[Phylobase-devl] stalled ...

Steven Kembel steve.kembel at gmail.com
Thu Jan 15 20:54:40 CET 2009

Hi Ben,

>> 2. see what we can do to detect & fix problems with unrooted trees:
>> this includes a lot of Steve's "to do" list (sorting out nodeId,
>> nNode, etc.)
>  ???

I can look at this but probably won't get a chance to do so for a week  
if anyone else wants to tackle it. If we've settled on the nodeId/edge  
order question it should just be a matter of checking things like  
nNode in construction and print methods to make sure they work with  
unrooted trees.

>> 6. with some input from Emmanuel, implement SOME form of
>> checking/consistency rule for ordering when importing/exporting
>> from/to ape
>   NOT DONE. Volunteers?

It sounded like pruningwise is maybe subtly different than preorder so  
not sure what to do on import from ape but for export to ape can we  
simply reorder the tree preorder?

>> 2. adding metadata/annotation slots, although if we know
>> their GENERAL form it would be nice to add them to phylo4[d]
>> objects now because adding slots later breaks backward compatibility
>> of saved objects (but we may just have to bite the bullet and
>> do it later).  In particular if these were slots of type list()
>> we could be vague about what we were going to put in (at the
>> cost of less-strong typing of the objects)
>  Could add as list() if we can agree on names for the slots,
> how many.

I think a single @metadata slot should be enough, if it's a list we  
can put whatever else we want in there in the future. An annotation  
slot is tricky, if annotations are going to be attached to nodes/edges  
they can be phylo4d data, but if they apply to the whole tree they can  
be metadata, so just a @metadata slot may be enough?

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