[Dynamite] Is this working now then?

[Guy Slater]

On Sun, 5 Mar 2000, Ewan Birney wrote:

> 
> > > 
> > > At the risk of treading old ground here..
> > > 
> > > I vote for a lightweight sequence data structure containing two strings:
> > > name and sequence data. This accession number stuff has nothing to do with
> > > dynamic programming really. Besides -- having three different kinds of ID
> > > with apparently nothing to distinguish them is somewhat idiosyncratic.
> 
> 
> No no... last point *bad*.
> 
> Don't forget we are doing DB searching in this package. The DB searching
> package absolutely has to be able to handle the nice-ities of looping
> through a set of sequences and providing a data structure from which
> was can make decent output. One does need three names:
> 
> 	a) human-readable name to be shown, does not have to be
> unique (display_id)
> 
> 	b) supposed unique 'biological' name, (without the database
> part, as we should know what database we searched) which needs to be
> reported in the output for the output to be useful to a computer
> (accession_number)
> 
> 	c) a unique id for this implementation, which the implementation
> has complete control of - for example, byte position in a file munged
> into a string.
> 
> 
> All three names are **absolutely required**. I have walked this road many
> times and I now know you need three "names" for different functions.
> It may look mad, but it certainly is not mad.
> 
> 
> This offends people again and again - and so they insist on one name - and
> then they find they need three parts to that name - so they munge a string
> together into that one string and they the have the affront to claim that
> we need structured munging rules of "display|accession|implementation" to
> allow people to know how to decode this munged name when they should have
> **let the datastructure have three names** in the first place.

I would have thought you wouldn't need any identifiers for the DP itself,
but only for alignment display, database searching, etc.

Again, I think we need to have a list of all objects,
to make it easier to mark out the territory of each of them ...

Guy.
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