Figure 1

API architecture. An overview of the core classes that form the API. Abstract classes that require further implementation by a developer are shown in green and have italicized text. Most class names contain the word 'Biological', and so for brevity, this word has been replaced by an asterisk. Objects with a logical interaction are denoted by thick dotted lines, objects that are intrinsically related are denoted with a dashed line, object inheritance is shown using a solid line (with the arrow pointing to the superclass), and alternating dotted-dashed lines indicate an object that throws a specific exception (with the arrow pointing to the exception).