[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 ---
http://bugzilla.open-bio.org/show_bug.cgi?id=2456
cheers-
MAJ
----- 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 
inB:T:Node::remove_Descendent?


>
> 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!
>
> -c
>
> 



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