[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1165 (fwd)

[Hilmar Lapp]

It probably is a lesson for the future. I suggest that from now on we
will not include modules in stable releases that lack a rigorous
test. That means, if there's no test for Computation.pm that passes
at the time 1.0.1 is up, Computation.pm should be removed from that
branch.

    -hilmar

--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> I'm not sure anyone even uses Bio::SeqFeature::Computation ... 
> Anyone?
> None of the other bioperl modules do at this point.
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> ---------- Forwarded message ----------
> Date: Fri, 19 Apr 2002 15:11:38 -0400
> From: bioperl-bugs@bioperl.org
> To: bioperl-guts-l@bioperl.org
> Subject: [Bioperl-guts-l] Notification: incoming/1165
> 
> JitterBug notification
> 
> new message incoming/1165
> 
> Message summary for PR#1165
> 	From: mingyi.liu@gpc-biotech.com
> 	Subject: Computation module lacks test and has various bugs
> 	Date: Fri, 19 Apr 2002 15:11:37 -0400
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From mingyi.liu@gpc-biotech.com Fri Apr 19 15:11:37 2002
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g3JJBbkO029596
> 	for <bioperl-bugs@pw600a.bioperl.org>; Fri, 19 Apr 2002 15:11:37
> -0400
> Date: Fri, 19 Apr 2002 15:11:37 -0400
> Message-Id: <200204191911.g3JJBbkO029596@pw600a.bioperl.org>
> From: mingyi.liu@gpc-biotech.com
> To: bioperl-bugs@bioperl.org
> Subject: Computation module lacks test and has various bugs
> 
> Full_Name: Mingyi Liu
> Module: Bio::SeqFeature::Computation
> Version: 1.0
> PerlVer: 5.6.1
> OS: Win2K
> Submission from: cambridge.gpc-biotech.com (63.74.162.108)
> 
> 
> score function in the module Bio::SeqFeature::Computation should be
> changed to:
> 
> sub score {
>    my ($self, $value) = @_;
>    if (defined $value) {
>      if (!ref($value)) { $self->add_score_value('default', $value);
> }
>    } else {
>       return ($self->each_score_value('default'))[0];
>    }
> }
> 
> Or else a value of 0 causes problem, which btw also illustrates the
> lack of
> tolerance for non-standard (but not error) situations.  This module
> seriously
> lack any test.  It doesn't look good for upgrading to 1.0.
> 
> Another big problem is that both Bio::SeqFeature::Generic and
> Bio::SeqFeature::Computation deals with a score parameter, but
> Generic takes a
> scalar, and Computation takes a hash, which causes a big problem in
> new method
> (Computation's new calls Generic's) because Computation's score
> method only
> deals with a hash situation. So I added the if(!ref($value)) above.
> 
> 
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> 
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> 


=====
----------------------------------------------------------
Hilmar Lapp                         email: lapp@gnf.org
GNF, San Diego, Ca. 92121           phone: +1-858-812-1757
----------------------------------------------------------

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