NAME

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

SYNOPSIS

         use strict;
         my $stats = Bio::Align::PairwiseStatistics->new();

         # get alignment object of two sequences somehow
         my $pwaln;
         print $stats->number_of_comparable_bases($pwaln);
         my $score = $stats->score_nuc($pwaln);

DESCRIPTION

       Calculate pairwise statistics.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

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

   number_of_comparable_bases
        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>

   number_of_differences
        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>

   number_of_gaps
        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>

   score_nuc
        Title   : score_nuc
        Usage   : my $score = $stat->score_nuc($aln);
                    or
                  my $score = $stat->score_nuc(
                    -aln =>$aln,
                    -match    => 1,
                    -mismatch => -1,
                    -gap_open => -1,
                    -gap_ext  => -1
                  );
        Function: Calculate the score of an alignment of 2 nucleic acid sequences. The
                  scoring parameters can be specified. Otherwise the blastn default
                  parameters are used: match = 2, mismatch = -3, gap opening = -5, gap
                  extension = -2
        Returns : alignment score (number)
        Args    : L<Bio::Align::AlignI>
                  match score [optional]
                  mismatch score [optional]
                  gap opening score [optional]
                  gap extension score [optional]