[Biojava-l] [newio] Proposed event-notification interfaces

[Matthew Pocock]

Hi Ann.

Ann Loraine wrote:

> Please allow in-between residues annotations as well as
> on-top-of residues annotations.
>
> For instance, in-between annotations are useful for mapping splice
> sites onto alignments.  On-top-of anotations are useful for flagging
> individual residues.

The current location frame-work is effectively built around the concept of
sets of symbol indecies. Thus, there is no 'between'. This has caused
problems for edit operations - GappedSymbolList for example is a bit tortuous
in its definition of where to insert new gap characters. If you want to think
of the current locations in terms of between-ness, then the min represents
between it and the previous symbol, and max represents between it an the
following symbol. Since min < max, there is no way to represent 'between'.

The options are

a) A completely new position object. Pros - it can look however you want it
to. Cons - it will not play well with locations

b) A location implementation that is empty, and still represents a gap
emediately before min & emediately after max, and where max = min-1? Pros -
this would fit the current math cleanly, and would let you add features to
splice-sites. Cons - it kind-of breaks the Location concept.

c) A location implementation where max = min + 1, but is empty and represents
the position between the two indecies. Pros - nothing broken. Cons - We would
have to adjust the Location docs to state that min & max are not contained in
the location in this very special case - no biggie.

My vote is c). What about you?

Matthew

> I hope this is useful!
>
> -Ann
>
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