[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer

[Mark Johnson]

> I think a 4in1 would still be possible. Presumably at some point you
> know which one you will run, so let the user set everything in the
> single new() even if it doesn't make sense, but then form argument
> strings with


<SNIP>

Something like that occurred to me while driving home last night.  That
ought to separate things cleanly enough, especially if I validate the
options against the selected program.  I'm wasn't really thrilled with the
idea of code duplication between multiple modules, either.

All that said, if these Glimmer things are different programs with
> different uses (and not simply different versions of the same thing with
> the same function), by all means make separate modules.
>

It's a 'family' of gene predictors, two eukaryotic, two prokaryotic.
They're just similar enough to need similar solutions, and just different
enough to be slightly annoying.  8)