The Zenautics Matrix Project 0.02 Beta (Default branch)


 
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Old 04-25-2008
The Zenautics Matrix Project 0.02 Beta (Default branch)

The Zenautics Matrix Project is a matrix/vectorclass for C++. It supports real and complex datafor nearly all matrix algebra calculations. It isoptimized for the double type (std::complex). Itworks well with small and large matrices. It iseasy to use and get started. It features plotting,FFT/IFFT, and more.License: BSD License (revised)Changes:
Some inner loop optimizations for speed. A few new functions.Image

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TFBS::Matrix(3pm)					User Contributed Perl Documentation					 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 perl v5.14.2 2008-01-24 TFBS::Matrix(3pm)