[Bioperl-l] sequence trace index data

[Robson Francisco de Souza]

	Hi,

On Thu, 19 Dec 2002, Ewan Birney wrote:
> I suspect we should make a Bio::Seq::Read object and have a 
> Bio::Seq::SeqWithQualityI which both Bio::Seq::SeqWithQuality (bases 
> and quality values) and Bio::Seq::Read (trace file with called bases and 
> trace points).

	Just a thought: Bio::Seq::SeqWithQuality objects aggregate a
Bio::PrimarySeq and a Bio::Seq::PrimaryQual object. The last one holds the
quality array and is-a Bio::Seq:QualI. Should there be also a
Bio::Seq::TraceI and a Bio::Seq::PrimaryTrace object and should
Bio::Seq::Read aggregate a Bio::PrimarySeq and a Bio::Seq::PrimaryTrace?
	I must confess that I don't like this path. What about adding a
general holder for base-associated data, able to associate even several
values to each base in a sequence? I mean, tomorrow we may need to
annotate another data for all o almost all sequences in a huge sequence
and Bio::SeqFeatures will not be pratical for this task. We could have a
simple interface for sequence objects which can associate arrays of values
to intervals in a sequence... ooops! Isn't this a feature tag? Well, I
don't think so... but the ideia is just that: a set of methods to
associate arrays of values to intervals in sequences and, even better,
features. This general interface could be built in a way that
Bio::Seq::PrimaryQual and Bio::Seq::Read could inherit from it.

					Robson

> Bio::Seq::SeqWithQualityI should probably inheriet from Bio::PrimarySeqI
> 
> 
> 
> Whilst you are in there - any chance of you squashing bugs 1267, 1268 in 
> Bugzilla?
> 
> 
> 
> > 
> > Chad Matsalla
> > _______________________________________________
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
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