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.\" ========================================================================
.\"
.IX Title "TFBS::PatternGen 3"
.TH TFBS::PatternGen 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
TFBS::PatternGen \- a base class for pattern generators
.SH "DESCRIPTION"
.IX Header "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.
.SS "pattern"
.IX Subsection "pattern"
.Vb 10
\& 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.
.Ve
.SS "patternSet"
.IX Subsection "patternSet"
.Vb 7
\& 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
.Ve
.SS "all_patterns"
.IX Subsection "all_patterns"
.Vb 8
\& 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
.Ve