Layout-class: SBML type "Layout"

Description

Contains the glyphs and other graphical objects that compose an SBML layout. Layouts are not part of the core SBML specification. See the reference for the SBML layout extension specification.

Arguments

Instantiation

Objects can be created by calls of the form new("Layout", ...).

Slots

id:: Object of class "character" uniquely identifying this component.
dimensions:: Object of class "Dimensions" specifing the size of the layout.
compartmentGlyphs:: Object of class "list" containing the CompartmentGlyphs. The names of the list correspond to the IDs of the elements.
speciesGlyphs:: Object of class "list" containing the SpeciesGlyphs. The names of the list correspond to the IDs of the elements.
reactionGlyphs:: Object of class "list" containing the ReactionGlyphs. The names of the list correspond to the IDs of the elements.
textGlyphs:: Object of class "list" containing the TextGlyphs. The names of the list correspond to the IDs of the elements.
additionalGraphicalObjects:: Object of class "list" containing the additional GraphicalObjects that are not bound to any model component. The names of the list correspond to the IDs of the elements.
metaId:: Object of class "character" that is an XML ID "described" by an RDF resource. This links an SBML element to an RDF resource. RDF may appear anywhere in an SBML element, but is usually placed inside the annotation element.
notes:: Object of class "character" containing user-readable XHTML notes about an element.
annotation:: Object of class "character" containing additional machine-readable information about an element, usually as RDF, such as BioPAX. This is where application-specific data belongs.
cvTerms:: Object of class "list" containing instances of CVTerm associated with this element.
sboTerm:: Object of class "integer" identifying a term in the Systems Biology Ontology (SBO).

Extends

Class "SBase", directly.

Methods

id: signature(object = "Layout"): gets the id slot
id<-: signature(object = "Layout"): sets the id slot
additionalGraphicalObjects: signature(object = "Layout"): gets the additionalGraphicalObjects slot
additionalGraphicalObjects<-: signature(object = "Layout"): sets the additionalGraphicalObjects slot
compartmentGlyphs: signature(object = "Layout"): gets the compartmentGlyphs slot
compartmentGlyphs<-: signature(object = "Layout"): sets the compartmentGlyphs slot
dimensions: signature(object = "Layout"): gets the dimensions slot
dimensions<-: signature(object = "Layout"): sets the dimensions slot
reactionGlyphs: signature(object = "Layout"): gets the reactionGlyphs slot
reactionGlyphs<-: signature(object = "Layout"): sets the reactionGlyphs slot
speciesGlyphs: signature(object = "Layout"): gets the speciesGlyphs slot
speciesGlyphs<-: signature(object = "Layout"): sets the speciesGlyphs slot
textGlyphs: signature(object = "Layout"): gets the textGlyphs slot
textGlyphs<-: signature(object = "Layout"): sets the textGlyphs slot

References

http://projects.villa-bosch.de/bcb/sbml