[Bioperl-l] Bio::Seq::SeqWithQuality status

Chris Fields cjfields at illinois.edu
Tue Jan 13 19:31:49 EST 2009


Okay, but that still doesn't answer the more significant question,  
mainly why this wasn't added to the appropriate file when the  
deprecation warning was added.  And when are we supposed to remove the  
module (now? 1.7?).

Looks like Heikki added the deprecation warning with r9002 (7/11/2005)  
which predates 1.5.1.  We can remove it now but I think it's probably  
best to wait until 1.7 since we're almost 3 RCs into a release.


On Jan 13, 2009, at 1:37 PM, Florent Angly wrote:

> There is a line in the Bio::Seq::SeqWithQuality code that causes  
> this module to display a warning mentioning that the module is  
> deprecated:
> l. 231:    $self->deprecated("deprecated class - use  
> Bio::Seq::Quality instead");
> I just updated the documentation so that is is clearer to everyone  
> (incl. me).
> Florent
> Chris Fields wrote:
>> What is the current status of this module?  Florent Angly has  
>> marked this as deprecated on main trunk (in the POD) but it hasn't  
>> been added to the DEPRECATED list, nor can I find any discussion on  
>> the mail list about deprecating this module (normally a  
>> prerequisite for doing so).
>> chris

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