Provided by: libtfbs-perl_0.7.1-2_amd64 bug


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


       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.


       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

       Boris Lenhard <> Modified by Eivind Valen


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

        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

        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

        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

        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

        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

        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

        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

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