[Bioperl-l] Feature/Annotation rollback finished

Chris Fields cjfields at uiuc.edu
Thu Aug 30 13:27:46 EDT 2007


display_text() is really a hack for explicitly getting the same  
output one would have expected from stringification overload for any  
Bio::AnnotationI (you can also use callbacks on it for customizing it  
if needed, but that's not important here).  It works depending on the  
context of what you're trying to accomplish, but it might be best to  
use value() specifically in places where you expect only using  
Bio::Annotation::Simple.

chris

On Aug 30, 2007, at 11:28 AM, Scott Cain wrote:

> Hi Hilmar,
>
> I'm using it as Chris suggested: where I had be depending on ""
> overloading.  I think in most places, I am using it on
> Bio::Annotation::SimpleValue to get the string that is the simple  
> value.
> On more complex data types, I am using other methods built into those
> classes to extract useful stuff for inserting into the database.
>
> Scott
>
>
>
> On Thu, 2007-08-30 at 12:07 -0400, Hilmar Lapp wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>>
>> On Aug 30, 2007, at 11:46 AM, Scott Cain wrote:
>>
>>> Good news!  I only had to add a few defineds and a few
>>> display_texts and
>>> I was able to successfully create a database and load the yeast GFF3
>>
>> Scott - I'm a little worried - what are you using the display_text()
>> calls for? There is no method to set a property that would be
>> returned here, so you only have control over that if you override the
>> method in a custom AnnotationI class.
>>
>> 	-hilmar
>> - --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.3 (Darwin)
>>
>> iD8DBQFG1us5uV6N2JxL7qsRAicFAKCFCHPORyK9273X8u2/gbaZCNpEHgCeMovA
>> OtZghop1tET5iMqnwXzL+lk=
>> =NVrK
>> -----END PGP SIGNATURE-----
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                    
> cain.cshl at gmail.com
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list