The Layout Layer

The layout layer defines a geometric description of the elements of the topology layer. The layout layer of a diagram is defined by an instance of the interface ReactionNetLayout. This interfaces defines a mapping for each element of a ReactionNet to an appropiate layout object which contains the geometric description of its graphical representation.

The interface CompoundLayout defines the geometric description of the graphical representation of a compound. In yWays the graphical representation of a compound is a shape. Usually the graphical representation is a reactangel containing a text label with the name of the compound. The geometric description of this shape is defined by the coordinates of the bounding box of the shape.

The interface ReactionLayout defines the geometric description of the graphical representation of a reaction. The graphical representation of a reaction is much more commplex than the graphical representation of a compound. It is defined as a set of curves with special properties, we refer to this set as hyperedge. The hyperedge contains one special curve which is called skeleton. One endpoint of the skeleton is called skeleton source, the other one skeleton target. For each main substrat of the reaction there is a curve connecting the shape of the compound to the skeleton source. We call this curve connection line. Similarly each main product is connected with a curve to the skeleton target. Additionaly, for each co-compound of the reaction there is a curve connecting the shape of the co-compound to a point on the skeleton. Note that this points needs not to be the skeleton source, resp. the skeleton target, as it is the case for main compounds.

As an example for the graphical representation of compounds and reactions, the following figure shows a reaction with the main substrats Citrate, CoA and the main products Oxaloacetate, Acetyl-Coa. There is a cosubstrat H2O and a catalyst denoted by the EC number "4.1.3.7".