TFBS::PatternGen(3pm)

NAME

TFBS::PatternGen - a base class for pattern generators

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