[Bioperl-l] Changes to Bio::SeqI broke Bio::Graphics

[Hilmar Lapp]

Lincoln correct me if this is wrong, but I guess that 'lightweight 
interface' is more or less Bio::SeqFeatureI.

One could duplicate (well, probably remove a few methods?) 
Bio::SeqFeatureI as Bio::SeqFeature::RenderableFeatureI ... Is that 
what you were thinking of?

	-hilmar

On Monday, November 11, 2002, at 12:25 PM, Matthew Pocock wrote:

> Rather than all this kludging to make sequences look like features 
> so that they can be rendered, could you instead define the renderer 
> in terms of some light-weigth interface for the data you need to 
> render something and adapt both features and sequences to that 
> interface? That way, you can later decide to render traces, 
> barcharts, pictures by just providing an apropreate adaptor.
>
> Just my 2p
>
> Matthew
>
> Hilmar Lapp wrote:
>> I was thinking of doing exactly that, just don't have time. I'd 
>> have called it Bio::SeqFeature::SeqAdaptor, because basically the 
>> pattern is to adapt a Bio::SeqI object to the Bio::SeqFeatureI 
>> interface. Hence,
>>     Bio::SeqFeature::SeqAdaptor is-a Bio::SeqFeatureI, Bio::SeqI
>> Bio::SeqI would be implemented by composition, as you say. With 
>> this you'd be able to look at any seq object as if it were a 
>> feature. I believe Lincoln has already accomplished a similar 
>> thing in Bio::DB::GFF::Feature even though it's not explicit. Not 
>> sure though.
>> The only downside of this is that it could potentially be 
>> expensive if you want to disguise very many sequences.
>>     -hilmar
>> On Saturday, November 9, 2002, at 04:53 AM, Ewan Birney wrote:
>>> On Fri, 8 Nov 2002, Lincoln Stein wrote:
>>>
>>>>>
>>>>> Why? So that they looked like sequence features? I still think 
>>>>> it is wrong
>>>>> to have Bio::SeqI inherieting from Bio::RangeI.
>>>>
>>>>
>>>> When rendering the features of a sequence, it looks nice to have 
>>>> a single
>>>> feature that goes all the way across the whole sequence labeled 
>>>> with the
>>>> display_id of the sequence.  When Bio::SeqI had start() and 
>>>> end() features,
>>>> this was sufficient to pass the sequence object to the drawing 
>>>> code and get
>>>> the desired effect.
>>>>
>>>
>>> I think this is changing the sequence interface for a specific 
>>> use case. I
>>> would claim a better pattern here is:
>>>
>>>
>>>   Bio::SeqFeature::SequenceExtent
>>>
>>> which is-a Bio::SeqFeatureI and has-a Bio::SeqI and chains the 
>>> call to
>>> "end" to "length" and also "has_tags" etc to something sensible in
>>> Bio::AnnotationCollection.
>>>
>>> I am happy to write this. Does this sound like a better solution?
>>>
>>>
>>>
>>>
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>> -- -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
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>
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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