[Biococoa-dev] Subclassing BCSequence really needed?

[Alexander Griekspoor]

Just a few ideas in between the praying that are website will withstand 
being slashdotted ;-)

> 1. Should we have just one BCSequenceReader class, which takes care of 
> all various file formats, or should we subclass for each format? I'm 
> not sure yet what the best solution is.
Given the large number of different formats, I'm a bit afraid that we 
will end up with way to many subclasses It might also be a problem to 
have a general "find-out-what-format-it-is-and-handle-it" method, 
although this could be handled in a superclass. I'm not sure on this 
one either.
>
> 2. Some formats can contain multiple seqeuences (eg fasta). Should we 
> return an NSArray of BCSequences only in those cases, or to be more 
> consistent for all formats? I suggest the latter.
I love consistency, but we can have some convenience methods to get 
only the first or a range of sequences.
>
> 3. Do we need an additional class that holds the BCSequence plus all 
> other info, or should everything go into the BCSequence class?
Good question, I would tend to go with everything in BCSequence to 
avoid another wrapper, after all it is a property of the BCSequence...
Cheers,
Alex
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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
                    Web: http://www.mekentosj.com

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