[Bioperl-l] New analysis interface; name space question

[Heikki Lehvaslaiho]

Last night Martin Senger committed a new versions of Bio::AnalysisI and
Bio::SimpleAnalysisI files.

The AnalysisI is great for full blown analysis servers like SOAPLab
Martin is working on. I felt that a downscaled version would be a great
help for wrapping simpler services. 

The result was Bio::AnalysisI. It is not that different from
Bio::Tools::Run::WrapperBase methods and gives the implementation ways
to define meta data about the application and input and output options.

I've taken Richard Adams contributed script that wraps NetPhos Web
server and turned that into the first SimpleAnalysisI implementation. 

I'd like to commit that module, but we have not really had the
discussion about the name space. Last time this turned up was a while
ago but there was just one opinion expressed:

http://bioperl.org/pipermail/bioperl-l/2002-September/009499.html

Now I do not think that we should categorise modules by the access
method, so I am not proposing Bio::WWW name space. However, Bio::Tools
name space is too full and messy, as was pointed out a while ago.

Users are used to Bio::Tools directory, so how about:

Bio::Tools::Analysis
Bio::Tools::Analysis::Protein
Bio::Tools::Analysis::Protein::NetPhos

and:
Bio::Tools::AnalysisParser
(NetPhos module contains its own parser, so nothing into here 
from NetPhos)

We could add more when needed: 
Bio::Tools::Analysis::Nucleotide,  ...?

Some options:

- Last level is too deep: put all modules into Bio::Tools::Analysis
- Let's not use Tools, create Bio::Analysis and Bio::Analysis::Protein,
  and Bio::AnalysisParser,


	-Heikki






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     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
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