tfbs::patterni(3pm) [debian man page]

TFBS::PatternI(3pm)					User Contributed Perl Documentation				       TFBS::PatternI(3pm)

NAME

       TFBS::PatternI - interface definition for all pattern objects (currently includes matrices and word (consensus and regular expressions )

DESCRIPTION

       TFBS::PatternI is a draft class that should contain general interface for matrix and other (future) pattern objects. It is not defined and
       not used yet, as I need to ponder over certain unresolved issues in general pattern definition. User feedback is more than welcome.

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard
       Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

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

   ID
	Title	: ID
	Usage	: my $ID = $icm->ID()
		  $pfm->ID('M00119');
	Function: Get/set on the ID of the pattern (unique in a DB or a set)
	Returns : pattern ID (a string)
	Args	: none for get, string for set

   name
	Title	: name
	Usage	: my $name = $pwm->name()
		  $pfm->name('PPARgamma');
	Function: Get/set on the name of the pattern
	Returns : pattern name (a string)
	Args	: none for get, string for set

   class
	Title	: class
	Usage	: my $class = $pwm->class()
		  $pfm->class('forkhead');
	Function: Get/set on the structural class of the pattern
	Returns : class name (a string)
	Args	: none for get, string for set

   tag
	Title	: tag
	Usage	: my $acc = $pwm->tag('acc')
		  $pfm->tag(source => "Gibbs");
	Function: Get/set on the structural class of the pattern
	Returns : tag value (a scalar/reference)
	Args	: tag name (string) for get,
		  tag name (string) and value (any scalar/reference) for set

   all_tags
	Title	: all_tags
	Usage	: my %tag = $pfm->all_tags();
	Function: get a hash of all tags for a matrix
	Returns : a hash of all tag values keyed by tag name
	Args	: none

   delete_tag
	Title	: delete_tag
	Usage	: $pfm->delete_tag('score');
	Function: get a hash of all tags for a matrix
	Returns : nothing
	Args	: a string (tag name)

perl v5.14.2							    2008-01-24						       TFBS::PatternI(3pm)

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)