[Biojava-dev] The future of BioJava

[george waldon]

Hello,

All this is very exciting. I would certainly contribute to something like that. A few remarks that come to my mind while reading all these emails.

I noticed that the tutorial has seriously improved – thanks for the work. I remember my initial steps going to understanding Symbol and cross-alphabets (…)  Still, from time to time, I have difficulties with basic things that are not intuitive to me such as “token”, e.g. Alphabet.getTokenizarion(“token”) or SymbolTokenization.tokenizeSymbolList(SymbolList). 

I am surprised by the all the requests to use String instead of SymbolList. The CookBook tells precisely, and with code examples, how to make most of all basic operations. Maybe someone could illustrate the new kind of code versus the old one? I bet many newbies (and older one) actually get their answer in the Cookbook.

Richard wrote:
>It is suggested that development stops on the existing Biojava(…)
Well, I don’t think the license can let you do that :-)  
Writing new code might be easier but certainly making old code better will improve the level of code abstraction. Therefore I am promoting improving existing Biojava code versus hazardous code rewrite. I can see some of the initial steps on the roadmap:
- Switch to Subversion repository
- Change of the build process compatible with creation of modules
- Improving testing frame (mentioned several times)
- Creation of white papers for coding practices, build releases, (others?)

Then maybe the proper work of restructuring Biojava may start. We can either divide the existing mammoth into multiple modules at first or - my preference – building modules one by one by selectively picking classes. This way it will be easy to find out classes that can be deprecated (by lack of users) and we can even have a deprecated module at the end. Some coupling may need to loosen up. We will also need a list of API change for developers who will use the newer version.  I am sure that the kind of data structures proposed by Richard could find their place as well as some of the proposed patterns (beans, others?)

Anyway, all these are simple ideas. I am not an expert in build process, but I can help with improving javadocs, writing examples and test cases. I have also a fair knowledge of the molecular biology package.

Hope it helps,
George