[Bioperl-l] [Gmod-schema] beginning work on SeqIO::chadoxml

Hilmar Lapp hlapp at gmx.net
Fri Feb 2 11:45:30 EST 2007


There must be at least a stub for next_seq(). It may throw a not- 
implemented exception, but it should not just be absent.

	-hilmar

On Feb 2, 2007, at 11:37 AM, Chris Fields wrote:

> I was going to suggest maybe allowing one to switch out XML  
> handlers/writers based on the style (ala XML::SAX), but I see that  
> chadoxml currently uses XML::Writer and there is no next_seq()  
> implemented.  Oh well...
>
> chris
>
> On Feb 2, 2007, at 10:03 AM, Scott Cain wrote:
>
>> Hi Hilmar,
>>
>> That is a good idea; when I started down this road, it felt like  
>> there
>> would only be a few things that I might want to allow to be  
>> different,
>> but I think you are right that having one standard implementation  
>> that
>> can be subclassed for legacy systems is a good thing.
>>
>> Scott
>>
>>
>> On Fri, 2007-02-02 at 10:09 -0500, Hilmar Lapp wrote:
>>> On Feb 1, 2007, at 2:55 PM, Scott Cain wrote:
>>>
>>>> The second main change was to introduce a -flybase_compat argument
>>>> when
>>>> initializing the Bio::SeqIO writer, so that 'old style' cv and  
>>>> cvterms
>>>> (that are compatable with flybase) will be used, but now the  
>>>> default
>>>> will be to use current standards:
>>>
>>> Just my $0.02 ... obviously, Flybase may be the only organization
>>> that uses an 'old style' or any other way not compliant with  
>>> 'current
>>> standards' (presumably SO), but if it's not the only one then this
>>> approach won't scale.
>>>
>>> Also, an argument -flybase_compat suggests to the unsuspecting that
>>> this is an endorsed flavor of the standard and fine to use for
>>> everyone else too.
>>>
>>> If Flybase is idiosyncratic in this way, why not make chadoxml.pm
>>> compliant with the standard as we all want it, keep it free from
>>> litter caused by usage of old versions of SO, and create a second
>>> module fb-chadoxml.pm that inherits from the first and merely
>>> overrides a few things so that it works for Flybase. This way, other
>>> organizations with similar needs can follow the path and create  
>>> their
>>> own xyz-chadoxml.pm, rather than having to muck around in the
>>> chadoxml.pm that comes with the distribution.
>>>
>>> I'm not sure I fully grasp the underlying issue, so I may not make
>>> much sense here. Apologies if that's the case ...
>>>
>>> 	-hilmar
>> -- 
>> --------------------------------------------------------------------- 
>> ---
>> Scott Cain, Ph. D.                                    
>> cain.cshl at gmail.com
>> GMOD Coordinator (http://www.gmod.org/)                      
>> 216-392-3087
>> Cold Spring Harbor Laboratory
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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