[BioRuby] GSOC: phyloXML for BioRuby: Profiling

[Christian M Zmasek]

Hi, Diana:

Great analysis!

>
> The reason I am using Bio::Tree#parent is because I have to keep track 
> of the current node I am parsing. When I have reached </clade> element 
> i set the current_node to the parent of the node I just parsed.
>
> I see here two options.
>
> 1) Keep track of the current node myself (by putting references in an 
> array and pushing and poping accordingly). Thus I won't have to call 
> the Bio::Tree#parent method.
As a temporary solution, you could try this.


>
> 2) Update Bio::Tree/ Bio::Node class so that nodes contain references 
> to their parents. (thus not needing to  call breadth first search).

This seems a better (long term) solution, but _might_ be out of scope 
for this summer project.

Christian