Support NLMSA requerying with subintervals of original query sequence.

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See issue #34, comment 7:

> 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.

Original issue reported on code.google.com by the.good...@gmail.com on 7 Sep 2009 at 12:20

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Original comment by alexande...@gmail.com on 11 Sep 2009 at 6:28

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Original comment by alexande...@gmail.com on 11 Sep 2009 at 6:29