[Biococoa-dev] Design question
Alexander Griekspoor
mek at mekentosj.com
Thu Aug 5 14:21:31 EDT 2004
Just to illustrate the principle: look at
http://www.biojava.org/docs/api/index.html
and lookup their RestrictionEnzyme class in the "All Classes" list on
the left. It's exactly the way I propose to do as well. Also click on
the "Use" button on top of the page once you have the RestrictionEnzyme
class in opened. You'll see that they have "controller objects" as
well. We could make a SharedRestrictionEnzymeManager as well, one that
could return all listed enzymes for instance, or which you could ask
for details about a specific enzyme.
Another example: Go again to the mainpage which the link above points
to. Check out the core biological class "org.biojava.bio.seq" and
you'll see that they have a class called DNATools and RNATools. This is
where a lot of general methods could go into. Finally, it would be an
idea as well to add a number of protocols that would group certain
related classes (like NSCoding, NSCopying, does for the foundation
frameworks).
Again, enough stuff to think about and a lot of design work, but these
guys at BioJava have done many things along the lines we were thinking
as well, and it seems to work very nicely...
Alex
Op 5-aug-04 om 16:45 heeft John Timmer het volgende geschreven:
> I'm going to be writing two methods: One gives a list of all ORFs
> over a
> certain size given the size and a DNA sequence, the second will list
> all
> sites in a sequence, given a site and the sequence.
>
> The question is: how to return the list?
>
> I could see three options:
> The sites could be handled as an NSIndexSet, but that won't work for
> the
> ORFs and is 10.3 only.
> Another option would be to store Ranges as NSValues and return an
> array of
> them. This would be very convenient internally, but wouldn't allow
> convenient saving of the information, since NSValues would need to be
> encoded before saving.
> The final thing would be to add a category to NSDictionary that would
> add
> the methods "storeRangeInDictionary" and "retrieveRangeFromDictionary"
> that
> would just make length and location keys in a dictionary.
>
> Does anyone have a preference about how to handle it?
>
> Cheers,
>
> John
>
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** Alexander Griekspoor **
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The Netherlands Cancer Institute
Department of Tumorbiology (H4)
Plesmanlaan 121, 1066 CX, Amsterdam
Tel: + 31 20 - 512 2023
Fax: + 31 20 - 512 2029
AIM: mekentosj at mac.com
E-mail: a.griekspoor at nki.nl
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