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

[Jason Stajich]

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.


_______________________________________________
Bioperl-guts-l mailing list
Bioperl-guts-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-guts-l