[Bioperl-l] Unwise elimination of nodes inB:T:Node::remove_Descendent?

Chris Fields cjfields at illinois.edu
Fri Feb 6 23:09:22 EST 2009


Mark,

Saw some errors pop up when running Tree tests (see the attachment on  
the bug report).  They may be due to bad test data and not your patch  
so it'll need further investigating; a few appear to be the same test  
data using in various TreeIO formats.

chris

On Feb 6, 2009, at 7:13 PM, Mark A. Jensen wrote:

> 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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