NAME

       TFBS::Matrix - base class for matrix patterns, containing methods common to all

DESCRIPTION

       TFBS::Matrix is a base class consisting of universal constructor called by its subclasses
       (TFBS::Matrix::*), and matrix manipulation methods that are independent of the matrix
       type. It is not meant to be instantiated itself.

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

       Boris Lenhard <Boris.Lenhard@cgb.ki.se> Modified by Eivind Valen eivind.valen@gmail.com

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       preceded with an underscore.

   matrix
        Title   : matrix
        Usage   : my $matrix = $pwm->matrix();
                  $pwm->matrix( [ [12, 3, 0, 0, 4, 0],
                                  [ 0, 0, 0,11, 7, 0],
                                  [ 0, 9,12, 0, 0, 0],
                                  [ 0, 0, 0, 1, 1,12]
                                ]);

        Function: get/set for the matrix data
        Returns : a reference to 2D array of integers(PFM) or floats (ICM, PWM)
        Args    : none for get;
                  a four line string, reference to 2D array, or a 2D piddle for set

   pdl_matrix
        Title   : pdl_matrix
        Usage   : my $pdl = $pwm->pdl_matrix();
        Function: access the PDL matrix used to store the actual
                  matrix data directly
        Returns : a PDL object, aka a piddle
        Args    : none

   revcom
        Title   : revcom
        Usage   : my $revcom_pfm = $pfm->revcom();
        Function: create a matrix pattern object which is reverse complement
                   of the current one
        Returns : a TFBS::Matrix::* object of the same type as the one
                   the method acted upon
        Args    : none

   rawprint
        Title   : rawprint
        Usage   : my $rawstring = $pfm->rawprint);
        Function: convert matrix data to a simple tab-separated format
        Returns : a four-line string of tab-separated integers or floats
        Args    : none

   prettyprint
        Title   : prettyprint
        Usage   : my $prettystring = $pfm->prettyprint();
        Function: convert matrix data to a human-readable string format
        Returns : a four-line string with nucleotides and aligned numbers
        Args    : none

   STAMPprint
        Title   : STAMPprint
        Usage   : my $STAMPstring = $pfm->STAMPprint();
        Function: Convert the matrix to STAMP readable format
        Returns : A string of the matrix in a TRANSFAC like format for STAMP
        Args    : none

   length
        Title   : length
        Usage   : my $pattern_length = $pfm->length;
        Function: gets the pattern length in nucleotides
                   (i.e. number of columns in the matrix)
        Returns : an integer
        Args    : none

   randomize_columns
        Title   : randomize_columns
        Usage   : $pfm->randomize_columns();
        Function: Randomizes the columns of a matrix (in place).
        Returns : Nothing
        Args    : none