[pygr-notify] Issue 34 in pygr: Refactor BLAST support as a mapping

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Comment #7 on issue 34 by alexander.alekseyenko: Refactor BLAST support as  
a mapping
http://code.google.com/p/pygr/issues/detail?id=34

> If we go this route, we could
> easily add a property to the NLMSASlice that gets the original
> NLMSA, allowing the user to requery with subintervals of the original
> query sequence.  Seems like a reasonable idea.

I was looking for this feature for quite some time. Makes life easier.  
However, in my
opinion the requerying should eventually happen on the level of NLMSASlice.  
Also one
thing I don't get is why NLMSA and NLMSASlice have different interfaces.  
Intuitively
they are the same thing: collections of interval tuples. This is especially  
true for
directional NLMSAs, but could also be envisaged for undirectional ones.

BTW, requerying the NLMSASlice is a kind of a JOIN query: e.g.
sl1 = msa[s1[a:b]]
sl2 = sl1[sl1[c:b]]

could be the same as:
overlap(msa[s1[a:b]], msa[s1[c:b]])

One could also think of doing
sl1 = msa[sl[a:b]]
sl2 = sl1[s2[c:b]]

as
overlap(msa[sl1[a:b]], msa[s2[c:b]])
Note here we trying to JOIN two NLMSASlices created via queries of totally  
different
things.

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