Re: STRUCT_REF_SEQ_DIF

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It gets kind of messy to handle deletions purely by alignment of the
segments that do align, since you then don't have an aligned segment
to refer to to define what was deleted.  You can cure this
implicitly when there are aligned segments before and after the
deletion, but you are kind of stuck if the deletions are at one
end or the other, and really stuck when those deletions have outlying
insertions with no further outlying alignments.   All of this
gets trivial when you are able to specify what is going on residue
by residue and are allowed to match up a given residue on either
side against "."  I am not saying it is impossible to do it the
other way, just more difficult and in need of a lot of clarifying
semantics.

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