Bioperl-guts: I'm back... status report ...

Steven E. Brenner brenner@hyper.stanford.edu
Mon, 24 Aug 1998 14:23:00 -0700


> steveb rightly points out that there are different 'modes' for the
> formatting: I can think of at least three:
> 
> 	a) single sequence reading
> 	b) multiple sequence (ma reading)
> 	c) database looping

good point.

> In wise2 I have found the best way is to have each 'mode' produce
> a separate object (sequence, m.a. or sequence db stream) and then
> rely on the user to chose what s/he wants. Beneeath the scenes the
> m.a. or db stream can re-use the single sequence code but that is
> neither here nor there to the interface user...

seems to make sense -- i like this model.  we should think about how we
get the same code into different classes' methods.

> I propose to keep this model for bioperl - which does mean we should
> have a sequence db stream - I am really tempted to tie it to a filehandle
> to allow 

sequence db stream is for the "loops," take it.


> Don gilbert has written readseq and good coders write good code... great 
> coders reuse other people's code (quote from the cathederal and the
> bazaar) so ... I am still planning to integreate in somehow but in a way
> which will allow other formetting systems to work. 

OTOH, relying on C code will cause many people not to use the programs
(because compilation of C is much harder than just using a Perl module).
Therefore, I think that writing Perl code has much merit.

Steve

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