NAME

       Bio::Matrix::MatrixI - An interface for describing a Matrix

SYNOPSIS

         # Get a Matrix object

DESCRIPTION

       This is an interface describing how one should be able to interact with a matrix.  One can
       have a lot of information I suppose and this outline won't really work for PWM or PSSMs.
       We will have to derive a particular interface for those.

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 email or the web:

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

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

APPENDIX

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

   matrix_id
        Title   : matrix_id
        Usage   : my $id = $matrix->matrix_id
        Function: Get the matrix ID
        Returns : string value
        Args    :

   matrix_name
        Title   : matrix_name
        Usage   : my $name = $matrix->matrix_name();
        Function: Get the matrix name
        Returns : string value
        Args    :

   get_entry
        Title   : get_entry
        Usage   : my $entry = $matrix->get_entry($rowname,$columname)
        Function: Get the entry for a given row,column pair
        Returns : scalar
        Args    : $row name
                  $column name

   get_column
        Title   : get_column
        Usage   : my @row = $matrix->get_column('ALPHA');
        Function: Get a particular column
        Returns : Array (in array context) or arrayref (in scalar context)
                  of values
        Args    : name of the column

   get_row
        Title   : get_row
        Usage   : my @row = $matrix->get_row('ALPHA');
        Function: Get a particular row
        Returns : Array (in array context) or arrayref (in scalar context)
                  of values
        Args    : name of the row

   get_diagonal
        Title   : get_diagonal
        Usage   : my @diagonal = $matrix->get_diagonal;
        Function: Get the diagonal of the matrix
        Returns : Array (in array context) or arrayref (in scalar context)
        Args    : none

   column_num_for_name
        Title   : column_num_for_name
        Usage   : my $num = $matrix->column_num_for_name($name)
        Function: Gets the column number for a particular column name
        Returns : integer
        Args    : string

   row_num_for_name
        Title   : row_num_for_name
        Usage   : my $num = $matrix->row_num_for_name($name)
        Function: Gets the row number for a particular row name
        Returns : integer
        Args    : string

   num_rows
        Title   : num_rows
        Usage   : my $rowcount = $matrix->num_rows;
        Function: Get the number of rows
        Returns : integer
        Args    : none

   num_columns
        Title   : num_columns
        Usage   : my $colcount = $matrix->num_columns
        Function: Get the number of columns
        Returns : integer
        Args    : none

   reverse
        Title   : reverse
        Usage   : my $matrix = $matrix->reverse
        Function: Get the reverse of a matrix
        Returns :
        Args    :

   row_names
        Title   : row_names
        Usage   : my @rows = $matrix->row_names
        Function: The names of all the rows
        Returns : array in array context, arrayref in scalar context
        Args    : none

   column_names
        Title   : column_names
        Usage   : my @columns = $matrix->column_names
        Function: The names of all the columns
        Returns : array in array context, arrayref in scalar context
        Args    : none