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

Mark A. Jensen maj at fortinbras.us
Mon Feb 16 13:58:49 EST 2009


Chris et al-
Any objections to a commit on these mods, plus the .t changes?
Just pinging.
Mark
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Saturday, February 07, 2009 3:39 PM
Subject: Re: [Bioperl-l] Unwise elimination of 
nodesinB:T:Node::remove_Descendent?


> Ok- some modified tests and editorial analysis up under Bug #2456-
> cheers 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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>>> Bioperl-l at lists.open-bio.org
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>>
>>
>>
>
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