[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 
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 

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...

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 **
                  The Netherlands Cancer Institute
                  Department of Tumorbiology (H4)
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                       E-mail: a.griekspoor at nki.nl
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