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

Mark A. Jensen maj at fortinbras.us
Fri Feb 6 23:54:02 EST 2009


cheers Chris-- I'll check it out- MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 06, 2009 11:09 PM
Subject: Re: [Bioperl-l] Unwise elimination of nodes 
inB:T:Node::remove_Descendent?


> 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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>
>
> 



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