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.\" ========================================================================
.\"
.IX Title "TFBS::Matrix 3pm"
.TH TFBS::Matrix 3pm "2008-01-24" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
TFBS::Matrix \- base class for matrix patterns, containing methods common
to all
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
Modified by Eivind Valen eivind.valen@gmail.com
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "matrix"
.IX Subsection "matrix"
.Vb 7
\& 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
.Ve
.SS "pdl_matrix"
.IX Subsection "pdl_matrix"
.Vb 6
\& 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
.Ve
.SS "revcom"
.IX Subsection "revcom"
.Vb 7
\& 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
.Ve
.SS "rawprint"
.IX Subsection "rawprint"
.Vb 5
\& 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
.Ve
.SS "prettyprint"
.IX Subsection "prettyprint"
.Vb 5
\& 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
.Ve
.SS "length"
.IX Subsection "length"
.Vb 6
\& 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
.Ve
.SS "randomize_columns"
.IX Subsection "randomize_columns"
.Vb 5
\& Title   : randomize_columns
\& Usage   : $pfm\->randomize_columns();
\& Function: Randomizes the columns of a matrix
\& Returns : Nothing
\& Args    : none
.Ve