[BioRuby] GSOC: Bioruby PhyloXML update 12

[Christian M Zmasek]

Hi, Diana:

> 
>     * How does integration to the master branch goes? Is all i have to
>     do is pull_request on github?

I think so (never done this myself, though). Maybe the git experts can 
answer this?


>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>     returns incomplete data, since info for
>     Bio::Sequence#classification, Bio::Sequence#species,
>     Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>     it is not accessible from Sequence class. Should there be
>     PhyloXML::Node#to_biosequence method which would gather information
>     from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>     Bio::Sequence should not hold taxonomic information?

Good point. Personally, I would leave your 
PhyloXML::Sequence#to_biosequence as it is (and add a warning about this 
  to the documentation) and, in addition, create 
PhyloXML::Node#to_biosequence -- although, I would not call it 
to_biosequence but maybe something like extract_biosequence.
Needless to say, that an almost infinite number of "solutions" to this 
exists, without a clear "winner" (in my opinion).

Christian