Layout-class: SBML type "Layout"

In rsbml: R support for SBML, using libsbml

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.

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

Author(s)

Michael Lawrence

References

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

rsbml documentation built on Nov. 8, 2020, 8:09 p.m.