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:
The topology layer defines the structure of the biochemical network. The structure is mainly defined by a set of compounds and and a set of reactions. At this level reactions are defined as a transformation of one set of compounds into another set of compounds.
The layout layer defines a geometric description of the elements of the topology layer. This geometric description contains the coordinates of the geomtetric objects representing the elements of the topology layer.
The rendering layer provides information which defines the rendering of the diagram elements. The type of data stored in the rendering layer depends on the rendering device and the rendering mechanism used.
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 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:
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.