Package org.sbml.jsbml.ext.layout

Provides classes for the Layout package.

There is no formal SBML level 3 proposal but the classes implemented are derived from the Layout proposal by Gauges et al. as an annotation in SBMl level 2

Author:

Nicolas Rodriguez, Sebastian Fröhlich, Andreas Dräger, Clemens Wrzodek

Interface Summary

Interface	Description
IBoundingBox	Defines classes that are inside a BoundingBox, which specifies the position and the size of the object.
ICurve

Class Summary

Class	Description
AbstractReferenceGlyph	Abstract super class for all kinds of glyphs that graphically represent an instance of NamedSBase.
BoundingBox	The BoundingBox class specifies the required elements position and dimension.
CompartmentGlyph	The CompartmentGlyph class is derived from GraphicalObject and inherits its attributes.
CubicBezier	Represents smooth curves in the Layout package.
Curve	The Curve class describes how to connect elements in a diagram defined with the use of the Layout package.
CurveSegment	Parent class to LineSegment and CubicBezier.
Dimensions	A Dimensions is specified via the required attributes width, height and an optional attribute depth, all of which are of type double.
GeneralGlyph	The GeneralGlyph is used to facilitate the representation of elements other than Compartment, Species and Reaction and thus can be used for the display of relationships of Rule or elements defined by other SBML packages.
GraphicalObject	All the more specific layout elements (CompartmentGlyph, GeneralGlyph, SpeciesGlyph, ReactionGlyph, ReferenceGlyph, TextGlyph, and SpeciesReferenceGlyph) are derived from the class GraphicalObject.
Layout	The Layout class stores layout information for some or all elements of the Model as well as additional objects that need not be connected to the Model.
LayoutConstants	Contains some constants related to the layout package.
LayoutModelPlugin	The Layout package extends the Model class with the addition of one child element: the listOfLayouts.
LineSegment	The LineSegment class consists of the mandatory attribute xsi:type and two child elements of type Point.
NamedSBaseReferenceFilter	This is a special NameFilter that allows users to search for a AbstractReferenceGlyph that refers to a NamedSBase with the given identifier attribute.
Point	The representation of a point in the "layout" package.
ReactionGlyph	Analogous to how a Reaction object has to at least have one reactant or product, the ReactionGlyph has to at least have one SpeciesReferenceGlyph stored in the ReactionGlyph.listOfSpeciesReferenceGlyphs.
ReferenceGlyph	The ReferenceGlyph element describes the graphical connection between an arbitrary GraphicalObject (or derived element) and a GeneralGlyph (which would be an arrow or some curve in most cases).
SpeciesGlyph	The SpeciesGlyph class has an optional species attribute, in addition to to the attributes from GraphicalObject.
SpeciesReferenceGlyph	The SpeciesReferenceGlyph class describes the graphical connection between a SpeciesGlyph and a ReactionGlyph (which would be an arrow or some curve in most cases).
TextGlyph	The TextGlyph class describes the position and dimension of text labels.

Enum Summary

Enum	Description
CurveSegment.Type
SpeciesReferenceRole	Enumeration that defines the different SpeciesReferenceRoles that are encoded by the Layout package.