[Biococoa-dev] Sequence Structure

Alexander Griekspoor mek at mekentosj.com
Mon Jul 11 10:42:09 EDT 2005

> John, I am sure I speak for the others too that I would hate to see  
> you leave, so again, we should try all our efforts to come to a  
> good way out of this.
Yes, absolutely!! It would be really a pity to see you leave John.  
You have made absolutely a major contribution to the project, and it  
would be a shame to see a person leave with your experience and  
skills. I hope you decide to take the gamble, perhaps wait a bit till  
we can either see whether or not we are heading in the right  
direction, and jump back in. Already having the opinions and critical  
eye of someone who is sceptical about our approach would be very  

Again, I have been always in favour of first of all only 1 approach,  
either typed or untyped bcsequences, and I have always been in favour  
of typed sequences. I still would like to see only one approach, but  
recently I feel more and more attracted to the untyped sequences  
approach for several reasons:
- a uniform and simple interface for new developers (and ourselves).  
Trying (and failing) to explain our approach even to myself on the  
WWDC told me we were doing something wrong
- we have a way of typing in my opinion, the symbolsets, I'm  
convinced (at least hope) that this should be able to give enough  
typing and error checking, also during runtime (by explicit testing  
- it largely reduces the number of subclasses to only 2 (mutable vs  
immutable), and solves a problem I haven't seen a decent alternative  
for, the 2d-inheritance problem.

Perhaps I was most convinced by the appearance of more and more omni- 
graffle schemes. I couldn't understand a single one instantly, way to  
complex, way to many arrows, code-duplication all over, methods  
spread all over, difficult initializers, tricks, etc. For me they  
made only one thing really clear, not the structure we should pick,  
but the structure we should not pick.

Again, it would be a real pity to leave, if you want to use some of  
the classes like they are now in your own projects I would say go  
ahead, we'll work the license out later. We can always release the  
current "snapshot" under a bsd license. But I hope your needs are not  
immediate and that you are willing to hang around and see how things  
develop. I hope it will change your mind later, and that the  
framework can be of great use. In the mean time your advice would be  

On 11-jul-2005, at 15:25, Koen van der Drift wrote:
> On Jul 11, 2005, at 8:44 AM, John Timmer wrote:
>> Well, it's starting very poorly for me.  If I'm the only one  
>> arguing the
>> alternative, then I the majority should rule.  Unfortunately, that  
>> makes the
>> resulting framework a poor choice for my work/coding style, so I  
>> don't
>> expect I will use it for much more than sequence format  
>> translations and
>> perhaps alignments.  Since I won't be using the main classes, I  
>> doubt I'll
>> contribute much to their coding in the future.
> Well, that's not good news at all :(
> We should really try to find a solution for this situation. You  
> have contributed quite some code and it would be a shame to see you  
> leave because of this. I guess in your own project that uses  
> BioCocoa you could always create your own subclasses of BCSequence  
> to suit your needs, but that's a half baked solution, I admit.
> My understanding is that the main reason you prefer the typed  
> sequences, is that you can avoid sending the wrong type of sequence  
> to the wrong operation, is that correct?  Because this is  
> unavoidable for untyped sequences, we should do our best to find a  
> solution for this. Alex's suggestion, using the symbolset, seems a  
> good step forward. On the other hand, untyped sequences make  
> implementing the immutable/mutable classes much easier.
> John, I am sure I speak for the others too that I would hate to see  
> you leave, so again, we should try all our efforts to come to a  
> good way out of this.
> cheers,
> - Koen.
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                     ** Alexander Griekspoor **
              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

       Microsoft is not the answer,
       Microsoft is the question,
       NO is the answer


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