[Biojava-dev] Plans for next biojava release - modularization

[Andreas Prlic]

Hi Richard,

Do you think the BJ3 code could form the beginning of a new
biojava-sequence module and can become part of the next release?

Andreas

On Tue, May 12, 2009 at 1:26 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> The BJ3 code contains only as much code as is needed to represent
> sequences and to parse/write simple FASTA. It should be viewed as a
> concept. In particular the file parsing mechanism is quite flexible (if
> a little complex) but easily wrapped with simple one-liner utility
> methods to provide end-users with easier-to-use APIs.
>
> Sequence representation in BJ3 is done via the Collections API. It's set
> up in such a way that you can write something yourself that implements
> the List API and behaves like a List but internally uses a more compact
> or even offline storage mechanism to represent the sequence. This allows
> you to reuse sequences wherever Lists can be used, e.g. in Iterators or
> foreach-loops.
>
> Everything written so far has been documented here:
>
>  http://biojava.org/wiki/BioJava3:HowTo
>
> cheers,
> Richard
>
>
>
> On Sun, 2009-05-10 at 21:26 -0700, Andreas Prlic wrote:
>> Hi biojava-devs,
>>
>> It is time to start working on the next biojava release.  I  would
>> like to modularize the current code base and apply some of the ideas
>> that have emerged around Richard's "biojava 3" code. In principle the
>> idea is that all changes should be backwards compatible with the
>> interfaces provided by the current biojava 1.7 release.  Backwards
>> compatibility shall only be broken if the functionality is being
>> replaced with something that works better, and gets documented
>> accordingly. For the build functionality I would suggest to stick with
>> what Richard's biojava 3 code base already is providing. Since we will
>> try to be backwards compatible all code development should be part of
>> the biojava-trunk and the first step will be to move the ant-build
>> scripts to a maven build process. Following this procedure will allow
>> to use e.g. the code refactoring tools provided by Eclipse, which
>> should come in handy.
>>
>> The modules I would like to see should provide self-contained
>> functionality and cross dependencies should be restricted to a
>> minimum. I would suggest to have the following modules:
>>
>> biojava-core: Contains everything that can not easily be modularized
>> or nobody volunteers to become a module maintainer.
>> biojava-phylogeny: Scooter expressed some interested to provide such a
>> module and become package maintainer for it.
>> biojava-structure: Everything protein structure related. I would be
>> package maintainer.
>> biojava-blast: Blast parsing is a frequently requested functionality
>> and it would be good to have this code self-contained. A package
>> maintainer for this still will need to be nominated at a later stage.
>> Any suggestions for other modules?
>>
>> Let me know what you think about this.
>>
>> Andreas
>> _______________________________________________
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>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
>