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