[Biococoa-dev] Moving on

Charles Parnot charles.parnot at gmail.com
Sun Jul 10 20:21:41 EDT 2005

Sorry I should have replied to this earlier... The pace of the  
discussions is getting crazy...

On Jul 10, 2005, at 6:57 AM, Koen van der Drift wrote:

> Hi,
> We have discussed quite some issues last week, and I think we  
> should start thinking about putting this into the project. I will  
> try to summarize some points.
> 1. Now that we more or less agree on the fact that we will use  
> typed sequence, I want to bring up again the question whether we  
> keep the current structure of sequence classes, or we go back to  
> the regular superclass-subclass structure. If I remember correctly,  
> the main reason to create the pseudo class-cluster was to make it  
> possible that we only had to call BCSequence, instead of all the  
> subclasses. However, as mentioned before, this appeared to be  
> confusing since in some cases the subclasses are still being used.
> So we either stick to the current structure, and make really sure  
> that we only use BCSequence, or we go back to the old structure.  
> Charles put a lot of effort in creating the BCAbstractSequence/ 
> BCSequence classes, so I don't want to throw that out immediately.  
> However, since we agree on using typed sequences, it seems more  
> logical (and less confusing) to use the subclasses.

Don't worry! I will repeat what I said before: there is very little  
code for the placeholder trick to work. Most of the code in  
BCSequence is to provide the automatic guess of the sequence type,  
which we will reuse in the superclas anyway.

What I spent more time in was to clean the init methods, make it  
simpler and more consistent, and define one designated initializer,  
so that any modifications that affect all classes is in just one  
place. We will see what John has to say about that after he is done!!  
Anyway, like I said in another email, we will have to define a  
different dsignated initializer.

> 2. The main sequenceholder will be a char array that is private and  
> can only be accessed through a NSData/NSMutable data wrapper. At  
> this point it is still not clear how we will implement the  
> immutable/mutable sequences, but I suggest to just start with the  
> immutabe version, and take it from there.

Sorry I missed that earlier. We will have to find something...

> 3. I proposed to add a general object, BCStructureObject that will  
> allow to add different types of classes, such as atom and residue.  
> If there are no objections I can go ahead an add this as a  
> superclass for BCSymbol and BCAbstractSequence.

How about BCMolecule instead. Well, I guess having BCAtom a subclass  
of BCMolecule is a bit weird... Never mind :-)

Anyway, can you explain again the rationale to have a superclass for  
both BCSymbol and BCSequence? I know you already did explain it but I  
can't find the email.


Help science move fast forward:

Charles Parnot
charles.parnot at gmail.com

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