This document contains certain recommendations for the further development of the Java side of BioMoby. While the guidelines present in this document serve to present a uniform way of doing things, BioMoby developers are in no way bound to these recommendations. By presenting guidelines, we hope to outline ways that our developers can become more efficient, while also producing more maintainable code that ultimately will aid in the practical usage of jMoby by others in the BioMoby community.
Any open source software developer will agree that even the original author of a piece of software is not the only one maintaining a piece of code. More often than not, most maintenance of code is done by someone other than the original author1. Therefore, it is crucial that any developer using our code find it well written and well documented. If we plan to share our code with the open source community, then we should allow it to be used to the most of its capabilities. Now that BioMoby is growing, we should move away from source code obfuscation and start to move towards more readable and understandable source code. After all, jMoby is written in Java and not Perl.
To do: provide more explanations here and possible examples of the layout that is used below.