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It is intended that the methods in this code are inherited
by other modules.

=head2 Anatomy of a gene

A gene is a linear sequence of tokens which tell some unknown
system how to behave.  These methods all expect that a gene
is of the form:

 [ [ 'token0', 'token1', ...  ], .. other elements ignored ]

=head2 Using the module

To use the genetic sequences, you must write your own
implementations of the following methods along with some
way of turning your encoded sequence into something useful.

=over 4

=item generate_token

=back

You may also want to override the following methods:

=over 4

=item new

=item clone

=item render_gene

=back

The calling conventions for these methods are outlined below.

=head2 Mutation methods

Mutation methods are all named C<mutate_*>.  In general, the
first argument will be the number of mutations required, followed
by the positions in the genes which should be affected, followed
by the lengths of sequences within the gene which should be affected.
If positions are not defined, then random ones are chosen.  If
lengths are not defined, a length of 1 is assumed (ie. working on
single tokens only), if a length of 0 is requested, then a random
length is chosen.

If a mutation is attempted which could corrupt your gene (copying
from a region beyond the end of the gene for instance) then it
will be silently skipped.  Mutation methods all return the number
of mutations carried out (not the number of tokens affected).

=over 4

=item C<mutate([num, ref to hash of probs & methods])>

This will call at random one of the other mutation methods.
It will repeat itself I<num> times.  If passed a reference
to a hash as its second argument, it will use that to
decide which mutation to attempt.

This hash should contain keys which fit $1 in C<mutate_(.*)>
and values indicating the weight to be given to that method.
The module will normalise this nicely, so you do not have to.
This lets you define your own mutation methods in addition to
overriding any you do not like in the module.

=item C<mutate_insert([num, pos])>

Inserts a single token into the string at position I<pos>.
The token will be randomly generated by the calling object's 
C<generate_token> method.

=item C<mutate_overwrite([num, pos1, pos2, len])>

Copies a section of the gene (starting at I<pos1>, length I<len>)
and writes it back into the gene, overwriting current elements,
starting at I<pos2>.

=item C<mutate_reverse([num, pos, len])>

Takes a sequence within the gene and reverses the ordering of the
elements within that sequence.  Starts at position I<pos> for
length I<len>.

=item C<mutate_shuffle([num, pos1, pos2, len])>

This takes a sequence (starting at I<pos1> length I<len>)
 from within a gene and moves
it to another position (starting at I<pos2>).  Odd things might occur if the
position to move the sequence into lies within the
section to be moved, but the module will try its hardest
to cause a mutation.

=item C<mutate_duplicate([num, pos1, pos2, length])>

This copies a portion of the gene starting at I<pos1> of length
I<length> and then splices it into the gene before I<pos2>.

=item C<mutate_remove([num, pos, length]))>

Deletes I<length> tokens from the gene, starting at I<pos>. Repeats
I<num> times.

=item C<mutate_minor([num, pos])>

This will mutate a single token at position I<pos> in the gene 
into one of the same type (as decided by the object's C<generate_token>
method).

=item C<mutate_major([num, pos])>

This changes a single token into a token of any token type.
Token at postition I<pos>.  The token is produced by the object's
C<generate_token> method.

=item C<mutate_switch([num, pos1, pos2, len1, len2])>

This takes two sequences within the gene and swaps them
into each other's position.  The first starts at I<pos1>
with length I<len1> and the second at I<pos2> with length
I<len2>.  If the two sequences overlap, then no mutation will
be attempted.

=back

The following methods are also provided, but you will probably
want to overide them for your own genetic sequences.

=over 4

=item C<generate_token([current token])>

This is used by the mutation methods when changing tokens or 
creating new ones.  It is expected to return a single token.
If a minor mutation is being attempted, then the method will
also be passed the current token.

The provided version of this method returns a random character
from 'a'..'z' as both the token type and token.

=item C<clone()>

This returns a copy of the gene as a new object.  If you are using
nested genes, or other references as your tokens, then you may need
to produce your own version which will deep copy your structure.

=item C<new>

This returns an empty gene, into which you can put things.  If you
want to initialise your gene, or anything useful like that, then
you will need another one of these.

=item C<render_gene>

This is useful for debugging, returns a serialised summary of the
gene.

=back

=head1 AUTHOR

This module was written by Alex Gough (F<alex@rcon.org>).

=head1 SEE ALSO

If you are encoding something which must maintain a correct
syntax (executable code, regular expressions, formal poems)