Bioperl: Start of alignment debate...

[Gordon D. Pusch]

Lincoln Stein <lstein@cshl.org> wrote:

> Steve Chervitz writes:
[...]
>> Not all alignments need to be editable. Removing editability and 
>> using factories to create new alignments would simplify the alignment 
>> object itself. Having a class of immutable alignments would also ensure 
>> that a given alignment hasn't been mangled, when this is important.
>
> I think that the representation of alignments should be designed
> with editability in mind.  It might be hard to add editability after
> the fact.

I think I'm going to agree with Lincoln on this one --- it seems to me that
editability is something that can more easily be removed than added...

If one wants an ``immutable'' alignment class, it makes more sense to me
to make it a derived class of the general (``mutable'') alignment class,
rather than the other way round...


--  Gordon D. Pusch   <pusch@mcs.anl.gov>

Disclaimer:  I'm a consultant collaborating with Argonne researchers;
I don't speak for ANL or the DOE --- and they *certainly* don't speak
for =ME= !!!

Claimer:  I report =ALL= SPAMvertisers to their ISP --- =NO= exceptions !!!

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