[Bioperl-l] zero length sequence in PrimarySeq

[Heikki Lehvaslaiho]

Hilmar Lapp wrote:
> 
> Heikki Lehvaslaiho wrote:
> >
> > If you reset the sequence of a PrimarySeq to a zero length after first
> > setting it to some value and you had not set moltype, method _guess_type
> > got called and threw an exception. I've now fixed it in both 07 branch and
> > main trunk by conditionally calling _guess_type only if the sequence ne ''.
> >
> > One could argue that one should always set the moltype but I think that is
> > expecting a bit too much from a casual user.
> >
> > One alternative would be for _guess_type to silently do nothing rather than
> > throw an exception.
> >
> > If you feel that some other implementation of the fix is better than the
> > one I did, feel free to change the code, but please keep the functionality.
> >
> 
> I have to admit that I am not happy with this change. It renders
> the sequence object in an undetermined state, because then there
> is no way to find out what type of sequence it is, which is
> against the API definition.
> 
> So, I suggest to do one of the following:
> 1) Change the API definition of moltype() such that there is an
> additional type 'unknown' allowed.
> 2) Change the code such that it retains the last active moltype if
> the sequence is reset to zero length. (This then still requires a
> moltype be supplied at initialization with a zero length seq,
> which I'm a strong supporter of.)
> 
> I'd rather prefer option 2), because it seems cleaner to me, and I
> don't see the use case that really needs option 1).
> 
> What do you think?

Your option 2) is the way I changed it into. The objects does keep the last
active moltype. See the code below:

-----------------------------------------
use Bio::PrimarySeq;

$a = new Bio::PrimarySeq;
print $a->seq, ": ", $a->moltype, "\n";

$a->seq('a');
print $a->seq, ": ", $a->moltype, "\n";

$a->seq('');
print $a->seq, ": ", $a->moltype, "\n";
-----------------------------------------

The output is:

----------
:
a: dna
: dna
----------

All objects need to be able to be created without any attributes set, don't
you agree?  The moltype remains undef until explicitly set or seq is set.

OK?

	-Heikki


>         Hilmar
> --
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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