[pyphy] Mavric Tk version

[Rick Ree]

On Thu, 13 May 1999, Danny Rice wrote:

> Hello, I downloaded
> http://theopenlab.uml.edu/mavric/mavric-19990428.tar.gz and got the
> example scripts to run.  By upgrading to linux redhat 6.0 all the
> required python related programs were installed.  I had to make a
> couple trivial changes to get main.py to work.

> It might be worth mentioning in the README what gtest.py and testdi.py
> do.  An example phylip alignment file in the examples directory would
> be good.

I'll look into doing this.  In fact, the README file in CVS could use a
total rewrite, to reflect the stuff that Thomas has been doing.

I have sort of neglected the scripts in the examples directory, too.  They
are out of date.  The file 'mavric.py' in the source directory is now the
Gnome/Gtk app to run.

> I noticed that if you try to collapse a node that is a polytomy the
> branch leading to that node disappears and this error is printed:

I'll look into fixing this too :)

> So I thought I would download the latest cvs stuff and have a look.  I
> would like to start using the treeviewer but the example main.py
> didn't seem to take quoted taxa names containing space.  At least it
> had some problems with my trees.  I thought this might be pretty easy
> to fix.

Right.  The code that reads newick-formatted trees could be improved a
lot.  I still haven't incorporated Thomas' suggestion for reading
bootstraps _and_ branchlengths, either  :(

Right now, the newick reader class parses the input
character-by-character.  Python 1.5.2 has tokenizer support (shlex) that
could be used to parse trees (and other data files), but I don't know if
requiring everyone to upgrade is worth it.

>  I know c and perl but haven't messed with python nor cvs.
> Anyway I have a couple questions about cvs.

I'm a cvs newbie also, so maybe someone else can give you the skinny.

> By the way,  I think this little treeviewer already rules.

Thanks!  Check out the Tk version -- it has some nice features that I'll
try and incorporate into the Gtk version :) 

--Rick