[Biopython-dev] [Bug 3047] PhyloXML, behavior on setting color and width doesn't match docstring or spec

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http://bugzilla.open-bio.org/show_bug.cgi?id=3047





------- Comment #7 from eric.talevich at gmail.com  2010-04-07 01:38 EST -------
(In reply to comment #3)
> (In reply to comment #2)
> > (In reply to comment #0)
> > > From the Clade docstring:
> > > 
> > > "Both 'color' and 'width' elements apply for the whole clade unless
> > > overwritten in-sub clades.
> > 
> > What is the bug? The docstring doesn't say the property will be explicitly
> > cascaded down to the sub-clades, which seems to be your interpretation.
> > Isn't that implicit when interpreting (drawing) the tree?
> > 
> > Peter
> > 
> 
> I suppose one could maintain that it's the responsibility of user code to
> enforce the behavior specified in the docstring, although I think that's a
> recipe for incompatibilities.  However, neither of the two available user codes
> I'm aware of (archaeoptryx or biopython's  Phylo.draw_graphviz) actually
> implement it.  It's better to just change the docstring, I think.
> 


That's my interpretation of it -- the color attribute is meant to be handled
that way by whatever code uses it for drawing.

Which means two things should happen before closing this bug:

 - Change the docstring to indicate *user code* is supposed to handle colors
and widths in a cascading fashion

 - Fix draw_graphviz (actually to_networkx) to cascade colors down branches,
like the Archaeopteryx GUI does


By the way, thanks for phyloXMLtools.py -- I'll take a closer look when I have
some time.


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