Linux Certif

Toute la documentation sur la certification Linux LPI

TFBS::Matrix.3pm

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
 
 

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
  Returns : Nothing
  Args    : none