[Bioperl-l] Deprecated methods

Chris Fields cjfields at illinois.edu
Wed Jan 14 00:08:29 EST 2009

Just ack'ed through the code and I have found many methods are noted  
as deprecated in bioperl, however they aren't clearly scheduled for  
removal in any future version.  Should we revise  
Bio::Root::Root::deprecated to accept two arguments (text and bp  
version) to check against the Root::Version and convert a dep warning  
to a throw if the version matches up?  Something like:

# maybe check against both 1.x and 1.00x?
$self->deprecated(-text => 'Use of foo() is deprecated.  Use set_foo()  
instead', -version => 1.7);

I don't think this'll break current code as _rearrange would just  
default the first argument to '-text' if the order is indicated.


More information about the Bioperl-l mailing list