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.
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