[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.
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