NAME

       Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix

SYNOPSIS

         use Bio::Matrix::IO;
         my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
                                          -file   => 'nucmatrix.txt');
         my $matrix = $parser->next_matrix;
         my $gap_open = $parser->gap_open;
         my $gap_continue = $parser->gap_continue;

DESCRIPTION

       Use to read in and write out substitution matrix files suitable for use by mlagan.

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 - Sendu Bala

       Email bix@sendu.me.uk

APPENDIX

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

   new
        Title   : new
        Usage   : my $obj = Bio::Matrix::IO::mlagan->new();
        Function: Builds a new Bio::Matrix::IO::mlagan object
        Returns : an instance of Bio::Matrix::IO::mlagan
        Args    :

   next_matrix
        Title   : next_matrix
        Usage   : my $matrix = $obj->next_matrix();
        Function: parses a matrix file
        Returns : L<Bio::Matrix::Mlagan>
        Args    : none

   write_matrix
        Title   : write_matrix
        Usage   : $obj->write_matrix($matrix)
        Function: Write out a matrix in mlagan format
        Returns : n/a
        Args    : L<Bio::Matrix::Generic>