[Biojava-dev] hierarchical vs flat module organisation

[Scooter Willis]

Andreas
 
I think the organization should make the most sense to the user of BioJava and should be functionally grouped. I show up looking for specific biology algorithms/code. Blast, Sequence Alignment, Tree construction etc. In that module I would then find different features that I can then explore to solve the problem. The question becomes would I pick a module based on how it solved the problem. Given that BioJava does not have a native solution do to BLAST nor does the developer want to deal with all the configuration the BLAST-web services call simply becomes the only choice. The results of parsing a BLAST output and making a BLAST web service call should be the same structured result where I would then use other BioJava api's against the results.
 
I think we should group by function an that gives the developer a collection of tools to work with.
 
Scooter

________________________________

From: biojava-dev-bounces at lists.open-bio.org on behalf of Andreas Prlic
Sent: Thu 5/28/2009 12:53 PM
To: biojava-dev
Subject: [Biojava-dev] hierarchical vs flat module organisation



Hi,

from the different posts it seems there are two types of suggestions
for how to organize modules: hierarchical vs. flat.

I wonder if the best way to organize this is to mix the designs. There
could be few top-level modules like core, webservices, phylo,
structure. These would be equivalent to projects in the workspace.
These can then contain-submodules like

webservices-blast-ebi
webservices-blast-ncbi
webservices-whatever

or
structure-core
structure-viewers

The submodules would be sub-folders in the projects.

Any thoughts on that?

Andreas
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