[Bioperl-l] Unwise elimination of nodes inB:T:Node::remove_Descendent?
Mark A. Jensen
maj at fortinbras.us
Fri Feb 6 20:13:17 EST 2009
Interested parties please have a look at fixes ---
----- Original Message -----
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Hilmar Lapp" <hlapp at gmx.net>; <bioperl-l at lists.open-bio.org>
Sent: Friday, February 06, 2009 4:11 PM
Subject: Re: [Bioperl-l] Unwise elimination of nodes
> On Feb 6, 2009, at 8:59 AM, Mark A. Jensen wrote:
>>> I suppose the best way to deal with some of these questions (and ensure
>>> Node/Tree is acting as expected) is to come up with several vetted test
>>> cases indicating what we expect the proper behavior to be for
>>> remove_Descendant(), contract_linear_paths(), and any other problematic
>>> Node/Tree/TreeFunctionI methods. In fact, I highly recommend any code
>>> changes like this add tests to the test suite demonstrating the issue.
>> I can work the example of the thread into a test, adding some
>> of the points brought in by Hilmar-
> Any other areas of worry?
>>> Possibly related to all this is a fairly significant lingering bug dealing
>>> with Bio::Tree::TreeFunctionsI::reroot()
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2456 ). Any takers?
>> I take this one, if I have those privileges ( it is a privilege to serve,
>> isn't it?)...
> Cool, thanks Mark!
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