[BioRuby] Alignment plugin

[Pjotr Prins]

On Mon, Apr 26, 2010 at 06:25:31PM +0100, Rutger Vos wrote:
> If you buy this line of thinking (YMMV), you might agree that a single
> sequence may need complicated helper objects and coordinate systems to
> keep track of the sort of mapping semantics that come into play once
> the sequence becomes homologized with others as building blocks for
> alignments/matrices.
> 
> I hope all this makes some amount of sense :-)

Ah, it does make sense, coming from phylogeny. And is in fact very
useful for some other project I have in mind, that has to do with
mosaic evolution.

Maybe Ruby is not the greatest language for this. You would want
built-in type checking and generics. And objects passed into the
structure.

However, I think these ideas can be combined. The only real difference
I see is that sequences have some type of objects (annotations) that
apply to a range of nucleotides/amino acids. I think the concept of
range is valuable.

And rather than some elaborate scheme of calculating/mapping
positions for every operation, I would champion immutable values that
just get copied to a new structure. E.g. if one would like delete
some data we would not do that in place and try to correct every
single position of linked helper objects every time. The heuristic
should be to created a new copy with its helpers, that is correct.

Pj.