[Biococoa-dev] Sequence factory

[John Timmer]

> Sound fine with me, just checking if that is what you had in mind :)
> Although I am not sure how to deal with the skippingNonBases part.
> Probably that should be replaced by passing the right symbol set
> instead?

Chiming in from just north of London - happy holidays all!

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 or
not.  I know it allows ambiguous bases - there's no "strict" version.

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 objects,
it was best to create them only once, so I made a factory.  It seems that
the main decision on when to use one here is based on modularity of code,
rather than practical time/memory issues.  Is this accurate?

Now back to my regularly scheduled vacation....

JT

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