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.
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?
> 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.
>>> On 6/11/08 4:50 PM, "Jason Stajich" <JASON_STAJICH at BERKELEY.EDU>
>>> 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 :
>>> 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 Stajich
>>> Miller Research Fellow
>>> University of California, Berkeley
>>> lab: 510.642.8441
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> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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