[Bioperl-l] Re: issues with _rearrange

[Jason Stajich]

> There does seem to be a lot of work going on to make sure that ->verbose()
> can be overridden ...
>
I don't think that verbose needs to be permitted to be overridden, but we
need an easy way to see debugging only for a specific class or object so I
don't want to go back to the old (pre 0.7) way of only having a global debug
option.

The functionality provided in Root is as following, every object should be
able to call the following. Verbose is the only method that needs state.

'debug'   which will print msg to STDERR if verbose is > 0
'verbose' warns are ignored when this is < 0 and warns become throw when
          verbose > 1
'throw'  Throw a warning, these can be caught
'warn'   Print a warning to stderr
'deprecated' will print deprecation warnings in a standard way
'warn/throw_not_implemented' For interfaces, standard msg about un
                             implemented methods

There are some housekeeping methods for dealing with properly cleaning up
objects, this has to do with chaining a set of calls in the DESTROY block
which can get hairy with multiple inheritance.  Design refactoring may
remove this dependancy but this was Hilmar and my own workarounds
implemented for the time being.

> -Aaron

>
> P.S. with my now dead laptop unavailable for awhile, I'd really like some
> list lurker to contact me about implementing some of these things; no
> bioinformatics knowledge necessary!  Your chance to become a BioPerl hero!
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu