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lib/Bio/Polloc/RuleI.pm  view on Meta::CPAN

=over

=item 

Gets/sets the type of rule

=item Arguments

Value (str).  Can be: pattern, profile, repeat, tandemrepeat, similarity, coding,
boolean, composition, crispr.  See the corresponding C<Bio::Polloc::Rule::*> objects
for further details.

Some variations can be introduced, like case variations or short versions like
B<patt> or B<rep>.

=item Return

Value (str).  The type of the rule, or C<undef> if undefined.  The value returned
is undef or a string from the above list, regardless of the input variations.

=item Throws

L<Bio::Polloc::Polloc::Error> if an unsupported type is received.

=back

=cut

sub type {
   my($self,$value) = @_;
   if($value){
      my $v = $self->_qualify_type($value);
      $self->throw("Attempting to set an invalid type of rule",$value) unless $v;
      $self->{'_type'} = $v;
   }
   return $self->{'_type'};
}



=head2 context

=over

=item 

Gets/sets the context of the rule.

The context is a reference to an array of two elements (I<int> or I<str>),
the first being:
   1 => with respect to the start of the sequence
   0 => somewhere within the sequence (ignores the second)
  -1 => with respect to the end of the sequence

And the second being the number of residues from the reference point.  The second
value can be positive, negative, or zero.

=item Arguments

Three integers, or one integer equal to zero.  Please note that this function is
extremely tolerant, and tries to guess the context regardless of the input.

=item Returns

A reference to the array described above.

=back

=cut

sub context {
   my($self,@args) = @_;
   if($#args>=0){
      $self->{'_context'} = [$args[0]+0, $args[1]+0, $args[2]+0];
   }
   $self->{'_context'} ||= [0,0,0];
   if($self->{'_context'}->[0] < 0) {$self->{'_context'}->[0] = -1;}
   elsif($self->{'_context'}->[0] > 0) {$self->{'_context'}->[0] = 1;}
   else {$self->{'_context'}->[0] = 0;}
   $self->{'_context'}->[1]+=0;
   return $self->{'_context'};
}

=head2 value

=over

=item 

Gets/sets the value of the rule

=item Arguments

Value (mix)

=item Returns

Value (mix)

=item Note

This function relies on C<_qualify_value>

=item Throws

L<Bio::Polloc::Polloc:Error> if unsupported value is received

=back

=cut

sub value {
   my($self,$value) = @_;
   if(defined $value){
      my $v = $self->_qualify_value($value);
      defined $v or $self->throw("Bad rule value", $value);
      $self->{'_value'} = $v;
   }
   return $self->{'_value'};
}