[Bioperl-l] Changes to Bio::SeqI broke Bio::Graphics

Hilmar Lapp hlapp@gnf.org
Thu, 7 Nov 2002 11:40:04 -0800

We could put those methods back with a deprecation warning, and not have RangeI in @ISA.

The problem with that is that it's not solely about forwarding to some other method ... There is really no other place for these properties unless you use Bio::LocatableSeq (Aaron et al, is this correct?).

Generally, in the ideal case the HOWTOs don't go much beyond what's being tested for in the test cases...


> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Thursday, November 07, 2002 11:28 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Changes to Bio::SeqI broke Bio::Graphics
> Hi All,
> The recent removal of RangeI from Bio::SeqI caused all my
> Bio::Graphics HOWTO examples to fail (about eight of them).  It also
> broke some other scripts that I use routinely.  I was relying on the
> object returned by Bio::SeqIO to implement start and end methods.
> I've fixed the HOWTOs, but the extent of the damage leads me to wonder
> how many other people might have made the same mistake.  It occurs to
> me that we may be breaking a *lot* of scripts out there.
> Lincoln
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