Re: [Wg-phyloinformatics] Summer of Code: project summaries

Hi,
Just writing to summarize the final product of this summer. (even though it's overdue)
The phyloXML support in BioPerl project is finished officially,
I've created three new modules,
Bio::TreeIO::phyloxml,
Bio::Tree::AnnotatableNode,
and Bio::Annotation::Relation.
The parsing is done for all elements except for <ProteinDomain>
And the validation step is still missing.
I'm planning to add those in in the future.

I was contemplating to make a Bio::Annotation::XML till the end,
But decided not to since there was already a new module Bio::Annotation::TagTree, that looked like the
same thing.
Currently, the module does not use TagTree, it uses nested AnnotationCollections instead, because
TagTree was a temporary stub at the time.
There are methods in phyloxml that seem out of place there,
For example, the print_annotation and print_attr functions that print the annotations in phyloXML format.
Or the read_annotation function that reads the value of the annotation for a certain object.
I feel like these functions should go with the Annotation object,
But since there were no Annotation object that is phyloXML specific,
I just put them in the TreeIO::phyloxml.
This may change too in the future.

The documentations are all finished and can be seen in
http://www.bioperl.org/wiki/Module:Bio::TreeIO::phyloxml
http://www.bioperl.org/wiki/Module:Bio::Tree::AnnotatableNode
http://www.bioperl.org/wiki/Module:Bio::Annotation::Relation