[Bioperl-l] PrimarySeqI and IdentifiableI

[Shawn]

On Sat, 2002-09-07 at 03:14, Hilmar Lapp wrote:
> Done.
> 
> As an aside, I also fixed PrimarySeq::is_circular() which would not 
> allow you to reset the property to non-circular (why was this?).
> 
> All tests pass except RepeatMasker.t, the reason of which seems to 
> be unrelated to these changes:


Sorry about that, I forgot to commit a file.

shawn


> 
> ------------- EXCEPTION  -------------
> MSG: Could not open t/data/repeatmasker.fa.out for reading: No such 
> file or directory
> STACK Bio::Root::IO::_initialize_io blib/lib/Bio/Root/IO.pm:259
> STACK Bio::Tools::RepeatMasker::new Bio/Tools/RepeatMasker.pm:93
> STACK toplevel t/RepeatMasker.t:27
> 
> --------------------------------------

> 
> 	-hilmar
> 
> On Friday, September 6, 2002, at 09:51  AM, Ewan Birney wrote:
> 
> > On Fri, 6 Sep 2002, Hilmar Lapp wrote:
> >
> >>
> >>
> >>> -----Original Message-----
> >>> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> >>> Sent: Friday, September 06, 2002 12:32 AM
> >>> To: Hilmar Lapp
> >>> Cc: Bioperl
> >>> Subject: Re: [Bioperl-l] PrimarySeqI and IdentifiableI
> >>>
> >>>
> >>> On Thu, 5 Sep 2002, Hilmar Lapp wrote:
> >>>
> >> [...]
> >>>>
> >>>> I'll have to fix Bio::Seq anyway (I guess there's little doubt it
> >>>> should be Identifiable), but if we decide to separate IdentifiableI
> >>>> (and DescribableI) from PrimarySeqI, I'll fix that right away, too.
> >>>
> >>> It is a good question - I would say that they should
> >>> implement the methods
> >>> but could easily pass back "" strings. What is the other solution - A
> >>> composition solution? Then clients have to test whether
> >>>
> >>> $seq->identifier() is undef?
> >>>
> >>
> >> No, not composition (although that's an option too). By separation I
> >> rather meant that then you can't assume that if 
> >> obj->isa("Bio::PrimarySeqI")
> >> is true $obj->isa("Bio::IdentifiableI") will be true, too.
> >> You'd have to test for this separately before safely calling the
> >> IdentifiableI methods. So, a PrimarySeqI implementation could opt
> >> not to implement IdentifiableI.
> >>
> >> Right now having tested for isa("Bio::PrimarySeqI") implies having
> >> tested for isa("Bio::IdentifiableI").
> >
> >
> > Aha. I am ok with this. Go for it.
> >
> >
> >>
> >> 	-hilmar
> >>
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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