[Bioperl-l] adding seqfeatures in Bio::Seq

[Hilmar Lapp]

Just to exemplify how useful the recent changes can be I thought I'd 
add one of my problems and how easy it is solved now: the way I 
rewrote the biosql-adaptor code, the seq object attached to the 
features of a Bio::Seq got out-of-sync with the sequence (i.e., they 
became different disconnected objects). The way to re-sync that is 
now as simple as 1 line:

        $seq->add_SeqFeature($seq->flush_SeqFeatures());

and this goes automatically all the way down to sub-features etc.

	-hilmar

On Friday, September 27, 2002, at 11:19 AM, Hilmar Lapp wrote:

>
> On Thursday, September 26, 2002, at 05:44 PM, Jason Stajich wrote:
>
> <deleted encouragement even though it lifted my spirit 
> substantially - thanks Jason>
>
>>
>>
>> On Thu, 26 Sep 2002, Hilmar Lapp wrote:
>>
>>>
> <snip>
>>> I could also fix 4) such that $feat->attach_seq(undef) would de-tach
>>> a previously attached seq. However, to me the most sensible solution
>>> is also the simplest one: remove the restriction in
>>> Seq::add_SeqFeature().
>>>
>>> Comments? Thoughts? Objections?
>>
>> I think this is sensible -- I guess that 1.2 is going to be a bit 
>> cleaner
>> than 1.0 as you have done a really good job pushing these things 
>> out to
>> the edges.
>>
>
> Being the impatient that I am, I took your vote and the lack of 
> outcries as consensus and  committed this change. If this was too 
> fast and there is no consensus, I'll reverse it and make seqs 
> de-tachable from features (but please, there is [silent] 
> consensus? :)
>
> 	-hilmar
>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
--
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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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