[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1167 (fwd)

[Jason Stajich]

It's really helpful when you provide constructive comments - if you're not
happy with the state of toolkit we'd welcome contributors rather than just
complaining about a 'buggy' release.  Join us in making the toolkit
better!

As for your points:

1) Sorry, this is the wrong interpretation of how the modules are used -
   the annotation framework has
   changed to the interface Bio::AnnotationCollectionI which allows us to
   be more flexible about the types of annotations stored, rather than
   requiring a new function for each type.  This change is mentioned in
   the Changelog for 0.9.2.   Future changes to the annotation system will
   more fully link in the Bio::Biblio to the annotation objects.

2) At this point no one uses Bio::SeqFeature::Computation because it is a
   newish module that Mark Fiers wanted to see included.  We'd welcome
   improvements and tests for this module - if you write it and submit to
   the list we'll add it to the repository.

Thanks.
-jason
-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Fri, 19 Apr 2002 16:36:11 -0400
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1167

JitterBug notification

new message incoming/1167

Message summary for PR#1167
	From: mingyi.liu@gpc-biotech.com
	Subject: Bugs in genbank.pm
	Date: Fri, 19 Apr 2002 16:36:10 -0400
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From mingyi.liu@gpc-biotech.com Fri Apr 19 16:36:11 2002
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Date: Fri, 19 Apr 2002 16:36:10 -0400
Message-Id: <200204192036.g3JKaAkO030177@pw600a.bioperl.org>
From: mingyi.liu@gpc-biotech.com
To: bioperl-bugs@bioperl.org
Subject: Bugs in genbank.pm

Full_Name: Mingyi Liu
Module: Bio::SeqIO::genbank
Version: 1.0
PerlVer: 5.6.1
OS: Win2K
Submission from: cambridge.gpc-biotech.com (63.74.162.108)


Two bugs:

1. get_Annotations('reference') and get_Annotations('comment') should be changed
to each_Reference and each_Comment.

2. _print_GenBank_FTHelper should add error checking that if a feature's primary
tag is longer than maximum, then truncate it automatically instead of throwing
an exception in _write_line_GenBank_regex.

V1.0's even more buggy than a beta version.  Any code testing should've found
these bugs (including the ones in Computation.pm)!


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