[Bioperl-l] Recoding Bio::SimpleAlign

Bernd Web bernd.web at gmail.com
Sat Jul 17 08:21:46 EDT 2010

Dear Jun,

Thanks for your work on this.
Just a few remarks.
-is changing methods names indeed needed? this will break existing
code (for some time)
-i am not sure how naming is generally done now in BioPerl, but is
used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has
an "_" followed by a capital. I'd stick with each_seq like names.  You
now changed it too  "each_Seq" but gap_char for example remained
gap_char. But surely others know better how/if to change naming.

> 2. gap chars/missing chars are more consistent in the package
> Default values for gap char and missing char are now set in the package.
> Calling/Setting gap char should be made by calling $aln->gap_char("-").
So the change here is that now the default values are actually set in
new, instead of setting a the default by calling gap_char.

> Another example, the method is renamed to give a clearer information.
> $aln->purge is renamed into $aln->remove_redundant_Seqs
Purge to me is a clear name in aln context ;-)

> $aln->splice_by_seq_pos is renamed to $aln->remove_gaps
But there was already a remove_gaps method.
$aln2 = $aln->remove_gaps
 Function  : Creates an aligment with gaps removed

Title   : splice_by_seq_pos
 Usage   : $status = splice_by_seq_pos(1);
 Function: splices all aligned sequences where the specified sequence
           has gaps.

So remove_gaps now takes an optional argument to indicate a
'reference' sequence for splicing?


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