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

Chris Fields cjfields at illinois.edu
Fri Feb 6 16:11:18 EST 2009


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


More information about the Bioperl-l mailing list