[Bioperl-l] [Wg-phyloinformatics] Re: phyloXML weekly report

Chris Fields cjfields at illinois.edu
Fri Aug 15 10:12:10 EDT 2008


The method get_all_annotation_keys() is present in  
AnnotationCollectionI but not get_all_Annotations(), though I doubt it  
is set up for recursive retrieval (something that might be worth  
testing).  I don't have a problem adding this in.  Hilmar, thoughts?

chris

On Aug 15, 2008, at 1:11 AM, Han, Mira wrote:

>
> Hi,
> I've fixed the get_deep_Annotations() to get_nested_Annotations()
> It has arguments -keys and -recursive,
> And behaves exactly like get_Annotations() when recursive is not set  
> (tested by replacing the get_Annotations() in the Annotation.t)
> I made it a new function instead of modifying get_Annotations()  
> because I wasn't sure how to modify it to be backwards compatible.
> I thought of adding the function to the interface  
> AnnotationCollectionI,
> But it seemed like get_all_Annotations() was missing from the  
> interface as well,
> So decided to ask if it should be added to the interface at all.
> Isn't it possible that certain implementations of the interface has  
> functions that are only specific to that implementation?
>
> Mira
>
>
> On 8/12/08 12:00 AM, "Mira Han" <mirhan at indiana.edu> wrote:
>
>
> Oh yes,
> I meant get_Annotations,
> I want a get_Annotations that is recursive and passes the keys to  
> the recursive calls.
>
>
>
> On 8/11/08 11:54 PM, "Hilmar Lapp" <hlapp at duke.edu> wrote:
>
> Hi Mira -
>
> On Aug 11, 2008, at 11:46 PM, Han, Mira wrote:
>
>> Yes it is true that it's similar to get_all_Annotations, it's
>> basically a recursive version of it.
>
>
> I suppose you mean get_Annotations(), right? (get_all_Annotations() is
> already recursive)
>
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> ===========================================================
>
>
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






More information about the Bioperl-l mailing list