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is trusted.  This is useful for non-directed features like repeats,
which context is actually directed.

=item -alldetected I<bool (int)>

Include all detected features (even these overlapping with input features).

=item -feature I<bool (int)>

Should I include the feature region in the search? 0 by default.

=item -lensd I<float>

Number of Standar Deviations (SD) tolerated as half of the range of lengths
for a feature.  The average (Avg) and the standard deviation of the length
are calculated based on all the stored features, and the Avg+(SD*lensd) is
considered as the largest possible new feature.  No minimum length constraint
is given, unless explicitly set with -minlen.  This argument is ignored if
C<-maxlen> is explicitly set.  Default is 1.5.

=item -maxlen I<int>

Maximum length of a new feature in number of residues.  If zero (0) evaluates
C<-lensd> instead.  Default is 0.

=item -minlen I<int>

Minimum length of a new feature in number of residues.  Default is 0.

=item -similarity I<float>

Minimum fraction of similarity to include a found region. 0.8 by default.

=item -oneside I<bool (int)>

Should I consider features with only one of the sides?  Takes effect only if
both -upstream and -downstream are defined. 0 by default.

=item -algorithm I<str>

=over

=item C<blast>

Use BLAST to search (after multiple alignment and consensus calculation of
queries).  Default algorithm.

=item C<hmmer>

Use HMMer to search (after multiple alignment and C<hmmbuild> of query
sequences).

=back

=item -score I<int>

Minimum score for either algorithms B<blast> and B<hmmer>. 20 by default.

=item -consensusperc I<float>

Minimum percentage a residue must appear in order to include it in the
consensus used as query.  60 by default.  Only if -algorithm blast.

=item -e I<float>

If C<-algorithm> B<blast>, maximum e-value.  0.1 by default.

=item -p I<str>

If C<-algorithm> B<blast>, program used (C<[t]blast[npx]>).  B<blastn> by
default.

=back

=item Throws

L<Bio::Polloc::Polloc::Error> if unexpected input,

=back

=cut

sub extension {
   my ($self, @args) = @_;
   return $self->{'_groupextension'} unless $#args>=0;
   @args = split /\s+/, $args[0] if $#args == 0;
   $self->throw("Odd number of elements, impossible to build key-value pairs", \@args)
   	unless $#args%2;
   my %f = @args;
   $f{'-function'} ||= 'context';
   $f{'-algorithm'} ||= 'blast';
   ($f{'-feature'} ||= 0) += 0;
   ($f{'-downstream'} ||= 0) += 0;
   ($f{'-upstream'} ||= 0) += 0;
   ($f{'-detectstrand'} ||= 0) += 0;
   ($f{'-alldetected'} ||= 0) += 0;
   ($f{'-oneside'} ||= 0) += 0;
   $f{'-lensd'} = defined $f{'-lensd'} ? $f{'-lensd'}+0 : 1.5;
   $f{'-maxlen'} = defined $f{'-maxlen'} ? $f{'-maxlen'}+0 : 0;
   $f{'-minlen'} = defined $f{'-minlen'} ? $f{'-minlen'}+0 : 0;
   $f{'-similarity'} = defined $f{'-similarity'} ? $f{'-similarity'}+0 : 0.8;
   $f{'-score'} = defined $f{'-score'} ? $f{'-score'}+0 : 20;
   $f{'-consensusperc'} = defined $f{'-consensusperc'} ? $f{'-consensusperc'}+0 : 60;
   $f{'-e'} = defined $f{'-e'} ? $f{'-e'}+0 : 0.1;
   $f{'-p'} = 'blastn' unless defined $f{'-p'};
   $self->{'_groupextension'} = \%f;
   return $self->{'_groupextension'};
}


=head2 extend

=over

=item 

Extends a group based on the arguments provided by L<Bio::Polloc::GroupCriteria->extension>.

=item Arguments

=over