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

[Hilmar Lapp]

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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--
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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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