[Bioperl-l] Problem solved: Sorting alphabetically in simple align objects

[Heikki Lehvaslaiho]

Anthony,

You seem to be right. ("/","-") is the default for that function, so 
I changed the lines into:  
    $nse = $seq->get_nse;

and wrote some tests into the SimpleAlign.t file and added you as a
contributor to SimpleAlign.pm.

Thanks for spotting this.

	-Heikki

On Fri, 2002-11-29 at 16:12, AUnderwood@phls.org.uk wrote:
> I've find the problem in that was preventing sorting in alignments
> 
> in the Simplealign.pm module there are two identical lines in the
> sort_alphabetically and each_alphabetically methods that need to be changed:
> 
> $nse = $seq->get_nse("-","-"); needs to be changed to $nse = $seq->get_nse("/","-"); 
> 
>  other wise the keys in the _order hash are messed up so that when it comes
> to do anything with the sequences the values can not be referenced by the
> keys since they are different ot the keys in teh _seq hash.
> 
> I think this is what is happening anyway. I am fairly new to
> perl/programming so I am on the steep part of the learning curve when it
> comes to  objects and methods. I am not sure how to update stuff in the CVS
> bioper-live but if those in the know think this fix is OK tehn maybe the
> Simplealign.pm module can be update.
> 
> Anthony
> 
> Dr Anthony Underwood
> Bioinformatics Unit
> Central Public Health Laboratory
> 61 Colindale Avenue
> London
> NW9 5HT
> t:    0208 2004400 ext. 3618
> f:    0208 3583138
> e: aunderwood@phls.org.uk
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________