Chapter 4. The Core

Table of Contents

The Topology Layer
The Layout Layer
Rendering Layer

In this chapter contains a description of the core. The core contains the data structures that are used in yWays to represent biochemical pathways and their visualizations. All classes and interfaces of the core are part of the package yWays.base or yWays.layout.

To represent a diagram of a biochemical network, yWays follows a layererd approach which defines three different layers of information:

Every layer is defined by a set of interfaces. For every interface a default implementation is provided, which has the same name as the interface followed by Impl.

The Topology Layer

The topology layer defines the structure of the biochemical network. The topological layer of a diagram is defined by an instance of the interface ReactionNet.

There are two main types of elements at this layer: compounds and reactions. Compounds are represented by the the interface Compound and are the basic entity. Reactions are represented by the interface ReactionNet and are interpreted as a transformation of compounds. Mathematically speaking a compound is a relation over the set of compounds. A reaction partitions the compounds participating in it in three main groups:

  • Substrats

  • Products

  • Catalysts

There is the following chemical interpretation for the above definitions: A reaction corresponds to a chemical reaction in which the substrats are transformed into the products. The transformation is done with the help of some catalysts. If the reaction is reversible, the products can also be transformed into the substrats with the same catalysts.

The groups Substrats and Products are further refined to emphasize the importance of the corresponding compound in a certain reaction. The group substrats can be divided into main-substrats and co-substrats, the group products into main-products and co-products.