[Bioperl-l] Use of Root.pm versus RootI.pm

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Tue Oct 3 04:30:06 UTC 2006

My understanding is that all Bioperl-compliant classes should inherit 
from Bio::Root::Root, not Bio::Root::RootI.

Additionally, if functions such as throw() or _rearrange() are to be 
used without a class instance reference, they are to be used as class 
methods via Bio::Root::Root, not Bio::Root::RootI.

Is this correct?

My naive audit of bioperl-live CVS brought up the following statistics:

# Root.pm
/cvs/bioperl-live $ grep -r 'use Bio::Root::Root;' Bio | wc -l
/cvs/bioperl-live $ grep -r 'use base.*Bio::Root::Root' Bio | wc -l

# RootI.pm
/cvs/bioperl-live $ grep -r 'use Bio::Root::RootI;' Bio | wc -l
/cvs/bioperl-live $ grep -r 'use base.*Bio::Root::RootI' Bio | wc -l

My guess would be that all RootI should be changed to plain Root ?

Any help appreciated,

Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia

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