMLExtension
	Base class for SBML Level 3 package plug-ins. More...
class	SBMLExtensionException
	Exception used by package extensions More...
class	SBMLExtensionRegistry
	Registry where package extensions are registered. More...
class	SBMLExternalValidator
	More...
class	SBMLFileResolver
	comp Resolves documents stored on a file system. More...
class	SBMLFunctionDefinitionConverter
	Converter to expand user-defined functions in-line. More...
class	SBMLIdConverter
	Converter for replacing object identifiers. More...
class	SBMLInferUnitsConverter
	Converter for inferring and setting parameter units. More...
class	SBMLInitialAssignmentConverter
	Converter that removes SBML initial assignments. More...
class	SBMLLevel1Version1Converter
	Whole-document SBML Level/Version converter. More...
class	SBMLLevelVersionConverter
	Whole-document SBML Level/Version converter. More...
class	SBMLLocalParameterConverter
	Converter to turn local parameters into global ones. More...
class	SBMLNamespaces
	Set of SBML Level + Version + namespace triples. More...
class	SBMLNamespacesList
class	SBMLReactionConverter
	Converter to replace reactions with SBML rate rules. More...
class	SBMLReader
	File and text-string SBML reader. More...
class	SBMLResolver
	comp Base class for SBML resolvers. More...
class	SBMLResolverRegistry
	comp Registry of all SBML resolvers. More...
class	SBMLRuleConverter
	Converter that sorts SBML rules and assignments. More...
class	SBMLStripPackageConverter
	Converter that removes SBML Level 3 packages. More...
class	SBMLUnitsConverter
	Converts a model's existing units to SI units. More...
class	SBMLUri
	comp Utility class for handling URIs. More...
class	SBMLValidator
	Base class for SBML validators. More...
class	SBMLWriter
	File and text-string SBML writer. More...
class	SBO
	Facilities for using the Systems Biology Ontology. More...
class	SimpleSpeciesReference
	Abstract class for references to species in reactions. More...
class	Species
	An SBML species – a pool of entities. More...
class	SpeciesFeature
	multi Defines a feature of a multi Species. More...
class	SpeciesFeatureType
	multi Defines a template for referencing SpeciesFeature objects. More...
class	SpeciesFeatureValue
	multi Defines a particular value for a SpeciesFeature. More...
class	SpeciesGlyph
	layout A glyph for an SBML species. More...
class	SpeciesReference
	A reference to an SBML species in a reaction. More...
class	SpeciesReferenceGlyph
	layout A glyph for an SBML species reference. More...
class	SpeciesType
	A species type in SBML Level 2. More...
class	SpeciesTypeComponentIndex
	multi Identifies a component within a MultiSpeciesType. More...
class	SpeciesTypeComponentMapInProduct
	multi Distinguishes between components in reactants versus products. More...
class	SpeciesTypeInstance
	multi Allows construction of structured MultiSpeciesType objects. More...
class	StoichiometryMath
	Stochiometry expressions in SBML Level 2 reactions. More...
class	StringSet
class	Style
	render Abstract base class for local and global styles. More...
class	SubListOfSpeciesFeatures
	multi Defines a set of SpeciesFeature objects. More...
class	Submodel
	comp A model instance inside another model. More...
class	SWIGTYPE_p_double
class	SWIGTYPE_p_ExpectedAttributes
class	SWIGTYPE_p_f_p_Model_p_SBMLErrorLog_p_void__int
class	SWIGTYPE_p_FormulaUnitsData
class	SWIGTYPE_p_int
class	SWIGTYPE_p_packageErrorTableEntryV2
class	SWIGTYPE_p_PrefixTransformer
class	SWIGTYPE_p_std__stringstream
class	SWIGTYPE_p_std__vectorT_ASTBasePlugin_p_t
class	SWIGTYPE_p_std__vectorT_std__string_t
class	SWIGTYPE_p_std__vectorT_unsigned_int_t
class	SWIGTYPE_p_std__vectorT_XMLError_p_t
class	SWIGTYPE_p_StringBuffer_t
class	SWIGTYPE_p_UnitFormulaFormatter
class	SWIGTYPE_p_void
class	SyntaxChecker
	Methods for checking the validity of SBML identifiers. More...
class	Text
	render Representation of text elements. More...
class	TextGlyph
	layout A glyph for a text label. More...
class	Transformation
	render Implementation of a 3D transformation matrix. More...
class	Transformation2D
	render Implementation of a 2D transformation matrix. More...
class	Transition
	qual A transition of a QualitativeSpecies. More...
class	Trigger
	The trigger expression for an SBML event. More...
class	Unit
	A single unit referenced in an SBML unit definition. More...
class	UnitDefinition
	A definition of a unit used in an SBML model. More...
class	XMLAttributes
	A list of attributes on an XML element. More...
class	XMLConstructorException
	Exceptions thrown by some libSBML constructors. More...
class	XMLError
	XML-level errors, warnings and other diagnostics. More...
class	XMLErrorLog
	Log of diagnostics reported during XML processing. More...
class	XMLInputStream
	An interface to an XML input stream. More...
class	XMLNamespaces
	An XML Namespace. More...
class	XMLNode
	A node in libSBML's XML document tree. More...
class	XMLOutputStream
	Interface to an XML output stream. More...
class	XMLOwningOutputFileStream
class	XMLOwningOutputStringStream
class	XMLToken
	A token in an XML stream. More...
class	XMLTriple
	A qualified XML name. More...