[Bioperl-l] SearchIO and result of StandAloneBlast

[Steve Chervitz]

--- Catherine Letondal <letondal@pasteur.fr> wrote:
> ...
> Thanks for the explanations!
> 
> We are upgrading our bioperl course to bioperl 1.0, and we are trying to
> figure out how 
> all the classes work together. The 1st result is a big headache :-), and the
> 2nd one is a 
> diagram, for which I would be very happy to get a little feedback:
>
http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/figures/searchio-class.png
> Is it correct?
> ("old" Bio::Tools::Blast and BPlite are not included)

Great job at making sense of a complex set of modules. One glitch is that you
show BlastHSP as inheriting from Bio::SeqFeature::SimilarityPair. Actually,
HSPI inherits from SimilarityPair (the ISA statement of BlastHSP doesn't need
to include SimilarityPair, which probably mislead you and can be fixed ;). I
can see BPlite and BPpsilite and the attendant SeqAnalysisParserI stuff,
contrary to what you say.

Another tip, you might want to make the diagram conform to official UML. Check
out the class diagram at http://bio.perl.org/images/bioperl.pdf (for some
reason, the image goes blank whenever I zoom in, but the birds-eye view looks
promising).

> This is of course not going to be the 1st diagram to show to students in
> order to
> use the new Blast parsers! It's just intended to show the architecture.
> BTW, what do you think about adding some information about classes in the
> documentation?
> (eventhough the ISA statement is more precise)

Yes, more information about class relationships would be great to include in
the docs. Single-level inheritance in included automatically in the docs
generated at http://doc.bioperl.org/releases/bioperl-1.0/, which is a good
start.

Steve

> Thanks a lot for all this work,
> 
> --
> Catherine Letondal -- Pasteur Institute Computing Center
> _______________________________________________


=====
Steve Chervitz
sac@bioperl.org

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