Langue: en

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 3 (Bibliothèques de fonctions)


Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments


   use strict;
   my $stats = Bio::Align::DNAStatistics->new();
   # get alignment object of two sequences somehow
   my $pwaln;
   print $stats->number_of_comparable_bases($pwaln);


Calculate pairwise statistics.


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  Title   : number_of_comparable_bases
  Usage   : my $bases = $stat->number_of_comparable_bases($aln);
  Function: Returns the count of the number of bases that can be
            compared (L) in this alignment ( length - gaps)
  Returns : integer
  Args    : L<Bio::Align::AlignI>


  Title   : number_of_differences
  Usage   : my $nd = $stat->number_of_distances($aln);
  Function: Returns the number of differences between two sequences
  Returns : integer
  Args    : L<Bio::Align::AlignI>


  Title   : number_of_gaps
  Usage   : my $nd = $stat->number_of_gaps($aln);
  Function: Returns the number of gapped positions among sequences in alignment
  Returns : integer
  Args    : L<Bio::Align::AlignI>