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 Throws    : n/a

=cut

sub revcom {  shift->throw_not_implemented; }

=head2 recognition_length

 Title     : recognition_length
 Usage     : $re->recognition_length();
 Function  : Get the length of the RECOGNITION sequence.
             This is the total recognition sequence,
             inluding the ambiguous codes.
 Returns   : An integer
 Argument  : Nothing

See also: L<non_ambiguous_length>

=cut

sub recognition_length {  shift->throw_not_implemented; }

=head2 non_ambiguous_length

 Title     : non_ambiguous_length
 Usage     : $re->non_ambiguous_length();
 Function  : Get the nonambiguous length of the RECOGNITION sequence.
             This is the total recognition sequence,
             excluding the ambiguous codes.
 Returns   : An integer
 Argument  : Nothing

See also: L<non_ambiguous_length>

=cut

sub non_ambiguous_length {  shift->throw_not_implemented; }

=head2 cutter

 Title    : cutter
 Usage    : $re->cutter
 Function : Returns the "cutter" value of the recognition site.

            This is a value relative to site length and lack of
            ambiguity codes. Hence: 'RCATGY' is a five (5) cutter site
            and 'CCTNAGG' a six cutter

            This measure correlates to the frequency of the enzyme
            cuts much better than plain recognition site length.

 Example  : $re->cutter
 Returns  : integer or float number
 Args     : none

Why is this better than just stripping the ambiguous codes? Think about
it like this: You have a random sequence; all nucleotides are equally
probable. You have a four nucleotide re site. The probability of that
site finding a match is one out of 4^4 or 256, meaning that on average
a four cutter finds a match every 256 nucleotides. For a six cutter,
the average fragment length is 4^6 or 4096. In the case of ambiguity
codes the chances are finding the match are better: an R (A|T) has 1/2
chance of finding a match in a random sequence. Therefore, for RGCGCY
the probability is one out of (2*4*4*4*4*2) which exactly the same as
for a five cutter! Cutter, although it can have non-integer values
turns out to be a useful and simple measure.

From bug 2178: VHDB are ambiguity symbols that match three different
nucleotides, so they contribute less to the effective recognition sequence
length than e.g. Y which matches only two nucleotides. A symbol which matches n
of the 4 nucleotides has an effective length of 1 - log(n) / log(4).

=cut

sub cutter {  shift->throw_not_implemented; }

=head2 is_palindromic

 Title     : is_palindromic
 Usage     : $re->is_palindromic();
 Function  : Determines if the recognition sequence is palindromic
           : for the current restriction enzyme.
 Returns   : Boolean
 Argument  : n/a
 Throws    : n/a

A palindromic site (EcoRI):

  5-GAATTC-3
  3-CTTAAG-5

=cut

sub is_palindromic {  shift->throw_not_implemented; }

=head2 overhang

 Title     : overhang
 Usage     : $re->overhang();
 Function  : Determines the overhang of the restriction enzyme
 Returns   : "5'", "3'", "blunt" of undef
 Argument  : n/a
 Throws    : n/a

A blunt site in SmaI returns C<blunt>

  5' C C C^G G G 3'
  3' G G G^C C C 5'

A 5' overhang in EcoRI returns C<5'>

  5' G^A A T T C 3'
  3' C T T A A^G 5'

A 3' overhang in KpnI returns C<3'>

  5' G G T A C^C 3'
  3' C^C A T G G 5'

=cut