Bioperl-guts: seq reimplementation

Ewan Birney birney@sanger.ac.uk
Sat, 21 Aug 1999 01:01:37 +0100 (BST)


On Fri, 20 Aug 1999, Lovitt, Corey -PMC-CA wrote:

> Ewan,
> Sorry to be late in the discussion of the Bio::Seq reworking.

Fine...

> 
> Has by chance, anyone brought up the notion of making the Bio::Seq class an
> abstract class and implementing concrete subclasses of it such as DNASeq,
> AASeq, RNASeq etc.  Common functionality could be stuck into the base class
> and the specialized methods such as 'translate', and 'reverse_translate'
> would have natural locations within the hierarchy.  In addition, one could
> associate legal alphabets with each subclass if you chose.

Yup. This has been discussed. I sort of rejected it for two reasons:

	a) it changes alot of the semantics from the old seq object
	b) we've done fine with a single object for a long time and 
I think the main argument to doing it is to "make the object model look 
nice", which is a good thing, but not necessary.

I can imagine in the future inhereiting off the Seq object in to Protein
and DNA classes.

> 
> This would throw the onus on the caller to instantiate the correct sequence
> object (potential draw back for integration with the existing code base).
> However, it would likely simplify the Bio::Seq code overall.
> 

more objects... we are only really talking about the complement and
translate functions. Not that much simplification. 


I think we are cool with this set up, though I understand your idea and
appreciate it.




> Cheers,
> corey
> 
> 
> -----Original Message-----
> From: Ewan Birney [mailto:birney@sanger.ac.uk]
> Sent: Saturday, August 14, 1999 11:16 AM
> To: bioperl guts
> Subject: Bioperl-guts: seq reimplementation
> 
> 
> 
> A final proposal is up at
> 
> http://bio.perl.org/Projects/Sequence/reimpl.html
> 
> I am going to start to get to work on the basis of this proposal,
> assumming that people are ok with it (and only minor changes).
> Notice I need some ideas about
> 
> 	- case of sequence characters (so petty! and yet so important!)
> 
> 	- alphabet paranoia
> 
> I have encorporated many ideas given to me about this. Notice
> the backward compatibility functions which throw warnings, and
> the lack of translate but a descriptive error message.
> 
> 
> 
> 
> 
> Ewan Birney
> <birney@sanger.ac.uk>
> http://www.sanger.ac.uk/Users/birney/
> 
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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