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

[Jason Stajich]

changes checked in - the default params to get_nse are ('/','-') so this
can be simplified to use get_nse().  See guts list for full diffs.

Also fixed simplealign using deprecated API as well.

Need to do good once over of ALL the scripts before 1.2 is released to
find these problems sooner.

Volunteers?

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

On Fri, 29 Nov 2002 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
>
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