[Bioperl-l] treexml

miraceti miraceti at gmail.com
Wed Jun 11 20:50:22 EDT 2008


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.


On Wed, Jun 11, 2008 at 5:01 PM, Chris Fields <cjfields at uiuc.edu> wrote:

>
> On Jun 11, 2008, at 3:50 PM, Jason Stajich 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.
>>
>
> I agree; it simplifies the interface, even if it sacrifices small
> conveniences.
>
>  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.
>>
>
> Not sure myself; maybe this was part of Sendu's Taxonomy overhaul a while
> back?
>
>  -jason
>> --
>> Jason Stajich
>> Miller Research Fellow
>> University of California, Berkeley
>> lab: 510.642.8441
>> http://pmb.berkeley.edu/~taylor/people/js.html
>> http://fungalgenomes.or
>>
>
> -c
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
>
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