[Bioperl-l] GFF handling in SeqFeatureI

[Hilmar Lapp]

Today saw an excellent (well, that's my personal view :)
coproduction of 3 people: Matthew provided Bio::Tools::GFF as a
starter for a class in charge of parsing/producing GFF format,
Jason added fixes and tests, and I finally added lots of
documentation and a couple of public methods to make it a fully
flexible GFF hub. Check it out and comment if you're concerned
with GFF.

I also fully adopted this module in SeqFeatureI and
SeqFeature::Generic. These two modules now don't any GFF
parsing/formatting themselves, but instead delegate to a
Bio::Tools::GFF object. You can set the GFF interpreter via
SeqFeature::Generic->gff_format($mygffio), both as class and as
instance method (see POD). There is no distinction between GFF2
and GFF1 anymore in SeqFeatureI and descendants, it's the GFF
interpreter object that makes the distinction. The only exception
is -gff1_string as possible named parameter to
SeqFeature::Generic->new(), which will automatically install a GFF
interpreter initialized to GFF version 1 (the default it version
2).

I was wondering whether to put gff_format() to SeqFeatureI or
SeqFeature::Generic. The first option may seem better, but it
would change the interface, which is why I refrained from it. If
people think there's no problem changing the interface, I'll go
ahead and move it to SeqFeatureI.

All tests pass so far.

	Hilmar

-- 
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Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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