NAME

       Bio::Matrix::Mlagan - A generic matrix with mlagan fields

SYNOPSIS

         # See L<Bio::Matrix::Generic> for most methods.
         # These are relevant for mlagan IO:
         $matrix->gap_open(-400);
         $matrix->gap_continue(-25);

DESCRIPTION

       This is based on Bio::Matrix::Generic, differing by storing gap_open and gap_continue data members to
       allow mlagan IO (see Bio::Matrix::IO::mlagan).  (Those values are 'outside' the matrix.)

       It also limits the structure to a 6x6 matrix with row & column names 'A', 'C', 'G', 'T', '.' and 'N'.

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://redmine.open-bio.org/projects/bioperl/

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::Generic->new();
        Function: Builds a new Bio::Matrix::Generic object
        Returns : an instance of Bio::Matrix::Generic
        Args    : -values            => arrayref of arrayrefs of data initialization
                  -matrix_id         => id of the matrix
                  -matrix_name       => name of the matrix
                  -matrix_init_value => default value to initialize empty cells
                  -gap_open          => gap open penalty (int)
                  -gap_continue      => gap continue penalty (int)

                  NB: -rownames and -colnames should not be given here, since they are
                  always being set to 'A', 'C', 'G', 'T', '.' and 'N'.

   gap_open
        Title   : gap_open
        Usage   : $obj->gap_open(-400);
        Function: Get/set the gap open amount.
        Returns : int
        Args    : none to get, OR int to set

   gap_continue
        Title   : gap_continue
        Usage   : $obj->gap_continue(-25);
        Function: Get/set the gap continue amount.
        Returns : int
        Args    : none to get, OR int to set

   add_row
        Title   : add_row
        Usage   : Do not use
        Function: This generic method is not suitable for mlagan, where the number of
                  rows is fixed.
        Returns : Warning
        Args    : none

   remove_row
        Title   : remove_row
        Usage   : Do not use
        Function: This generic method is not suitable for mlagan, where the number of
                  rows is fixed.
        Returns : Warning
        Args    : none

   add_column
        Title   : add_column
        Usage   : Do not use
        Function: This generic method is not suitable for mlagan, where the number of
                  columns is fixed.
        Returns : Warning
        Args    : none

   remove_column
        Title   : remove_column
        Usage   : Do not use
        Function: This generic method is not suitable for mlagan, where the number of
                  columns is fixed.
        Returns : Warning
        Args    : none