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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