[BioRuby] Bioruby PhyloXML update

[Raoul JP Bonnal]

Hi Diana,
a portability issue.
Have you guys verified if LibXML::XML is it running on JRuby ? I don't 
think so because it's implemented in C. A solution could be
this http://github.com/mguterl/libxml-jruby/tree/master but today I 
can't access to it, probably due to my network problems.

Some test, 1 year ago - last post -:
http://www.nabble.com/comparing-xml-parsing-in-JRuby-and-MRI-td16268560.html#a16268560

this is the test code - good portability example too - :
https://svn.concord.org/svn/projects/trunk/common/ruby/xml_benchmarks/xml_benchmarks.rb

Cheers.

Diana Jaunzeikare ha scritto:
> Hi all!
>
> Here is what was done during community bonding period:
>
>    - subscribed to mailing lists
>    - created a blog <http://latvianlinuxgirl.blogspot.com/>
>    - got familiar with Git (this was particularly useful:
>    http://www.gitcasts.com/posts/railsconf-git-talk )
>    - created GitHub account and forked bioruby project.
>    - made first commit by adding sample phyloxml data files from
>    www.phyloxml.org
>    - reviewed BioPerl phyloXML implementation (also
>    http://www.bioperl.org/wiki/HOWTO:Trees )
>    - got familiar with libxml-ruby. Wrote simple program using both
>    LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml file.
>    - reviewed Ruby classes - Bio:Tree, Bio::Pathways
>    - After discussions in mailing lists it has been agreed to use
>    LibXML-ruby library, the LibXML::XML::Reader class
>
>
> This weeks plan:
>
>    - Start writing parser using LibXML::XML::Reader. It should return a
>    Bio::Tree object.
>    - Implement function next_tree to parse and return the next phylogeny.
>    - Design Tree::Node object for containing phyloxml elements.
>    - Start mapping phyloxml elements to Bio::Tree::Node, start with
>    taxonomy, branch_length, scientific_name
>    - Write simple unit tests.
>