[BioRuby] GSOC: phyloXML for BioRuby: Profiling
Christian M Zmasek
czmasek at burnham.org
Mon Jun 29 21:26:23 UTC 2009
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
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