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

[AUnderwood@PHLS.org.uk]

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