[Biococoa-dev] Design question

John Timmer jtimmer at bellatlantic.net
Fri Aug 6 18:37:01 EDT 2004

> In the last few messages I missed any mention of a BCSequence class
> that more or less functions as the center of the framework. It's main
> member is then probably an NSString representing the sequence (DNA,
> RNA, protein). This is easy because they all are single character based
> sequences (unlike eg glycans).

I had sent out an RTF file with some ideas on how to construct the class -
if you hadn't gotten it, let me know and I'll resend it.  It hadn't
triggered any discussion yet, but I'd assumed that was because it was all
ideas and no code yet.

> Additionally this class could have an NSMutableArray member consisting
> of objects that represent each single base, amino acid. Whenever the
> NSString is edited, the NSMutableArray is updated, and vice versa.
I'm curious as to what this adds that a string doesn't.  The string itself
acts like an array for most purposes other than sorting, which is a bad idea
for sequences ;).  Creating enough individual objects for storing a long
sequence is going to be very processor/memory intensive - I'd imagine making
an array out of a BAC sequence would bring my laptop to its knees.  If there
are a few specific array methods that you'd like to have for the sequence,
I'll happily code them using the NSString contents.

I'm hoping to put the last of the methods I have lying around into the
BCUtils this weekend, and get started on implementing the sequence class
ideas I've got next week.

Relevant to this, I'm planning on using a few enumerations (ie -
BCDNASequence, BCProteinSequence, BCRNASequence), but haven't done so in
ObjC before.  Where do they get defined, and does anybody have some code
they're willing to share with me to make sure I don't screw that up?

Meanwhile, I still can't log into my ssh account and my request for help
from bioinformatics.org has gone unanswered.  Sigh....



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