[Bioperl-l] TreeFunctionsI::findnode_by_id ?

Jason Stajich jason at bioperl.org
Fri Aug 15 19:00:04 EDT 2008


I think D.

There should probably only be one find_node function.

findnode_by_id was written by Ramiro for the re-rooting code and I  
guess it wasn't checked to reduce unneeded functions.  I don't have  
any problems removing/deprecating it but will need to update the code  
that depends on it to use find_node properly.

-jason
On Aug 14, 2008, at 6:14 AM, Heikki Lehvaslaiho wrote:

> A generic method for retrieving nodes from a Bio::Tree::TreeI  
> objects is
> Bio::Tree::TreeFunctionsI::find_node. It defaults to searching the  
> 'id'
> attribute unless a field is given. I can retrieve nodes based on  
> internal id
> like this:
>
>   $tree->find_node(-internal_id => $internal_id);
>
> I now found Bio::Tree::TreeFunctionsI::findnode_by_id() that  
> retrieves by id.
> However, the POD documentation claims that it retrieves by internal  
> id.
>
> What needs to be done?
>
> A. Fix the doc to speak about id
> B. Fix to code to retrieve by internal_id
> C. Fix the doc and create findnode_by_internal_id()
> C. Remove findnode_by_id() as redundant and confusing
> D. Deprecate findnode_by_id() as redundant and confusing
>
> There are no tests for findnode_by_id() which to me tilts selection  
> to D and A
> for now.
>
> Any other opinions?
>
> 	-Heikki
>
>
> -- 
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Jason Stajich
jason at bioperl.org





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