[Bioperl-l] treexml

Chris Fields cjfields at uiuc.edu
Thu Jun 12 13:03:55 EDT 2008


Yes, that sounds correct to me.  I could see this being useful for  
other rich tree file formats so it probably should be genericized.

chris

On Jun 12, 2008, at 8:58 AM, Hilmar Lapp wrote:

> I agree with implementing Bio::AnnotatableI. I'm not sure we need to  
> have a node class specifically tailored to PhyloXML but maybe we do.
>
> But even if we do, the annotatable capability sounds generic enough  
> for having a Bio::Tree::AnnotatableNode, from which  
> Bio::Tree::NodePhyloXML would inherit and do all the things that are  
> really specific to PhyloXML?
>
> 	-hilmar
>
> On Jun 11, 2008, at 8:56 PM, Jason Stajich wrote:
>>
>> On Jun 11, 2008, at 5:48 PM, Han, Mira wrote:
>>
>>>
>>> I can remove the TreePhyloXML class,
>>> And use the tag functions for Bio::Tree::TreeI.
>>> Yeah, it seems like TreePhyloXML is overkill.
>>> I don't know about the node though.
>>> I think it would be cleaner to have a NodePhyloXML,
>>> Since there are much more than scalar values that will be  
>>> connected to the node,
>>> Such as annotations, sequences, etc.
>>
>> Mira -
>> That sounds quite fine to me.  I agree that the NodePhyloXML is  
>> probably going to be different enough from the generic Node object  
>> to justify making a sub-class.  You may want to inherit from the  
>> interfaces like Bio::AnnotatableI in the NodePhyloXML if you are  
>> attaching annotations, etc.
>>
>> For example I do this for the Bio::Tree::AlleleNode which are nodes  
>> in a tree and also Individuals from a Population for popgen analyses.
>>
>> -jason
>>>
>>>
>>> On 6/11/08 4:50 PM, "Jason Stajich" <JASON_STAJICH at BERKELEY.EDU>  
>>> wrote:
>>>
>>> Hey Mira -
>>>
>>> Looks like things are going well. I just wanted to check and see  
>>> if it is totally necessary to create new classes or if you can use  
>>> the get/set tag/value pair interface that already exists?
>>>
>>> These are the functions that are present in Bio::Tree::TreeI and  
>>> Bio::Tree::NodeI :
>>> add_tag_value
>>> remove_tag
>>> get_all_tags
>>> get_tag_values
>>> has_tag
>>>
>>> These are the same functions we use in SeqFeatureI interface as  
>>> well.  It is just possible to re-use these rather than making a  
>>> new function for every data type - this way we don't have to  
>>> change the interface for different richness of data.
>>>
>>> BTW (and this may be me who did it, but maybe Sendu remembers) - I  
>>> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does  
>>> anyone know? Trees are containers around a set of Nodes which are  
>>> linked together to form a tree and the Tree object holds a pointer  
>>> to the root node.
>>>
>>> -jason
>>>
>>> --
>>> Jason Stajich
>>> Miller Research Fellow
>>> University of California, Berkeley
>>> lab: 510.642.8441
>>> http://pmb.berkeley.edu/~taylor/people/js.html
>>> http://fungalgenomes.org
>>>
>>>
>>>
>>>
>>
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>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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