[Biococoa-dev] Sequence factory
Koen van der Drift
kvddrift at earthlink.net
Fri Dec 24 13:31:19 EST 2004
On Dec 24, 2004, at 12:28 PM, John Timmer wrote:
> Skipping non-bases just means whether or not to allow undefined
> symbols in
> with your valid bases or not. I don't know how symbol sets would
> create the
> equivalent of that, and I can't remember whether that code allows gaps
> not. I know it allows ambiguous bases - there's no "strict" version.
What I meant was, how do we pass the skippingNonBases value to the
BCSequenceFactory and then back to initWithFoo. If we use symbolsets,
then we could eg have a 'strict' symbol set, which only allows
ambiguous and unambiguous symbols, and a non-strict symbol set which
also allows gaps and undefined symbols. Right now BCSymbolSet only
supplies strict symbolsets, but it shouldn't be a problem to add one
that also contains gap and undefined.
> Basically just wanted to be clear on what I was doing when I wrote the
> method, just in case it gets replaced.
> One little question on factories for my own edification - in other
> code I
> wrote, I decided when to make a factory based on the number of objects
> I had
> to create in order to get something to work. If I needed a lot of
> it was best to create them only once, so I made a factory.
John, I am confused which 'factory' you are referring to. Do you mean
> It seems that
> the main decision on when to use one here is based on modularity of
> rather than practical time/memory issues. Is this accurate?
The idea is to *always* use BCSequenceFactory, although it is hidden
from the users, by the convenience methods that Alex proposed.
BTW, what is you guys opinion on adding a BCSymbolListFactory class as
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