[Biococoa-dev] Moving on

Koen van der Drift kvddrift at earthlink.net
Sun Jul 10 09:57:23 EDT 2005


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.

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.

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.

let me know what you guys think, and if I left anything out.


- Koen.

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