Reference

TFBS::PatternGen(3pm)

a base class for pattern generators

NAME

TFBS::PatternGen - a base class for pattern generators

DESCRIPTION

TFBS::PatternGen is a base class 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

History