[Bioperl-l] is the Bio::Align::AlignI doc right?

[Mark A. Jensen]

Hi Ben-- you are correct, someone brought this up a while back
and it was corrected in revision 15841. MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Thursday, February 25, 2010 7:35 AM
Subject: [Bioperl-l] is the Bio::Align::AlignI doc right?


> below is a Bio::Align::AlignI example found here:
>
> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number
>
>
> Title   : column_from_residue_number
> Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
> Function:
>
>           This function gives the position in the alignment
>           (i.e. column number) of the given residue number in the
>           sequence with the given name. For example, for the
>           alignment
>
>             Seq1/91-97 AC..DEF.GH
>             Seq2/24-30 ACGG.RTY..
>             Seq3/43-51 AC.DDEFGHI
>
>           column_from_residue_number( "Seq1", 94 ) returns 5.
>           column_from_residue_number( "Seq2", 25 ) returns 2.
>           column_from_residue_number( "Seq3", 50 ) returns 9.
>
>
> Perhaps I am simply misunderstanding the method, but shouldnt the first
> example return 6, not 5?
>
> E is the 94th residue.  It is in the 6th column.  Am I missing something?
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