[Bioperl-l] Bio::SeqFeature::Annotated API change

Sendu Bala bix at sendu.me.uk
Fri Oct 12 11:06:30 EDT 2007

Chris Fields wrote:
> On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:
>> Chris Fields wrote:
>>> B::SF::A violated the SeqFeatureI interface from the get-go by
>>> returning objects.
>> On that note, the other major change I'd propose is to make
>> B::SF::A inherit from B::SeqFeatureI. I really need this for RangeI
>> methods.
> It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,
> which itself is-a SeqFeatureI.  We might want to run the tests on
> that but a quick inheritance tree check on my ends seems to confirm
> that.  If the Range methods don't work there may be an issue within
> B::SF::A (which wouldn't surprise me).

Sorry, I was looking at the docs on the website and for whatever reason
its failing to display all the inherited modules. If RangeI methods
don't work I'll post back, but for now assume they do (I'm not in a
position to test right now).

> My inclination is [snip]

I still don't really understand what the deal is with all these modules,
so I'll leave it your hands to make further recommendations and take action.

 From my limited understanding what you said seems reasonable, except for
excluding FeatureIO completely. At least, I'd really like to see it in
1.6; it would be a shame to miss it just because of Annotated. Worst
case, isn't Generic 'good enough' as a replacement?

> The GMOD meeting is a few weeks away, where I assume some things will
> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
> saving; maybe retooling it would be in our best interests, but it
> needs a decent roadmap to move forward.

Agreed. I guess we'll wait for the results of that meeting? Is anyone 
going planning to discuss this issue?

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