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

NAME

       TFBS::PatternGen - a base class for pattern generators

DESCRIPTION

       TFBS::PatternGen is a base classs providing methods common to all pattern generating modules. It is meant to be inherited by a concrete
       pattern generator, which must have its own constructor.

   pattern
	Title	: pattern
	Usage	: my $pattern_obj = $patterngen->pattern()
	Function: retrieves a pattern object produced by the pattern generator
	Returns : a pattern object (currently available pattern generators
		  return a TFBS::Matrix::PFM object)
	Args	: none
	Warning : If a pattern generator produces more than one pattern,
		  this method call returns only the first one and prints
		  a warning on STDERR, In those cases you should use
		  I<all_patterns> or I<patternSet> methods.

   patternSet
	Title	: patternSet
	Usage	: my $patternSet = $patterngen->patternSet()
	Function: retrieves a pattern set object containing all the patterns
		  produced by the pattern generator
	Returns : a pattern set object (currently available pattern generators
		  return a TFBS::MatrixSet object)
	Args	: none

   all_patterns
	Title	: all_patterns
	Usage	: my @patterns = $patterngen->all_patterns()
	Function: retrieves an array of pattern objects
		  produced by the pattern generator
	Returns : an array of pattern set objects (currently available
		  pattern generators return an array of
		  TFBS::Matrix::PFM objects)
	Args	: none

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