Layout-class {rsbml} | R Documentation

## 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.

### 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 `CompartmentGlyph`s. The names of the list correspond to the IDs of the elements.

`speciesGlyphs`:

  Object of class `"list"` containing the `SpeciesGlyph`s. The names of the list correspond to the IDs of the elements.

`reactionGlyphs`:

  Object of class `"list"` containing the `ReactionGlyph`s. The names of the list correspond to the IDs of the elements.

`textGlyphs`:

  Object of class `"list"` containing the `TextGlyph`s. The names of the list correspond to the IDs of the elements.

`additionalGraphicalObjects`:

  Object of class `"list"` containing the additional `GraphicalObject`s 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

[Package rsbml version 2.44.0 Index]