[Bioperl-l] {SPECS] Sequence meta data

[Robson Francisco de Souza]

	Hi Heikki,

On 31 Mar 2003, Heikki Lehvaslaiho wrote:
...snip...
> NAME
>     Bio::Seq::MetaI - Interface for sequence objects with residue-based
> meta
>     information
> 
...snip...
> DESCRIPTION
>     The length of the meta data sequence is not dependent on the amount 
>     of the quality information. The meta information always covers all 
>     the residues, but a blank value is used to denote unavailable 
>     information. If necessary the implementation quietly truncates or 
>     extends metain formation with blank values. Definition of blank is 
>     implementation dependent. Gaps in MSAs should not have meta 
>     information.

	Isn't such a restriction a drawback? Do you really think it's
necessary? I think it would be nice being able to associate meta data to
gap positions... maybe annotations or qualities (like phrap does)...

>     At this point a residue in a sequence object can have only one meta
>     value. If you need more, use multiple copies of the sequence object.

	Why? You create Bio::Seq::MetaI objects by blessing sequence
objects and latter attaching a data structure holding the meta data,
either a string, anonymous hash or array. If you extend the interface a
little more you could allow named meta data sets, like

	$meta_values = $obj->meta($new_name, $new_values);

and an access call would be like

	$meta_values = $obj->meta($new_name);	

	Of course this forces users to name all meta data but this way you
won't need extra, redundant copies of the sequence object, which may need
a lot of space.
	Hope I haven't missed the point :). Nice modules! :)
	Cheers,
			Robson